@article{Gogoi2022b,
title = {Transition from inhomogeneous limit cycles to oscillation death in nonlinear oscillators with similarity-dependent coupling},
author = {P B Gogoi and S Kumarasamy and A Prasad and R Ramaswamy},
url = {https://doi.org/10.1063/5.0100595},
doi = {10.1063/5.0100595},
issn = {1054-1500},
year  = {2022},
date = {2022-11-21},
journal = {Chaos},
volume = {32},
pages = {113138},
abstract = {We consider a system of coupled nonlinear oscillators in which the interaction is modulated by a measure of the similarity between the oscillators. Such a coupling is common in treating spatially mobile dynamical systems where the interaction is distance dependent or in resonance-enhanced interactions, for instance. For a system of Stuart–Landau oscillators coupled in this manner, we observe a novel route to oscillation death via a Hopf bifurcation. The individual oscillators are confined to inhomogeneous limit cycles initially and are damped to different fixed points after the bifurcation. Analytical and numerical results are presented for this case, while numerical results are presented for coupled Rössler and Sprott oscillators.},
keywords = {Complex Behaviour},
pubstate = {published},
tppubtype = {article}
}
@article{Pandey2022,
title = {Modeling of indirect cell–cell interaction networks mediated by IFN- γ/IL-4 cytokines involved in atopic dermatitis},
author = {R Pandey and A Jangid and R Gayathri Vinjamuri and R Ramaswamy},
url = {https://doi.org/10.1016/j.jtbi.2022.111291},
doi = {https://doi.org/10.1016/j.jtbi.2022.111291},
issn = {1095-8541},
year  = {2022},
date = {2022-09-24},
journal = {Journal of Theoretical Biology},
volume = {556},
pages = {111921},
abstract = {Atopic dermatitis (AD) is an immune-driven inflammatory skin disease that is 
      known to have a significantly high life-time prevalence in the human population. 
      T-helper (Th) immune cells play a key role in the pathogenesis of AD which is 
      marked by defects in the skin barrier function along with a significant increase 
      in the population of either Th1 or Th2 sub-types of Th cells. The progression of 
      AD from the acute to chronic phase is still poorly understood, and here we 
      explore the mechanism of this transition through the study of a mathematical 
      model for indirect cell-cell interactions among Th and skin cells via the 
      secreted cytokines IFNγ and IL-4, both known to have therapeutic potential. An 
      increase in the level of cytokine IFN γ can catalyse the transition of AD from an 
      acute to a chronic stage, while an increase in the level of cytokine IL-4 has the 
      reverse effect. In our model, the transition of AD from the acute to chronic 
      stage and vice versa can be abrupt (switch-like) with hysteresis: this bistable 
      behaviour can potentially be used to keep AD in the acute phase since therapy 
      based on suppression of IFNγ can retard the transition to the chronic phase.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Singha2022,
title = {Phase-locking in k-partite networks of delay-coupled oscillators},
author = {J Singha and R Ramaswamy},
url = {https://www.sciencedirect.com/science/article/pii/S0960077922001576},
doi = {https://doi.org/10.1016/j.chaos.2022.111947},
issn = {0960-0779},
year  = {2022},
date = {2022-03-11},
journal = {Chaos, Solitons, and Fractals},
volume = {157},
pages = {111947},
abstract = {We examine the dynamics of an ensemble of phase oscillators that are divided in k sets, with time-delayed coupling interactions only between oscillators in different sets or partitions. The network of interactions thus forms a k−partite graph. A variety of phase-locked states are observed; these include, in addition to the fully synchronized in-phase solution, splay cluster solutions in which all oscillators within a partition are synchronised and the phase differences between oscillators in different partitions are integer multiples of 2π/k. Such solutions exist independent of the delay and we determine the generalised stability criteria for the existence of these phase-locked solutions. With increase in time-delay, there is an increase in multistability, the generic solutions coexisting with a number of other partially synchronized solutions. The Ott-Antonsen ansatz is applied for the special case of a symmetric k−partite graph to obtain a single time-delayed differential equation for the attracting synchronization manifold. Agreement with numerical results for the specific case of oscillators on a tripartite lattice (the k=3 case) is excellent.},
keywords = {Delay coupling, Network},
pubstate = {published},
tppubtype = {article}
}
@article{Bilal2022,
title = {A higher-dimensional generalization of the Lozi map: bifurcations and dynamics},
author = {S Bilal and R Ramaswamy},
url = {https://doi.org/10.1080/10236198.2022.2041625},
doi = {10.1080/10236198.2022.2041625},
issn = {1023-6198},
year  = {2022},
date = {2022-02-23},
journal = {Journal of Difference Equations and Applications},
volume = {28},
pages = {1-12},
abstract = {We generalize the two-dimensional Lozi map in order to systematically obtain piecewise continuous maps in three and higher dimensions. Similar to higher dimensional generalizations of the related Hénon map, these higher dimensional Lozi maps support hyperchaotic dynamics. We carry out a bifurcation analysis and investigate the dynamics through both numerical and analytical means. The analysis is extended to a sequence of approximations that smooth the discontinuity of the derivatives in the Lozi map.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Wontchui2022,
title = {Intermingled attractors in an asymmetrically driven modified Chua oscillator},
author = {T T Wontchui and M E Sone and S R Ujjwal and J Y Effa and H P E Fouda and R Ramaswamy},
url = {https://pubs.aip.org/aip/cha/article/32/1/013106/2835551/Intermingled-attractors-in-an-asymmetrically},
doi = {10.1063/5.0069232},
issn = {1054-1500},
year  = {2022},
date = {2022-01-03},
journal = {Chaos},
volume = {32},
number = {1},
abstract = {Understanding the asymptotic behavior of a dynamical system when system parameters are varied remains a key challenge in nonlinear dynamics. We explore the dynamics of a multistable dynamical system (the response) coupled unidirectionally to a chaotic drive. In the absence of coupling, the dynamics of the response system consists of simple attractors, namely, fixed points and periodic orbits, and there could be chaotic motion depending on system parameters. Importantly, the boundaries of the basins of attraction for these attractors are all smooth. When the drive is coupled to the response, the entire dynamics becomes chaotic: distinct multistable chaos and bistable chaos are observed. In both cases, we observe a mixture of synchronous and desynchronous states and a mixture of synchronous states only. The response system displays a much richer, complex dynamics. We describe and analyze the corresponding basins of attraction using the required criteria. Riddled and intermingled structures are revealed.},
keywords = {Chaos, Lorenz, Lyapunov exponent, Multistability},
pubstate = {published},
tppubtype = {article}
}
@article{Jangid2021,
title = {A Stochastic Model of Homeostasis: the roles of noise and nuclear positioning in deciding cell fate},
author = {A Jangid and S Selvarajan and R Ramaswamy},
url = {https://www.sciencedirect.com/science/article/pii/S2589004221011676},
doi = {https://doi.org/10.1016/j.isci.2021.103199},
issn = {2589-0042},
year  = {2021},
date = {2021-10-22},
journal = {iScience},
volume = {24},
number = {10},
abstract = {We study a population-based cellular model that starts from a single stem cell that divides stochastically to give rise to either daughter stem cells or differentiated daughter cells. There are three main components in the model: nucleus position, the underlying gene-regulatory network, and stochastic segregation of transcription factors in the daughter cells. The proportion of self-renewal and differentiated cell lines as a function of the nucleus position which in turn decides the plane of cleavage is studied. Both nuclear position and noise play an important role in determining the stem cell genealogies. We have observed both long and short genealogies in model simulation, and these compare well with experimental results from neuroblast and B-cell division. Symmetric divisions are observed in apical nuclei, while asymmetric division occurs when the nucleus is toward the base. In this model, the number of clones decreases over time, although the average clone size increases.},
keywords = {Stochastic dynamics, Theoretical biology},
pubstate = {published},
tppubtype = {article}
}
@article{jangid1,
title = {Transition and identification of pathological states in p53 dynamics for therapeutic intervention},
author = {A Jangid and Md Z Malik and R Ramaswamy and RK Brojen Singh },
url = {https://www.nature.com/articles/s41598-021-82054-1},
doi = {10.1038/s41598-021-82054-1},
issn = {2045-2322},
year  = {2021},
date = {2021-01-27},
journal = {Scientific Reports},
volume = {11},
pages = {2349},
abstract = {We study a minimal model of the stress-driven p53 regulatory network that includes competition between active and mutant forms of the tumor-suppressor gene p53. Depending on the nature and level of the external stress signal, four distinct dynamical states of p53 are observed. These states can be distinguished by different dynamical properties which associate to active, apoptotic, pre-malignant and cancer states. Transitions between any two states, active, apoptotic, and cancer, are found to be unidirectional and irreversible if the stress signal is either oscillatory or constant. When the signal decays exponentially, the apoptotic state vanishes, and for low stress the pre-malignant state is bounded by two critical points, allowing the system to transition reversibly from the active to the pre-malignant state. For significantly large stress, the range of the pre-malignant state expands, and the system moves to irreversible cancerous state, which is a stable attractor. This suggests that identification of the pre-malignant state may be important both for therapeutic intervention as well as for drug delivery.},
keywords = {p53 dynamics, systems biology, therapeutics},
pubstate = {published},
tppubtype = {article}
}
@article{sahoo1,
title = {Ageing in mixed populations of Stuart–Landau oscillators: the role of diversity},
author = {S Sahoo and V Varshney and A Prasad and R. Ramaswamy},
url = {https://iopscience.iop.org/article/10.1088/1751-8121/ab4a21},
doi = {10.1088/1751-8121/ab4a21},
issn = {1751-8121},
year  = {2019},
date = {2019-10-21},
journal = {Journal of Physics A:  Mathematical and Theoretical},
volume = {52},
pages = {464001},
abstract = {The phenomenon of ageing in a population of autonomous oscillators, namely the increase in the number of inactive (or non-oscillatory) units due to coupling interactions is studied in a population of globally coupled Stuart–Landau oscillators. The initial populations are prepared either as a mixture of active and inactive oscillators or as an ensemble of active oscillators with a mixture of distinct frequencies. The ageing transition does not depend on whether the coupling breaks gauge symmetry or not, but is affected by the degree of diversity in the ensemble, namely the existence of different types of subsystems that can cause oscillation quenching when coupled. The scaling exponents depend on the nature of the coupling interaction.},
keywords = {ageing, phase transition, scaling, stasis},
pubstate = {published},
tppubtype = {article}
}
@book{KosambiLetters2019,
title = {A Fragmented Feminism: The Life and Letters of Anandibai Joshee by Meera Kosambi},
editor = { R Ramaswamy and M Kolhatkar and A Mukherji},
url = {https://www.taylorfrancis.com/books/9780429266386},
doi = {10.4324/9780429266386},
isbn = {9780429266386 },
year  = {2019},
date = {2019-08-30},
publisher = {Routledge, UK},
edition = {First Edition},
abstract = {"This book is a search for ‘the real Anandibai Joshee’ —— a search in which the readers are invited to participate."

In her short and eventful life, Anandibai Joshee, the first Indian woman to earn a medical degree, broke many stereotypes. Literate at a time when it was taboo for a girl to attend school or even ‘pick up a paper’, she was courageous, articulate, and assertive. And ambitious. Fuelled by a desire to improve the healthcare that was available to Indian women at that time, she travelled across the seas to the United States to study medicine.

Meera Kosambi’s biography of Anandibai is more than just a retelling of the life of a woman who was ahead of her times. Drawing on a host of narratives, Kosambi recovers Anandibai’s many voices that have been submerged in history — that of a conflicted feminist, a nationalist, and a reformer among others — and her engagement with the world at large.

This volume is a testament to Meera Kosambi’s commitment to social history. When she passed away in 2015, she left an incomplete manuscript that has painstakingly been put together by the editors. Drawing on archival research, including a host of Anandibai’s letters, her poems in Marathi, newspaper reports and rare photographs, this book will be of immense interest to scholars and researchers of modern Indian history, sociology, gender, and South Asian studies.},
keywords = {Anandibai, Book, Kosambi},
pubstate = {published},
tppubtype = {book}
}
@article{PhysRevE.98.032217,
title = {Design strategies for generalized synchronization},
author = {S Chishti and R Ramaswamy },
url = {https://link.aps.org/doi/10.1103/PhysRevE.98.032217},
doi = {10.1103/PhysRevE.98.032217},
issn = {2470-0053 },
year  = {2018},
date = {2018-09-24},
journal = {Physical Review E},
volume = {98},
pages = {032217},
abstract = {We describe a general procedure to couple two dynamical systems so as to guide their joint dynamics onto a specific transversally stable invariant submanifold in the phase space. This method can thus be viewed as a means of constraining the dynamics, with the coupling functions providing the forces of constraint, which results in the coupled systems being in generalized synchronization. The required coupling functions are, however, not uniquely defined and can therefore be chosen in order to satisfy a desired design criterion.},
keywords = {Generalized Synchronization, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{PhysRevE.98.022212,
title = {Dynamical effects of breaking rotational symmetry in counter-rotating Stuart-Landau oscillators},
author = {N Punetha and V Varshney and S Sahoo and G Saxena and A Prasad and R Ramaswamy},
url = {https://ramramaswamy.org/papers/174.pdf},
doi = {10.1103/PhysRevE.98.022212},
issn = {2470-0053 },
year  = {2018},
date = {2018-08-01},
journal = {Physical Review E},
volume = {98},
pages = {022212},
publisher = {American Physical Society},
abstract = {Stuart-Landau oscillators can be coupled so as to either preserve or destroy the rotational symmetry that the 
uncoupled system possesses. We examine some of the simplest cases of such couplings for a system of two 
nonidentical oscillators. When the coupling breaks the rotational invariance, there is a qualitative difference 
between oscillators wherein the phase velocity has the same sign (termed co-rotation) or opposite signs (termed 
counter-rotation). In the regime of oscillation death the relative sense of the phase rotations plays a major role. 
In particular, when rotational invariance is broken, counter-rotation or phase velocities of opposite signs appear 
to destabilize existing fixed points, thereby preserving and possibly extending the range of oscillatory behaviour. 
The dynamical “frustration” induced by counter-rotations can thus suppress oscillation quenching when coupling 
breaks the symmetry.},
keywords = {Amplitude Death, Landau-Stuart, Oscillation Quenching, Symmetry Breaking},
pubstate = {published},
tppubtype = {article}
}
@article{Donepudi2018,
title = {The collective dynamics of NF-kB in cellular ensembles},
author = {D Raviteja and R Ramaswamy},
url = {https://ramramaswamy.org/papers/172.pdf},
doi = {10.1140/epjst/e2018-800014-7},
issn = {1951-6355},
year  = {2018},
date = {2018-01-01},
journal = {The European Physical Journal Special Topics},
volume = {227},
pages = {851-863},
abstract = {textlessh3 class=ä-plus-plus"textgreaterAbstracttextless/h3textgreater textlessp class=ä-plus-plus"textgreater The transcription factor NF ‚àí textlessem class=ä-plus-plus"textgreater$kappa$textless/emtextgreaterB is a crucial component in inflammatory signalling. Its dynamics is known to be oscillatory and has been extensively studied. Using a recently developed model of NF ‚àí textlessem class=ä-plus-plus"textgreater$kappa$textless/emtextgreaterB regulation, we examine the collective dynamics of a network of NF ‚àí textlessem class=ä-plus-plus"textgreater$kappa$textless/emtextgreaterB oscillators that are coupled exogenously by a common drive (in this case a periodically varying cytokine signal corresponding to the TNF molecule concentration). There is multistability owing to the overlapping of Arnol'd tongues in each of the oscillators, and thus the collective dynamics exhibit a variety of complex dynamical states. We also study the case of a globally (mean field) coupled network and observe that the ensemble can display global synchronisation, cluster synchronisation and splay states. In addition, there can be dynamical chimeras, namely coexisting synchronised and desynchronized clusters. The basins of attraction of these different collective states are studied and the parametric dependence in the basin uncertainty is examined. 
 textless/ptextgreater},
keywords = {Cellular Ensembles, Computational Biology, systems biology},
pubstate = {published},
tppubtype = {article}
}
@article{Kumar2018,
title = {Chemistry at the Nanoscale: When Every Reaction is a Discrete Event},
author = {A B R Kumar and R Ramaswamy},
url = {https://ramramaswamy.org/papers/169.pdf},
doi = {10.1007/s12045-018-0592-4},
issn = {0973-712X},
year  = {2018},
date = {2018-01-01},
journal = {Resonance},
volume = {23},
pages = {23-40},
abstract = {Traditionally the kinetics of a chemical reaction has been stud- ied as a set of coupled ordinary differential equations. The law of mass action, a tried and tested principle for reactions involving macroscopic quantities of reactants, gives rise to de- terministic equations in which the variables are species con- centrations. In recent years, though, as smaller and smaller systems – such as an individual biological cell, say – can be studied quantitatively, the importance of molecular discrete- ness in chemical reactions has increasingly been realized. This is particularly true when the system is far from the ‘thermo- dynamic limit' when the numbers of all reacting molecular species involved are several orders of magnitude smaller than Avogadro's number. In such situations, each reaction has to be treated as a probabilistic ‘event' that occurs by chance when the appropriate reactants collide. Explicitly accounting for such processes has led to the development of sophisticated statistical methods for simulation of chemical reactions, particularly those occurring at the cellular and sub-cellular level. In this article, we describe this approach, the so-called stochastic simulation algorithm, and discuss applications to study the dynamics of model regulatory networks.},
keywords = {Chemical Kinetics, Gillespie's Algorithm, Stochasticity, Synthetic Gene Oscillators},
pubstate = {published},
tppubtype = {article}
}
@article{Donepudi2018a,
title = {By-product group benefits of non-kin resource-sharing in vampire bats},
author = {D Raviteja and R Ramaswamy},
url = {https://ramramaswamy.org/papers/171.pdf},
doi = {10.1088/1742-6596/1090/1/012002},
issn = {1742-6596},
year  = {2018},
date = {2018-01-01},
journal = {Journal of Physics: Conference Series},
volume = {1090},
pages = {012002},
abstract = {We develop an agent based model (ABM) to simulate the behaviour of a colony of vampire bats (Order: Chiroptera) and study the by-product group benefits that result from resource-sharing among related as well as unrelated members of the colony. Such cooperative behaviour can lead to unexpected group benefits; there is an increase the inclusive fitness of related members of the colony (namely kin) and can have direct benefit when shared with unrelated members (namely non-kin). Sharing can also provides by-product benefits when individuals have a shared (or group) interest. 
 
Our study focuses on the contrast in the group estimates between sharing and non-sharing populations. For constant ecological resources, sharing behaviour can increase the sustainable population size, increase the total resource stored in the population, and reduce the average resource required per individual, compared to a non-sharing population. (The extent of the increase or decrease will depend on the parameters of the model). This increased carrying capacity due to resource sharing can increase the fitness of individuals in the group. The increase in cooperativity has a nonlinear effect on group benefits: Substantial group benefits are shown only after a cooperativity threshold, and it increases exponentially to a maximum thereafter.},
keywords = {Conference, Optimisation, Population Dynamics, Resource Management},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2018,
title = {Modeling long lifespans in eusocial insect populations},
author = {R Ramaswamy and D Raviteja},
url = {https://ramramaswamy.org/papers/171.pdf},
doi = {10.1101/408211},
year  = {2018},
date = {2018-01-01},
journal = {bioRxiv},
pages = {408211},
abstract = {Along with division of labour, and life-history complexities, a characteristic of eusocial insect societies is the greatly extended lifespan for queens. The colony structure reduces the extrinsic mortality of the queen, and according to classical evolutionary theories of ageing, this greatly increases the lifespan. We explore the relationship between the evolution of longevity and the evolution of eusociality by introducing age-structure into a previously proposed evolutionary model and also define an associated agent-based model. A set of three population structures are defined: (i) solitary with all reproductive individuals, (ii) monogynous eusocial with a single queen, and (iii) polygynous eusocial, with multiple queens. In order to compare the relative fitnesses, we compete all possible pairs of these strategies as well as all three together, analysing the effects of parameters such as the probability of progeny migration, group benefits, and extrinsic mortality on the evolution of long lifespans. Simulations suggest that long lifespans appear to evolve only in eusocial populations, and further, that long lifespans enlarge the region of parameter space where eusociality evolves. When all three population strategies compete, the agent-based simulations indicate that solitary strategies are largely confined to shorter lifespans. For long lifespan strategies, the solitary behaviour results only for extreme (very low or very high) migration probability. For median and small values of migration probability, the polygynous eusocial and monogynous eusocial strategies give advantage to the population respectively. For a given migration probability, with an increase in lifespan, the dominant strategy changes from solitary to polygynous to monogynous eusociality. The evolution of a long lifespan is thus closely linked to the evolution of eusociality, and our results are in accord with the observation that the breeding female in monogynous eusocial species has a longer lifespan than those in solitary or polygynous eusocial species.},
keywords = {systems biology},
pubstate = {published},
tppubtype = {article}
}
@article{Yadav2017,
title = {Emergent organization in a model market},
author = {A C Yadav and K Manchanda and R Ramaswamy
},
url = {https://www.sciencedirect.com/science/article/pii/S0378437117303321},
doi = {10.1016/j.physa.2017.04.029},
issn = {0378-4371},
year  = {2017},
date = {2017-09-15},
journal = {Physica A: Statistical Mechanics and its Applications},
volume = {482},
pages = {118 },
abstract = {We study the collective behaviour of interacting agents in a simple model of market economics that was originally introduced by Nørrelykke and Bak. A general theoretical framework for interacting traders on an arbitrary network is presented, with the interaction consisting of buying (namely consumption) and selling (namely production) of commodities. Extremal dynamics is introduced by having the agent with least profit in the market readjust prices, causing the market to self-organize. In addition to examining this model market on regular lattices in two-dimensions, we also study the cases of random complex networks both with and without community structures. Fluctuations in an activity signal exhibit properties that are characteristic of avalanches observed in models of self-organized criticality, and these can be described by power–law distributions when the system is in the critical state.},
keywords = {emergent phenomenon, self-organization, statistical physics},
pubstate = {published},
tppubtype = {article}
}
@article{Yadav2017b,
title = {A general mechanism for the 1/f noise},
author = {A C Yadav and R Ramaswamy and D Dhar},
url = {https://doi.org/10.1103/PhysRevE.96.022215},
doi = {10.1103/PhysRevE.96.022215},
issn = {2470-0053 },
year  = {2017},
date = {2017-08-24},
journal = {Physical Review E},
volume = {96},
number = {2},
pages = {022215},
abstract = { },
keywords = {Sandpile, statistical physics},
pubstate = {published},
tppubtype = {article}
}
@article{Ujjwal2017,
title = {Emergence of chimeras through induced multistability},
author = {S R Ujjwal and N Punetha and A Prasad and R Ramaswamy},
url = {https://ramramaswamy.org/papers/165.pdf},
doi = {10.1103/PhysRevE.95.032203},
issn = {2470-0053},
year  = {2017},
date = {2017-01-01},
journal = {Physical Review E},
volume = {95},
pages = {032203 },
abstract = {Chimeras, namely coexisting desynchronous and synchronized dynamics, are formed in an ensemble of identically coupled identical chaotic oscillators when the coupling induces multiple stable attractors, and further when the basins of the different attractors are intertwined in a complex manner. When there is coupling-induced multistability, an ensemble of identical chaotic oscillators—with global coupling, or also under the influence of common noise or an external drive (chaotic, periodic, or quasiperiodic)—inevitably exhibits chimeric behavior. Induced multistability in the system leads to the formation of distinct subpopulations, one or more of which support synchronized dynamics, while in others the motion is asynchronous or incoherent. We study the mechanism for the emergence of such chimeric states, and we discuss the generality of our results.},
keywords = {Chimeras, Multistability, Quasiperiodicity},
pubstate = {published},
tppubtype = {article}
}
@article{Wontchui2017,
title = {Coupled Lorenz oscillators near the Hopf boundary: Multistability, intermingled basins, and quasiriddling},
author = {T T Wontchui and J Y Effa and H P E Fouda and S R Ujjwal and R Ramaswamy },
url = {https://ramramaswamy.org/papers/166.pdf},
doi = {10.1103/PhysRevE.96.062203},
issn = {2470-0053},
year  = {2017},
date = {2017-01-01},
journal = {Physical Review E},
volume = {96},
pages = {062203},
abstract = {textcopyright 2017 American Physical Society. We investigate the dynamics of coupled identical chaotic Lorenz oscillators just above the subcritical Hopf bifurcation. In the absence of coupling, the motion is on a strange chaotic attractor and the fixed points of the system are all unstable. With the coupling, the unstable fixed points are converted into chaotic attractors, and the system can exhibit a multiplicity of coexisting attractors. Depending on the strength of the coupling, the motion of the individual oscillators can be synchronized (both in and out of phase) or desynchronized and in addition there can be mixed phases. We find that the basins have a complex structure: the state that is asymptotically reached shows extreme sensitivity to initial conditions. The basins of attraction of these different states are characterized using a variety of measures and depending on the strength of the coupling, they are intermingled or quasiriddled.},
keywords = {Intermingled Basins, Lorenz, Multistability, Quasiriddling},
pubstate = {published},
tppubtype = {article}
}
@article{Manchanda2017,
title = {Collective dynamics in heterogeneous networks of neuronal cellular automata},
author = {K Manchanda and A Bose and R Ramaswamy},
url = {https://ramramaswamy.org/papers/167.pdf},
doi = {10.1016/j.physa.2017.06.021},
issn = {0378-4371},
year  = {2017},
date = {2017-01-01},
journal = {Physica A: Statistical Mechanics and its Applications},
volume = {487},
pages = {111},
publisher = {Elsevier B.V.},
abstract = {We examine the collective dynamics of heterogeneous random networks of model neuronal cellular automata. Each automaton has b active states, a single silent state and r‚àíb‚àí1 refractory states, and can show ‚Äòspiking' or ‚Äòbursting' behavior, depending on the values of b. We show that phase transitions that occur in the dynamical activity can be related to phase transitions in the structure of Erdõs‚ÄìRényi graphs as a function of edge probability. Different forms of heterogeneity allow distinct structural phase transitions to become relevant. We also show that the dynamics on the network can be described by a semi-annealed process and, as a result, can be related to the Boolean Lyapunov exponent.},
keywords = {Binary Mixtures, Cellular automata, Discrete Dynamics, Lyapunov exponent, Network Motif},
pubstate = {published},
tppubtype = {article}
}
@article{Sharma2017,
title = {Time-delayed conjugate coupling in dynamical systems},
author = {Amit Sharma and Manish Dev Shrimali and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/168.pdf},
doi = {10.1140/epjst/e2017-70026-4},
issn = {19516401},
year  = {2017},
date = {2017-01-01},
journal = {European Physical Journal: Special Topics},
volume = {226},
number = {9},
pages = {1903--1910},
abstract = {textcopyright 2017, EDP Sciences and Springer-Verlag GmbH Germany. We study the effect of time-delay when the coupling between nonlinear systems is “conjugate”, namely through dissimilar variables. This form of coupling can induce anomalous transitions such as the emergence of oscillatory dynamics between regimes of amplitude death and oscillation death. The specific cases of coupled Landau-Stuart oscillators as well as a predator-prey model system with cross-predation are discussed. The dynamical behaviour is analyzed numerically and the regions corresponding to different asymptotic states are identified in parameter space.},
keywords = {Amplitude Death, Landau-Stuart, Oscillation Death, Time Delay},
pubstate = {published},
tppubtype = {article}
}
@article{Ujjwal2017b,
title = {Symmetries and symmetry-breaking in oscillator ensembles},
author = {Sangeeta R Ujjwal and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/.pdf},
year  = {2017},
date = {2017-01-01},
journal = {Physics News},
volume = {47},
number = {2},
pages = {11--16},
keywords = {Chaos Theory, Symmetry Breaking},
pubstate = {published},
tppubtype = {article}
}
@book{KosambiEssays2016,
title = {Adventures Into the Unknown: Essays},
editor = {Ram Ramaswamy},
url = {https://threeessays.com/books/adventures-into-the-unknown/},
isbn = {978-93-83968-11-4},
year  = {2016},
date = {2016-06-01},
publisher = {Three Essays Collective},
address = {Gurugram, India},
edition = {First Edition},
abstract = {As the essays in this collection testify, even half a century after his death in 1966, D D Kosambi continues to be provocative, instructive, and contemporary. Many of the arguments that he makes in his two didactic and hitherto unpublished essays are insightful and incisive, and display, in a new setting, the range of his scholarship and the breadth of his interests. The other essays that are included here are his passionate advocacy of solar energy, and his posthumously published autobiographical essay that outlines his credo, and that lends its title to the book.},
keywords = {Book, Kosambi},
pubstate = {published},
tppubtype = {book}
}
@book{KosambiMaths2016,
title = {D.D. Kosambi: Selected Works in Mathematics and Statistics},
editor = {Ramaswamy, Ramakrishna},
url = {https://www.springer.com/gp/book/9788132236740
},
doi = {10.1007/978-81-322-3676-4},
isbn = {978-81-322-3676-4},
year  = {2016},
date = {2016-01-01},
publisher = {Springer India},
edition = {First Edition},
