Publications

@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{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{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}
}