• Somdatta Sinha

Articles written in Pramana – Journal of Physics

• Dynamics of simple one-dimensional maps under perturbation

It is known that the one-dimensional discrete maps having single-humped nonlinear functions with the same order of maximum belong to a single class that shows the universal behaviour of a cascade of period-doubling bifurcations from stability to chaos with the change of parameters. This paper concerns studies of the dynamics exhibited by some of these simple one-dimensional maps under constant perturbations. We show that the “universality” in their dynamics breaks down under constant perturbations with the logistic map showing different dynamics compared to the other maps. Thus these maps can be classified into two types with respect to their response to constant perturbations. Unidimensional discrete maps are interchangeably used as models for specific processes in many disciplines due to the similarity in their dynamics. These results prove that the differences in their behaviour under perturbations need to be taken into consideration before using them for modelling any real process.

• Analysis of protein folds using protein contact networks

Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out the biophysical and biochemical functions. Proteins are defined as having a common fold' if they have major secondary structural elements with same topological connections. It is known that folding mechanisms are largely determined by a protein's topology rather than its interatomic interactions. The native state protein structures can, thus, be modelled, using a graph-theoretical approach, as coarse-grained networks of amino acid residues as nodes' and the inter-residue interactions/contacts as `links'. Using the network representation of protein structures and their 2D contact maps, we have identified the conserved contact patterns (groups of contacts) representing two typical folds – the EF-hand and the ubiquitin-like folds. Our results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein's contact map alone.

• Synchronization in multicell systems exhibiting dynamic plasticity

Collective behaviour in multicell systems arises from exchange of chemicals/signals between cells and may be different from their intrinsic behaviour. These chemicals are products of regulated networks of biochemical pathways that underlie cellular functions, and can exhibit a variety of dynamics arising from the non-linearity of the reaction processes. We have addressed the emergent synchronization properties of a ring of cells, diffusively coupled by the end product of an intracellular model biochemical pathway exhibiting non-robust birhythmic behaviour. The aim is to examine the role of intercellular interaction in stabilizing the non-robust dynamics in the emergent collective behaviour in the ring of cells. We show that, irrespective of the inherent frequencies of individual cells, depending on the coupling strength, the collective behaviour does synchronize to only one type of oscillations above a threshold number of cells. Using two perturbation analyses, we also show that this emergent synchronized dynamical state is fairly robust under external perturbations. Thus, the inherent plasticity in the oscillatory phenotypes in these model cells may get suppressed to exhibit collective dynamics of a single type in a multicell system, but environmental influences can sometimes expose this underlying plasticity in its collective dynamics.

• Collective dynamics of multicellular systems

We have studied the collective behaviour of a one-dimensional ring of cells for conditions when the individual uncoupled cells show stable, bistable and oscillatory dynamics. We show that the global dynamics of this model multicellular system depends on the system size, coupling strength and the intrinsic dynamics of the cells. The intrinsic variability in dynamics of the constituent cells are suppressed to stable dynamics, or modiﬁed to intermittency under different conditions. This simple model study reveals that cell–cell communication, system size and intrinsic cellular dynamics can lead to evolution of collective dynamics in structured multicellular biological systems that is signiﬁcantly different from its constituent single-cell behaviour.

• PNLD 2013: Conference summary and a perspective

• # Pramana – Journal of Physics

Volume 94, 2019
All articles
Continuous Article Publishing mode

• # Editorial Note on Continuous Article Publication

Posted on July 25, 2019