abstract = {This book fills an important gap in studies on D. D. Kosambi. For the first time, the mathematical work of Kosambi is described, collected and presented in a manner that is accessible to non-mathematicians as well. A number of his papers that are difficult to obtain in these areas are made available here. In addition, there are essays by Kosambi that have not been published earlier as well as some of his lesser known works. Each of the twenty four papers is prefaced by a commentary on the significance of the work, and where possible, extracts from technical reviews by other mathematicians.},
keywords = {Book, Kosambi},
pubstate = {published},
tppubtype = {book}
}
@article{Ujjwal2016,
title = {Phase oscillators in modular networks: The effect of nonlocal coupling},
author = {Sangeeta Rani Ujjwal and Nirmal Punetha and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/161.pdf},
doi = {10.1103/PhysRevE.93.012207},
issn = {24700053},
year  = {2016},
date = {2016-01-01},
journal = {Physical Review E},
volume = {93},
number = {1},
pages = {1--10},
abstract = {We study the dynamics of nonlocally coupled phase oscillators in a modular network. The interactions include a phase lag, $alpha$. Depending on the various parameters the system exhibits a number of different dynamical states. In addition to global synchrony there can also be modular synchrony when each module can synchronize separately to a different frequency. There can also be multicluster frequency chimeras, namely coherent domains consisting of modules that are separately synchronized to different frequencies, coexisting with modules within which the dynamics is desynchronized. We apply the Ott-Antonsen ansatz in order to reduce the effective dimensionality and thereby carry out a detailed analysis of the different dynamical states.},
keywords = {Modular Network, Nonlocal Coupling, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Ujjwal2016a,
title = {Driving-induced multistability in coupled chaotic oscillators: Symmetries and riddled basins},
author = {Sangeeta Rani Ujjwal and Nirmal Punetha and Ram Ramaswamy and Manish Agrawal and Awadhesh Prasad},
url = {http://dx.doi.org/10.1063/1.4954022},
doi = {10.1063/1.4954022},
issn = {10541500},
year  = {2016},
date = {2016-01-01},
journal = {Chaos},
volume = {26},
number = {6},
abstract = {The human brain, power grids, arrays of coupled lasers and the Amazon rainforest are all characterized by multistability. The likelihood that these systems will remain in the most desirable of their many stable states depends on their stability against significant perturbations, particularly in a state space populated by undesirable states. Here we claim that the traditional linearization-based approach to stability is too local to adequately assess how stable a state is. Instead, we quantify it in terms of basin stability, a new measure related to the volume of the basin of attraction. Basin stability is non-local, nonlinear and easily applicable, even to high-dimensional systems. It provides a long-sought-after explanation for the surprisingly regular topologies of neural networks and power grids, which have eluded theoretical description based solely on linear stability. We anticipate that basin stability will provide a powerful tool for complex systems studies, including the assessment of multistable climatic tipping elements.},
keywords = {Chaos, Multistability, Riddled Basins},
pubstate = {published},
tppubtype = {article}
}
@article{Kumar2016,
title = {Synchronization properties of coupled chaotic neurons: The role of random shared input},
author = {Rupesh Kumar and Shakir Bilal and Ram Ramaswamy},
url = {http://dx.doi.org/10.1063/1.4954377},
doi = {10.1063/1.4954377},
issn = {10541500},
year  = {2016},
date = {2016-01-01},
journal = {Chaos},
volume = {26},
number = {6},
abstract = {textcopyright 2016 Author(s). Spike-time correlations of neighbouring neurons depend on their intrinsic firing properties as well as on the inputs they share. Studies have shown that periodically firing neurons, when subjected to random shared input, exhibit asynchronicity. Here, we study the effect of random shared input on the synchronization of weakly coupled chaotic neurons. The cases of so-called electrical and chemical coupling are both considered, and we observe a wide range of synchronization behaviour. When subjected to identical shared random input, there is a decrease in the threshold coupling strength needed for chaotic neurons to synchronize in-phase. The system also supports lag-synchronous states, and for these, we find that shared input can cause desynchronization. We carry out a master stability function analysis for a network of such neurons and show agreement with the numerical simulations. The contrasting role of shared random input for complete and lag synchronized neurons is useful in understanding spike-time correlations observed in many areas of the brain.},
keywords = {Neurons, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Jafri2016,
title = {Generalized synchrony of coupled stochastic processes with multiplicative noise},
author = {Haider Hasan Jafri and K.Brojen R Singh and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/164.pdf},
doi = {10.1103/PhysRevE.94.052216},
issn = {24700053},
year  = {2016},
date = {2016-01-01},
journal = {Physical Review E},
volume = {94},
number = {5},
pages = {1--8},
abstract = {textcopyright 2016 American Physical Society. We study the effect of multiplicative noise in dynamical flows arising from the coupling of stochastic processes with intrinsic noise. Situations wherein such systems arise naturally are in chemical or biological oscillators that are coupled to each other in a drive-response configuration. Above a coupling threshold we find that there is a strong correlation between the drive and the response: This is a stochastic analog of the phenomenon of generalised synchronization. Since the dynamical fluctuations are large when there is intrinsic noise, it is necessary to employ measures that are sensitive to correlations between the variables of drive and the response, the permutation entropy, or the mutual information in order to detect the transition to generalized synchrony in such systems.},
keywords = {Generalized Synchronization, Stochasticity},
pubstate = {published},
tppubtype = {article}
}
@article{Agrawal2015,
title = { Erratum: Driving-induced bistability in coupled chaotic attractors [Phys. Rev. E 87 , 042909 (2013)] },
author = {Manish Agrawal and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/148e.pdf},
doi = {10.1103/PhysRevE.87.042909},
issn = {1539-3755},
year  = {2015},
date = {2015-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {92},
number = {4},
pages = {49903},
abstract = {We examine the effects of symmetry-preserving and -breaking interactions in a drive-response system where the response has an invariant symmetry in the absence of the drive. Subsequent to the onset of generalized synchronization, we find that there can be more than one stable attractor. Numerical as well as analytical results establish the presence of phase synchrony in such coexisting attractors. These results are robust to external noise.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Punetha2015,
title = {Delay-induced remote synchronization in bipartite networks of phase oscillators},
author = {Nirmal Punetha and Sangeeta Rani Ujjwal and Fatihcan M Atay and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/159.pdf},
doi = {10.1103/PhysRevE.91.022922},
issn = {15502376},
year  = {2015},
date = {2015-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {91},
number = {2},
pages = {1--7},
abstract = {We study a system of mismatched oscillators on a bipartite topology with time-delay coupling, and analyze the synchronized states. For a range of parameters, when all oscillators lock to a common frequency, we find solutions such that systems within a partition are in complete synchrony, while there is lag synchronization between the partitions. Outside this range, such a solution does not exist and instead one observes scenarios of remote synchronization—namely, chimeras and individual synchronization, where either one or both of the partitions are synchronized independently. In the absence of time delay such states are not observed in phase oscillators.},
keywords = {Bipartite Network, Delay, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Punetha2015a,
title = {Bipartite networks of oscillators with distributed delays: Synchronization branches and multistability},
author = {Nirmal Punetha and Ramakrishna Ramaswamy and Fatihcan M Atay},
url = {https://ramramaswamy.org/papers/160.pdf},
doi = {10.1103/PhysRevE.91.042906},
issn = {15502376},
year  = {2015},
date = {2015-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {91},
number = {4},
pages = {1--10},
abstract = {We study synchronization in bipartite networks of phase oscillators with general nonlinear coupling and distributed time delays. Phase-locked solutions are shown to arise, where the oscillators in each partition are perfectly synchronized among themselves but can have a phase difference with the other partition, with the phase difference necessarily being either zero or $pi$ radians. Analytical conditions for the stability of both types of solutions are obtained and solution branches are explicitly calculated, revealing that the network can have several coexisting stable solutions. With increasing value of the mean delay, the system exhibits hysteresis, phase flips, final state sensitivity, and an extreme form of multistability where the numbers of stable in-phase and antiphase synchronous solutions with distinct frequencies grow without bound. The theory is applied to networks of Landau-Stuart and Rossler oscillators and shown to accurately predict both in-phase and antiphase synchronous behavior in appropriate parameter ranges.},
keywords = {Bipartite Network, Multistability, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Shastri2015,
title = {Towards gender equity in physics in India: Initiatives, investigations, and questions},
author = {P Shastri and A Kurup and L Resmi and R Ramaswamy and S Ubale and S Bagchi and S Rao and S Narasimhan},
url = {https://ramramaswamy.org/papers/OA24.pdf},
doi = {10.1063/1.4937669},
issn = {15517616},
year  = {2015},
date = {2015-01-01},
journal = {AIP Conference Proceedings},
volume = {1697},
pages = {53--56},
abstract = {Initiatives towards gender parity in the sciences in India have occurred$backslash$nboth at national, governmental levels and at local, institutional$backslash$nlevels. A gender gap persists in physics, but data suggest that this gap$backslash$nis due neither to lack of interest in science nor to a lack of career$backslash$ngoals in science among girls. We outline investigations that are$backslash$nimportant to pursue and recommendations that build on the existing$backslash$nscience interest and the impact of initiatives so far.},
keywords = {Gender Equity},
pubstate = {published},
tppubtype = {article}
}
@article{Bilal2014,
title = {Synchronization and amplitude death in hypernetworks},
author = {Shakir Bilal and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/155.pdf},
doi = {10.1103/PhysRevE.89.062923},
issn = {15502376},
year  = {2014},
date = {2014-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {89},
number = {6},
pages = {1--6},
abstract = {We study dynamical systems on a hypernetwork, namely by coupling them through several variables. For the case when the coupling(s) are all linear, a comprehensive analysis of the master stability function (MSF) for synchronized dynamics is presented and, through application to a number of paradigmatic examples, the typical forms of the MSF are discussed. The MSF formalism for hypernetworks also provides a framework to study synchronization in systems that are diffusively coupled through dissimilar variables - the so-called conjugate coupling that can lead to amplitude or oscillation death. textcopyright 2014 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Srivastava2014,
title = {Two-layer modular analysis of gene and protein networks in breast cancer},
author = {Alok Srivastava and Suraj Kumar and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/156.pdf},
doi = {10.1186/1752-0509-8-81},
issn = {17520509},
year  = {2014},
date = {2014-01-01},
journal = {BMC Systems Biology},
volume = {8},
number = {1},
pages = {1--15},
abstract = {Background: Genomic, proteomic and high-throughput gene expression data, when integrated, can be used to map the interaction networks between genes and proteins. Different approaches have been used to analyze these networks, especially in cancer, where mutations in biologically related genes that encode mutually interacting proteins are believed to be involved. This system of integrated networks as a whole exhibits emergent biological properties that are not obvious at the individual network level. We analyze the system in terms of modules, namely a set of densely interconnected nodes that can be further divided into submodules that are expected to participate in multiple biological activities in coordinated manner.Results: In the present work we construct two layers of the breast cancer network: the gene layer, where the correlation network of breast cancer genes is analyzed to identify gene modules, and the protein layer, where each gene module is extended to map out the network of expressed proteins and their interactions in order to identify submodules. Each module and its associated submodules are analyzed to test the robustness of their topological distribution. The constituent biological phenomena are explored through the use of the Gene Ontology. We thus construct a " network of networks" , and demonstrate that both the gene and protein interaction networks are modular in nature. By focusing on the ontological classification, we are able to determine the entire GO profiles that are distributed at different levels of hierarchy. Within each submodule most of the proteins are biologically correlated, and participate in groups of distinct biological activities.Conclusions: The present approach is an effective method for discovering coherent gene modules and protein submodules. We show that this also provides a means of determining biological pathways (both novel and as well those that have been reported previously) that are related, in the present instance, to breast cancer. Similar strategies are likely to be useful in the analysis of other diseases as well. textcopyright 2014 Srivastava et al.; licensee BioMed Central Ltd.},
keywords = {Gene expression, Gene ontology, Modules, Networks, Protein-protein interaction},
pubstate = {published},
tppubtype = {article}
}
@article{Karnatak2014,
title = {Conjugate coupling in ecosystems: Cross-predation stabilizes food webs},
author = {Rajat Karnatak and Ram Ramaswamy and Ulrike Feudel},
url = {http://dx.doi.org/10.1016/j.chaos.2014.07.003},
doi = {10.1016/j.chaos.2014.07.003},
issn = {09600779},
year  = {2014},
date = {2014-01-01},
journal = {Chaos, Solitons and Fractals},
volume = {68},
pages = {48--57},
publisher = {Elsevier Ltd},
abstract = {We study the dynamics of two predator-prey systems that are coupled via cross-predation, in which each predator consumes also the other prey. This setup constitutes a model system in which conjugate coupling emerges naturally and denotes the transition from two separate food chains to a food web. We show that cross-predation of a certain strength leads to amplitude death stabilizing the food web in a new equilibrium. },
keywords = {Conjugate Coupling, Population Dynamics, Predator-Prey},
pubstate = {published},
tppubtype = {article}
}
@article{Punetha2014,
title = {Phase-locked regimes in delay-coupled oscillator networks},
author = {Nirmal Punetha and Awadhesh Prasad and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/158.pdf},
doi = {10.1063/1.4897360},
issn = {10541500},
year  = {2014},
date = {2014-01-01},
journal = {Chaos},
volume = {24},
number = {4},
abstract = {textcopyright 2014 AIP Publishing LLC. For an ensemble of globally coupled oscillators with time-delayed interactions, an explicit relation for the frequency of synchronized dynamics corresponding to different phase behaviors is obtained. One class of solutions corresponds to globally synchronized in-phase oscillations. The other class of solutions have mixed phases, and these can be either randomly distributed or can be a splay state, namely with phases distributed uniformly on a circle. In the strong coupling limit and for larger networks, the in-phase synchronized configuration alone remains. Upon variation of the coupling strength or the size of the system, the frequency can change discontinuously, when there is a transition from one class of solutions to another. This can be from the in-phase state to a mixed-phase state, but can also occur between two in-phase configurations of different frequency. Analytical and numerical results are presented for coupled Landau-Stuart oscillators, while numerical results are shown for Rössler and FitzHugh-Nagumo systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Saxena2014,
title = {Amplitude death: The cessation of oscillations in coupled nonlinear dynamical systems},
author = {Garima Saxena and Nirmal Punetha and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/RC44.pdf},
doi = {10.1063/1.4865354},
issn = {15517616},
year  = {2014},
date = {2014-01-01},
journal = {AIP Conference Proceedings},
volume = {1582},
pages = {158--171},
abstract = {Here we extend a recent review (Physics Reports $backslash$bf 521, 205 (2012)) of amplitude death, namely the suppression of oscillations due to the coupling interactions between nonlinear dynamical systems. This is an important emergent phenomenon that is operative under a variety of scenarios. We summarize results of recent studies that have significantly added to our understanding of the mechanisms that underlie the process, and also discuss the phase--flip transition, a characteristic and unusual effect that occurs in the transient dynamics as the oscillations die out.},
keywords = {Amplitude quenching, Bifurcation, Control Network, Fixed-point solution, Interaction, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Manchanda2013,
title = {Scaling behavior in probabilistic neuronal cellular automata},
author = {Kaustubh Manchanda and Avinash Chand Yadav and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/146.pdf},
doi = {10.1103/PhysRevE.87.012704},
issn = {15393755},
year  = {2013},
date = {2013-01-01},
journal = {Physical Review E},
volume = {87},
number = {1},
pages = {1--6},
abstract = {We study a neural network model of interacting stochastic discrete two-state cellular automata on a regular lattice. The system is externally tuned to a critical point which varies with the degree of stochasticity (or the effective temperature). There are avalanches of neuronal activity, namely, spatially and temporally contiguous sites of activity; a detailed numerical study of these activity avalanches is presented, and single, joint, and marginal probability distributions are computed. At the critical point, we find that the scaling exponents for the variables are in good agreement with a mean-field theory. textcopyright 2013 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Bilal2013,
title = {Quasiperiodically driven maps in the low-dissipation limit},
author = {Shakir Bilal and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/147.pdf},
doi = {10.1103/PhysRevE.87.034901},
issn = {15393755},
year  = {2013},
date = {2013-01-01},
journal = {Physical Review E},
volume = {87},
number = {3},
pages = {3--6},
abstract = {We study the quasiperiodically driven Hénon and Standard maps in the weak dissipative limit. In the absence of forcing, there are a large number of coexisting periodic attractors. Although chaotic attractors can also be found, these typically have vanishingly small basins of attraction. Quasiperiodic forcing reduces the multistability in the system, and as the bifurcation parameter is varied, strange nonchaotic attractors (SNAs) are created. The attractor basin for SNAs appears to be the largest among those of all coexisting attractors at such a transition. textcopyright 2013 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Agrawal2013,
title = {Driving-induced bistability in coupled chaotic attractors},
author = {Manish Agrawal and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/148.pdf},
doi = {10.1103/PhysRevE.87.042909},
issn = {15393755},
year  = {2013},
date = {2013-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {87},
number = {4},
pages = {1--5},
abstract = {We examine the effects of symmetry--preserving and breaking interactions in a drive--response system where the response has an invariant symmetry in the absence of the drive. Subsequent to the onset of generalized synchronization, we find that there can be more than one stable attractor. Numerical, as well as analytical results establish the presence of phase synchrony in such coexisting attractors. These results are robust to external noise.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Keller2013,
title = {Nature of weak generalized synchronization in chaotically driven maps},
author = {Gerhard Keller and Haider H Jafri and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/149.pdf},
doi = {10.1103/PhysRevE.87.042913},
issn = {15393755},
year  = {2013},
date = {2013-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {87},
number = {4},
pages = {1--7},
abstract = {Weak generalized synchrony in a drive-response system occurs when the response dynamics is a unique but nondifferentiable function of the drive, in a manner that is similar to the formation of strange nonchaotic attractors in quasiperiodically driven dynamical systems. We consider a chaotically driven monotone map and examine the geometry of the limit set formed in the regime of weak generalized synchronization. The fractal dimension of the set of zeros is studied both analytically and numerically. We further examine the stable and unstable sets formed and measure the regularity of the coupling function. The stability index as well as the dimension spectrum of the equilibrium measure can be computed analytically.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{BILAL2013b,
title = {The generalized time-delayed Hénon map: Bifurcations and dynamics},
author = {Shakir Bilal and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/150.pdf},
doi = {10.1142/s0218127413500454},
issn = {0218-1274},
year  = {2013},
date = {2013-01-01},
journal = {International Journal of Bifurcation and Chaos},
volume = {23},
number = {03},
pages = {1350045},
abstract = {We analyze the bifurcations of a family of time-delayed Hénon maps of increasing dimension and determine the regions where the motion is attracted to different dynamical states. As a function of parameters that govern nonlinearity and dissipation, boundaries that confine asymptotic periodic motion are determined analytically, and we examine their dependence on the dimension d. For large d these boundaries converge. In low dimensions both the period-doubling and quasiperiodic routes to chaos coexist in the parameter space, but for high dimensions the latter predominates and prior to the onset of chaos, the systems exhibit multistability. When the nonlinearity parameter is varied, the dimension of chaotic attractors in the systems changes smoothly with increasing number of non-negative Lyapunov exponents. textcopyright 2013 World Scientific Publishing Company.},
keywords = {cient, di ff eomorphism, dissipative map, high dimension, limiting, normal form coe ffi},
pubstate = {published},
tppubtype = {article}
}
@article{Saxena2013,
title = {Amplitude death phenomena in delay-coupled Hamiltonian systems},
author = {Garima Saxena and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/151.pdf},
doi = {10.1103/PhysRevE.87.052912},
issn = {15393755},
year  = {2013},
date = {2013-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {87},
number = {5},
pages = {1--5},
abstract = {Hamiltonian systems, when coupled via time-delayed interactions, do not remain conservative. In the uncoupled system, the motion can typically be periodic, quasiperiodic, or chaotic. This changes drastically when delay coupling is introduced since now attractors can be created in the phase space. In particular, for sufficiently strong coupling there can be amplitude death (AD), namely, the stabilization of point attractors and the cessation of oscillatory motion. The approach to the state of AD or oscillation death is also accompanied by a phase flip in the transient dynamics. A discussion and analysis of the phenomenology is made through an application to the specific cases of harmonic as well as anharmonic coupled oscillators, in particular the Hénon-Heiles system.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ujjwal2013,
title = {Chimeras with multiple coherent regions},
author = {Sangeeta Rani Ujjwal and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/152.pdf},
doi = {10.1103/PhysRevE.88.032902},
issn = {15393755},
year  = {2013},
date = {2013-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {88},
number = {3},
abstract = {We study chimeric states in a coupled phase oscillator system with piecewise linear nonlocal coupling. By modifying the details of the coupling, it is possible to obtain multiple chimeric states with a specified number of coherent regions and with specified phase relationships. The case of a two-component chimera is illustrated and the generalization to arbitrary chimeric configurations is discussed. The phase relations between the two clusters of phase oscillators is described in some detail. textcopyright 2013 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{ChandYadav2013,
title = {Memoryless nonlinear response: A simple mechanism for the 1/f noise},
author = {Avinash {Chand Yadav} and Ramakrishna Ramaswamy and Deepak Dhar},
url = {https://ramramaswamy.org/papers/153.pdf},
doi = {10.1209/0295-5075/103/60004},
issn = {02955075},
year  = {2013},
date = {2013-01-01},
journal = {Epl},
volume = {103},
number = {6},
abstract = {Discovering the mechanism underlying the ubiquity of "1/f$alpha$" noise has been a long-standing problem. The wide range of systems in which the fluctuations show the implied long-time correlations suggests the existence of some simple and general mechanism that is independent of the details of any specific system. We argue here that a memoryless nonlinear response suffices to explain the observed nontrivial values of $alpha$: a random input noisy signal S(t) with a power spectrum varying as 1/f$alpha$′, when fed to an element with such a response function R, gives an output that can have a power spectrum 1/f$alpha$with$alpha$ ≤ $alpha$ ′. As an illustrative example, we show that an input Brownian noise ($alpha$′=2) acting on a device with a sigmoidal response function R(S)=sgn, (S)Sx with x textless 1, produces an output with $alpha$= 3/2+x, for0 textless x textless 1/2 discussion is easily extended to more general types of input noise as well as more general response functions. textcopyright Copyright EPLA, 2013.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kumar2013,
title = {Local Properties of Vigilance States: EMD Analysis of EEG Signals during Sleep-Waking States of Freely Moving Rats},
author = {Rupesh Kumar and Ram Ramaswamy and Birendra {Nath Mallick}},
url = {https://ramramaswamy.org/papers/154.pdf},
doi = {10.1371/journal.pone.0078174},
issn = {19326203},
year  = {2013},
date = {2013-01-01},
journal = {PLoS ONE},
volume = {8},
number = {10},
pages = {1--13},
abstract = {Understanding the inherent dynamics of the EEG associated to sleep-waking can provide insights into its basic neural regulation. By characterizing the local properties of the EEG using power spectrum, empirical mode decomposition (EMD) and Hilbert-spectral analysis, we can examine the dynamics over a range of time-scales. We analyzed rat EEG during wake, NREMS and REMS using these methods. The average instantaneous phase, power spectral density (PSD) of intrinsic mode functions (IMFs) and the energy content in various frequency bands show characteristic changes in each of the vigilance states. The 2nd and 7th IMFs show changes in PSD for wake and REMS, suggesting that those modes may carry wake- and REMS-associated cognitive, conscious and behavior-specific information of an individual even though the EEG may appear similar. The energy content in $theta$2 (6 Hz-9 Hz) band of the 1st IMF for REMS is larger than that of wake. The decrease in the phase function of IMFs from wake to REMS to NREMS indicates decrease of the mean frequency in these states, respectively. The rate of information processing in waking state is more in the time scale described by the first three IMFs than in REMS state. However, for IMF5-IMF7, the rate is more for REMS than that for wake. We obtained Hilbert-Huang spectral entropy, which is a suitable measure of information processing in each of these state-specific EEG. It is possible to evaluate the complex dynamics of the EEG in each of the vigilance states by applying measures based on EMD and Hilbert-transform. Our results suggest that the EMD based nonlinear measures of the EEG can provide useful estimates of the information possessed by various oscillations associated with the vigilance states. Further, the EMD-based spectral measures may have implications in understanding anatamo-physiological correlates of sleep-waking behavior and clinical diagnosis of sleep-pathology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Shastri2013,
title = {Gender diversity in physics in India: Interventions so far and recommendations for the future},
author = {P Shastri and R Ramaswamy and S Narasimhan and S Rao and S Ubale and S Kulkarni},
url = {https://ramramaswamy.org/papers/OA15.pdf},
doi = {10.1063/1.4794242},
issn = {0094243X},
year  = {2013},
date = {2013-01-01},
journal = {AIP Conference Proceedings},
volume = {1517},
pages = {106--107},
abstract = {Several governmental policy initiatives have already taken shape in India during the last few years to address the gender imbalance in the sciences. These initiatives and the barriers to gender inequity that persist in physics are summarized. Recommendations that build upon the positive impact of these initiatives and address the gaps are outlined. Several of the inferences presented use data for the sciences in general when physics-specific data are not available.textcopyright 2013 American Institute of Physics.},
keywords = {Gender Equity},
pubstate = {published},
tppubtype = {article}
}
@article{Jafri2012,
title = {Phantom instabilities in adiabatically driven systems: Dynamical sensitivity to computational precision},
author = {H H Jafri, T U Singh and R Ramaswamy},
url = {https://pubs.aip.org/aip/cha/article-pdf/doi/10.1063/1.4732542/14604784/033103\_1\_online.pdf},
doi = {10.1063/1.4732542},
issn = {1054-1500},
year  = {2012},
date = {2012-09-01},
journal = {Chaos},
volume = {22},
number = {3},
pages = {033103},
abstract = {We study the robustness of dynamical phenomena in adiabatically driven nonlinear mappings with skew-product structure. Deviations from true orbits are observed when computations are performed with inadequate numerical precision for monotone, periodic, or quasiperiodic driving. The effect of slow modulation is to “freeze” orbits in long intervals of purely contracting or purely expanding dynamics in the phase space. When computations are carried out with low precision, numerical errors build up phantom instabilities which ultimately force trajectories to depart from the true motion. Thus, the dynamics observed with finite precision computation shows sensitivity to numerical precision: the minimum accuracy required to obtain “true” trajectories is proportional to an internal timescale that can be defined for the adiabatic system.},
keywords = {phantom instabilities},
pubstate = {published},
tppubtype = {article}
}
@book{Mandakini2012,
title = {The Girl’s Guide to a Life in Science},
editor = {Mandakini Dubey, Ram RAmaswamy, Rohini Godbole},
url = {https://zubaanbooks.com/shop/the-girls-guide-to-a-life-in-science/},
isbn = {9789381017111},
year  = {2012},
date = {2012-01-01},
publisher = {Zubaan Books, New Delhi and Indian Academy of Sciences, Bangalore},
edition = {First Edition},
abstract = {Inspiring, informative, insightful? meet some of India's most celebrated female scientists. What led them to choose their particular field? Who encouraged them? What were their struggles? What are their sources of inspiration? What are the key questions at the cutting edge of modern research? Why choose a life in science at all? From astrophysics to zoology, learn what it takes to make a career in science.

