2022 |
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| 214. | Gogoi, P B; Kumarasamy, S; Prasad, A; Ramaswamy, R Transition from inhomogeneous limit cycles to oscillation death in nonlinear oscillators with similarity-dependent coupling Journal Article Chaos, 32 , pp. 113138, 2022, ISSN: 1054-1500. Abstract | Links | BibTeX | Tags: Complex Behaviour @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} } 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. |
| 213. | Pandey, R; Jangid, A; Vinjamuri, Gayathri R; Ramaswamy, R Modeling of indirect cell–cell interaction networks mediated by IFN- γ/IL-4 cytokines involved in atopic dermatitis Journal Article Journal of Theoretical Biology, 556 , pp. 111921, 2022, ISSN: 1095-8541. Abstract | Links | BibTeX | Tags: @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} } 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. |
| 212. | Singha, J; Ramaswamy, R Phase-locking in k-partite networks of delay-coupled oscillators Journal Article Chaos, Solitons, and Fractals, 157 , pp. 111947, 2022, ISSN: 0960-0779. Abstract | Links | BibTeX | Tags: Delay coupling, Network @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} } 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. |
| 211. | Bilal, S; Ramaswamy, R A higher-dimensional generalization of the Lozi map: bifurcations and dynamics Journal Article Journal of Difference Equations and Applications, 28 , pp. 1-12, 2022, ISSN: 1023-6198. Abstract | Links | BibTeX | Tags: @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} } 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. |
| 210. | Wontchui, T T; Sone, M E; Ujjwal, S R; Effa, J Y; Fouda, H P E; Ramaswamy, R Intermingled attractors in an asymmetrically driven modified Chua oscillator Journal Article Chaos, 32 (1), 2022, ISSN: 1054-1500. Abstract | Links | BibTeX | Tags: Chaos, Lorenz, Lyapunov exponent, Multistability @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} } 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. |
2021 |
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| 209. | Jangid, A; Selvarajan, S; Ramaswamy, R A Stochastic Model of Homeostasis: the roles of noise and nuclear positioning in deciding cell fate Journal Article iScience, 24 (10), 2021, ISSN: 2589-0042. Abstract | Links | BibTeX | Tags: Stochastic dynamics, Theoretical biology @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} } 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. |
| 208. | Jangid, A; Malik, Md Z; Ramaswamy, R; Singh, RK Brojen Transition and identification of pathological states in p53 dynamics for therapeutic intervention Journal Article Scientific Reports, 11 , pp. 2349, 2021, ISSN: 2045-2322. Abstract | Links | BibTeX | Tags: p53 dynamics, systems biology, therapeutics @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} } 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. |
2019 |
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| 207. | Sahoo, S; Varshney, V; Prasad, A; Ramaswamy, R Ageing in mixed populations of Stuart–Landau oscillators: the role of diversity Journal Article Journal of Physics A: Mathematical and Theoretical, 52 , pp. 464001, 2019, ISSN: 1751-8121. Abstract | Links | BibTeX | Tags: ageing, phase transition, scaling, stasis @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} } 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. |
| 206. | Ramaswamy, R; Kolhatkar, M; Mukherji, A (Ed.) A Fragmented Feminism: The Life and Letters of Anandibai Joshee by Meera Kosambi Book First Edition, Routledge, UK, 2019, ISBN: 9780429266386 . Abstract | Links | BibTeX | Tags: Anandibai, Book, Kosambi @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} } "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. |
2018 |
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| 205. | Chishti, S; Ramaswamy, R Design strategies for generalized synchronization Journal Article Physical Review E, 98 , pp. 032217, 2018, ISSN: 2470-0053 . Abstract | Links | BibTeX | Tags: Generalized Synchronization, Synchronization @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} } 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. |
