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Aravind Chandrasekaran

Publications and source records attributed to Aravind Chandrasekaran.

2 recordsLinked to original sources

Actin reorganization throughout the cell cycle mediated by motor proteins

Cortical actin networks are highly dynamic and play critical roles in shaping the mechanical properties of cells. The actin cytoskeleton undergoes significant reorganization over the course of the cell cycle, when cortical actin transitions between open patched meshworks, homogeneous distributions, and aligned bundles. Several types of myosin motor proteins, characterized by different kinetic parameters, have been involved in this reorganization of actin filaments. Given the limitations in studying the interactions of actin with myosin in vivo, we propose stochastic agent-based model simulations and develop a set of data analysis measures to assess how myosin motor proteins mediate various actin organizations. In particular, we identify individual motor parameters, such as motor binding rate and step size, that generate actin networks with different levels of contractility and different patterns of myosin motor localization. In simulations where two motor populations with distinct kinetic parameters interact with the same actin network, we find that motors may act in a complementary way, by tuning the actin network organization, or in an antagonistic way, where one motor emerges as dominant. This modeling and data analysis framework also uncovers parameter regimes where spatial segregation between motor populations is achieved. By allowing for changes in kinetic rates during the actin-myosin dynamic simulations, our work suggests that certain actin-myosin organizations may require additional regulation beyond mediation by motor proteins in order to reconfigure the cytoskeleton network on experimentally-observed timescales.

q-bio.QM

Segmental Lennard-Jones Interactions for Semi-flexible Polymer Networks

Simulating soft matter systems such as the cytoskeleton can enable deep understanding of experimentally observed phenomena. One challenge of modeling such systems is realistic description of the steric repulsion between nearby polymers. Previous models of the polymeric excluded volume interaction have the deficit of being non-analytic, being computationally expensive, or allowing polymers to erroneously cross each other. A recent solution to these issues, implemented in the MEDYAN simulation platform, uses analytical expressions obtained from integrating an interaction kernel along the lengths of two polymer segments to describe their repulsion. Here, we extend this model by re-deriving it for lower-dimensional geometrical configurations, deriving similar expressions using a steeper interaction kernel, comparing it to other commonly used potentials, and showing how to parameterize these models. We also generalize this new integrated style of potential by introducing a segmental Lennard-Jones potential, which enables modelling both attractive and repulsive interactions in semi-flexible polymer networks. These results can be further generalized to facilitate the development of effective interaction potentials for other finite elements in simulations of soft-matter systems.

cond-mat.soft