Telugu translation, by A V Padmakara Reddy: Vignanashastra Rangamlo Mahila Sphoorthipradatalu, (Emesco Books, Vijaywada, 2013).},
keywords = {Book, Women in Science},
pubstate = {published},
tppubtype = {book}
}
@article{Banerjee2012,
title = {Enhancing synchrony in chaotic oscillators by dynamic relaying},
author = {Ranjib Banerjee and Dibakar Ghosh and E Padmanaban and R Ramaswamy and L M Pecora and Syamal K Dana},
url = {https://ramramaswamy.org/papers/140.pdf},
doi = {10.1103/PhysRevE.85.027201},
issn = {15393755},
year  = {2012},
date = {2012-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {85},
number = {2},
pages = {5--9},
abstract = {In a chain of mutually coupled oscillators, the coupling threshold for synchronization between the outermost identical oscillators decreases when a type of impurity (in terms of parameter mismatch) is introduced in the inner oscillator(s). The outer oscillators interact indirectly via dynamic relaying, mediated by the inner oscillator(s). We confirm this enhancing of critical coupling in the chaotic regimes of the Lorenz system, in the Rössler system in the absence of coupling delay, and in the Mackey-Glass system with delay coupling. The enhancing effect is experimentally verified in the electronic circuit of Rössler oscillators. textcopyright 2012 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Punetha2012,
title = {Frequency discontinuity and amplitude death with time-delay asymmetry},
author = {Nirmal Punetha and Rajat Karnatak and Awadhesh Prasad and Jürgen Kurths and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/141.pdf},
doi = {10.1103/PhysRevE.85.046204},
issn = {15393755},
year  = {2012},
date = {2012-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {85},
number = {4},
pages = {1--8},
abstract = {We consider oscillators coupled with asymmetric time delays, namely, when the speed of information transfer is direction dependent. As the coupling parameter is varied, there is a regime of amplitude death within which there is a phase-flip transition. At this transition the frequency changes discontinuously, but unlike the equal delay case when the relative phase difference changes by $pi$, here the phase difference changes by an arbitrary value that depends on the difference in delays. We consider asymmetric delays in coupled Landau-Stuart oscillators and Rössler oscillators. Analytical estimates of phase synchronization frequencies and phase differences are obtained by separating the evolution equations into phase and amplitude components. Eigenvalues and eigenvectors of the Jacobian matrix in the neighborhood of the transition also show an ävoided crossing," as has been observed in previous studies with symmetric delays. textcopyright 2012 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Yadav2012,
title = {Power spectrum of mass and activity fluctuations in a sandpile},
author = {Avinash Chand Yadav and Ramakrishna Ramaswamy and Deepak Dhar},
url = {https://ramramaswamy.org/papers/142.pdf},
doi = {10.1103/PhysRevE.85.061114},
issn = {15393755},
year  = {2012},
date = {2012-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {85},
number = {6},
pages = {1--8},
abstract = {We consider a directed Abelian sandpile on a strip of size 2√ón, driven by adding a grain randomly at the left boundary after every T timesteps. We establish the exact equivalence of the problem of mass fluctuations in the steady state and the number of zeros in the ternary-base representation of the position of a random walker on a ring of size 3n. We find that while the fluctuations of mass have a power spectrum that varies as 1/f for frequencies in the range 3 -2n f 1/T, the activity fluctuations in the same frequency range have a power spectrum that is linear in f. textcopyright 2012 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Rawal2012,
title = { Distribution of MGEs and their insertion sites in the Macaca mulatta genome },
author = {Kamal Rawal and Avantika Priya and Aman Malik and Radhika Bahl and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/144.pdf},
doi = {10.4161/mge.21074},
year  = {2012},
date = {2012-01-01},
journal = {Mobile Genetic Elements},
volume = {2},
number = {3},
pages = {133--141},
abstract = {Mobile genetic elements (MGEs) are fragments of DNA that can move around within the genome through retrotransposition. These are responsible for various important events such as gene inactivation, transduction, regulation of gene expression and genome expansion. The present work involves the identification and study of the distribution of Alu and L1 retrotransposons in the genome of Macaca mulatta, an extensively used organism in biomedical studies. We also make comparisons with MGE distributions in other primate genomes and study the physicochemical properties of the local DNA structure around the transposon insertion site using ELAN. The present work also includes computational testing of the pre-insertion loci in order to detect unique features based on DNA structure, thermodynamic considerations and protein interaction measures. Although there is significant sequence divergence between the elements of M. mulatta and H. sapiens, their genome wide distribution is very similar; comparing the distribution of L1's in all available X chromosome sequences suggests a common mechanism behind the spread of MGE's in primate genomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Alam2012,
title = {Stochastic synchronization of interacting pathways in testosterone model},
author = {Md Jahoor Alam and Gurumayum Reenaroy Devi and K.Brojen R Singh and R Ramaswamy and Sonu Chand Thakur and Indrajit B Sharma},
url = {http://dx.doi.org/10.1016/j.compbiolchem.2012.08.001},
doi = {10.1016/j.compbiolchem.2012.08.001},
issn = {14769271},
year  = {2012},
date = {2012-01-01},
journal = {Computational Biology and Chemistry},
volume = {41},
pages = {10--17},
publisher = {Elsevier Ltd},
abstract = {We examine the possibilities of various coupling mechanisms among a group of identical stochastic oscillators via Chemical Langevin formalism where each oscillator is modeled by stochastic model of testosterone (T) releasing pathway. Our results show that the rate of synchrony among the coupled oscillators depends on various parameters namely fluctuating factor, coupling constants $epsilon$, and interestingly on system size. The results show that synchronization is achieved much faster in classical deterministic system rather than stochastic system. Then we do large scale simulation of such coupled pathways using stochastic simulation algorithm and the detection of synchrony is measured by various order parameters such as synchronization manifolds, phase plots etc and found that the proper synchrony of the oscillators is maintained in different coupling mechanisms and support our theoretical claims. We also found that the coupling constant follows power law behavior with the systems size (V) by $epsilon$ ∼ AV-$gamma$, where $gamma$ = 1 and A is a constant. We also examine the phase transition like behavior in all coupling mechanisms that we have considered for simulation. The behavior of the system is also investigated at thermodynamic limit; where V→ ∞, molecular population, N→ ∞ but NV→finite, to see the role of noise in information processing and found the destructive role in the rate of synchronization. textcopyright 2012 Elsevier Ltd. All rights reserved.},
keywords = {Cell signaling, Coupling, Intercellular communication, Intracellular communication, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2012,
title = {Integrating mathematics and history : The scholarship of D D Kosambi},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/OA13.pdf},
year  = {2012},
date = {2012-01-01},
journal = {Economic & Political Weekly },
volume = {xlvii},
number = {3},
pages = {58--62},
abstract = {Today, D D Kosambi’s significance as a historian greatly
overshadows his reputation and contributions in
mathematics. Kosambi simultaneously worked in both
areas for much of his adult life, and to understand the
body of his work either in the social sciences or in
mathematics, an appreciation of the complementarity of
his interests is essential. An understanding of Kosambi
the historian can only be enhanced by an appreciation of
Kosambi the mathematician. In a fundamental way,
Kosambi embodied the multidisciplinary approach,
channelling diverse interests – indeed combining them
– to create scholarship of high order.},
keywords = {Kosambi, Mathematics and History},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2012a,
title = {Science at the interface : UoH ' s quest for innovation and excellence},
author = {Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/OA14.pdf
http://AcademicExecutives.elsevier.com},
year  = {2012},
date = {2012-01-01},
journal = {The Academic Executive Brief},
volume = {2},
number = {2},
pages = {16--17},
keywords = {Innovation, UoH},
pubstate = {published},
tppubtype = {article}
}
@article{Saxena2012,
title = {Amplitude death: The emergence of stationarity in coupled nonlinear systems},
author = {Garima Saxena and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/RC43.pdf},
doi = {10.1016/j.physrep.2012.09.003},
issn = {03701573},
year  = {2012},
date = {2012-01-01},
journal = {Physics Reports},
volume = {521},
number = {5},
pages = {205--228},
abstract = {When nonlinear dynamical systems are coupled, depending on the intrinsic dynamics and the manner in which the coupling is organized, a host of novel phenomena can arise. In this context, an important emergent phenomenon is the complete suppression of oscillations, formally termed amplitude death (AD). Oscillations of the entire system cease as a consequence of the interaction, leading to stationary behavior. The fixed points which the coupling stabilizes can be the otherwise unstable fixed points of the uncoupled system or can correspond to novel stationary points. Such behavior is of relevance in areas ranging from laser physics to the dynamics of biological systems. In this review we discuss the characteristics of the different coupling strategies and scenarios that lead to AD in a variety of different situations, and draw attention to several open issues and challenging problems for further study. textcopyright 2012 Elsevier B.V.},
keywords = {Amplitude quenching, Bifurcation, Control, Fixed-point solution, Interaction, Network, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Manchanda2011,
title = {Order parameter for the transition from strong to weak generalized synchrony from empirical mode decomposition analysis},
author = {Kaustubh Manchanda and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/134.pdf},
doi = {10.1103/PhysRevE.83.066201},
issn = {15393755},
year  = {2011},
date = {2011-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {83},
number = {6},
pages = {1--6},
abstract = {We examine driven nonlinear dynamical systems that are known to be in a state of generalized synchronization with an external drive. The chaotic time series of the response system are subject to empirical mode decomposition analysis. The instantaneous intrinsic mode frequencies (and their variance) present in these signals provide suitable order parameters for detecting the transition between the regimes of strong and weak generalized synchrony. Application is made to a variety of chaotically driven flows as well as maps. textcopyright 2011 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sharma2011,
title = {Phase-flip transition in relay-coupled nonlinear oscillators},
author = {Amit Sharma and Manish Dev Shrimali and Awadhesh Prasad and Ram Ramaswamy and Ulrike Feudel},
url = {https://ramramaswamy.org/papers/135.pdf},
doi = {10.1103/PhysRevE.84.016226},
issn = {15393755},
year  = {2011},
date = {2011-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {84},
number = {1},
pages = {1--5},
abstract = {We study the dynamics of oscillators that are coupled in relay; namely, through an intermediary oscillator. From previous studies it is known that the oscillators show a transition from in-phase to out-of-phase oscillations or vice versa when the interactions involve a time delay. Here we show that, in the absence of time delay, relay coupling through conjugate variables has the same effect. However, this phase-flip transition does not occur abruptly at a certain critical value of the coupling parameter. Instead we find a parameter region around the phase-flip transition where bistability occurs. In this parameter interval in-phase and out-of-phase oscillations coexist with changing sizes of their basins of attraction. Further increase of the coupling strength leads to amplitude death and subsequently to the stabilization of a fixed point. These transitions are characterized through various quantities such as the average phase difference and crossings in the spectrum of Lyapunov exponents. Numerical results are presented for a specific case of coupled Rössler-like oscillators. textcopyright 2011 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Rawal2011,
title = {Genome-wide analysis of mobile genetic element insertion sites},
author = {Kamal Rawal and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/136.pdf},
doi = {10.1093/nar/gkr337},
issn = {03051048},
year  = {2011},
date = {2011-01-01},
journal = {Nucleic Acids Research},
volume = {39},
number = {16},
pages = {6864--6878},
abstract = {Mobile genetic elements (MGEs) account for a significant fraction of eukaryotic genomes and are implicated in altered gene expression and disease. We present an efficient computational protocol for MGE insertion site analysis. ELAN, the suite of tools described here uses standard techniques to identify different MGEs and their distribution on the genome. One component, DNASCANNER analyses known insertion sites of MGEs for the presence of signals that are based on a combination of local physical and chemical properties. ISF (insertion site finder) is a machine-learning tool that incorporates information derived from DNASCANNER. ISF permits classification of a given DNA sequence as a potential insertion site or not, using a support vector machine. We have studied the genomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Entamoeba histolytica via a protocol whereby DNASCANNER is used to identify a common set of statistically important signals flanking the insertion sites in the various genomes. These are used in ISF for insertion site prediction, and the current accuracy of the tool is over 65. We find similar signals at gene boundaries and splice sites. Together, these data are suggestive of a common insertion mechanism that operates in a variety of eukaryotes. textcopyright 2011 The Author(s).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Singh2011,
title = {Excitable Nodes on Random Graphs: Relating Dynamics to Network Structure},
author = {Thounaojam Umeshkanta Singh and Kaustubh Manchanda and Ramakrishna Ramaswamy and Amitabha Bose},
url = {https://ramramaswamy.org/papers/137.pdf},
doi = {10.1137/100802864},
year  = {2011},
date = {2011-01-01},
journal = {SIAM Journal on Applied Dynamical Systems},
volume = {10},
number = {3},
pages = {987--1012},
abstract = {Rhythmic activity in complex systems is generated and sustained through interactions among the constituent units. In this paper we study the interplay between topology and dynamics of excitable nodes on random networks. The nodal dynamics are discrete, each node being in three possible states: active, refractory, or silent. Loading rules are defined whereby a subset of active nodes may be able to convert a silent node into an active one at the next time step. In the case of simple loading (SL) a silent node becomes active if it receives input from any neighbor. In the majority rules (MR) loading, a silent node fires when the majority of its neighbors are active. We address the question of whether a particular network design pattern confers dynamical advantage for the generation and sustainment of rhythmic activity. We find that the intrinsic properties of a node and the rules for interaction between them determine which structural features of the graph permit sustained activity. With SL the level of activity in the graph increases monotonically with the probability of connections between nodes, while for MR, the level of activity may be either monotonic or nonmonotonic, depending on parameters. Copyright textcopyright by SIAM.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Agrawal2011,
title = {Relaying phase synchrony in chaotic oscillator chains},
author = {Manish Agrawal and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/138.pdf},
doi = {10.1103/PhysRevE.84.056205},
issn = {15393755},
year  = {2011},
date = {2011-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {84},
number = {5},
pages = {1--6},
abstract = {We study the manner in which the effect of an external drive is transmitted through mutually coupled response systems by examining the phase synchrony between the drive and the response. Two different coupling schemes are used. Homogeneous couplings are via the same variables while heterogeneous couplings are through different variables. With the latter scenario, synchronization regimes are truncated with an increasing number of mutually coupled oscillators in contrast to homogeneous coupling schemes. Our results are illustrated for systems of coupled chaotic Rössler oscillators. textcopyright 2011 American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Vaz2011,
title = {Micrornas modulate the dynamics of the NF-$kappa$B signaling pathway},
author = {Candida Vaz and Arvind Singh Mer and Alok Bhattacharya and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/139.pdf},
doi = {10.1371/journal.pone.0027774},
issn = {19326203},
year  = {2011},
date = {2011-01-01},
journal = {PLoS ONE},
volume = {6},
number = {11},
abstract = {Background: NF-$kappa$B, a major transcription factor involved in mammalian inflammatory signaling, is primarily involved in regulation of response to inflammatory cytokines and pathogens. Its levels are tightly regulated since uncontrolled inflammatory response can cause serious diseases. Mathematical models have been useful in revealing the underlying mechanisms, the dynamics, and other aspects of regulation in NF-$kappa$B signaling. The recognition that miRNAs are important regulators of gene expression, and that a number of miRNAs target different components of the NF-$kappa$B network, motivate the incorporation of miRNA regulated steps in existing mathematical models to help understand the quantitative aspects of miRNA mediated regulation. Methodology/Principal findings: In this study, two separate scenarios of miRNA regulation within an existing model are considered. In the first, miRNAs target adaptor proteins involved in the synthesis of IKK that serves as the NF-$kappa$B activator. In the second, miRNAs target different isoforms of I$kappa$B that act as NF-$kappa$B inhibitors. Simulations are carried out under two different conditions: when all three isoforms of I$kappa$B are present (wild type), and when only one isoform (I$kappa$B$alpha$) is present (knockout type). In both scenarios, oscillations in the NF-$kappa$B levels are observed and are found to be dependent on the levels of miRNAs. Conclusions/Significance: Computational modeling can provide fresh insights into intricate regulatory processes. The introduction of miRNAs affects the dynamics of the NF-$kappa$B signaling pathway in a manner that depends on the role of the target. This "fine-tuning" property of miRNAs helps to keep the system in check and prevents it from becoming uncontrolled. The results are consistent with earlier experimental findings. textcopyright 2011 Vaz, et al.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Manchanda2011a,
title = {Dynamics of excitable nodes on random graphs},
author = {K Manchanda and Umeshkanta T Singh and R Ramaswamy},
url = {https://ramramaswamy.org/papers/RC40.pdf},
doi = {10.1007/s12043-011-0180-6},
issn = {03044289},
year  = {2011},
date = {2011-01-01},
journal = {Pramana - Journal of Physics},
volume = {77},
number = {5},
pages = {803--809},
abstract = {We study the interplay of topology and dynamics of excitable nodes on random networks. Comparison is made between systems grown by purely random (Erd?os-Rényi) rules and those grown by the Achlioptas process. For a given size, the growth mechanism affects both the thresholds for the emergence of different structural features as well as the level of dynamical activity supported on the network. textcopyright Indian Academy of Sciences.},
keywords = {Excitable nodes, Networks, Rhythmic activity},
pubstate = {published},
tppubtype = {article}
}
@article{Saxena2011,
title = {The effect of finite response-time in coupled dynamical systems},
author = {Garima Saxena and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/RC41.pdf},
doi = {10.1007/s12043-011-0179-z},
issn = {03044289},
year  = {2011},
date = {2011-01-01},
journal = {Pramana - Journal of Physics},
volume = {77},
number = {5},
pages = {865--871},
abstract = {The paper investigates synchronization in unidirectionally coupled dynamical systems wherein the influence of drive on response is cumulative: coupling signals are integrated over a time interval t . A major consequence of integrative coupling is that the onset of the generalized and phase synchronization occurs at higher coupling compared to the instantaneous (t = 0) case. The critical coupling strength at which synchronization sets in is found to increase with t . The systems explored are the chaotic Rössler and limit cycle (the Landau-Stuart model) oscillators. For coupled Rössler oscillators the region of generalized synchrony in the phase space is intercepted by an asynchronous region which corresponds to anomalous generalized synchronization. textcopyright Indian Academy of Sciences.},
keywords = {Distributed delay, Drive-response, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Singh2011a,
title = {Spectral analysis of long noncoding RNAs},
author = {Vikram Singh and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/RC42.pdf},
doi = {10.5176/978-981-08-8119-1_bicb27},
isbn = {9789810881191},
year  = {2011},
date = {2011-01-01},
number = {Table I},
pages = {978--981},
keywords = {detrended fluctuation analysis, DNA, power spectrum analysis, RNA, wavelet transforms},
pubstate = {published},
tppubtype = {article}
}
@article{Cruz2010,
title = {The phase–flip transition in coupled electrochemical cells},
author = {J M Cruz, J Escalona, P Parmananda, R Karnatak, A Prasad, and R
Ramaswamy
},
url = {https://doi.org/10.1103/PhysRevE.81.046213},
doi = {10.1103/PhysRevE.81.046213},
year  = {2010},
date = {2010-04-26},
journal = {Physical Review E},
volume = {81},
number = {4},
pages = {046213},
abstract = {Time delay is introduced in the coupling between a pair of electrochemical cells. As coupling parameters are varied, the anodic current in the two cells oscillate in synchrony in regimes of periodic as well as chaotic dynamics. When the time delay is varied a phase-flip transition is observed: the relative phase between the synchronized oscillations changes abruptly by 
π
. This is accompanied by an experimentally measurable discontinuous change in the frequency of the synchronized oscillators.},
keywords = {electrochemical cells, phase transition},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad2010b,
title = {Amplitude death in nonlinear oscillators with nonlinear coupling},
author = {A Prasad, M Dhamala, B M Adhikari, and R Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevE.81.027201},
doi = {10.1103/PhysRevE.81.027201},
year  = {2010},
date = {2010-02-08},
journal = {Physical Review E},
volume = {81},
number = {2},
pages = {027201},
abstract = {Amplitude death is the cessation of oscillations that occurs in coupled nonlinear systems when fixed points are stabilized as a consequence of the interaction. We show here that this phenomenon is very general: it occurs in nonlinearly coupled systems in the absence of parameter mismatch or time delay although time-delayed interactions can enhance the effect. Application is made to synaptically coupled model neurons, nonlinearly coupled Rössler oscillators, as well as to networks of nonlinear oscillators with nonlinear coupling. By suitably designing the nonlinear coupling, arbitrary steady states can be stabilized.},
keywords = {Amplitude Death, Coupled Oscillators},
pubstate = {published},
tppubtype = {article}
}
@article{Agrawal2010,
title = { Quasiperiodic forcing of coupled chaotic systems},
author = {M Agrawal, A Prasad, and R Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevE.81.026202},
doi = {10.1103/PhysRevE.81.026202},
year  = {2010},
date = {2010-02-04},
journal = {Physical Review E},
volume = {81},
number = {2},
pages = {026202},
abstract = {We study the manner in which the effect of quasiperiodic modulation is transmitted in a coupled nonlinear dynamical system. A system of Rössler oscillators is considered, one of which is subject to driving, and the dynamics of other oscillators which are, in effect, indirectly forced is observed. Strange nonchaotic dynamics is known to arise only in quasiperiodically driven systems, and thus the transmitted effect is apparent when such motion is seen in subsystems that are not directly modulated. We also find instances of imperfect phase synchronization with forcing, where the system transits from one phase synchronized state to another, with arbitrary phase slips. The stability of phase synchrony for arbitrary initial conditions with identical forcing is observed as a general property of strange nonchaotic motion.},
keywords = {Quasiperiodicity, Strange nonchaotic attractors, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Singh2010b,
title = {Transition to weak generalized synchrony in chaotically driven flows},
author = {T U Singh, H H Jafri, and R Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevE.81.016208},
doi = {10.1103/PhysRevE.81.016208},
year  = {2010},
date = {2010-01-14},
journal = {Physical Review E},
volume = {81},
number = {1},
pages = {016208},
abstract = {We study regimes of strong and weak generalized synchronization in chaotically forced nonlinear flows. The transition between these dynamical states can occur via a number of different routes, and here we examine the onset of weak generalized synchrony through intermittency and blowout bifurcations. The quantitative characterization of this dynamical transition is facilitated by measures that have been developed for the study of strange nonchaotic motion. Weak and strong generalized synchronous motion show contrasting sensitivity to parametric variation and have distinct distributions of finite-time Lyapunov exponents.},
keywords = {Chaos Theory, Generalized Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Shrimali2010,
title = {Delay-coupled discrete maps: Synchronization, bistability, and quasiperiodicity},
author = {Manish Dev Shrimali and Rangoli Sharan and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/129.pdf},
doi = {10.1016/j.physleta.2010.04.048},
issn = {03759601},
year  = {2010},
date = {2010-01-01},
journal = {Physics Letters, Section A: General, Atomic and Solid State Physics},
volume = {374},
number = {26},
pages = {2636--2639},
abstract = {The synchronization transition is studied in delay-coupled logistic maps. For low coupling, in-phase and out-of-phase synchronous dynamics coexist, and with increasing coupling there is a regime of quasiperiodicity before eventual attraction to a fixed point at a critical value of coupling that depends on the nonlinearity. The presence of a region of asynchrony separating two synchronized regimes-termed anomalous behaviour-has been observed earlier in continuous systems and is shown here to occur in delay mappings as well. There are regions of in-phase, anti-phase, and out-of-phase dynamics of periodic as well as chaotic attractors. textcopyright 2010 Elsevier B.V.},
keywords = {Coupled maps, Delay coupling, Synchronization},
pubstate = {published},
tppubtype = {article}
}
@article{Saxena2010,
title = {Dynamical effects of integrative time-delay coupling},
author = {Garima Saxena and Awadhesh Prasad and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/130.pdf},
doi = {10.1103/PhysRevE.82.017201},
issn = {15393755},
year  = {2010},
date = {2010-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {82},
number = {1},
pages = {1--4},
abstract = {We study coupled dynamical systems wherein the influence of one system on the other is cumulative: coupling signals are integrated over a time interval $tau$. A major consequence of integrative coupling is that amplitude death occurs over a wider range and in a single region in parameter space. For coupled limit cycle oscillators (the Landau-Stuart model) we obtain an analytic estimate for the boundary of this region while for coupled chaotic Lorenz oscillators numerical results are presented. For given $tau$ we find that there is a critical coupling strength at which the frequency of oscillations changes discontinuously. textcopyright 2010 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad2010,
title = {Targeted control of amplitude dynamics in coupled nonlinear oscillators},
author = {Awadhesh Prasad and Mukeshwar Dhamala and Bhim Mani Adhikari and Ramkrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/131.pdf},
doi = {10.1103/PhysRevE.82.027201},
issn = {15393755},
year  = {2010},
date = {2010-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {82},
number = {2},
pages = {8--11},
abstract = {We propose a general strategy for designing coupling functions in order to achieve a desired amplitude dynamics in coupled nonlinear oscillators. The target dynamics achieved by the proposed control schemes is a fixed-point motion at a desired amplitude level or a periodic motion at a desired frequency. The control schemes are illustrated with Rössler and Hindmarsh-Rose oscillators. textcopyright 2010 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karnatak2010,
title = {Nature of the phase-flip transition in the synchronized approach to amplitude death},
author = {Rajat Karnatak and Nirmal Punetha and Awadhesh Prasad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/132.pdf},
doi = {10.1103/PhysRevE.82.046219},
issn = {15393755},
year  = {2010},
date = {2010-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {82},
number = {4},
pages = {1--5},
abstract = {We study the dynamics of time-delay coupled limit-cycle oscillators in the amplitude death regime. Through a detailed analysis of the Jacobian at the fixed point, we show that the phase-flip transition, namely, the abrupt change from in-phase synchronized dynamics to antiphase synchronized dynamics, is associated with an interchange of the imaginary parts of complex pairs of eigenvalues at an ävoided crossing" of Lyapunov exponents as a parameter is varied. An order parameter for the transition is constructed through the eigenvectors of the Jacobian. textcopyright 2010 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Singh2010,
title = {Stochastic synchronization of circadian rhythms},
author = {Raj Kumar Brojen Singh and Vikram Singh and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/133.pdf},
doi = {10.1007/s11424-010-0208-x},
issn = {10096124},
year  = {2010},
date = {2010-01-01},
journal = {Journal of Systems Science and Complexity},
volume = {23},
number = {5},
pages = {978--988},
abstract = {Models of circadian genetic oscillators involving interlinked feedback processes in molecular level genetic networks in Drosophila melanogaster and Neurospora crassa are studied, and mechanisms whereby synchronization can arise in an assembly of cells are examined. The individual subcellular circadian oscillatory processes are stochastic in nature due to the small numbers of molecules that are involved, and are subject to large fluctuations. The authors investigate and present the simulations of the stochastic dynamics of ensembles of clock-regulating proteins in different nuclei that communicate via ancillary small molecules, environmental parameters, additive cellular noise, or through diffusive processes. The results show that the emergence of collective oscillations is a macroscopic observable which has its origins in the microscopic coupling between distinct cellular oscillators. textcopyright The Editorial Office of JSSC & Springer-Verlag Berlin Heidelberg 2010.},
keywords = {Coupling, Stochastic dynamics, Synchrony},
pubstate = {published},
tppubtype = {article}
}
@article{Gopinathan2009,
title = {Bridging the gender gap in Indian science},
author = {Asha Gopinathan},
url = {https://ramramaswamy.org/papers/27.8 1082-1084 Books and Arts.pdf},
doi = {10.1038/4601082a},
issn = {0028-0836},
year  = {2009},
date = {2009-01-01},
journal = {Nature},
volume = {460},
number = {7259},
pages = {1082--1082},
abstract = {A set of biographies reveals the trials and triumphs of India's women researchers, says Asha Gopinathan.},
keywords = {Gender Equity},
pubstate = {published},
tppubtype = {article}
}
@article{Nandi2009,
title = {miRNA-regulated dynamics in circadian oscillator models},
author = {Amitabha Nandi and Candida Vaz and Alok Bhattacharya and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/121.pdf},
doi = {10.1186/1752-0509-3-45},
issn = {17520509},
year  = {2009},
date = {2009-01-01},
journal = {BMC Systems Biology},
volume = {3},
pages = {1--16},
abstract = {Background: We have studied the dynamics of miRNA regulation in two models of circadian oscillators. miRNAs are a class of small RNA molecules (18-24 nucleotides) that are known to regulate gene expression at the post-transcriptional level by reducing the amount of proteins produced by translation. This is done either by blocking translation or by degradation of mRNAs, the latter being mainly due to the initiation of a set of processes induced by formation of the miRNA:mRNA complex. Although miRNAs are known to regulate a large number of fundamental biological processes such as growth and development, their role in the dynamics of regulation is not completely understood. In exceptional cases, in particular, they can also up-regulate gene expression. Results: We have studied simple biological systems wherein oscillations originate from negative auto regulation of gene expression. The regulation of gene expression by miRNAs is introduced into these models and the dynamics is studied via standard stochastic simulation techniques. We find that in addition to a reduction in the amplitude of the oscillation, inclusion of miRNAs in the models has the effect of altering the frequency of oscillation and thereby regulating the dynamics of protein production. Conclusion: miRNAs can have a profound effect on the dynamics of regulatory modules, both by control of amplitude, namely by affecting the level of gene expression, as well as by control or alteration of frequency, namely by interference with the temporal sequence of gene production or delivery. We believe that our results are valid for a variety of regulatory systems, beyond the exemplars discussed here. textcopyright 2009 Nandi et al; licensee BioMed Central Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Nandi2009a,
title = {Design strategies for the creation of aperiodic nonchaotic attractors},
author = {Amitabha Nandi and Sourav K Bhowmick and Syamal K Dana and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/122.pdf},
doi = {10.1063/1.3194250},
issn = {10541500},
year  = {2009},
date = {2009-01-01},
journal = {Chaos},
volume = {19},
number = {3},
pages = {1--8},
abstract = {Parametric modulation in nonlinear dynamical systems can give rise to attractors on which the dynamics is aperiodic and nonchaotic, namely, with largest Lyapunov exponent being nonpositive. We describe a procedure for creating such attractors by using random modulation or pseudorandom binary sequences with arbitrarily long recurrence times. As a consequence the attractors are geometrically fractal and the motion is aperiodic on experimentally accessible time scales. A practical realization of such attractors is demonstrated in an experiment using electronic circuits. textcopyright 2009 American Institute of Physics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karnatak2009,
title = {Synchronization regimes in conjugate coupled chaotic oscillators},
author = {Rajat Karnatak and Ram Ramaswamy and Awadhesh Prasad},
url = {https://ramramaswamy.org/papers/123.pdf},
doi = {10.1063/1.3236385},
issn = {10541500},
year  = {2009},
date = {2009-01-01},
journal = {Chaos},
volume = {19},
number = {3},
pages = {1--5},
abstract = {Nonlinear oscillators that are mutually coupled via dissimilar (or conjugate) variables display distinct regimes of synchronous behavior. In identical chaotic oscillators diffusively coupled in this manner, complete synchronization occurs only by chaos suppression when the coupled subsystems drive each other into a regime of periodic dynamics. Furthermore, the coupling does not vanish but acts as an "internal" drive. When the oscillators are mismatched, phase synchronization occurs, while in a master slave configuration, generalized synchrony results. These effects are demonstrated in a system of coupled chaotic Rossler oscillators.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kelkar2009,
title = {Characterisation of inactivation domains and evolutionary strata in human X chromosome through markov segmentation},
author = {Ashwin Kelkar and Vivek Thakur and Ramakrishna Ramaswamy and Deepti Deobagkar},
url = {https://ramramaswamy.org/papers/124.pdf},
doi = {10.1371/journal.pone.0007885},
issn = {19326203},
year  = {2009},
date = {2009-01-01},
journal = {PLoS ONE},
volume = {4},
number = {11},
abstract = {Markov segmentation is a method of identifying compositionally different subsequences in a given symbolic sequence. We have applied this technique to the DNA sequence of the human X chromosome to analyze its compositional structure. The human X chromosome is known to have acquired DNA through distinct evolutionary events and is believed to be composed of five evolutionary strata. In addition, in female mammals all copies of X chromosome in excess of one are transcriptionally inactivated. The location of a gene is correlated with its ability to undergo inactivation, but correlations between evolutionary strata and inactivation domains are less clear. Our analysis provides an accurate estimate of the location of stratum boundaries and gives a highresolution map of compositionally different regions on the X chromosome. This leads to the identification of a novel stratum, as well as segments wherein a group of genes either undergo inactivation or escape inactivation in toto. We identify oligomers that appear to be unique to inactivation domains alone.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{,
title = {Brainstem tests not},
url = {https://ramramaswamy.org/papers/128.pdf},
year  = {2009},
date = {2009-01-01},
journal = {Nature},
volume = {461},
number = {October},
pages = {80045},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2009,
title = {Women in mathematics: the indian experience},
author = {R Ramaswamy},
url = {https://ramramaswamy.org/papers/dani.pdf},
year  = {2009},
date = {2009-01-01},
pages = {1--4},
keywords = {Women in Mathematics},
pubstate = {published},
tppubtype = {article}
}
@book{Rohini2008,
title = {Lilavati’s Daughters: The women scientists of India},
editor = {Rohini Godbole, Ram Ramaswamy},
url = {https://ramramaswamy.org/books/Leelavati-daughters-2018.pdf
https://archive.org/details/A0560IASLeelavathisDaughterFullBook/page/n20},
year  = {2008},
date = {2008-11-01},
publisher = {Indian Academy of Sciences, Bangalore, November 2008},
address = {Bangalore, India},
abstract = {This initiative of the Women in Science (WiS) Panel relates to
mentoring of young women who are potentially looking for careers in
science, engineering, medicine etc.