| 204. | Punetha, N; Varshney, V; Sahoo, S; Saxena, G; Prasad, A; Ramaswamy, R Dynamical effects of breaking rotational symmetry in counter-rotating Stuart-Landau oscillators Journal Article Physical Review E, 98 , pp. 022212, 2018, ISSN: 2470-0053 . Abstract | Links | BibTeX | Tags: Amplitude Death, Landau-Stuart, Oscillation Quenching, Symmetry Breaking @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} } 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. |
| 203. | Raviteja, D; Ramaswamy, R The collective dynamics of NF-kB in cellular ensembles Journal Article The European Physical Journal Special Topics, 227 , pp. 851-863, 2018, ISSN: 1951-6355. Abstract | Links | BibTeX | Tags: Cellular Ensembles, Computational Biology, systems biology @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} } 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 |
| 202. | Kumar, A B R; Ramaswamy, R Chemistry at the Nanoscale: When Every Reaction is a Discrete Event Journal Article Resonance, 23 , pp. 23-40, 2018, ISSN: 0973-712X. Abstract | Links | BibTeX | Tags: Chemical Kinetics, Gillespie’s Algorithm, Stochasticity, Synthetic Gene Oscillators @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 ‚Äì such as an individual biological cell, say ‚Äì 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 ‚Äòthermo- 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 ‚Äòevent’ 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} } 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 ‚Äì such as an individual biological cell, say ‚Äì 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 ‚Äòthermo- 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 ‚Äòevent’ 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. |
| 201. | Raviteja, D; Ramaswamy, R By-product group benefits of non-kin resource-sharing in vampire bats Journal Article Journal of Physics: Conference Series, 1090 , pp. 012002, 2018, ISSN: 1742-6596. Abstract | Links | BibTeX | Tags: Conference, Optimisation, Population Dynamics, Resource Management @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} } 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. |
| 200. | Ramaswamy, R; Raviteja, D Modeling long lifespans in eusocial insect populations Journal Article bioRxiv, pp. 408211, 2018. Abstract | Links | BibTeX | Tags: systems biology @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} } 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. |
2017 |
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| 199. | Yadav, A C; Manchanda, K; Ramaswamy, R Emergent organization in a model market Journal Article Physica A: Statistical Mechanics and its Applications, 482 , pp. 118 , 2017, ISSN: 0378-4371. Abstract | Links | BibTeX | Tags: emergent phenomenon, self-organization, statistical physics @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} } 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. |
| 198. | Yadav, A C; Ramaswamy, R; Dhar, D A general mechanism for the 1/f noise Journal Article Physical Review E, 96 (2), pp. 022215, 2017, ISSN: 2470-0053 . Abstract | Links | BibTeX | Tags: Sandpile, statistical physics @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} } |
| 197. | Ujjwal, S R; Punetha, N; Prasad, A; Ramaswamy, R Emergence of chimeras through induced multistability Journal Article Physical Review E, 95 , pp. 032203 , 2017, ISSN: 2470-0053. Abstract | Links | BibTeX | Tags: Chimeras, Multistability, Quasiperiodicity @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} } 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. |
| 196. | Wontchui, T T; Effa, J Y; Fouda, H P E; Ujjwal, S R; Ramaswamy, R Coupled Lorenz oscillators near the Hopf boundary: Multistability, intermingled basins, and quasiriddling Journal Article Physical Review E, 96 , pp. 062203, 2017, ISSN: 2470-0053. Abstract | Links | BibTeX | Tags: Intermingled Basins, Lorenz, Multistability, Quasiriddling @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} } 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. |
| 195. | Manchanda, K; Bose, A; Ramaswamy, R Collective dynamics in heterogeneous networks of neuronal cellular automata Journal Article Physica A: Statistical Mechanics and its Applications, 487 , pp. 111, 2017, ISSN: 0378-4371. Abstract | Links | BibTeX | Tags: Binary Mixtures, Cellular automata, Discrete Dynamics, Lyapunov exponent, Network Motif @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} } 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. |