WiS has compiled a collection of essays on the lives of Indian women
scientists in the form a book titled 'Lilavati's Daughters: The Women
Scientists of India'. The book contains brief biographical and
autobiographical sketches of about one hundred women scientists from
India. Covering a range of disciplines, in these essays the women
scientists talk of what brought them to science, what kept their
interest alive, and what has helped them achieve some measure of
distinction in their careers.

The Panel of Women in Science hopes that this collection would
represent our cultural diversity as well as cover a large range of
disciplines so that any woman student could gain from the insights and
experiences of women to whom they can relate at many levels.

The book 'Lilavati's Daughters: The Women Scientists of India' was
successfully released during the Inaugural session of the Annual meeting
of the Indian Academy of Sciences on 31st October, 2008, by Dr. D.
Balasubramanian, President of IAS, at the Indian Institute of
Technology, New Delhi.

Lilavati's Daughters: The Women Scientists of India

Our inspiration for this drive was from the book "One Hundred Reasons
to be a Scientist", a volume of essays put together by Prof. K R
Sreenivasan, Director of the International Center for Theoretical
Physics, Trieste.
},
keywords = {Book, Women in Science},
pubstate = {published},
tppubtype = {book}
}
@article{Prasad2008b,
title = {The effect of time–delay on anomalous phase synchronization},
author = {A Prasad, J Kurths and R Ramaswamy},
url = {https://doi.org/10.1016/j.physleta.2008.08.043},
doi = {10.1016/j.physleta.2008.08.043},
year  = {2008},
date = {2008-09-29},
journal = {Physics Letters A},
volume = {372},
number = {40},
pages = {6150-6154},
abstract = {Anomalous phase synchronization in nonidentical interacting oscillators is manifest as the increase of frequency disorder prior to synchronization. We show that this effect can be enhanced when a time-delay is included in the coupling. In systems of limit-cycle and chaotic oscillators we find that the regions of phase disorder and phase synchronization can be interwoven in the parameter space such that as a function of coupling or time-delay the system shows transitions from phase ordering to disorder and back.},
keywords = {Synchronization, Time Delay},
pubstate = {published},
tppubtype = {article}
}
@article{Gupta2008,
title = {Analytical signal analysis of strange nonchaotic dynamics},
author = {Kopal Gupta and Awadhesh Prasad and Harinder P Singh and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/115.pdf},
doi = {10.1103/PhysRevE.77.046220},
issn = {15393755},
year  = {2008},
date = {2008-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {77},
number = {4},
pages = {1--6},
abstract = {We apply an analytical signal analysis to strange nonchaotic dynamics. Through this technique it is possible to obtain the spectrum of instantaneous intrinsic mode frequencies that are present in a given signal. We find that the second-mode frequency and its variance are good order parameters for dynamical transitions from quasiperiodic tori to strange nonchaotic attractors (SNAs) and from SNAs to chaotic attractors. Phase fluctuation analysis shows that SNAs and chaotic attractors behave identically within short time windows as a consequence of local instabilities in the dynamics. In longer time windows, however, the globally stable character of SNAs becomes apparent. This methodology can be of great utility in the analysis of experimental time series, and representative applications are made to signals obtained from Rössler and Duffing oscillators. textcopyright 2008 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad2008,
title = {Universal occurrence of the phase-flip bifurcation in time-delay coupled systems},
author = {Awadhesh Prasad and Syamal Kumar Dana and Rajat Karnatak and Jürgen Kurths and Bernd Blasius and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/116.pdf},
doi = {10.1063/1.2905146},
issn = {10541500},
year  = {2008},
date = {2008-01-01},
journal = {Chaos},
volume = {18},
number = {2},
pages = {1--8},
abstract = {Recently, the phase-flip bifurcation has been described as a fundamental transition in time-delay coupled, phase-synchronized nonlinear dynamical systems. The bifurcation is characterized by a change of the synchronized dynamics from being in-phase to antiphase, or vice versa; the phase-difference between the oscillators undergoes a jump of pi as a function of the coupling strength or the time delay. This phase-flip is accompanied by discontinuous changes in the frequency of the synchronized oscillators, and in the largest negative Lyapunov exponent or its derivative. Here we illustrate the phenomenology of the bifurcation for several classes of nonlinear oscillators, in the regimes of both periodic and chaotic dynamics. We present extensive numerical simulations and compute the oscillation frequencies and the Lyapunov spectra as a function of the coupling strength. In particular, our simulations provide clear evidence of the phase-flip bifurcation in excitable laser and Fitzhugh-Nagumo neuronal models, and in diffusively coupled predator-prey models with either limit cycle or chaotic dynamics. Our analysis demonstrates marked jumps of the time-delayed and instantaneous fluxes between the two interacting oscillators across the bifurcation; this has strong implications for the performance of the system as well as for practical applications. We further construct an electronic circuit consisting of two coupled Chua oscillators and provide the first formal experimental demonstration of the bifurcation. In totality, our study demonstrates that the phase-flip phenomenon is of broad relevance and importance for a wide range of physical and natural systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Singh2008,
title = {Coexisting attractors in periodically modulated logistic maps},
author = {Thounaojam Umeshkanta Singh and Amitabha Nandi and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/117.pdf},
doi = {10.1103/PhysRevE.77.066217},
issn = {15393755},
year  = {2008},
date = {2008-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {77},
number = {6},
pages = {1--8},
abstract = {We consider the logistic map wherein the nonlinearity parameter is periodically modulated. For low periods, there is multistability, namely two or more distinct dynamical attractors coexist. The case of period 2 is treated in detail, and it is shown how an extension of the kneading theory for one-dimensional maps can be applied in order to analyze the origin of bistability, and to demarcate the principal regions of bistability in the phase space. When the period of the modulation is increased-and here we choose periods which are the Fibonacci numbers-the measure of multistable regions decreases. The limit of quasiperiodic driving is approached in two different ways, by increasing the period and keeping the drive dichotomous, or by increasing the period and varying the modulation sinusoidally. In the former case, we find that multistability persists in small regions of the phase space, while in the latter, there is no evidence of multistability but strange nonchaotic attractors are created. textcopyright 2008 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Singh2008a,
title = {Scenarios for generalized synchronization with chaotic driving},
author = {Thounaojam Umeshkanta Singh and Amitabha Nandi and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/118.pdf},
doi = {10.1103/PhysRevE.78.025205},
issn = {15393755},
year  = {2008},
date = {2008-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {78},
number = {2},
pages = {1--4},
abstract = {In chaotically driven nonlinear dynamical systems, weak generalized synchrony can arise through distinct scenarios or routes in a manner similar to the onset of low-dimensional chaos or the creation of strange nonchaotic attractors in quasiperiodically driven systems. The limit sets of the dynamics for weak generalized synchronization are nonchaotic-the Lyapunov exponent is nonpositive-and are geometrically strange. Quantitative measures related to the parameter sensitivity exponent and finite-time Lyapunov exponent distributions can be defined in order to characterize generalized synchronization. textcopyright 2008 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{SHRIMALI2008,
title = {the Nature of Attractor Basins in Multistable Systems},
author = {Manish Dev Shrimali and Awadhesh Prasad and Ram Ramaswamy and Ulrike Feudel},
url = {https://ramramaswamy.org/papers/119.pdf},
doi = {10.1142/s0218127408021269},
issn = {0218-1274},
year  = {2008},
date = {2008-01-01},
journal = {International Journal of Bifurcation and Chaos},
volume = {18},
number = {06},
pages = {1675--1688},
abstract = {In systems that exhibit multistability, namely those that have more than one coexisting attractor, the basins of attraction evolve in specific ways with the creation of each new attractor. These multiple attractors can be created via different mechanisms. When an attractor is formed via a saddle-node bifurcation, the size of its basin increases as a power-law in the bifurcation parameter. In systems with weak dissipation, the basins of low-order periodic attractors increase linearly, while those of high-order periodic attractors decay exponentially as the dissipation is increased. These general features are illustrated for autonomous as well as driven mappings. In addition, the boundaries of the basins can also change from being smooth to fractal when a new attractor appears. Transitions in the basin boundary morphology are reflected in abrupt changes in the dependence of the uncertainty exponent on the bifurcation parameter. textcopyright 2008 World Scientific Publishing Company.},
keywords = {attractor basins, multistable systems},
pubstate = {published},
tppubtype = {article}
}
@article{Alexe2007,
title = {Data perturbation independent diagnosis and validation of breast-cancer subtypes using clustering and patterns},
author = {G Alexe G S Dalgin R Ramaswamy C Delisi and G Bhanot},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2675483/},
year  = {2007},
date = {2007-02-19},
journal = { Cancer Informatics Online},
volume = {2},
pages = {243-274},
abstract = {Molecular stratification of disease based on expression levels of sets of genes can help guide therapeutic decisions if such classifications can be shown to be stable against variations in sample source and data perturbation. Classifications inferred from one set of samples in one lab should be able to consistently stratify a different set of samples in another lab. We present a method for assessing such stability and apply it to the breast cancer (BCA) datasets of Sorlie et al. 2003 and Ma et al. 2003. We find that within the now commonly accepted BCA categories identified by Sorlie et al. Luminal A and Basal are robust, but Luminal B and ERBB2+ are not. In particular, 36% of the samples identified as Luminal B and 55% identified as ERBB2+ cannot be assigned an accurate category because the classification is sensitive to data perturbation. We identify a "core cluster" of samples for each category, and from these we determine "patterns" of gene expression that distinguish the core clusters from each other. We find that the best markers for Luminal A and Basal are (ESR1, LIV1, GATA-3) and (CCNE1, LAD1, KRT5), respectively. Pathways enriched in the patterns regulate apoptosis, tissue remodeling and the immune response. We use a different dataset (Ma et al. 2003) to test the accuracy with which samples can be allocated to the four disease subtypes. We find, as expected, that the classification of samples identified as Luminal A and Basal is robust but classification into the other two subtypes is not.},
keywords = {breast cancer, clusters},
pubstate = {published},
tppubtype = {article}
}
@article{Tiwari2007,
title = {Prediction of probable genes by Fourier analysis of genomic sequences},
author = {Shrish Tiwari and S Ramachandran and Alok Bhattacharya and Sudha Bhattacharya and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/064.pdf},
doi = {10.1093/bioinformatics/13.3.263},
issn = {1367-4803},
year  = {2007},
date = {2007-01-01},
journal = {Bioinformatics},
volume = {13},
number = {3},
pages = {263--270},
abstract = {Motivation: The major signal in coding regions of genomic sequences is a three-base periodicity. Our aim is to use Fourier techniques to analyse this periodicity, and thereby to develop a tool to recognize coding regions in genomic DNA. Result: The three-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f = 1/3 in the Fourier (or power) spectrum. From extensive spectral analysis of DNA sequences of total length over 5.5 million base pairs from a wide variety or organisms (including the human genome), and by separately examining coding and non-coding sequences, we find that the relative height of the peak at f = 1/3 in the Fourier spectrum is a good discriminator of coding potential. This feature utilized by us to detect probable coding regions in DNA sequences, by examining the local signal-to-noise ratio of the peak within a sliding window. While the overall accuracy is comparable to that of other techniques currently in use, the measure that is presently proposed is independent of training sets or existing database information, and can thus find general application. Availability: A computer program coding open reading frames and exonic regions in genomic sequences has been developed, and is available on request.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Thakur2007,
title = {Markov models of genome segmentation},
author = {Vivek Thakur and Rajeev K Azad and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/111.pdf},
doi = {10.1103/PhysRevE.75.011915},
issn = {15393755},
year  = {2007},
date = {2007-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {75},
number = {1},
pages = {1--10},
abstract = {We introduce Markov models for segmentation of symbolic sequences, extending a segmentation procedure based on the Jensen-Shannon divergence that has been introduced earlier. Higher-order Markov models are more sensitive to the details of local patterns and in application to genome analysis, this makes it possible to segment a sequence at positions that are biologically meaningful. We show the advantage of higher-order Markov-model-based segmentation procedures in detecting compositional inhomogeneity in chimeric DNA sequences constructed from genomes of diverse species, and in application to the E. coli K12 genome, boundaries of genomic islands, cryptic prophages, and horizontally acquired regions are accurately identified. textcopyright 2007 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ngamga2007,
title = {Recurrence analysis of strange nonchaotic dynamics},
author = {E J Ngamga and A Nandi and R Ramaswamy and M C Romano and M Thiel and J Kurths},
url = {https://ramramaswamy.org/papers/112.pdf},
doi = {10.1103/PhysRevE.75.036222},
issn = {15393755},
year  = {2007},
date = {2007-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {75},
number = {3},
pages = {1--8},
abstract = {We present methods to detect the transitions from quasiperiodic to chaotic motion via strange nonchaotic attractors (SNAs). These procedures are based on the time needed by the system to recur to a previously visited state and a quantification of the synchronization of trajectories on SNAs. The applicability of these techniques is demonstrated by detecting the transition to SNAs or the transition from SNAs to chaos in representative quasiperiodically forced discrete maps. The fractalization transition to SNAs-for which most existing diagnostics are inadequate-is clearly detected by recurrence analysis. These methods are robust to additive noise, and thus can be used in analyzing experimental time series. textcopyright 2007 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karnatak2007,
title = {Amplitude death in the absence of time delays in identical coupled oscillators},
author = {Rajat Karnatak and Ram Ramaswamy and Awadhesh Prasad},
url = {https://ramramaswamy.org/papers/113.pdf},
doi = {10.1103/PhysRevE.76.035201},
issn = {15393755},
year  = {2007},
date = {2007-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {76},
number = {3},
pages = {1--4},
abstract = {We study the dynamics of oscillators that are mutually coupled via dissimilar (or "conjugate") variables and find that this form of coupling leads to a regime of amplitude death. Analytic estimates are obtained for coupled Landau-Stuart oscillators, and this is supplemented by numerics for this system as well as for coupled Lorenz oscillators. Time delay does not appear to be necessary to cause amplitude death when conjugate variables are employed in coupling identical systems. Coupled chaotic oscillators also show multistability prior to amplitude death, and the basins of the coexisting attractors appear to be riddled. This behavior is quantified: an appropriately defined uncertainty exponent in the coupled Lorenz system is shown to be zero. textcopyright 2007 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Nandi2007,
title = {Effective mechanisms for the synchronization of stochastic oscillators},
author = {Amitabha Nandi and G Santhosh and K.Brojen R Singh and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/114.pdf},
doi = {10.1103/PhysRevE.76.041136},
issn = {15393755},
year  = {2007},
date = {2007-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {76},
number = {4},
pages = {1--10},
abstract = {The emergence of synchronization is a phenomenon that is ubiquitous in a wide variety of natural systems. Such behavior is also often robust: systems subject to large stochastic fluctuations and which possess a range of internal time scales are capable of exhibiting sustained correlated dynamics. Here we study model chemical reactions and genetic networks that have stochastic oscillatory dynamics, and discuss microscopic mechanisms through which two or more such distinct stochastic processes can be coupled so as to result in the phase synchronization of their dynamical variables. We also consider the effect of time delay in the interaction and show that for suitable choices of the delay parameter, in-phase or antiphase synchronization can occur. textcopyright 2007 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gupta2006,
title = {Adaptive targeting of chaotic response in periodically stimulated neural systems},
author = {Kopal Gupta and Harinder P Singh and B Biswal and R Ramaswamy},
url = {https://ramramaswamy.org/papers/106.pdf},
doi = {10.1063/1.2204749},
issn = {10541500},
year  = {2006},
date = {2006-01-01},
journal = {Chaos},
volume = {16},
number = {2},
pages = {1--7},
abstract = {We demonstrate a technique for the enhancement of chaos in a computational model of a periodically stimulated excitable neuron. Änticontrol" of chaos is achieved through intermittent adaptive intervention, which is based on finite-time Lyapunov exponents measured from the time series. Our results suggest that an adaptive strategy for chaos anticontrol is viable for increasing the complexity in physiological systems that are typically both noisy and nonstationary. textcopyright 2006 American Institute of Physics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Haimovich2006,
title = {Wavelet Analysis of DNA Walks},
author = {Adrian D Haimovich and Bruce Byrne and Ramakrishna Ramaswamy and William J Welsh},
url = {https://ramramaswamy.org/papers/107.pdf},
doi = {10.1089/cmb.2006.13.1289},
issn = {1066-5277},
year  = {2006},
date = {2006-01-01},
journal = {Journal of Computational Biology},
volume = {13},
number = {7},
pages = {1289--1298},
abstract = {A wavelet transform of the DNA "walk" constructed from a genomic sequence offers a direct visualization of short and long-range patterns in nucleotide sequences. We study sequences that encode diverse biological functions, taken from a variety of genomes. Pattern irregularities in the transform are frequently associated with sequences of biological interest. Exonic regions, for example, visualize differently under wavelet analysis than introns, and ribosomal RNA regions display distinct universal signatures. DNA walk wavelet analysis can provide a sensitive and rapid assessment of the putative biological significance of genomic DNA. textcopyright Mary Ann Liebert, Inc.},
keywords = {dna walk, genomic analysis, sequence analysis, wavelet transform},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad2006,
title = {Phase-flip bifurcation induced by time delay},
author = {Awadhesh Prasad and Jürgen Kurths and Syamal Kumar Dana and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/108.pdf},
doi = {10.1103/PhysRevE.74.035204},
issn = {15393755},
year  = {2006},
date = {2006-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {74},
number = {3},
pages = {2--5},
abstract = {We present a general bifurcation in the synchronized dynamics of time-delay-coupled nonlinear oscillators. The relative phase between the oscillators jumps from zero to $pi$ as a function of the coupling; this phase-flip bifurcation is accompanied by a discontinuous change in the frequency of the synchronized oscillators. This phenomenon is of broad relevance, being observed in regimes of oscillator death as well as in periodic, quasiperiodic, and chaotic dynamics. Time-delay coupling is necessary for the phase-flip bifurcation. We illustrate the phenomenon, and present analytical results for paradigmatic nonlinear systems. Possible applications are discussed. textcopyright 2006 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mandal2006,
title = {Identification of insertion hot spots for non-LTR retrotransposons: Computational and biochemical application to Entamoeba histolytica},
author = {Prabhat K Mandal and Kamal Rawal and Ram Ramaswamy and Alok Bhattacharya and Sudha Bhattacharya},
url = {https://ramramaswamy.org/papers/109.pdf},
doi = {10.1093/nar/gkl710},
issn = {03051048},
year  = {2006},
date = {2006-01-01},
journal = {Nucleic Acids Research},
volume = {34},
number = {20},
pages = {5752--5763},
abstract = {The genome of the human pathogen Entamoeba histolytica contains non-long terminal repeat (LTR) retrotransposons, the EhLINEs and EhSINEs, which lack targeted insertion. We investigated the importance of local DNA structure, and sequence preference of the element-encoded endonuclease (EN) in selecting target sites for retrotransposon insertion. Pre-insertion loci were tested computationally to detect unique features based on DNA structure, thermodynamic considerations and protein interaction measures. Target sites could readily be distinguished from other genomic sites based on these criteria. The contribution of the EhLINE1-encoded EN in target site selection was investigated biochemically. The sequence-specificity of the EN was tested in vitro with a variety of mutated substrates. It was possible to assign a consensus sequence, 5′-GCATT-3′, which was efficiently nicked between A-T and T-T. The upstream G residue enhanced EN activity, possibly serving to limit retrotransposition in the A+T-rich E.histolytica genome. Mutated substrates with poor EN activity showed structural differences compared with normal substrates. Analysis of retrotransposon insertion sites from a variety of organisms showed that, in general, regions of favorable DNA structure were recognized for retrotransposition. A combination of favorable DNA structure and preferred EN nicking sequence in the vicinity of this structure may determine the genomic hotspots for retrotransposition. textcopyright 2006 Oxford University Press.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Datta2005,
title = {Critical localization and strange nonchaotic dynamics: The Fibonacci chain},
author = {S Datta, S S Negi, R Ramaswamy, and U Feudel
},
url = {https://doi.org/10.48550/arXiv.nlin/0104054},
doi = {10.48550/arXiv.nlin/0104054},
year  = {2005},
date = {2005-01-01},
journal = {International Journal of Bifurcation and Chaos},
volume = {15},
number = {4},
pages = {1493-1501},
abstract = {The discrete Schrödinger equation with a quasiperiodic dichotomous potential specified by the Fibonacci sequence is known to have a singular continuous eigenvalue spectrum with all states being critically localized. This equation can be transformed into a quasiperiodic skew product dynamical system. In this iterative mapping which is entirely equivalent to the Schrödinger problem, critically localized states correspond to fractal attractors which have all Lyapunov exponents equal to zero. This provides an alternate means of studying the spectrum, as has been done earlier for the Harper equation. We study the spectrum of the Fibonacci system and describe the scaling of gap widths with potential strength.},
keywords = {Strange nonchaotic attractors},
pubstate = {published},
tppubtype = {article}
}
@article{Ghosh2005,
title = {Cluster-weighted modeling: Estimation of the Lyapunov spectrum in driven systems},
author = {Anandamohan Ghosh and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/099.pdf},
doi = {10.1103/PhysRevE.71.016224},
issn = {15393755},
year  = {2005},
date = {2005-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {71},
number = {1},
pages = {1--6},
abstract = {Cluster-weighted modeling based techniques are shown to be accurate, efficient, and robust in application to the problem of computing the Lyapunov spectrum from time-series data. We develop a method that is appropriate for application to driven nonlinear dynamical systems and show, in particular, that it is possible to estimate both global and local Lyapunov exponents through this technique. For dynamics on strange nonchaotic attractors, the present approach correctly determines a largest Lyapunov exponent that is negative. textcopyright2005 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mudi2005,
title = {Spectral signatures of the diffusional anomaly in water},
author = {Anirban Mudi and Charusita Chakravarty and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/100.pdf},
doi = {10.1063/1.1860555},
issn = {00219606},
year  = {2005},
date = {2005-01-01},
journal = {Journal of Chemical Physics},
volume = {122},
number = {10},
pages = {1--8},
abstract = {Power spectra for various tagged particle quantities in bulk extended simple point charge model water [H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987)] are shown to have a regime with 1f$alpha$ dependence on frequency f with $alpha$ lying between 1 and 1.5 if the dynamical changes in the particular observable are sensitive to the multiple time-scale behavior of the hydrogen-bond network. The variations in mobility associated with the diffusional anomaly are mirrored in the scaling exponent $alpha$ associated with this multiple time-scale behavior, suggesting that monitoring of 1f$alpha$ behavior is a simple and direct method for linking phenomena on three distinctive length and time scales: the local molecular environment, hydrogen-bond network reorganizations, and the diffusivity. Our results indicate that experimental studies of supercooled water to probe the density dependence of 1f$alpha$ spectral features, or equivalent stretched exponential behavior in time-correlation functions, will be of interest. textcopyright 2005 American Institute of Physics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Nandi2005,
title = {The phase-modulated logistic map},
author = {Amitabha Nandi and Debabrata Dutta and Jayanta K Bhattacharjee and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/101.pdf},
doi = {10.1063/1.1914755},
issn = {10541500},
year  = {2005},
date = {2005-01-01},
journal = {Chaos},
volume = {15},
number = {2},
pages = {1--9},
abstract = {We study the logistic mapping with the nonlinearity parameter varied through a delayed feedback mechanism. This history dependent modulation through a phaselike variable offers an enhanced possibility for stabilization of periodic dynamics. Study of the system as a function of nonlinearity and modulation parameters reveals new phenomena: In addition to period-doubling and tangent bifurcations, there can be bifurcations where the period increases by unity. These are extensions of crises that arise in nonlinear dynamical systems. Periodic orbits in this system can be systematized via the kneading theory, which in the present case extends the analysis of Metropolis, Stein, and Stein for unimodal maps. textcopyright 2005 American Institute of Physics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Santhosh2005,
title = {Thermal transport in low-dimensional lattices with nearest- and next-nearest-neighbour coupling},
author = {G Santhosh and Deepak Kumar and R Ramaswamy},
url = {https://ramramaswamy.org/papers/103.pdf},
doi = {10.1088/1742-5468/2005/07/P07005},
issn = {17425468},
year  = {2005},
date = {2005-01-01},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
number = {7},
pages = {71--80},
abstract = {We examine the effect of increasing the range of interaction on the anomalous transport properties of classical low-dimensional lattices coupled to thermal baths at different temperatures. We consider one-dimensional next-nearest-neighbour (NNN) interactions as well as a zig-zag model of two chains with nonlinearity of Fermi-Pasta-Ulam (namely quartic + quadratic) type. As in the case of linear chains with nearest-neighbour coupling, the thermal conductivity diverges as a power of the system size. The characteristic exponents are, however, distinct, and appear to depend on the strength of the coupling. textcopyright 2005 IOP Publishing Ltd.},
keywords = {Transport processes/heat transfer (theory)},
pubstate = {published},
tppubtype = {article}
}
@article{Shrimali2005,
title = {Basin bifurcations in quasiperiodically forced coupled systems},
author = {Manish Dev Shrimali and Awadhesh Prasad and Ram Ramaswamy and Ulrike Feudel},
url = {https://ramramaswamy.org/papers/105.pdf},
doi = {10.1103/PhysRevE.72.036215},
issn = {15393755},
year  = {2005},
date = {2005-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {72},
number = {3},
pages = {1--8},
abstract = {We study the effect of quasiperiodic forcing on a system of coupled identical logistic maps. Upon a variation of system parameters, a variety of different dynamical regimes can be observed, including phenomena such as bistability and multistability. At the bifurcation to bistability, in a manner reminiscent of attractor expansion at interior crises, there is an abrupt change in the size of attractor basins. In the bistable region, attractor basins undergo additional bifurcations wherein holes and islands are created within the basins when system parameters change. These can be understood by examining critical surfaces for the coupled system. textcopyright 2005 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2005,
title = {The natural effectiveness of mathematics in the biological sciences},
author = {R Ramaswamy},
url = {https://ramramaswamy.org/papers/R34.pdf},
issn = {00113891},
year  = {2005},
date = {2005-01-01},
journal = {Current Science},
volume = {88},
number = {3},
pages = {381--387},
abstract = {An increasingly quantitative approach within the biological sciences has been accompanied by a greater degree of mathematical sophistication. However, there is a need for new paradigms within which to treat an array of biological phenomena such as life, development, evolution or cognition. Topics such as game theory, chaos theory and complexity studies are now commonly used in biology, if not yet as analytic tools, as frameworks within which some biological processes can be understood. In addition, there have been great advances in unravelling the mechanism of biological processes from the fundamental cellular level upwards that have also required the input of very advanced methods of mathematical analysis. These range from the combinatorics needed in genome sequencing, to the complex transforms needed for image reconstruction in tomography. In this article, I discuss some of these applications, and also whether there is any framework other than mathematics within which the human mind can comprehend natural phenomena.},
keywords = {General Science, Mathematics},
pubstate = {published},
tppubtype = {article}
}
@article{Gupte2005,
title = {A perspective on nonlinear dynamics},
author = {Neelima Gupte and Ramakrishna Ramaswamy and Rajarshi Roy},
url = {https://ramramaswamy.org/papers/R35.pdf},
issn = {03044289},
year  = {2005},
date = {2005-01-01},
journal = {Pramana - Journal of Physics},
volume = {64},
number = {3 SPEC. ISS.},
pages = {307--313},
abstract = {We present a brief report on the conference, a summary of the proceedings, and a discussion on the field of nonlinear science studies and its current frontiers. textcopyright Indian Academy of Sciences.},
keywords = {Conference summary, Review},
pubstate = {published},
tppubtype = {article}
}
@article{Alexe2005,
title = {A robust meta-classification strategy for cancer diagnosis from gene expression data},
author = {Gabriela Alexe and Ramakrishna Ramaswamy and Gyan Bhanot and Jorge Lepre and Gustavo Stolovitzky and Babu Venkataraghavan and Arnold J Levine},
url = {https://ramramaswamy.org/papers/R37.pdf},
doi = {10.1109/CSB.2005.7},
isbn = {0769523447},
year  = {2005},
date = {2005-01-01},
journal = {Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005},
volume = {2005},
pages = {322--325},
abstract = {One of the major challenges in cancer diagnosis from microarray data is to develop robust classification models which are independent of the analysis techniques used and can combine data from different laboratories. We propose a metaclassification scheme which uses a robust multivariate gene selection procedure and integrates the results of several machine learning tools trained on raw and pattern data. We validate our method by applying it to distinguish diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) on two independent datasets: the HuGeneFL Affmetrixy dataset of Shipp et al. (www.genome.wi.mit.du/MPR /lymphoma) and the Hu95Av2 Affymetrix dataset (DallaFavera's laboratory, Columbia University). Our meta-classification technique achieves higher predictive accuracies than each of the individual classifiers trained on the same dataset and is robust against various data perturbations. We also find that combinations of p53 responsive genes (e.g., p53, PLK1 and CDK2) are highly predictive of the phenotype. textcopyright 2005 IEEE.},
keywords = {Bioinformatics, cancer diagnosis},
pubstate = {published},
tppubtype = {article}
}
@article{Azad2004,
title = {Symbol sequence analysis of climatic time signals},
author = {R Azad, J Subba Rao, and R Ramaswamy},
url = {https://doi.org/10.1016/j.nonrwa.2003.11.003},
doi = {10.1016/j.nonrwa.2003.11.003},
year  = {2004},
date = {2004-07-01},
journal = {Nonlinear Analysis: Real World Applications },
volume = {5},
number = {3},
pages = {487-500},
abstract = {The conditional entropy of two symbolic sequences encoded faithfully from different chaotic time signal data is minimised at zero relative shift of the two signals if the signals have their origin in same underlying dynamics. We show that this minimum in conditional entropies E(Z/X) and E(X/Z) obtained after suitably ‘coarse–graining’ the time signals of, say, variables X and Z have marked differences depending upon the degree of dynamical coupling of the variables in the model. This technique has also been shown to be useful in studying delayed dependences of time signals. Application is made to climate data of four meteorological stations in India, namely New Delhi, Jaipur, Sundernagar and Chennai in order to determine (a) the commonality of underlying dynamics, (b) relative strength of dynamical coupling of different variables and (c) the delay implicit in the dynamics. The method appears robust to measurement noise.},
keywords = {climate, dynamical coupling, entropy, Time Delay},
pubstate = {published},
tppubtype = {article}
}
@article{Samanta2004,
title = {Approach to equilibrium in adiabatically evolving potentials},
author = {H S Samanta, J K Bhattacharjee, and R Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevE.69.056114},
doi = {10.1103/PhysRevE.69.056114},
year  = {2004},
date = {2004-05-25},
journal = {Physical Review E},
volume = {69},
number = {5},
pages = {056114},
abstract = {For a potential function (in one dimension) which evolves from a specified initial form 
V
i
(
x
)
 to a different 
V
f
(
x
)
 asymptotically, we study the evolution, in an overdamped dynamics, of an initial probability density to its final equilibrium. There can be unexpected effects that can arise from the time dependence. We choose a time variation of the form 
V
(
x
,
t
)
=
V
f
(
x
)
+
(
V
i
−
V
f
)
e
−
λ
t
. For a 
V
f
(
x
)
, which is double welled and a 
V
i
(
x
)
 which is simple harmonic, we show that, in particular, if the evolution is adiabatic, this results in a decrease in the Kramers time characteristic of Vf(x)
. Thus the time dependence makes diffusion over a barrier more efficient. There can also be interesting resonance effects when 
Vi(x)
 and 
Vf(x)
 are two harmonic potentials displaced with respect to each other that arise from the coincidence of the intrinsic time scale characterizing the potential variation and the Kramers time. Both these features are illustrated through representative examples.},
keywords = {Adiabatic switching},
pubstate = {published},
tppubtype = {article}
}
@article{Sharma2004,
title = {Spectral repeat finders (SRF): Identification of repetitive sequences using Fourier transformation},
author = {Deepak Sharma and Biju Issac and G P S Raghava and R Ramaswamy},
url = {https://ramramaswamy.org/papers/095.pdf},
doi = {10.1093/bioinformatics/bth103},
issn = {13674803},
year  = {2004},
date = {2004-01-01},
journal = {Bioinformatics},
volume = {20},
number = {9},
pages = {1405--1412},
abstract = {Repetitive DNA sequences, besides having a variety of regulatory functions, are one of the principal causes of genomic instability. Understanding their origin and evolution is of fundamental importance for genome studies. The identification of repeats and their units helps in deducing the intra-genomic dynamics as an important feature of comparative genomics. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Datta2004,
title = {On the dynamics of the critical Harper map},
author = {S Datta and T Jäger and G Keller and R Ramaswamy},
url = {https://ramramaswamy.org/papers/096.pdf},
doi = {10.1088/0951-7715/17/6/017},
issn = {09517715},
year  = {2004},
date = {2004-01-01},
journal = {Nonlinearity},
volume = {17},
number = {6},
pages = {2315--2323},
abstract = {We examine the behaviour of typical orbits in the Harper map, a quasiperiodically driven skew-product dynamical system in two dimensions. When the map is critical, namely when all Lyapunov exponents vanish, the dynamics is parabolic.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Singh2004,
title = {The role of heterogeneity on the spatiotemporal dynamics of host-parasite metapopulation},
author = {Brajendra K Singh and Subba J Rao and R Ramaswamy and Somdatta Sinha},
url = {https://ramramaswamy.org/papers/097.pdf},
doi = {10.1016/j.ecolmodel.2004.04.031},
issn = {03043800},
year  = {2004},
date = {2004-01-01},
journal = {Ecological Modelling},
volume = {180},
number = {2-3},
pages = {435--443},
abstract = {Subpopulations of organisms in different habitat patches may differ from each other in biotic (e.g., inherent growth rate and interaction strength) and abiotic (e.g., climatic and landscape pattern) components. Such heterogeneity can influence the mode and extent of dispersal of individuals among these subpopulations, which, in turn, may regulate their spatiotemporal dynamics. We have modelled a homogeneous metapopulation of the interacting host and parasite system, with closed boundary and dispersal limited to nearest neighbours, using the spatially explicit coupled map lattice approach. We have studied the role of heterogeneity in terms of landscape fragmentation and demographic heterogeneity on the spatiotemporal dynamics. The homogeneous metapopulation shows spatiotemporally synchronous dynamics in the long-term, which is independent of the exact forms of the dispersal function considered commonly. The primary role of both types of heterogeneity is to resist evolution of spatiotemporal synchrony in the lattice, and the dynamics in the metapopulation remains asynchronous for a very long time. Spatiotemporal synchrony in species population may be detrimental to persistence and is a potential problem for conservation biologists. Thus, evolution and maintenance of ecological and demographic diversity in nature seem to aid in species persistence at a metapopulation level. textcopyright 2004 Elsevier B.V. All rights reserved.},
keywords = {Asynchrony, Coupled map lattice, Demographic heterogeneity, Dispersal, Landscape fragmentation},
pubstate = {published},
tppubtype = {article}
}
@article{Datta2004a,
title = {Fractalization route to strange nonchaotic dynamics},
author = {Sandip Datta and Ramakrishna Ramaswamy and Awadhesh Prasad},
url = {https://ramramaswamy.org/papers/098.pdf},
doi = {10.1103/PhysRevE.70.046203},
issn = {1063651X},
year  = {2004},
date = {2004-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {70},
number = {4},
pages = {9},
abstract = {The process of fractalization route to strange nonchaotic dynamics was examined. It was demonstrated that a cascade of attractor merger crises precedes the creation of the fractal attractor. The unstable sets for the fractalization process were investigated using a sequence of rational approximations. The unstable sets were found to be created through a cascade of period-doubling bifurcations, and collision of chaotic bands with them caused a cascade of interior merging crisis whereby the fractalization process takes place.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mudi2003,
title = {Signatures of multiple time-scale behaviour in the power spectra of water},
author = {Anirban Mudi and Ramakrishna Ramaswamy and Charusita Chakravarty},
url = {https://ramramaswamy.org/papers/089.pdf},
doi = {10.1016/S0009-2614(03)01006-6},
issn = {00092614},
year  = {2003},
date = {2003-01-01},
journal = {Chemical Physics Letters},
volume = {376},
number = {5-6},
pages = {683--689},
abstract = {Power spectra associated with fluctuations in the tagged particle potential and kinetic energies are analysed for bulk SPC/E water for a range of temperatures along the 1.0 g/cm3 isochore. Fluctuations in the tagged particle potential energies give rise to 1/f$alpha$ noise, indicative of multiple time-scale behaviour, over a temperature-dependent frequency regime. In contrast, the tagged particle centre-of-mass and rotational kinetic energies, which are indicative of the magnitude of local thermal fluctuations, do not show any evidence of 1/f$alpha$ behaviour. textcopyright 2003 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Datta2003,
title = {Thermodynamics of critical strange nonchaotic attractors},
author = {Sandip Datta and Ashutosh Sharma and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/090.pdf},
doi = {10.1103/PhysRevE.68.036104},
issn = {1063651X},
year  = {2003},
date = {2003-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {68},
number = {3},
pages = {361041--361046},
abstract = {Thermodynamics of critical strange nonchaotic attractors (SNA) was studied. A static phase transition in the free energy was observed in critical SNAs in the Harper systems. Results showed that the Tsallis nonextensive entropy which is known to characterize the thermodynamics of systems with leading Lyapunov exponent zero was a subadditive for the critical states.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad2003,
title = {Strange nonchaotic attractors in driven excitable systems},
author = {Awadhesh Prasad and Bibudhananda Biswal and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/091.pdf},
doi = {10.1103/PhysRevE.68.037201},
issn = {1063651X},
year  = {2003},
date = {2003-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {68},
number = {3},
pages = {4},
abstract = {Through quasiperiodic forcing, an excitable system can be driven into a regime of spiking behavior that is both aperiodic and stable. This is a consequence of strange nonchaotic dynamics: the motion of the system is on a fractal attractor and the largest Lyapunov exponent is negative.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Datta2003a,
title = {Non-Gaussian Fluctuations of Local Lyapunov Exponents at Intermittency},
author = {Sandip Datta and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/092.pdf},
doi = {10.1023/A:1025783023529},
issn = {00224715},
year  = {2003},
date = {2003-01-01},
journal = {Journal of Statistical Physics},
volume = {113},
number = {1-2},
pages = {283--295},
abstract = {In intermittent dynamical systems, the distributions of local Lyapunov exponents are markedly non-Gaussian and tend to be asymmetric and fat-tailed. A comparative analysis of the different time-scales in intermittency provides a heuristic explanation for the origin of the exponential tails, for which we also obtain an analytic expression deriving from a more quantitative theory. Application is made to several examples of discrete dynamical systems displaying intermittent dynamics.},
keywords = {Exponential tails, Finite time Lyapunov exponents, Intermittency},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2003,
title = {Analysis of DNA Sequences through Segmentation: Exploring the Mosaic via Statistical Measures},
author = {Ramakrishna Ramaswamy and Rajeev K Azad},
url = {https://ramramaswamy.org/papers/R31.pdf},
doi = {10.1238/physica.topical.106a00021},
issn = {0031-8949},
year  = {2003},
date = {2003-01-01},
journal = {Physica Scripta},
volume = {T106},
number = {1},
pages = {21},
abstract = {The Jensen-Shannon divergence provides a quantitative entropic measure through which genomic DNA can be divided into compositionally distinct domains by a standard recursive segmentation procedure. In this article we show the scaling behaviour observed in domain length distribution and further explore the significance of these domains in the context of gene location, in application to the segmentation of a complete bacterial genome. We also show that this entropic measure has the potential of detecting the horizontally transferred genes in a genome.},
keywords = {DNA, Statistical Measures},
pubstate = {published},
tppubtype = {article}
}
@article{NAYAK2002,
title = { Solid-liquid transition in model (HF)_n clusters },
url = {https://ramramaswamy.org/papers/061.pdf},
doi = {10.1080/002689796173705},
issn = {0026-8976},
year  = {2002},
date = {2002-01-01},
journal = {Molecular Physics},
volume = {89},
number = {3},
pages = {809--817},
abstract = {We study the stability, energetics and dynamics of small model hydrogen fluoride clusters (HF) n using isoergic molecular dynamics simulations. The largest Lyapunov exponent is computed over the energy range when the clusters melt, and is found to be more useful in defining the onset of melting than Lindemann's index. We also examine the power spectrum of potential energy fluctuations of clusters in the liquid state, which show 1/f dependence over a smaller frequency range than rare-gas clusters of comparable size. author = Nayak, Saroj K.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Chakravarty2002,
title = {Instantaneous normal mode spectra of quantum clusters},
author = {Charusita Chakravarty and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/063.pdf},
doi = {10.1063/1.473578},
issn = {0021-9606},
year  = {2002},
date = {2002-01-01},
journal = {The Journal of Chemical Physics},
volume = {106},
number = {13},
pages = {5564--5568},
abstract = {The spectrum of instantaneous normal mode (INM) frequencies of finite Lennard-Jones clusters is studied as a function of the extent of quantum delocalization. Configurations are sampled from the equilibrium distribution by a Fourier path integral Monte Carlo procedure. The INM spectra, average force constants and Einstein frequencies are shown to be interesting dynamical markers for the quantum delocalization-induced cluster solid-liquid transition. Comperisons are made with INM spectra of quantum and classical Lennard-Jones liquids. The methodology used here suggests a general strategy to obtain quantal analogs of various classical dynamical quantities. textcopyright 1997 American Institute of Physics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Hunjan2002,
title = {Global optimization by adiabatic switching},
author = {Jagtar S Hunjan and R Ramaswamy},
url = {https://ramramaswamy.org/papers/081.pdf},
doi = {10.3390/i3010030},
issn = {14220067},
year  = {2002},
date = {2002-01-01},
journal = {International Journal of Molecular Sciences},
volume = {3},
number = {1},
pages = {30--37},
abstract = {We apply a recently introduced method for global optimization to determine the ground state energy and configuration for model metallic clusters. The global minimum for a given N-atom cluster is found by following the damped dynamics of the N particle system on an evolving potential energy surface. In this application, the time dependent interatomic potential interpolates adiabatically between the Lennard-Jones (LJ) and the Sutton-Chen (SC) forms. Starting with an ensemble of initial conditions corresponding to the ground state configuration of the Lennard-Jones cluster, the system asymptotically reaches the ground state of the Sutton-Chen cluster. We describe the method and present results for specific cluster size N=15, when the ground state symmetry of LJ$_N$ and SC$_N$ differ.},
keywords = {Adiabatic switching, Atomic Clusters, Global optimization, Ground states},
pubstate = {published},
tppubtype = {article}
}
@article{Azad2002,
title = {Information-entropic analysis of chaotic time series: Determination of time-delays and dynamical coupling},
author = {Rajeev K Azad and J {Subba Rao} and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/093.pdf},
doi = {10.1016/S0960-0779(02)00003-6},
issn = {09600779},
year  = {2002},
date = {2002-01-01},
journal = {Chaos, Solitons and Fractals},
volume = {14},
number = {4},
pages = {633--641},
abstract = {By calculating the conditional entropy of two different chaotic time series, converted into symbolic sequences through the application of prescribed (but otherwise arbitrary) rules, it can be determined whether or not these originate from the same underlying dynamics. We show that by comparing the conditional entropy of a sequence, obtained by coarse-graining of a chaotic time series, with respect to shifted copies of itself, time-delays that may be inherent in the dynamics can be found. Application is made to time-series obtained from dynamical systems such as Mackey-Glass equation and Ikeda equation. The method appears equally effective in determining the dynamical coupling of climatic time signals. Our results are robust to additive noise, and can thus be applied even when the conversion from a time series to a symbolic sequence has a small proportion of errors. textcopyright 2002 Elsevier Science Ltd. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Aggarwal2002,
title = {Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER},
author = {Gautam Aggarwal and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/083.pdf},
doi = {10.1007/BF02703679},
issn = {02505991},
year  = {2002},
date = {2002-01-01},
journal = {Journal of Biosciences},
volume = {27},
number = {1 SUPPL. 1},
pages = {7--14},
abstract = {We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail.},
keywords = {GeneScan, GLIMMER},
pubstate = {published},
tppubtype = {article}
}
@article{Shrimali2002,
title = {Phase ordering at crises},
author = {Manish Dev Shrimali and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/084.pdf},
doi = {10.1016/S0375-9601(02)00179-2},
issn = {03759601},
year  = {2002},
date = {2002-01-01},
journal = {Physics Letters, Section A: General, Atomic and Solid State Physics},
volume = {295},
number = {5-6},
pages = {273--279},
abstract = {Phase order, namely the average direction of sequential iterations, is studied in the family of unimodal maps x → 1 - $mu$|x| z on the interval [-1, 1]. The average phase order or "magnetization" M is sensitive to local changes in the dynamics. At merging crises, this quantity increases from zero with the scaling behaviour M ∼ ($mu$ -$mu$ c ) 1/z , while at exterior crises, M decreases, also having the same scaling exponent. We find that the exponent z is governed by the singularities of the invariant density $rho$(x) at the edges of the interval: as x → ±1, $rho$(x) ∼ (1 - |x| z ) -$beta$ with $beta$ = 1 - 1/z. textcopyright 2002 Elsevier Science B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Azad2002a,
title = {Segmentation of genomic DNA through entropic divergence: Power laws and scaling},
author = {Rajeev K Azad and Pedro Bernaola-Galván and Ramakrishna Ramaswamy and Subba J Rao},
url = {https://ramramaswamy.org/papers/085.pdf},
doi = {10.1103/PhysRevE.65.051909},
issn = {1063651X},
year  = {2002},
date = {2002-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {65},
number = {5},
pages = {6},
abstract = {Genomic DNA is fragmented into segments using the Jensen-Shannon divergence. Use of this criterion results in the fragments being entropically homogeneous to within a predefined level of statistical significance. Application of this procedure is made to complete genomes of organisms from archaebacteria, eubacteria, and eukaryotes. The distribution of fragment lengths in bacterial and primitive eukaryotic DNAs shows two distinct regimes of power-law scaling. The characteristic length separating these two regimes appears to be an intrinsic property of the sequence rather than a finite-size artifact, and is independent of the significance level used in segmenting a given genome. Fragment length distributions obtained in the segmentation of the genomes of more highly evolved eukaryotes do not have such distinct regimes of power-law behavior. textcopyright 2002 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Azad2002b,
title = {Simplifying the mosaic description of DNA sequences},
author = {Rajeev K Azad and J {Subba Rao} and Wentian Li and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/086.pdf},
doi = {10.1103/PhysRevE.66.031913},
issn = {1063651X},
year  = {2002},
date = {2002-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {66},
number = {3},
pages = {1--6},
abstract = {By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbors, may, however, share compositional similarity with one or more distant (non-neighboring) domains. We thus obtain a coarse-grained description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly reducing its organizational complexity. This procedure gives a new means of evaluating genomic complexity as one examines organisms ranging from bacteria to human. The mosaic organization of DNA sequences could have originated from the insertion of fragments of one genome (the parasite) inside another (the host), and we present numerical experiments that are suggestive of this scenario. textcopyright 2002 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Hunjan2002a,
title = {Global optimization on an evolving energy landscape},
author = {J S Hunjan and S Sarkar and R Ramaswamy},
url = {https://ramramaswamy.org/papers/087.pdf},
doi = {10.1103/PhysRevE.66.046704},
issn = {15502376},
year  = {2002},
date = {2002-01-01},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
volume = {66},
number = {4},
pages = {046704/1--046704/4},
abstract = {Locating the global minimum of a complex potential energy surface is facilitated by considering a homotopy, namely, a family of surfaces that interpolate continuously from an arbitrary initial potential to the system under consideration. Different strategies can be used to follow the evolving minima. It is possible to enhance the probability of locating the global minimum through a heuristic choice of interpolation schemes and parameters, and the continuously evolving potential landscape reduces the probability of trapping in local minima. In application to a model problem, finding the ground-state configuration and the energy of rare-gas (Lennard-Jones) atomic clusters, we demonstrate the utility and the efficacy of this method. textcopyright 2002 The American Physical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2002,
title = {Symmetry-breaking in local lyapunov exponents},
author = {R Ramaswamy},
url = {https://ramramaswamy.org/papers/088.pdf},
doi = {10.1140/epjb/e2002-00313-8},
issn = {14346028},
year  = {2002},
date = {2002-01-01},
journal = {European Physical Journal B},
volume = {29},
number = {2},
pages = {339--343},
abstract = {Integrable dynamical systems, namely those having as many independent conserved quantities as freedoms, have all Lyapunov exponents equal to zero. Locally, the instantaneous or finite time Lyapunov exponents are nonzero, but owing to a symmetry, their global averages vanish. When the system becomes nonintegrable, this symmetry is broken. A parallel to this phenomenon occurs in mappings which derive from quasiperiodic Schrödinger problems in 1-dimension. For values of the energy such that the eigenstate is extended, the Lyapunov exponent is zero, while if the eigenstate is localized, the Lyapunov exponent becomes negative. This occurs by a breaking of the quasiperiodic symmetry of local Lyapunov exponents, and corresponds to a breaking of a symmetry of the wavefunction in extended and critical states.},
keywords = {05.45.-a Nonlinear dynamics and nonlinear dynamical systems, 05.45.Pq Numerical simulations of chaotic models, 71.30.+h Metal-insulator transitions and other electronic transitions},
pubstate = {published},
tppubtype = {article}
}
@article{Negi2001,
title = {Plethora of strange nonchaotic attractors},
author = {Surendra Singh Negi and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/079.pdf},
doi = {10.1007/s12043-001-0140-7},
issn = {03044289},
year  = {2001},
date = {2001-01-01},
journal = {Pramana - Journal of Physics},
volume = {56},
number = {1},
pages = {47--56},
abstract = {We show that it is possible to devise a large class of skew-product dynamical systems which have strange nonchaotic attractors (SNAs): the dynamics is asymptotically on fractal attractors and the largest Lyapunov exponent is non-positive. Furthermore, we show that quasiperiodic forcing, which has been a hallmark of essentially all hitherto known examples of such dynamics is not necessary for the creation of SNAs.},
keywords = {10, 42, 45, b, Fractals, Lyapunov exponent, nonchaotic, pacs nos 05, strange attractors},
pubstate = {published},
tppubtype = {article}
}
@article{Negi2001a,
title = {Critical states and fractal attractors in fractal tongues: Localization in the Harper map},
author = {Surendra Singh Negi and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/080.pdf},
doi = {10.1103/PhysRevE.64.045204},
issn = {1063651X},
year  = {2001},
date = {2001-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {64},
number = {4},
pages = {4},
abstract = {Eigenvalue spectrum of the Harper equation was analyzed using Harper map. Fractal attractors with nonpositive Lyapunov exponents in fractally organized tongue-like regions which originate from the Cantor set of eigenvalues were taken into consideration. The wave functions for critical and extended states have a quasiperiodic symmetry and correspond to energies in the gaps in the spectrum. The scaling properties of the gaps as a function of potential strength was determined by integer labeling of the gaps.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy2001,
title = {Genes, brains, and unpredictability: Developments in the sciences and reflections on what it means to be alive},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/R30.pdf},
issn = {00113891},
year  = {2001},
date = {2001-01-01},
journal = {Current Science},
volume = {80},
number = {11},
pages = {1381--1386},
abstract = {The most dramatic statement of the reductionist approach in the biological sciences is the ástonishing hypothesis' of Francis Crick that something as central to our sense of self, namely the human soul, is in effect 'no more than the behaviour of a vast assembly of nerve cells and their associated molecules'. Recent advances such as the sequencing of entire genomes (the human genome being a well-publicized example) or the elucidation of some of the neuronal mechanisms associated with memory, for instance, appear to support this point of view, that we can eventually possess the recipe for human individuality. This essay contends that the essential limitation of such a programme stems not from the remaining problems of working out the details, but from the fact that living systems are fundamentally complex. Drawing on the ideas of deterministic chaos and complexity theory, it is proposed that while the broad contours of the connection between biological functioning, genetic information and the organization of its nervous system will be accessible, the unique developmental trajectory of any organism - that which constitutes the essence of individuality and confers a notion of being alive - will remain beyond the realm of precise scientific prediction.},
keywords = {Brain, Genes},
pubstate = {published},
tppubtype = {article}
}
@article{Hunjan2000,
title = {Melting of the glassy mixed cluster, Ar9Xe10},
author = {J S Hunjan and R Ramaswamy
},
url = {http://nopr.niscpr.res.in/handle/123456789/25846},
issn = {0975-0975},
year  = {2000},
date = {2000-03-01},
journal = {Indian Journal of Chemistry A},
volume = {39},
abstract = {	We have studied the adiabatic instantaneous normal modes (INMs) for a mixed 19-particle cluster, Ar9Xe10 as a function of temperature. In finite clusters, the INM frequencies, which are well-separated, do not mix as a consequence of the noncrossing rule. The frequencies of the lowest few modes of the system progressively soften as the temperature is increased, and prior to melting, the lowest few modes become unstable: these INM frequencies become imaginary. Eigenvectors corresponding to the lowest modes that appear to be involved in the actual melting process are identified.},
keywords = {clusters, phase transition},
pubstate = {published},
tppubtype = {article}
}
@article{Bhattacharya2000,
title = {Identification of parasitic genes by computational methods},
author = {Alok Bhattacharya and Sudha Bhattacharya and Amita Joshi and Srinivasan Ramachandran and Ram Ramaswamy},
url = {https://ramramaswamy.org/papers/075.pdf},
doi = {10.1016/S0169-4758(99)01600-2},
issn = {01694758},
year  = {2000},
date = {2000-01-01},
journal = {Parasitology Today},
volume = {16},
number = {3},
pages = {127--131},
abstract = {A number of parasite genome projects are under way, and large amounts of nucleotide sequence data are becoming available for analysis. There is an urgent need for development of theoretical tools to analyze the genome data, including identification of protein-coding sequences. The majority of the methods developed to date require prior information about the genome before accurate predictions can be made. Because such information is not available for many parasites, these methods cannot be directly applied. In this article, Alok Bhattacharya and colleagues describe some of the gene-prediction methods commonly in use, and a new method, GeneScan, that they have developed for the analysis of parasite genomes. Copyright (C) 2000 Elsevier Science Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Venkatesan2000,
title = {Intermittency transitions to strange nonchaotic attractors in a quasiperiodically driven Duffing oscillator},
author = {A Venkatesan and M Lakshmanan and A Prasad and R Ramaswamy},
url = {https://ramramaswamy.org/papers/076.pdf},
doi = {10.1103/PhysRevE.61.3641},
issn = {1063651X},
year  = {2000},
date = {2000-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {61},
number = {4},
pages = {3641--3651},
abstract = {Different mechanisms for the creation of strange nonchaotic attractors (SNAs) are studied in a two-frequency parametrically driven Duffing oscillator. We focus on intermittency transitions in particular, and show that SNAs in this system are created through quasiperiodic saddle-node bifurcations (type-I intermittency) as well as through a quasiperiodic subharmonic bifurcation (type-III intermittency). The intermittent attractors are characterized via a number of Lyapunov measures including the behavior of the largest nontrivial Lyapunov exponent and its variance, as well as through distributions of finite-time Lyapunov exponents. These attractors are ubiquitous in quasiperiodically driven systems; the regions of occurrence of various SNAs are identified in a phase diagram of the Duffing system.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Negi2000,
title = {Bifurcations and transitions in the quasiperiodically driven logistic map},
author = {Surendra Singh Negi and Awadhesh Prasad and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/078.pdf},
doi = {10.1016/S0167-2789(00)00110-X},
issn = {01672789},
year  = {2000},
date = {2000-01-01},
journal = {Physica D: Nonlinear Phenomena},
volume = {145},
number = {1-2},
pages = {1--12},
abstract = {We discuss several bifurcation phenomena that occur in the quasiperiodically driven logistic map. This system can have strange nonchaotic attractors (SNAs) in addition to chaotic and regular attractors; on SNAs the dynamics is aperiodic, but the largest Lyapunov exponent is nonpositive. There are a number of different transitions that occur here, from periodic attractors to SNAs, from SNAs to chaotic attractors, etc. We describe some of these transitions by examining the behavior of the largest Lyapunov exponent, distributions of finite time Lyapunov exponents and the invariant densities in the phase space. textcopyright 2000 Elsevier Science B.V.},
keywords = {Lyapunov exponent, Quasiperiodically driven logistic map, Strange nonchaotic attractors},
pubstate = {published},
tppubtype = {article}
}
@article{Mehra1999,
title = {Melting behavior of heterogenous atomic clusters: Gapless coexisting phases in (Ar-Xe)13},
author = {Vishal Mehra and Awadhesh Prasad and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/070.pdf},
doi = {10.1063/1.478110},
issn = {00219606},
year  = {1999},
date = {1999-01-01},
journal = {Journal of Chemical Physics},
volume = {110},
number = {1},
pages = {501--507},
abstract = {We study the structural and dynamical aspects of 13-atom binary rare-gas clusters of Ar and Xe using constant-energy molecular dynamics simulations. The ground state geometry for ArnXe13-n},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ramakrishna1999,
title = {Gene identification in bacterial and organellar genomes using GeneScan},
author = {Ramaswamy Ramakrishna and Ramachandran Srinivasan},
url = {https://ramramaswamy.org/papers/071.pdf},
doi = {10.1016/S0097-8485(98)00034-5},
issn = {00978485},
year  = {1999},
date = {1999-01-01},
journal = {Computers and Chemistry},
volume = {23},
number = {2},
pages = {165--174},
abstract = {The performance of the GeneScan algorithm for gene identification has been improved by incorporation of a directed iterative scanning procedure. Application is made here to the cases of bacterial and organnellar genomes. The sensitivity of gene identification was 100% in Plasmodium falciparum plastid-like genome (35 kb) and in 98% in the Mycoplasma genitalium genome (∼580 kb) and the Haemophilus influenzae Rd genome (∼1.8 Mb). Sensitivity was found to improve in both the Open Reading Frames (ORFs) which have been identified as genes (by homology or by other methods) and those that are classified as hypothetical. False positive assignments (at the nucleotide level) were 0.25% in H. influenzae genome and 0.3% in M. genitalium. There were no false positive assignments in the plastid-like genome. The agreement between the GeneScan predictions and GeneMark predictions of putative ORFs was 97% in M. genitalium genome and 86% in H. influenzae genome. In terms of an exact match between predicted genes/ORFs and the annotation in the databank, GeneScan performance was evaluated to be between 72% and 90% in different genomes. We predict five putative ORFs that were not annotated earlier in the GenBank files for both M. genitalium and H. influenzae genomes. Our preliminary analysis of the newly sequenced G + C rich genome of Mycobacterium tuberculosis H37Rv also shows comparable sensitivity (99%). textcopyright 1999 Elsevier Science Ltd. All rights reserved.},
keywords = {Fourier, GeneScan, Haemophilus, Mycoplasma, Plasmodium},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad1999,
title = {Characteristic distributions of finite-time Lyapunov exponents},
author = {Awadhesh Prasad and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/072.pdf},
doi = {10.1103/PhysRevE.60.2761},
issn = {1063651X},
year  = {1999},
date = {1999-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {60},
number = {3},
pages = {2761--2766},
abstract = {We study the probability densities of finite-time or $backslash$local Lyapunov exponents (LLEs) in low-dimensional chaotic systems. While the multifractal formalism describes how these densities behave in the asymptotic or long-time limit, there are significant finite-size corrections which are coordinate dependent. Depending on the nature of the dynamical state, the distribution of local Lyapunov exponents has a characteristic shape. For intermittent dynamics, and at crises, dynamical correlations lead to distributions with stretched exponential tails, while for fully-developed chaos the probability density has a cusp. Exact results are presented for the logistic map, $x backslashto 4x(1-x)$. At intermittency the density is markedly asymmetric, while for `typical' chaos, it is known that the central limit theorem obtains and a Gaussian density results. Local analysis provides information on the variation of predictability on dynamical attractors. These densities, which are used to characterize the $backslash$sl nonuniform spatial organization on chaotic attractors are robust to noise and can therefore be measured from experimental data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad1999a,
title = {Collision and symmetry breaking in the transition to strange nonchaotic attractors},
author = {Awadhesh Prasad and Ramakrishna Ramaswamy and Indubala I Satija and Nausheen Shah},
url = {https://ramramaswamy.org/papers/073.pdf},
doi = {10.1103/PhysRevLett.83.4530},
issn = {10797114},
year  = {1999},
date = {1999-01-01},
journal = {Physical Review Letters},
volume = {83},
number = {22},
pages = {4530--4533},
abstract = {Strange nonchaotic attractors (SNAs) can be created due to the collision of an invariant curve with itself. This novel "homoclinic" transition to SNAs occurs in quasiperiodically driven maps which derive from the discrete Schrödinger equation for a particle in a quasiperiodic potential. In the classical dynamics, there is a transition from torus attractors to SNAs, which, in the quantum system, is manifest as the localization transition. This equivalence provides new insight into a variety of properties of SNAs, including its fractal measure. Further, there is a symmetry breaking associated with the creation of SNAs which rigorously shows that the Lyapunov exponent is nonpositive. We show that these characteristics associated with the appearance of SNA are robust and occur in a large class of systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Tsimring1999,
title = {Dynamics of a shallow fluidized bed},
author = {Lev S Tsimring and Ramakrishna Ramaswamy and Philip Sherman},
url = {https://ramramaswamy.org/papers/074.pdf},
doi = {10.1103/PhysRevE.60.7126},
issn = {1063651X},
year  = {1999},
date = {1999-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {60},
number = {6},
pages = {7126--7130},
abstract = {The results of the experimental study of the dynamics of a shallow fluidized bed are reported. The behavior of granular material is controlled by the interplay of two factors - levitation due to the upward airflow, and sliding back due to gravity. Near the threshold of instability, the system shows critical behavior with remarkably long transient dynamics. The experimental observations are compared with a simple cellular automata model.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Prasad1998,
title = {Strange nonchaotic attractors in the quasiperiodically forced logistic map},
author = {Awadhesh Prasad and Vishal Mehra and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/068.pdf},
doi = {10.1103/PhysRevE.57.1576},
issn = {1063651X},
year  = {1998},
date = {1998-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {57},
number = {2},
pages = {1576--1584},
abstract = {Different mechanisms for the creation of strange nonchaotic dynamics in the quasiperiodically forced logistic map are studied. These routes to strange nonchaos are characterized through the behavior of the largest nontrivial Lyapunov exponent, as well as through the characteristic distributions of finite-time Lyapunov exponents. Strange nonchaotic attractors can be created at a saddle-node bifurcation when the dynamics shows type-I intermittency; this intermittent transition, which is studied in detail, is characterized through scaling exponents. Band-merging crises through which dynamics remains nonchaotic are also studied, and correspondence is made with analogous behavior in the unforced logistic map. Robustness of these phenomena with respect to additive noise is investigated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1998,
title = {Targeting chaos through adaptive control},
author = {Ramakrishna Ramaswamy and Sudeshna Sinha and Neelima Gupte},
url = {https://ramramaswamy.org/papers/069.pdf},
doi = {10.1103/PhysRevE.57.R2507},
issn = {1063651X},
year  = {1998},
date = {1998-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {57},
number = {3},
pages = {R2507--R2510},
abstract = {We describe adaptive control algorithms whereby a chaotic dynamical system can be steered to a target state with desired characteristics. A specific implementation considered has the objective of directing the system to a state which is more chaotic or mixed than the uncontrolled one. This methodology is easy to implement in discrete or continuous dynamical systems. It is robust and efficient, and has the additional advantage that knowledge of the detailed behavior of the system is not required.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Tiwari1997,
title = {Prediction of probable genes by Fourier analysis of genomic sequences},
author = {S Tiwari, S Ramachandran, S Bhattacharya, A Bhattacharya and R Ramaswamy},
url = {https://doi.org/10.1093/bioinformatics/13.3.263},
doi = {10.1093/bioinformatics/13.3.263},
year  = {1997},
date = {1997-06-01},
journal = {Bioinformatics},
volume = {13},
number = {3},
pages = {263–270},
abstract = {Motivation: The major signal in coding regions of genomic sequences is a three-base periodicity. Our aim is to use Fourier techniques to analyse this periodicity, and thereby to develop a tool to recognize coding regions in genomic DNA.

Result: The three-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f = 1/3 in the Fourier (or power) spectrum. From extensive spectral analysis of DNA sequences of total length over 5.5 million base pairs from a wide variety or organisms (including the human genome), and by separately examining coding and non-coding sequences, we find that the relative height of the peak at f = 1/3 in the Fourier spectrum is a good discriminator of coding potential. This feature is utilized by us to detect probable coding regions in DNA sequences, by examining the local signal-to-noise ratio of the peak within a sliding window. While the overall accuracy is comparable to that of other techniques currently in use, the measure that is presently proposed is independent of training sets or existing database information, and can thus find general application.

Availability: A computer program GeneScan which locates coding open reading frames and exonic regions in genomic sequences has been developed, and is available on request},
keywords = {Fourier, Genes, GeneScan},
pubstate = {published},
tppubtype = {article}
}
@article{Chakravarty1997,
title = {Instantaneous normal mode spectra of quantum clusters},
author = {C Chakravarty and R Ramaswamy
},
url = {https://pubs.aip.org/aip/jcp/article-pdf/106/13/5564/10783293/5564\_1\_online.pdf},
doi = {10.1063/1.473578},
issn = {0021-9606},
year  = {1997},
date = {1997-04-01},
journal = {The Journal of Chemical Physics},
volume = {106},
number = {13},
pages = {5564–5568},
abstract = {The spectrum of instantaneous normal mode (INM) frequencies of finite Lennard-Jones clusters is studied as a function of the extent of quantum delocalization. Configurations are sampled from the equilibrium distribution by a Fourier path integral Monte Carlo procedure. The INM spectra, average force constants and Einstein frequencies are shown to be interesting dynamical markers for the quantum delocalization-induced cluster solid–liquid transition. Comparisons are made with INM spectra of quantum and classical Lennard-Jones liquids. The methodology used here suggests a general strategy to obtain quantal analogs of various classical dynamical quantities},
keywords = {lenard-jones, Monte Carlo, phase transition},
pubstate = {published},
tppubtype = {article}
}
@article{Mehra1997,
title = {Curvature fluctuations and the lyapunov exponent at melting},
author = {Vishal Mehra and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/065.pdf},
doi = {10.1103/PhysRevE.56.2508},
issn = {1063651X},
year  = {1997},
date = {1997-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {56},
number = {3},
pages = {2508--2517},
abstract = {We calculate the maximal Lyapunov exponent in constant-energy molecular-dynamics simulations at the melting transition for finite clusters of 6-13 panicles (model rare-gas and metallic systems) as well as for bulk rare-gas solids. For clusters, the Lyapunov exponent generally varies linearly with the total energy, but the slope changes sharply at the melting transition. In the bulk system, melting corresponds to a jump in the Lyapunov exponent, and this corresponds to a singularity in the variance of the curvature of the potential-energy surface. In these systems there are two mechanisms of chaos - local instability and parametric instability. We calculate the contribution of the parametric instability toward the chaoticity of these systems using a recently proposed formalism. The contribution of parametric instability is a continuous function of energy in small clusters but not in the bulk where the melting corresponds to a decrease in this quantity. This implies that the melting in small clusters does not lead to enhanced local instability.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Albanese1997,
title = {Intermittency route to strange nonchaotic attractors},
author = {C Albanese and P DellÁversana and F S Gaeta},
url = {https://ramramaswamy.org/papers/066.pdf},
doi = {10.1103/PhysRevLett.79.4151},
issn = {10797114},
year  = {1997},
date = {1997-01-01},
journal = {Physical Review Letters},
volume = {79},
number = {21},
pages = {4151--4154},
abstract = {Strange nonchaotic attractors (SNA) arise in quasiperiodically driven systems in the neighborhood of a saddle node bifurcation whereby a strange attractor is replaced by a periodic (torus) attractor. This transition is accompanied by Type-I intermittency. The largest nontrivial Lyapunov exponent $backslashLambda$ is a good order-parameter for this route from chaos to SNA to periodic motion: the signature is distinctive and unlike that for other routes to SNA. In particular, $backslashLambda$ changes sharply at the SNA to torus transition, as does the distribution of finite-time or N--step Lyapunov exponents, P($backslash$Lambda_N).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1997,
title = {Synchronization of strange nonchaotic attractors},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/067.pdf},
doi = {10.1103/PhysRevE.56.7294},
issn = {1063651X},
year  = {1997},
date = {1997-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {56},
number = {6},
pages = {7294--7296},
abstract = {Strange nonchaotic attractors (SNAs), which are realized in many quasiperiodically driven nonlinear systems, are strange (geometrically fractal) but nonchaotic (the largest nontrivial Lyapunov exponent is negative). Two such identical independent systems can be synchronized by in-phase driving: Because of the negative Lyapunov exponent, the systems converge to a common dynamics, which, because of the strangeness of the underlying attractor, is aperiodic. This feature, which is robust to external noise, can be used for applications such as secure communication. A possible implementation is discussed and its performance is evaluated. The use of SNAs rather than chaotic attractors can offer some advantages in experiments involving synchronization with aperiodic dynamics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mehra1996,
title = {Maximal Lyapunov exponent at crises},
author = {V Mehra and R Ramaswamy
},
url = {https://link.aps.org/doi/10.1103/PhysRevE.53.3420},
doi = {10.1103/PhysRevE.53.3420},
year  = {1996},
date = {1996-04-01},
journal = {Physical Review E},
volume = {53},
number = {4},
pages = {3420-3424},
abstract = {We study the variation of Lyapunov exponents of simple dynamical systems near attractor-widening and attractor-merging crises. The largest Lyapunov exponent has universal behavior, showing abrupt variation as a function of the control parameter as the system passes through the crisis point, either in the value itself, in the case of an attractor-widening crisis, or in the slope, for an attractor-merging crisis. The distribution of local Lyapunov exponents is very different for the two cases: the fluctuations remain constant through a merging crisis, but there is a dramatic increase in the fluctuations at a widening crisis.},
keywords = {Chaos Theory, Lyapunov exponent},
pubstate = {published},
tppubtype = {article}
}
@article{Nayak1996,
title = {Solid <==> liquid transition in model (HF)n clusters},
author = {S Nayak and R Ramaswamy
},
url = {https://doi.org/10.1080/002689796173705},
doi = {10.1080/002689796173705},
year  = {1996},
date = {1996-03-01},
journal = {Molecular Physics},
volume = {89},
number = {3},
pages = {809-817},
abstract = { We study the stability, energetics and dynamics of small model hydrogen fluoride clusters (HF) n using isoergic molecular dynamics simulations. The largest Lyapunov exponent is computed over the energy range when the clusters melt, and is found to be more useful in defining the onset of melting than Lindemann's index. We also examine the power spectrum of potential energy fluctuations of clusters in the liquid state, which show 1/f dependence over a smaller frequency range than rare-gas clusters of comparable size.},
keywords = {clusters, phase transition},
pubstate = {published},
tppubtype = {article}
}
@article{Tiwari1996b,
title = {Nos´e-Hoover dynamics of a nonintegrable Hamiltonian},
author = {S Tiwari and R Ramaswamy
},
url = {https://www.sciencedirect.com/science/article/pii/0166128095043098},
doi = {10.1016/0166-1280(95)04309-8},
issn = {0166-1280},
year  = {1996},
date = {1996-01-15},
journal = {Journal of Molecular Structure: THEOCHEM},
volume = {361},
number = {1},
pages = {111-116},
abstract = {We study the dynamics of a hamiltonian system with two degrees of freedom coupled to a Nosé-Hoover thermostat. In the absence of the thermostat, the system is quasi-integrable: at low energies, most of the motion is on two-dimensional tori, while at higher energies, the motion is mainly chaotic. Upon coupling to the thermostat the system becomes more chaotic, as evidenced by the magnitude of the largest Lyapunov exponent. In contrast to the case of isotropic oscillator systems coupled to thermostats, there is no evidence for a regime of integrable behaviour, even for large values of Q.},
keywords = {Lyapunov exponent, Nonintegrable Hamiltonian Systems},
pubstate = {published},
tppubtype = {article}
}
@article{Tiwari1996,
title = {Adaptive control in a resource management model},
author = {Shrish Tiwari and Ramakrishna Ramaswamy and J.Subba Rao},
url = {https://ramramaswamy.org/papers/056.pdf},
doi = {10.1016/0304-3800(94)00143-x},
issn = {03043800},
year  = {1996},
date = {1996-01-01},
journal = {Ecological Modelling},
volume = {84},
number = {1-3},
pages = {53--62},
abstract = {We cast a model of biological resource management as a problem of adaptive control in a nonlinear dynamical system. Optimisation of harvest, while ensuring that the resource population persists, is achieved through a simple algorithmic procedure which is remarkably robust under a variety of perturbations. textcopyright 1996 Elsevier Science B.V. All rights reserved.},
keywords = {Control, Optimization, Resource Management},
pubstate = {published},
tppubtype = {article}
}
@article{Schutz1996,
title = {Pairwise balance and invariant measures for generalized exclusion processes},
author = {Gunter M Schutz and Ramakrishna Ramaswamy and Mustansir Barma},
url = {https://ramramaswamy.org/papers/057.pdf},
doi = {10.1088/0305-4470/29/4/011},
issn = {03054470},
year  = {1996},
date = {1996-01-01},
journal = {Journal of Physics A: Mathematical and General},
volume = {29},
number = {4},
pages = {837--843},
abstract = {We characterize the steady state of a driven diffusive lattice gas in which each site holds several particles, and the dynamics is activated and asymmetric. Using a quantum Hamiltonian formalism, we show that for arbitrary transition rates the model has product invariant measure. In the steady state, a pairwise balance condition is shown to hold. Configurations n″ and n′ leading respectively into and out of a given configuration n are matched in pairs so that the flux of transitions from n″ to n is equal to the flux from n to n′. Pairwise balance is more general than the condition of detailed balance and holds in the non-equilibrium steady state of a number of stochastic models. textcopyright 1996 IOP Publishing Ltd.},
keywords = {Generalized Exclusion Processes, Invariant Measure},
pubstate = {published},
tppubtype = {article}
}
@article{Mahapatra1996,
title = {Quantum chaos in collinear (He,H+ 2 ) collisions},
author = {S Mahapatra and R Ramaswamy and N Sathyamurthy},
url = {https://ramramaswamy.org/papers/058.pdf},
issn = {00219606},
year  = {1996},
date = {1996-01-01},
journal = {Journal of Chemical Physics},
volume = {104},
number = {11},
pages = {3989--3997},
abstract = {The quasibound spectrum of the transition state in collinear (He, H2+) collisions is obtained from time-dependent wave packet calculations. Examination of short- and long-range correlations in the eigenvalue spectra through a study of the nearest neighbor spacing distribution, P(s), and the spectral rigidity, $Delta$3(L), reveals signatures of quantum chaotic behavior. Analysis in the time domain is carried out by computing the survival probability «P(t)» averaged over initial states and Hamiltonian. All these indicators show intermediate behavior between regular and chaotic. A quantitative comparison of «P(t)» with the results of random matrix theory provides an estimate of the fraction of phase space exhibiting chaotic behavior, in reasonable agreement with the classical dynamics. We also analyse the dynamical evolution of coherent Gaussian wave packets located initially in different regions of phase space and compute the survival probability, power spectrum and the volume of phase space over which the wave packet spreads and illustrate the different behaviors. textcopyright 1996 American Institute of Physics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Tadic1996,
title = {Defects in self-organized criticality: A directed coupled map lattice model},
author = {Bosiljka Tadi{ć} and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/060.pdf},
doi = {10.1103/PhysRevE.54.3157},
issn = {1063651X},
year  = {1996},
date = {1996-01-01},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
volume = {54},
number = {4},
pages = {3157--3164},
abstract = {We study a directed coupled map lattice model in d = 2 dimensions, with two degrees of freedom associated with each lattice site. The two freedoms are coupled at a fraction c of lattice bonds acting as quenched random defects. The system is driven (by adding "energy," say) in one of the degrees of freedom at the top of the lattice, and the relaxation rules depend on the local difference between the two variables at a lattice site. In the case of conservative dynamics, at any concentration of defects the system reaches a self-organized critical state with universal critical exponents close to the mean-field values $tau$t = 1, $tau$s = 2/3, and $tau$n= 1/2, for the integrated distributions of avalanche durations (t), size (s), and released energy (n), respectively. The probability distributions follow the general scaling form P(X,L) = L -$alpha$P(XL-DX), where $alpha$≈ 1 is the scaling exponent for the distribution of avalanche lengths, X stands for t, s, or n, and DX is the (independently determined) fractal dimension with respect to X. The distribution of current through the system is, however, nonuniversal, and does not show any apparent scaling form. In the case of nonconservative dynamics-obtained by incomplete energy transfer at the defect bonds-the system is driven out of the critical state. In the scaling region close to c = 0 the probability distributions exhibit the general scaling form P(X,c,L) = X-$tau$XP[X/$xi$X(c),XL-DX], where $tau$X= $alpha$/DX and the corresponding coherence length $xi$X(c) depends on the concentration of defect bonds c as $xi$X(c)∼c-DX.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gupta1996,
title = {Backbones of traffic jams},
author = {Himadri Shikhar Gupta and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/062.pdf},
doi = {10.1088/0305-4470/29/21/003},
issn = {03054470},
year  = {1996},
date = {1996-01-01},
journal = {Journal of Physics A: Mathematical and General},
volume = {29},
number = {21},
pages = {547--553},
abstract = {We study the jam phase of the deterministic traffic model in two dimensions. Within the jam phase, there is a phase transition, from a self-organized jam (formed by initial synchronization followed by jamming), to a random-jam structure. The backbone of the jam is defined and used to analyse self-organization in the jam. The fractal dimension and interparticle correlations on the backbone indicate a continous phase transition at density pc with critical exponent $mu$, which are characterized through simulations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Tadic1996a,
title = {Criticality in driven cellular automata with defects},
author = {Bosiljka Tadi{ć} and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/R13.pdf},
doi = {10.1016/0378-4371(95)00322-3},
issn = {03784371},
year  = {1996},
date = {1996-01-01},
journal = {Physica A: Statistical Mechanics and its Applications},
volume = {224},
number = {1-2},
pages = {188--198},
abstract = {We study three models of driven sandpile-type automata in the presence of quenched random defects. When the dynamics is conservative, all these models, termed the random sites (A), random bonds (B), and random slopes (C), self-organize into a critical state. For model C the concentration-dependent exponents are nonuniversal. In the case of nonconservative defects, the asymptotic state is subcritical. Possible defect-mediated nonequilibrium phase transitions are also discussed.},
keywords = {Cellular automata, Criticality},
pubstate = {published},
tppubtype = {article}
}
@article{Gade1995,
title = {Coupled maps on trees},
author = {P M Gade, H Cerdeira and R Ramaswamy
},
url = {https://link.aps.org/doi/10.1103/PhysRevE.52.2478},
doi = {10.1103/PhysRevE.52.2478},
year  = {1995},
date = {1995-09-01},
journal = {Physical Review E},
volume = {52},
number = {3},
pages = {2478--2485},
abstract = {We study coupled maps on a Cayley tree, with local (nearest-neighbor) interactions, and with a variety of boundary conditions. The homogeneous state (where every lattice site has the same value) and the node-synchronized state (where sites of a given generation have the same value) are both shown to occur for particular values of the parameters and coupling constants. We study the stability of these states and their domains of attraction. Since the number of sites that become synchronized is much higher compared to that on a regular lattice, control is easier to achieve. A general procedure is given to deduce the eigenvalue spectrum for these states. Perturbations of the synchronized state lead to different spatiotemporal structures. We find that a mean-field-like treatment is valid on this (effectively infinite dimensional) lattice.},
keywords = {Coupled map lattice, Coupled maps},
pubstate = {published},
tppubtype = {article}
}
@article{Nayak1995b,
title = {The maximal Lyapunov exponent in small atomic clusters},
author = {S K Nayak, R Ramaswamy and C Chakravarty},
url = {https://link.aps.org/doi/10.1103/PhysRevE.51.3376},
doi = {10.1103/PhysRevE.51.3376},
year  = {1995},
date = {1995-04-01},
journal = {Physical Review E},
volume = {51},
number = {4},
pages = {3376--3380},
abstract = {We study small clusters of atomic argon, 
Ar7 Ar13, and Ar55,  in the temperature range where they undergo a transition from a solidlike phase to a liquidlike phase. The signature of the phase transition is clearly seen as a dramatic increase in the largest Lyapunov exponent as the cluster ‘‘melts.},
keywords = {Atomic Clusters, Lyapunov exponent},
pubstate = {published},
tppubtype = {article}
}
@article{Nayak1995,
title = {1/ f Spectra in finite atomic clusters},
author = {Saroj K Nayak and Ramakrishna Ramaswamy and Charusita Chakravarty},
url = {https://ramramaswamy.org/papers/052.pdf},
doi = {10.1103/PhysRevLett.74.4181},
issn = {00319007},
year  = {1995},
date = {1995-01-01},
journal = {Physical Review Letters},
volume = {74},
number = {21},
pages = {4181--4184},
abstract = {We study small clusters of atomic argon, Ar7, Ar13, and Ar55, in the temperature range when they undergo a transition from a solidlike phase to a liquidlike phase. The power spectra of potential energy fluctuations of tagged atoms in the liquid state show 1/f behavior over a wide range of frequency f, unlike either the solid phase or bulk liquid, and suggest a new experimental means of detecting cluster melting. The origin of this temporal scale invariance is explored by studying the individual potential energy distributions, which are observed to become multimodal when the clusters melt. textcopyright 1995 The American Physical Society.},
keywords = {Atomic Clusters, Power Spectra},
pubstate = {published},
tppubtype = {article}
}
@article{Kumar1995,
title = {Overcoming the zero-point dilemma in quasiclassical trajectories: (He,H2+) as a test case},
author = {Sanjay Kumar and N Sathyamurthy and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/054.pdf},
doi = {10.1063/1.470430},
issn = {00219606},
year  = {1995},
date = {1995-01-01},
journal = {The Journal of Chemical Physics},
volume = {103},
number = {14},
pages = {6021--6028},
abstract = {We present a new technique for circumventing the problem of the zero-point leak in classical trajectories by extending the action-billiard approach of de Aguiar and Ozorio de Almeida [Nonlinearity 5, 523 (1992)]. In addition to demonstrating its utility in a model problem, we examine the application of various methods of overcoming the zero-point leak in the case of collinear He+H2 + collisions. We also show that not neglecting leaky trajectories gives, on an average, good agreement with quantal results for collinear as well as 3-dimensional collisions. textcopyright 1995 American Institute of Physics.},
keywords = {Action-Billiard},
pubstate = {published},
tppubtype = {article}
}
@article{Nayak1994b,
title = {Melting of (Ar–Xe)13 clusters: Surface-core effects},
author = {S K Nayak and R Ramaswamy},
url = {https://doi.org/10.1021/j100088a028},
doi = {10.1021/j100088a028},
issn = {0022-3654},
year  = {1994},
date = {1994-09-01},
journal = {Journal of Physical Chemistry},
volume = {98},
number = {37},
pages = {9260 - 9264},
abstract = {Potential energy fluctuations in the liquid phase of small atomic clusters (e.g. Ar13) have been seen to have
long-range temporal correlations. This is manifest in a power-law decay for the power spectrum, which has
a characteristic 1
//dependence on the frequency,/ (More precisely, the dependence is 1
//*, with a =
1.) In
order to understand the origin of this behavior, we study the melting of mixed rare-gas clusters Ar^Xe and
Xe^Ar (via molecular dynamics simulations). Substitution of atomic impurities introduces widely differing
time scales in the dynamics, and we show that long-lived memory-effects have their origins in hierarchical
relaxation processes arising in the motion of the atoms from the surface to the core and vice versa.
},
keywords = {clusters},
pubstate = {published},
tppubtype = {article}
}
@article{Nayak1994,
title = {Complex dynamics of atomic clusters},
author = {S Nayak and R Ramaswamy},
url = {https://doi.org/10.1007/BF02840767},
doi = {10.1007/BF02840767},
issn = {0973-7103},
year  = {1994},
date = {1994-04-01},
journal = {Proceedings of the Indian Academy of Sciences - Chemical Sciences},
volume = {106},
number = {2},
pages = {521–530},
abstract = {Potential energy fluctuations in small atomic clusters have long-ranged temporal correlations, which lead to l/f noise in the power spectra. The relaxation dynamics in clusters has a hierarchical organization, resulting from different processes at the surface and core. A cellular dynamical model is proposed to understand the origin of such fluctuations.},
keywords = {Atomic Clusters, relaxations},
pubstate = {published},
tppubtype = {article}
}
@article{Kertesz1994,
title = {Coarsening in a driven diffusive system with two species},
author = {J Kertész and R Ramaswamy},
url = {https://ramramaswamy.org/papers/050.pdf},
doi = {10.1209/0295-5075/28/9/001},
issn = {12864854},
year  = {1994},
date = {1994-01-01},
journal = {Epl},
volume = {28},
number = {9},
pages = {617--622},
abstract = {We study the dynamics of a lattice gas with two species of “charged” diffusing particles in the presence of an external field. There are several time scales characterizing the approach of the steady state. At short times diffusion smears out inhomogeneities. For fields such that the density is below the virtual (size-dependent) threshold of jamming, i.e. in the flow phase, this is the main relaxation mechanism. In addition, there are kinematic waves arising from the non-linear dependence of the current on the density. Above the threshold there is an instability leading to a multistrip structure of blockages: in each strip one type of particle prevents the other type from following the direction of the imposed field. The strips coarsen logarithmically slowly, until finally a single blockage remains. textcopyright 1994 IOP Publishing Ltd.},
keywords = {Driven Diffusive System},
pubstate = {published},
tppubtype = {article}
}
@article{Kudrolli1994,
title = {Signatures of chaos in quantum billiards: Microwave experiments},
author = {A Kudrolli, S Sridhar, A Pandey and R Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevE.49.R11},
doi = {10.1103/PhysRevE.49.R11},
year  = {1994},
date = {1994-01-01},
journal = {Physical Review E},
volume = {49},
number = {1},
pages = {R11--R14},
abstract = {The signatures of classical chaos and the role of periodic orbits in the wave-mechanical eigenvalue spectra of two-dimensional billiards are studied experimentally in microwave cavities. The survival probability for all the chaotic cavity data shows a ‘‘correlation hole,’’ in agreement with theory, that is absent for the integrable cavity. The spectral rigidity 
Δ
3
(L), which is a measure of long-range correlation, is shown to be particularly sensitive to the presence of marginally stable periodic orbits. Agreement with random-matrix theory is achieved only after excluding such orbits, which we do by constructing a special geometry, the Sinai stadium. Pseudointegrable geometries are also studied, and are found to display intermediate behavior.},
keywords = {Action-Billiard, Chaos, Quantum chaos},
pubstate = {published},
tppubtype = {article}
}
@conference{Barma1994,
title = {Field–induced transport in random media},
author = {M Barma and R Ramaswamy},
url = {https://link.springer.com/chapter/10.1007/3-540-58652-0_45},
year  = {1994},
date = {1994-01-01},
booktitle = {Non-Linearity and Breakdown in Soft Condensed Matter},
pages = {309-330},
publisher = {Springer},
address = {Calcutta, India},
abstract = {We review the problem of particle transport in random media in the presence of an external field. The random medium is modeled by the infinite cluster above the percolation threshold. The field imposes a preferred direction of motion along which diffusing particles (random walkers are more likely to move than against. Two kinds of traps occur - branches pointing in the direction of the field, and backbends, in which particles must move against the field. For noninteracting particles, the drift velocity is a nonmonotonic function of the biasing field, and the two kinds of traps make the current vanish above a threshold value of the bias. If there is hard-core repulsion between the particles, branches get filled up and eventually cease to be traps. Below the directed percolation threshold, transport is rate-limited by backbends, and the particle current flows predominantly along those paths on the percolation backbone on which the length of every backbend is bounded. The current is a nonmonotonic function of the biasing field. We also consider a different sort of interparticle interaction which leads to levels of particles equalising near backbend bottoms. The motion along a typical path is then described by 'drop-push' dynamics: between backbends, particles drop down, assisted by the field, and push those on the next backbend, possibly leading to a cascade of overflows. Drop-push dynamics has interesting connections with other lattice gas automata, and Monte Carlo simulations show that the model supports kinematic waves and exhibits interesting behaviour of time-dependent correlations.},
keywords = {Random Walk},
pubstate = {published},
tppubtype = {conference}
}
@article{Pandey1993,
title = {Symmetry-breaking in quantum chaotic systems},
author = {A Pandey, R Ramaswamy and P Shukla},
url = {https://doi.org/10.1007/BF02847320},
doi = {10.1007/BF02847320},
issn = {0973-7111},
year  = {1993},
date = {1993-07-01},
journal = {Pramana},
volume = {45},
number = {1},
pages = {75-81},
abstract = {We show, using semiclassical methods, that as a symmetry is broken, the transition between universality classes for the spectral correlations of quantum chaotic systems is governed by the same parametrization as in the theory of random matrices. The theory is quantitatively verified for the kicked rotor quantum map. We also provide an explicit substantiation of the random matrix hypothesis, namely that in the symmetry-adapted basis the symmetry-violating operator is random.},
keywords = {Quantum chaos, Symmetry Breaking},
pubstate = {published},
tppubtype = {article}
}
@article{Someda1993b,
title = {Decoupling surface analysis of classical irregular scattering and classification of its icicle structure},
author = {K Someda, R Ramaswamy and H Nakamura},
url = {https://pubs.aip.org/aip/jcp/article-pdf/98/2/1156/11047349/1156\_1\_online.pdf},
doi = {10.1063/1.464339},
issn = {0021-9606},
year  = {1993},
date = {1993-01-15},
journal = {The Journal of Chemical Physics},
volume = {98},
number = {2},
pages = {1156–1169 },
abstract = {Irregular scattering in molecular inelastic collision is analyzed classical mechanically by a novel method called ‘‘decoupling surface analysis.’’ Effective Hamiltonian of this analysis provides a phase space view of collision processes analogous to the Poincaré section of coupled‐oscillator systems. In this phase space view irregular scattering occurs in a stochastic layer formed around separatrix connected to resonance structure of the effective Hamiltonian. This circumstance is parallel to that in the coupled‐oscillator systems, in which stochastic motion is known to be connected to nonlinear resonance. The resonance structure in collision indicates trapping of classical trajectories in a certain dynamical well. The decoupling surface analysis suggests that the dynamical well is formed by a dip of stability exponents of trajectories as a function of time. By using a prototypical model exhibiting irregular scattering, a formal theoretical treatment is developed to analyze the structure of the fractal, termed icicle structure, observed in the plot of final vibrational action against the initial vibrational phase angle.},
keywords = {05.45.-a Nonlinear dynamics and nonlinear dynamical systems, Coupled Oscillators, Stochastic dynamics},
pubstate = {published},
tppubtype = {article}
}
@article{Tadi´c1992,
title = {Scaling behaviour in disordered sandpile automata},
author = {B Tadi´c, U Nowak, K Usadel, R Ramaswamy and S Padlewski
},
url = {https://link.aps.org/doi/10.1103/PhysRevA.45.8536},
doi = {10.1103/PhysRevA.45.8536},
year  = {1992},
date = {1992-06-01},
journal = {Physical Review A},
volume = {45},
number = {12},
pages = {8536--8545},
abstract = {We study numerically the scaling behavior of disordered sandpile automata with preferred direction on a two-dimensional square lattice. We consider two types of bulk defects that modify locally the dynamic rule: (i) a random distribution of holes, through which sand grains may leave the system, and (ii) several models with a random distribution of critical heights. We find that at large time and length scales the self-organized critical behavior, proved exactly in the pure model, is lost for any finite concentration of defects both in the model of random holes and in those models of random critical heights in which the dynamic rule violates the height conservation law. In the case of the random critical height model with the height-conserving dynamics, we find that self-organized criticality holds for the entire range of concentrations of defects, and it belongs to the same universality class as the pure model. In the case of random holes we analyze the scaling properties of the probability distributions P(T,p,L) and D(s,p,L) of avalanches of duration larger than T and size larger than s, respectively, at lattices with linear size L and concentration of defect sites p. We find that in general the following scaling forms apply: P(T)=
T
−
α
scrP(T/x,T/L) and D(s)=
s
−
τ
scrD(s/m,s/
L
ν
), where x≡x(p) and m≡m(p) are the characteristic duration (length) and the characteristic size (mass) of avalanches for a given concentration of defects.

The power-law behavior of the distributions still persists for length scales T≪x(p) and mass scales s≪m(p). The characteristic length x(p) and mass m(p) are finite for small concentrations of defects and diverge at p→0 according to the power law x(p)∼
p
−
μ
x
 and m(p)∼
p
−
μ
m
, with the numerically determined values of the exponents close to 
μ
x
=1 and 
μ
m
=1.5. The finite size of the lattice may affect the measured probability distributions if for a given concentration of defects the characteristic length x(p) exceeds the lattice size L. A finite-size scaling analysis for the mass distribution yields the exponent ν=1.5, while the duration of the avalanches scales linearly with the size. We also determine the exponent D=1.5 that connects the mass and the duration of avalanches.},
keywords = {Criticality, Fractals, Sandpile, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{Sasai1992,
title = {Long time fluctuation of liquid water: 1/f spectrum of energy fluctuation in hydrogen bond network rearrangement dynamics },
author = {M Sasai, I Ohmine and R Ramaswamy},
url = {https://pubs.aip.org/aip/jcp/article-pdf/96/4/3045/11026320/3045\_1\_online.pdf},
doi = {10.1063/1.461950},
issn = {0021-9606},
year  = {1992},
date = {1992-02-15},
journal = {The Journal of Chemical Physics},
volume = {96},
number = {4},
pages = {3045–3053},
abstract = {The power spectrum of the potential energy fluctuation of liquid water is examined and found to yield so‐called 1/f frequency dependence (f is frequency). This is in sharp contrast to spectra of simple liquids (e.g., liquid argon), which exhibit a near white spectrum. This indicates that there exists an extended multiplicity of hydrogen bond network relaxations in liquid water. A simple model of cellular dynamics is proposed to explain this frequency dependence. On the other hand, the cluster dynamics of argon also involves energy fluctuations of a 1/f type, resulting from various relaxation processes at core and surface.},
keywords = {clusters},
pubstate = {published},
tppubtype = {article}
}
@article{Pandey1991,
title = {Level spacings for harmonic oscillator systems},
author = {A Pandey and R Ramaswamy
},
url = {https://link.aps.org/doi/10.1103/PhysRevA.43.4237},
doi = {10.1103/PhysRevA.43.4237},
year  = {1991},
date = {1991-04-01},
journal = {Physical Review A},
volume = {43},
number = {8},
pages = {4237--4243},
abstract = {From the viewpoint of eigenvalue level statistics, harmonic-oscillator systems are unusual. Although integrable, these systems are nongeneric, and a spacing distribution does not exist even as the number of levels N→∞. The origins of this pathological behavior are explored using methods of number theory and ergodic analysis. However, such nongenericity is extremely fragile, and the smallest nonlinearity asymptotically restores generic behavior. These results are of relevance to the study of molecular spectra, as well as to the quasienergy spectra of integrable quantum maps.},
keywords = {Quantum State},
pubstate = {published},
tppubtype = {article}
}
@article{Sinha1990,
title = {Adaptive control in nonlinear dynamics},
author = {Sudeshna Sinha and Ramakrishna Ramaswamy and Subba J Rao},
url = {https://ramramaswamy.org/papers/040.pdf},
doi = {10.1016/0167-2789(90)90020-P},
issn = {01672789},
year  = {1990},
date = {1990-01-01},
journal = {Physica D: Nonlinear Phenomena},
volume = {43},
number = {1},
pages = {118--128},
abstract = {We extend an adaptive control algorithm recently suggested by Huberman and Lumer to multi-parameter and higher- dimensional nonlinear systems. This control mechanism is remarkably effective in returning a system to its original dynamics after a sudden perturbation in the system parameters changes the dynamical behaviour. We find that in all cases, the recovery time is linearly proportional to the inverse of control stiffness (for small stiffness). In higher dimensions there is an additional optimization problem since increasing stiffness beyond a certain value can retard recovery. The control of fixed point dynamics in systems capable of a wide variety of dynamical behaviour is demonstrated. We further suggest methods by which periodic motion such as limit cycles can be adaptively controlled, and demonstrate the robustness of the procedure in the presence of (additive) background noise. textcopyright 1990.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Dhar1989,
title = {An exactly solved model of self-organized critical phenomena},
author = {D Dhar and R Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevLett.63.1659},
doi = {10.1103/PhysRevLett.63.1659},
year  = {1989},
date = {1989-10-16},
journal = {PHYSICAL REVIEW LETTERS},
volume = {63},
number = {16},
pages = {1659--1662},
abstract = {We define a variant of the model of Bak, Tang, and Wiesenfeld of self-organized critial behavior by introducing a preferred direction. We characterize the critical state and, by establishing equivalence to a voter model, determine the critical exponents exactly in arbitrary dimension d. The upper critical dimension for this model is three. In two dimensions the model is equivalent to an earlier solved special case of directed percolation.},
keywords = {Criticality, Sandpile},
pubstate = {published},
tppubtype = {article}
}
@article{Mohan1989,
title = {Dimension analysis of climatic data},
author = {T R Krishna Mohan, J Subba Rao and R Ramaswamy},
url = {https://doi.org/10.1175/1520-0442(1989)002%3C1047:DAOCD%3E2.0.CO;2},
doi = {10.1175/1520-0442},
year  = {1989},
date = {1989-09-01},
journal = {Journal of Climate},
volume = {2},
number = {9},
pages = {1047–1057},
abstract = {It has been conjectured that the unpredictability of climatic systems is due to strange attractors (SAs) in the configuration space dynamics. One climatic record, the oxygen isotope ratio data from deep-sea cores that pertains to long periods on the order of one million years and provides direct correlation with the glaciation-deglaciation periods, seemed to indicate (under earlier analysis) a low dimensional attractor of correlation dimension D2 ≈ 3.1. Our present reanalysis of this data in light of recent methods suggested by Broomhead and King (BK) is at variance with that result. Two (model) four-variable systems that support chaotic strange attractors are examined using an analysis similar to BK to investigate the practical drawbacks of using a short time-series vis-a-vis the estimation of attractor dimension.},
keywords = {climate, fractal dimension},
pubstate = {published},
tppubtype = {article}
}
@article{Caldeira1989,
title = {Limits of weak damping of a quantum harmonic oscillator},
author = {A O Caldeira, H A Cerdeira and R Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevA.40.3438},
doi = {10.1103/PhysRevA.40.3438},
year  = {1989},
date = {1989-09-01},
journal = {Physical Review A},
volume = {40},
number = {6},
pages = {3438--3440},
abstract = {In this Brief Report we analyze the limit of very weak damping of a quantum-mechanical Brownian oscillator. It is shown that the propagator for the reduced density operator of the oscillator can be written as a double path integral of the same form as that obtained in the high-temperature limit. As a direct consequence, we can write a Fokker-Planck equation for the reduced density operator of the weakly damped oscillator (at any temperature) involving only the damping and a generalized diffusion constant in momentum space.},
keywords = {Quantum State},
pubstate = {published},
tppubtype = {article}
}
@article{Sinha1989,
title = {Spectral rigidity in atomic uranium},
author = {S Sinha and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/038.pdf},
doi = {10.1088/0953-4075/22/19/012},
issn = {09534075},
year  = {1989},
date = {1989-01-01},
journal = {Journal of Physics B: Atomic, Molecular and Optical Physics},
volume = {22},
number = {19},
pages = {2985--2990},
abstract = {The authors study the level statistics of parity-selected electronic states of atomic uranium (including autoionisation levels), obtained from recent photoionisation experiments. The spacings distribution which reflects short-range structure appears to be Poisson but spectral fluctuation measures reveal rigidity, and are consistent with a superposition of GOE sequences as is typically seen in nuclear spectra.},
keywords = {Control, Optimization},
pubstate = {published},
tppubtype = {article}
}
@article{Sinha1989b,
title = {Semiclassical quantization of resonant systems},
author = {S Sinha and R Ramaswamy
},
url = {https://doi.org/10.1080/00268978900101111},
doi = {10.1080/00268978900101111},
year  = {1989},
date = {1989-01-01},
journal = {Molecular Physics},
volume = {67},
number = {2},
pages = {335-346},
abstract = {Practical schemes of determining the energy eigenvalue spectrum of multimode resonant systems are suggested; these include an adaptation of the scaling (polynomial) interpolation technique, as well as an adiabatic-switching method.},
keywords = {Quantization},
pubstate = {published},
tppubtype = {article}
}
@article{Sinha1988,
title = {Complex behaviour of the repressible operon},
author = {Somdatta Sinha and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/034.pdf},
doi = {10.1016/S0022-5193(88)80217-0},
issn = {10958541},
year  = {1988},
date = {1988-01-01},
journal = {Journal of Theoretical Biology},
volume = {132},
number = {3},
pages = {307--318},
abstract = {The repressor-mediated repression process in bacteria is modelled using a gene-enzyme-endproduct control unit. A combined analytical-numerical study shows that the system, though stable normally, becomes unstable for super-repressing strains even at low values of the cooperativity of repression, provided demand for the endproduct saturates at large endproduct concentrations. In addition the system also shows bistability, i.e., the co-existence of a stable steady-state and a stable limit cycle. The tryptophan operon is used as a model system and the results are discussed in the light of differential regulation of gene expression in lower organisms, especially in mutant strains. textcopyright 1988 Academic Press Limited.},
keywords = {Bistability, Complex Behaviour, Gene, Operon},
pubstate = {published},
tppubtype = {article}
}
@article{Sinha1987b,
title = {On the dynamics of a controlled metabolic network and cellular behaviour},
author = {S Sinha and R Ramaswamy},
url = {https://www.sciencedirect.com/science/article/pii/0303264787900529},
doi = {10.1016/0303-2647},
issn = {0303-2647},
year  = {1987},
date = {1987-01-26},
journal = {Biosystems},
volume = {20},
number = {4},
pages = {341-354},
abstract = {The existence of elaborate control mechanisms for the various biochemical processes inside and within living cells is responsible for the coherent behaviour observed in its spatio-temporal organisation. Stability and sensitivity are both necessary properties of living systems and these are achieved through negetive and positive feedback loops as in other control systems. We have studied a three-step reaction scheme involving a negative and a positive feedback loop in the form of end-product inhibition and allosteric activation. The variety of behaviour exhibited by this system, under different conditions, includes steady state, simple limit cycle oscillations, complex oscillations and period bifurcations leading to random oscillations or chaos. The system also shows the existence of two distinct chaotic regimes under the variation of a single parameter. These results, in comparison with single biochemical control loops, show that new behaviours can be exhibited in a more complex network which are not seen in the single control loops. The results are discussed in the light of a diverse variety of cellular functions in normal and altered cells indicating the role of controlled metabolic network as the underlying basis for cellular behaviour.},
keywords = {Chaos, Control},
pubstate = {published},
tppubtype = {article}
}
@article{Sinha1987,
title = {Scaling of moments in rotational inelasticity},
author = {Sudeshna Sinha and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/030.pdf},
doi = {10.1016/0009-2614(87)87235-4},
issn = {00092614},
year  = {1987},
date = {1987-01-01},
journal = {Chemical Physics Letters},
volume = {135},
number = {1-2},
pages = {153--158},
abstract = {We report the scaling behaviour of rotational energy transfer moments. The quantum moments exhibit a polynomial scaling behaviour in the variable ji(ji+1), whereas the classical moments scale as a polynomial in Ji2, whereJi is the initial rotational quantum number or action. Applications are made to Li*2-rare gas collisions, as well as to a classical planar-rotor collision model. The scaling theory allows an accurate interpolation and extrapolation of experimental scattering data. textcopyright 1987.},
keywords = {Inelasticity, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1987,
title = {Transport in random networks in a field: Interacting particles},
author = {R Ramaswamy and M Barma},
url = {https://ramramaswamy.org/papers/031.pdf},
doi = {10.1088/0305-4470/20/10/039},
issn = {03054470},
year  = {1987},
date = {1987-01-01},
journal = {Journal of Physics A: Mathematical and General},
volume = {20},
number = {10},
pages = {2973--2987},
abstract = {Transport through a random medium in an external field is modelled by particles performing biased random walks on the infinite cluster above the percolation threshold. Steps are more likely in the direction of the field-say downward-than against. A particle is allowed to move only onto an empty site (particles interact via hard core exclusion). Branches that predominantly point downwards and backbends-backbone segments on which particles must move upwards-act as traps. The authors have studied the movement of interacting random walkers in branches and backbends by Monte Carlo simulations and also analytically. In the full network, the trap-limited current flows primarily through the part of the backbond composed of paths with the smallest backbends and its magnitude in high fields is estimated. Unlike in the absence of interactions, the drift velocity does not vanish in finite fields. However, it continues to show a non-monotonic dependence on the field over a sizeable range of density and percolation probability.},
keywords = {Monte Carlo, Random Network, Random Walk, Transport},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1987a,
title = {Fractal eigenfunctions in (classically) nonintegrable hamiltonian systems},
author = {R Ramaswamy and S Swaminathan},
url = {https://ramramaswamy.org/papers/033.pdf},
doi = {10.1209/0295-5075/4/2/001},
issn = {12864854},
year  = {1987},
date = {1987-01-01},
journal = {EPL},
volume = {4},
number = {2},
pages = {127--131},
abstract = {Bound-state eigenfunctions for a (classically) nonintegrable two degrees of freedom Hamiltonian system are studied. Between the de Broglie wavelength and a localization length, the probability density has a statistically fractal structure in some eigenstates. This novel characterization of eigenstates is intrinsically basis-set and coordinate independent and might therefore provide an objective approach to the question of quantum-chaotic behaviour. textcopyright IOP Publishing Ltd.},
keywords = {Fractals, Nonintegrable Hamiltonian Systems},
pubstate = {published},
tppubtype = {article}
}
@article{Barma1986,
title = {Escape times in interacting biased random walks},
author = {Mustansir Barma and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/028.pdf},
doi = {10.1007/BF01020653},
issn = {00224715},
year  = {1986},
date = {1986-01-01},
journal = {Journal of Statistical Physics},
volume = {43},
number = {3-4},
pages = {561--570},
abstract = {The dynamics of N particles with hard core exclusion performing biased random walks is studied on a one-dimensional lattice with a reflecting wall. The bias is toward the wall and the particles are placed initially on the N sites of the lattice closest to the wall. For N=1 the leading behavior of the first passage time TFP to a distant site l is known to follow the Kramers escape time formula TFP‚àº$łambda$l where $łambda$ is the ratio of hopping rates toward and away from the wall. For N textgreater 1 Monte Carlo and analytical results are presented to show that for the particle closest to the wall, the Kramers formula generalizes to TFR‚àº$łambda$IN. First passage times for the other particles are studied as well. A second question that is studied pertains to survival times Ts in the presence of an absorbing barrier placed at site l. In contrast to the first passage time, it is found that Ts follows the leading behavior $łambda$‚Ä≤ independent of N. textcopyright 1986 Plenum Publishing Corporation.},
keywords = {Bias, Random Walks, Survival Times},
pubstate = {published},
tppubtype = {article}
}
@article{Barma1986a,
title = {On backbends on percolation backbones},
author = {M Barma and R Ramaswamy},
url = {https://ramramaswamy.org/papers/029.pdf},
doi = {10.1088/0305-4470/19/10/009},
issn = {03054470},
year  = {1986},
date = {1986-01-01},
journal = {Journal of Physics A: General Physics},
volume = {19},
number = {10},
pages = {605--611},
abstract = {Just above the percolation concentration, a path on the backbone which leads from one side of the lattice to the other is not direct but zigzags through the lattice. Backbends are the portions of the zigzags which go backwards. They are important in the problem of particle transport in strong external fields, as they act as traps and limit the current. The threshold concentration for the proliferation of paths with backbends no longer than a given length L is defined as pb(L), with the limits pb(0) = pd (directed percolation) and pb(‚àû) = p c (ordinary percolation). The inverse function $zeta$(p) is the smallest integer such that, for given p between pc and pd, there are paths to infinity on which every backbend is smaller than $zeta$(p). This minimal backbend length is computed on a Bethe lattice and shown to diverge as (p-pc)-1/2. It is argued heuristically that on all lattices $zeta$(p) is proportional to the correlation length in the limit p‚Üípc. The chemical lengths of minimal backbend paths on the Bethe lattice are calculated. textcopyright 1986 The Institute of Physics.},
keywords = {Backbends, Percolation},
pubstate = {published},
tppubtype = {article}
}
@article{Raghavan1985,
title = {Rotational energy transfer in HF-Li collisions},
author = {K Raghavan, S Upadhyay, N Sathyamurthy and R Ramaswamy},
url = {https://pubs.aip.org/aip/jcp/article-pdf/83/4/1573/11110051/1573\_1\_online.pdf},
doi = {10.1063/1.449394},
issn = {0021-9606},
year  = {1985},
date = {1985-08-15},
journal = {The Journal of Chemical Physics},
volume = {83},
number = {4},
pages = {1573–1577},
abstract = {We report state‐to‐state integral inelastic cross sections for rotational energy transfer in rigid rotor HF–Li collisions, at a relative translational energy of 8.7 kcal mol−1. The results have been analyzed in terms of power gap law, information theoretic synthesis using energy and angular momentum constraints, and energy corrected sudden and energy corrected sudden‐power law scaling relations.},
keywords = {Perturbation},
pubstate = {published},
tppubtype = {article}
}
@article{Dhar1985z,
title = {Classical Diffusion on Eden Trees},
author = {Deepak Dhar and Ramakrishna Ramaswamy},
url = {https://link.aps.org/doi/10.1103/PhysRevLett.54.1346},
doi = {10.1103/PhysRevLett.54.1346},
year  = {1985},
date = {1985-04-01},
journal = {Phys. Rev. Lett.},
volume = {54},
pages = {1346--1349},
publisher = {American Physical Society},
abstract = {We study an aggregation process which gives rise to compact clusters with no loops. A generalization of the node-counting theorem, applicable to such branched graphs (trees), is proved. This is used to determine the spectral dimension of these clusters on square and cubic embedding lattices by Monte Carlo simulations. The results are explained in terms of the geometric structure of these trees.},
keywords = {Diffusion},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1985,
title = {A semiclassical quantization using arbitrary trajectories},
author = {R Ramaswamy
},
url = {https://pubs.aip.org/aip/jcp/article-pdf/82/2/747/15357383/747\_1\_online.pdf},
doi = {10.1063/1.448498},
issn = {0021-9606},
year  = {1985},
date = {1985-01-15},
journal = {The Journal of Chemical Physics},
volume = {82},
number = {2},
pages = {747–751},
abstract = {A simple method of obtaining the (first‐order) semiclassical eigenvalue spectrum from information pertaining to arbitrary nonquantizing tori is discussed. This method relies on the existence of a unique energy functional for tori, and the observation that for most typical potentials, the energy can be expressed as a polynomial function of the actions.},
keywords = {Quantization},
pubstate = {published},
tppubtype = {article}
}
@article{Bhargava1985,
title = {Quantum infomation from classical trajectories: Scaling deconvolution of moments in diatom-diatom collisions},
author = {Rajeev Bhargava and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/026.pdf},
doi = {10.1016/0301-0104(85)80077-X},
issn = {03010104},
year  = {1985},
date = {1985-01-01},
journal = {Chemical Physics},
volume = {95},
number = {2},
pages = {253--261},
abstract = {An inversion procedure to obtain quantal transition probabilities from the analysis of classical moments has been applied to various model diatom-diatom collision systems. This inversion relies on the use of a scaling theory to analyse classical moments and the subsequent use of a quantal scaling theory in interpretation of the classical scaling coefficients. We obtain transition probabilities that are in good agreement with exact quantum studies, and also compare favorably with other moment inversion schemes that have been described earlier in the literature. textcopyright 1985.},
keywords = {Quantum Information, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1984bb,
title = {Quasiperiodic quantum states},
author = {R Ramaswamy},
url = {https://pubs.aip.org/aip/jcp/article-pdf/80/12/6194/11014720/6194\_1\_online.pdf},
doi = {10.1063/1.446721},
issn = {0021-9606},
year  = {1984},
date = {1984-06-15},
journal = {The Journal of Chemical Physics},
volume = {80},
number = {12},
pages = {6194–6199 },
abstract = {We show that the Hose–Taylor criterion of quantum quasiperiodicity can be recovered from low‐order nondegenerate perturbation theory. It is seen that this mnemonic, which purports to identify energy levels which can be obtained by quantizing classical quasiperiodic motions, can lead to contradictions when applied to systems which are more semiclassical than that treated previously. These discrepancies arise since the criterion is both perturbation scheme and basis set dependent: the correlation between the semiclassical quantization and such a definition of quantum quasiperiodic behavior is not straightforward. As the underlying search is for a quantum KAM‐like theory (in particular for near‐separable systems which are typical of molecular vibrational Hamiltonians) some possibilities are discussed.},
keywords = {Perturbation, Quantum State},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1984b,
title = {The Scaling principle in classical inelastic collisions},
author = {R Ramaswamy},
url = {https://doi.org/10.1063/1.446995},
doi = {10.1063/1.446995},
issn = {0021-9606},
year  = {1984},
date = {1984-03-15},
journal = {The Journal of Chemical Physics},
volume = {80},
number = {6},
pages = {2462–2463},
abstract = {The scaling principle in classical molecular collisions given earlier by DePristo [J. Chem. Phys. 75, 3384 (1981)] is rederived. Using the method of variation of constants in classical mechanics, it is possible to obtain explicit expressions for the collision‐mapping function. A variety of related scaling forms are shown to result from this map.},
keywords = {molecular dynamics},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1984,
title = {Scaling behaviour in collinear atom-diatom collisions: energy transfer from high vibrational states},
author = {R Ramaswamy and R Bhargava},
url = {https://doi.org/10.1063/1.446837},
doi = {10.1063/1.446837},
issn = {0021-9606},
year  = {1984},
date = {1984-02-01},
journal = {The Journal of Chemical Physics},
volume = {80},
number = {3},
pages = {1095–1102},
abstract = {Classical energy transfer in a simple collinear collision system is studied within the framework of a recently derived classical scaling formalism. In the present system which corresponds to collinearly colliding I2 (Morse oscillator) + rare gas (He, Ar), a simple polynomial function in the initial vibrational quantum number of I2 scales the first moment of the energy transfer (ET). Using the computed ET moment from only five states as input, it is possible to predict that from any other bound state in the vibrational manifold 0≤n≤110. There is correspondence—in a limiting case—between the classical scaling law and the (quantum) energy corrected sudden scaling theory given earlier; this allows for the interpretation of the classical scaling coefficients and indicates that the higher order terms are necessary in order to account for multiquantum vibrational transitions in the V‐T process.},
keywords = {Interatomic Potential, Vibrational States},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1984z,
title = {Classical trajectory analysis in atom-triatom collisions: Continuous quantization and scaling behaviour},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/021.pdf},
year  = {1984},
date = {1984-01-01},
journal = {Chemical Physics},
volume = {88},
pages = {7-16},
keywords = {Collision Dynamics, Quantization, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1984y,
title = {Collision dynamics of non-integrable systems: Validity of classical scaling},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/022.pdf},
year  = {1984},
date = {1984-01-01},
journal = {Chemical Physics},
volume = {88},
pages = {17-25},
keywords = {Collision Dynamics, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1983,
title = {Chaotic motions in vibrating molecules: The generalized Henon-Heiles model},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/018.pdf},
doi = {10.1016/0301-0104(83)85046-0},
issn = {03010104},
year  = {1983},
date = {1983-01-01},
journal = {Chemical Physics},
volume = {76},
number = {1},
pages = {15--24},
abstract = {The method of avoided crossings is applied to a simple molecular model, the generalized Henon-Heiles system of coupled oscillators. The aim here is to determine the onset of wide-spread chaotic motions. The method is used to locate, in a simple manner, the resonances that lead to chaotic motions for different choices of parameters, wherein the frequencies of the unperturbed oscillators are in the ratio 3 : 4 and 7 : 13. The accuracy of the prediction is verified against numerical calculations of classical trajectories. textcopyright 1983.},
keywords = {Chaos, Henon-Heiles},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1981,
title = {Perturbative examination of avoided crossings},
author = {R Ramaswamy and R A Marcus},
url = {https://doi.org/10.1063/1.441201},
doi = {10.1063/1.441201},
issn = {0021-9606},
year  = {1981},
date = {1981-01-15},
journal = {The Journal of Chemical Physics},
volume = {74},
number = {2},
pages = {1379–1384},
abstract = {Quantum perturbation theory is used to examine the eigenvalues of a nonseparable Hamiltonian system in the classically regular and irregular regimes. As a function of the perturbation parameter, the eigenvalues obtained by exact (matrix diagonalization) methods undergo an avoided crossing. In the present paper perturbation theory is used as an approximate method to predict the locations of such avoided crossings in energy‐parameter space. The sparsity of such avoided crossings in the Hénon–Heiles system is seen to produce regular sequences in the eigenvalues even when the classical motion is predominantly chaotic.},
keywords = {Henon-Heiles, Nonintegrable Hamiltonian Systems, Perturbation},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1981b,
title = {The onset of chaotic motions in deterministic systems},
author = {R Ramaswamy and R A Marcus
},
url = {https://doi.org/10.1063/1.441202},
doi = {10.1063/1.441202},
issn = {0021-9606},
year  = {1981},
date = {1981-01-15},
journal = {The Journal of Chemical Physics},
volume = {74},
number = {2},
pages = {1385–1393},
abstract = {In the present paper the classical counterpart of the quantum avoided crossing method for detecting chaos is described using classical (Lie‐transform) perturbation theory and a grid of action variables. The results are applied to two systems of coupled oscillators with cubic and quartic nonlinearities. The plots of energy of members of the grid versus the perturbation parameter provide a visual description for predicting the onset of chaos.},
keywords = {Chaos, Coupled Oscillators, Perturbation},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1981z,
title = {A simple classical model of infrared multiphoton dissociation},
author = {Ramakrishna Ramaswamy Paul Siders and R A Marcus},
url = {https://ramramaswamy.org/papers/016.pdf},
year  = {1981},
date = {1981-01-01},
journal = {J. Chem. Phys.},
volume = {74},
number = {8},
pages = {4418-4425},
keywords = {Multiphoton Dissociation},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1981y,
title = {Classical methods in molecular scattering: A continuous quantization procedure },
author = {Ramakrishna Ramaswamy and Andrew E DePristo},
url = {https://ramramaswamy.org/papers/012.pdf},
year  = {1981},
date = {1981-01-01},
journal = {Chem. Phys. Lett.},
volume = {77},
number = {1},
pages = {190-194},
keywords = {Quantization, Scattering},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1981x,
title = {Continuous quantization procedure in quasiclassical scattering: Application to atom-Morse oscillator collisions},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/015.pdf},
year  = {1981},
date = {1981-01-01},
journal = {Pramana},
volume = {16},
number = {2},
pages = {139-146},
keywords = {Quantization, Scattering},
pubstate = {published},
tppubtype = {article}
}
@article{DePristo1981z,
title = {Concerning the scaling behaviour in the classical mechanics of non-reactive collisions: An analytic investigation},
author = {Andrew DePristo and Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/017.pdf},
year  = {1981},
date = {1981-01-01},
journal = {Chemical Physics},
volume = {57},
pages = {129-140},
keywords = {Collision Dynamics, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1980,
title = {Semiclassical quantization of multidimensional systems},
author = {R Ramaswamy, P Siders and R A Marcus
},
url = {https://doi.org/10.1063/1.439939},
doi = {10.1063/1.439939},
issn = {0021-9606},
year  = {1980},
date = {1980-11-15},
journal = {The Journal of Chemical Physics},
volume = {73},
number = {10},
pages = {5400–5401},
abstract = {Low order classical perturbation theory is used to obtain semiclassical eigenvalues for a system of three anharmonically coupled oscillators. The results in the low energy region studied here agree well with the ’’exact’’ quantum values. The latter had been calculated by matrix diagonalization using a large basis set.},
keywords = {Coupled Oscillators, Perturbation},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1980z,
title = {Dynamics of van der Waals molecules: A scaling theoretical analysis of I2*He},
author = {Ramakrishna Ramaswamy and Andrew E DePristo},
url = {https://ramramaswamy.org/papers/010.pdf},
doi = {10.1063/1.438915},
year  = {1980},
date = {1980-01-01},
journal = {J. Chem. Phys.},
volume = {72},
number = {1},
pages = {770},
keywords = {molecular dynamics, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{DePristo1979,
title = {Quantum number and energy scaling for non-reactive collisions},
author = {A E DePristo, S D Augustin, R Ramaswamy and H Rabitz
},
url = {https://doi.org/10.1063/1.438376},
doi = {10.1063/1.438376},
issn = {0021-9606},
year  = {1979},
date = {1979-07-15},
journal = {The Journal of Chemical Physics},
volume = {71},
number = {2},
pages = {850-865},
abstract = {Two new theoretical developments are presented in this article. First an energy corrected sudden (ECS) approximation is derived by explicitly incorporating both the internal energy level spacing and the finite collision duration into the sudden S‐matrix. An application of this ECS approximation to the calculation of rotationally inelastic cross sections is shown to yield accurate results for the H+–CN system. Second, a quantum number and energy scaling relationship for nonreactive S‐matrix elements is derived based on the ECS method. A few detailed illustrations are presented and scaling predictions are compared to exact results for R–T, V–T, and V–R, T processes in various atom–molecule systems. The agreement is uniformly very good — even when the sudden approximation is inaccurate. An important result occurs in the analysis of V–T processes: the effects of anharmonic wave functions (coupling) and decreasing vibrational energy gaps (energetics) are separated. Each factor makes significant contributions to the deviation of the anharmonic from the harmonic scaling relationship.},
keywords = {Scattering},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1979,
title = {Stochastic theory of collisions: Application to vibration–rotation inelasticity in CO–He},
author = {R Ramaswamy, S Augustin and H Rabitz},
url = {https://doi.org/10.1063/1.437706},
doi = {10.1063/1.437706},
issn = {0021-9606},
year  = {1979},
date = {1979-03-01},
journal = {The Journal of Chemical Physics},
volume = {70},
number = {5},
pages = {2455–2462},
abstract = {Vibration–rotation inelasticity in the CO–He collision system is studied within the stochastic formulation. Cross sections are obtained for purely rotational transitions using a modified electron gas potential. Vibration–rotation cross sections have been calculated in the energy range 2200 cm−1<E<4000 cm−1. At the higher energy, a total of 76 molecular states are energetically accessible. A comparison with earlier results is made, and coarse graining techniques for the treatment of large problems are utilized.},
keywords = {molecular dynamics, Stochasticity},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1979z,
title = {On the correlation of rotationally inelastic rates: A scaling theoretical analysis},
author = {R Ramaswamy and A E Z Depristo and H Rabitz},
url = {https://ramramaswamy.org/papers/009.pdf},
year  = {1979},
date = {1979-01-01},
journal = {Chem. Phys. Lett.},
volume = {61},
number = {3},
pages = {495--497},
keywords = {Inelasticity, molecular dynamics, scaling},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1978,
title = {Stochastic theory of intramolecular energy transfer},
author = {R Ramaswamy, S Augustin and H Rabitz},
url = {https://doi.org/10.1063/1.436544},
doi = {10.1063/1.436544},
issn = {0021-9606},
year  = {1978},
date = {1978-12-15},
journal = {The Journal of Chemical Physics},
volume = {69},
number = {12},
pages = {5509-5517},
abstract = {The problem of internal energy redistribution in an isolated polyatomic molecule is treated by a stochastic theory approach. The fundamental assumption of this work is that a random phase approximation is valid at specific time intervals. This results in the replacement of the Schrödinger equation by a master equation that governs the evolution of a probability distribution in the quantum levels of the molecule. No assumptions regarding the strength of the coupling are made, and the problem of energy conservation is specifically considered. A stochastic variable is introduced in order to satisfy the requirement that the total energy remain fixed. The further approximation of the master equation by a Fokker–Planck diffusion-like equation is outlined; the latter approach is particularly attractive for treating large molecules. Finally, the master‐equation theory is applied to a model problem representing a linearly constrained triatomic molecule, and the time evolution of an initially localized excitation is discussed.},
keywords = {energy conservation, probability, Stochasticity},
pubstate = {published},
tppubtype = {article}
}
@article{Green1978,
title = {Collisional excitation of interstellar molecules: H2},
author = {S Green, R Ramaswamy and H Rabitz
},
url = {https://ui.adsabs.harvard.edu/abs/1978ApJS...36..483G},
doi = {10.1086/190509},
year  = {1978},
date = {1978-04-01},
journal = {  Astrophysical Journal Supplement Series},
volume = {36},
pages = {483-496},
abstract = {Cross sections for the important rotational transitions in molecular hydrogen collisions are presented for rotational levels to j = 11 and energies to 20,000 K. These have been obtained from extensive theoretical calculations. The resulting cross sections are fitted to a simple polynomial in the energy, and the coefficients are tabulated for easy utilization.},
keywords = {hydrogen, interstellar gas, molecular dynamics, Scattering},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1978z,
title = {Rotational inelasticity in high-energy H2-H2 Collisions},
author = {Ramakrishna Ramaswamy Herschel Rabitz and Sheldon Green},
url = {https://ramramaswamy.org/papers/005.pdf},
year  = {1978},
date = {1978-01-01},
journal = {Chemical Physics},
volume = {28},
pages = {319-329},
keywords = {Inelasticity, molecular dynamics},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1977b,
title = {Low-temperature relaxation in gaseous H2 and D2},
author = {Ramakrishna Ramaswamy, Herschel Rabitz, Sheldon Green},
url = {https://doi.org/10.1063/1.434315},
doi = {10.1063/1.434315},
issn = {0021-9606},
year  = {1977},
date = {1977-04-01},
journal = {The Journal of Chemical Physics},
volume = {66},
number = {7},
pages = {3021-3030},
abstract = {Various potentials have been used for generating scattering cross sections for rotational transitions in hydrogen isotope systems. Low‐temperature rates were calculated and the relaxation times compared with the results of sound absorption experiments. It is seen that the existing potentials could still be improved since they do not exactly reproduce the experimental results.},
keywords = {isotopes, Scattering},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1977z,
title = {Electron momentum distributions and compton profiles of some molecules with FSGO model},
author = {S R Gadre R Ramaswamy and P T Narasimhan},
url = {https://ramramaswamy.org/papers/002.pdf},
year  = {1977},
date = {1977-01-01},
journal = {Pramana},
volume = {8},
number = {2},
pages = {99--107},
keywords = {molecular dynamics},
pubstate = {published},
tppubtype = {article}
}
@article{Ramaswamy1977,
title = {Vibration-rotation relaxation in bimolecular collisions with application to para-Hydrogen},
author = {R Ramaswamy and H Rabitz},
url = {https://doi.org/10.1063/1.433648},
doi = {10.1063/1.433648},
issn = {0021-9606},
year  = {1977},
date = {1977-01-01},
journal = {The Journal of Chemical Physics},
volume = {66},
number = {1},
pages = {152-159},
abstract = {Three‐dimensional quantum mechanical calculations in the effective potential approximation have been made on the para‐hydrogen system. At low temperatures, vib–rotationally inelastic collisions were examined while breathing sphere calculations were used to probe the high‐temperature regime. It was found that simultaneous vibrational and rotational processes contribute to the overall mechanism of vibrational relaxation. Collisionally induced intra‐ and intermolecular energy transfer is possible in the present calculation, and the corresponding cross sections are examined in detail. Rates are calculated from the cross sections and compared with experiment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Alexe2017,
title = {Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns},
author = {G Alexe and G S Dalgin and R Ramaswamy and C Delisi and G Bhanot},
url = {https://ramramaswamy.org/papers/110.pdf},
doi = {10.1177/117693510600200006},
issn = {1176-9351},
journal = {Cancer Informatics},
volume = {2},
pages = {117693510600200},
abstract = {Molecular stratification of disease based on expression levels of sets of genes can help guide therapeutic decisions if such classifications can be shown to be stable against variations in sample source and data perturbation. Classifications inferred from one set of samples in one lab should be able to consistently stratify a different set of samples in another lab. We present a method for assessing such stability and apply it to the breast cancer (BCA) datasets of Sorlie et al. 2003 and Ma et al. 2003. We find that within the now commonly accepted BCA categories identified by Sorlie et al. Luminal A and Basal are robust, but Luminal B and ERBB2+ are not. In particular, 36% of the samples identified as Luminal B and 55% identified as ERBB2+ cannot be assigned an accurate category because the classification is sensitive to data perturbation. We identify a "core cluster" of samples for each category, and from these we determine "patterns" of gene expression that distinguish the core clusters from each other. We find that the best markers for Luminal A and Basal are (ESR1, LIV1, GATA-3) and (CCNE1, LAD1, KRT5), respectively. Pathways enriched in the patterns regulate apoptosis, tissue remodeling and the immune response. We use a different dataset (Ma et al. 2003) to test the accuracy with which samples can be allocated to the four disease subtypes. We find, as expected, that the classification of samples identified as Luminal A and Basal is robust but classification into the other two subtypes is not.},
keywords = {breast cancer, clusters, diagnosis, multi-gene biomarkers, patterns},
pubstate = {published},
tppubtype = {article}
}
@article{Bhanot,
title = {Robust meta-analysis of genomic data for cancer diagnosis},
author = {Gabriela Bhanot Gyan Alexe and Babu Vengataraghavan and Jorge Lepre and Arnold J Levine and Gustavo Stolovitzky},
url = {https://ramramaswamy.org/papers/R36.pdf},
pages = {7--8},
keywords = {cancer diagnosis, combinatorial biomarkers, meta-analysis, meta-classifiers, patterns},
pubstate = {published},
tppubtype = {article}
}
@article{,
title = {Design strategies for generalized synchronization},
author = { },
url = { },
doi = { },
journal = { },
volume = { },
publisher = {American Physical Society},
abstract = { },
keywords = {Chaos, Coupled Lorenz System, Generalized Synchronization},
pubstate = {published},
tppubtype = {article}
}