Searcharxiv⌕ Search

arXiv subjects

Anirban Sain

Publications and source records attributed to Anirban Sain.

At least 19 recordsLinked to original sources
arXiv2026

From Flow to Form: Emergence of the Cytokinetic Ring via Active Cortical Dynamics

During cell division active flows occur in the cortex, a thin layer of gel like network of acto myosin filaments, beneath the cell surface. The cortical flow and the associated stresses bring about change in the cell shape, in particular a sharp invagination at the mid cell. Using 3D phase field simulation of an active deformable shell, which captures coupled dynamics of cortical velocity and nematic order, we show how a nematic like actomyosin ring spontaneously emerge at the equator and drive sharp invagination. We further demonstrate how different cortical flow patterns, including counter rotating flows emerge near the division furrow. We show that these flow patterns, often attributed to intrinsic chirality of actomyosin filaments can instead arise from bias in the initial nematic alignment, revealing a memory effect in the system. By analyzing a simpler model of activity gradient driven compressive flow on a flat interface we decipher the main ingredients for surface instability leading to invagination and counter moving flows.

cond-mat.soft↗
arXiv2025

Active chain spirograph: Dynamic patterns formed in extensible chains due to follower activity

Follower activity results in a large variety of conformational and dynamical states in active chains and filaments. These states are formed due to the coupling between chain geometry and the local activity. We study the origin and emergence of such patterns in noiseless, flexible active chains. In the overdamped limit, we observed a range of dynamical steady states for different chain lengths ($N$). The steady-state planar trajectories of the centre-of-mass of the chain include circles, periodic waves, and quasiperiodic, bound trajectories resembling spirographic patterns. In addition, out-of-plane initial configuration also leads to the formation of 3D structures, including globular and supercoiled helical structures. For the shortest chain with three segments $(N=3)$, the chain always moves in a circular trajectory. Such circular trajectories are also observed in the limit of large chain lengths $(N \gg 1)$. We analytically study the dynamical patterns in these two limiting cases, which show quantitative and qualitative matches with numerical simulations. Our analytical study also provides an estimate of the limiting $N$ where the large chain length behaviour is expected. These analyses reveal the existence of such intricately periodic patterns in active chains, arising due to the follower activity.

cond-mat.soft↗
arXiv2025

Actin driven morphogenesis in hydra

Hydra, a centimeter long cylindrical-shaped freshwater organism, has emerged as an interesting model system for studying morphogenesis in animals. Recently, fluorescent imaging of cytoskeletal actin filaments on the outer surface of hydra has revealed nematic-type arrangement of actin filaments. {Several topological defects in the nematic field have also been detected. In particular, aster-like +1 defects appear at the curved head of hydra and at the tip of its tentacles, while -1/2 defects are seen at the base of the tentacles. However, functional role of these defects in tissue development is not clear. Motivated by these observations, we here model hydra's epthelial tissue as a visco-elastic membrane and the tentacles as growing membrane tubes driven by a nematic interaction among actin. We consider the epithelial layer of hydra as a fluid membrane and carry out a non-equilibrium simulation which also includes membrane growth and polymerization of actin. We show that specific kind of defect at the head does not play any positive role in emergence of the tentacles. The reorganization of actin at the base and the tip of growing tentacles are consistent with other possible defect structures at the head as well. While it is known that regions of tentacle growth are hot spots of chemical signaling, involving Wnt3/$β$-catenin pathway, we propose that active polymerization of actin bundles could also be an important player in the growth of tubular tentacles. In addition to polymerization, fluidity of our model membrane, capturing effective fluidity of the epithelial tissue, turns out to be essential for enabling such growth.

cond-mat.soft↗
arXiv2022

Dynamics and stability of contractile actomyosin ring in the cell

Contraction of the cytokinetic ring during cell division leads to physical partitioning of a eukaryotic cell into two daughter cells. This involves flows of actin filaments and myosin motors in the growing membrane interface at the mid-plane of the dividing cell. Assuming boundary driven alignment of the acto-myosin filaments at the inner edge of the iterface we explore how the resulting active stresses influence the flow. Using the continuum gel theory framework, we obtain exact axisymmetric solutions of the dynamical equations. These solutions are consistent with experimental observations on closure rate. Using these solutions we perform linear stability analysis for the contracting ring under non-axisymmetric deformations. Our analysis shows that few low wave number modes, which are unstable during onset of the constriction, later on become stable when the ring shrinks to smaller radii, which is a generic feature of actomyosin ring closure. Our theory also captures how the effective tension in the ring decreases with its radius causing significant slow down in the contraction process at later times.

physics.bio-ph↗
arXiv2021

Membrane budding driven by intra-cellular ESCRT-III filaments

Exocytosis is a common transport mechanism via which cells transport out non-essential macro-molecules (cargo) into the extra cellular space. ESCRT-III proteins are known to help in this. They polymerize into a conical spring like structure and help deform the cell membrane locally into a bud which wrapps the outgoing cargo. we model this process using a continuum energy functional. It consists of elastic energies of the membrane and the semi-rigid ESCRT-III filament, favorable adhesion energy between the cargo and the membrane, and affinity among the ESCRT-III filaments. We take the free energy minimization route to identify the sequence of composite structures which form during the process. We show that membrane adhesion of the cargo is the driving force for this budding process and not the buckling of ESCRT-III filaments from flat spiral to conical spring shape. However ESCRT-III stabilizes the bud once it forms. Further we conclude that a non-equilibrium process is needed to pinch off/separate the stable bud (containing the cargo) from the cell body.

cond-mat.soft↗
arXiv2020

Chiral molecules on curved colloidal membranes

Colloidal membranes, self assembled monolayers of aligned rod like molecules, offer a template for designing membranes with definite shapes and curvature, and possibly new functionalities in the future. Often the constituent rods, due to their molecular chirality, are tilted with respect to the membrane normal. Spatial patterns of this tilt on curved membranes result from a competition among depletion forces, nematic interaction, molecular chirality and boundary effects. We present a covariant theory for the tilt pattern on minimal surfaces, like helicoids and catenoids, which have been generated in the laboratory only recently. We predict several non-uniform tilt patterns, some of which are consistent with experimental observations and some, which are yet to be discovered.

cond-mat.soft↗
arXiv2020

Poiseuille flow of soft polycrystals in 2D rough channels

Polycrystals are partially ordered solids where crystalline order extends over mesoscopic length scales, namely, the grain size. We study the Poisuielle flow of such materials in a rough channel. In general, similar to yield stress fluids, three distinct dynamical states, namely, flowing, stick-slip and jammed can be observed, with a yield threshold dependent on channel width. Importantly, the interplay between the finite channel width, and the intrinsic ordering scale (the grain size) leads to new type of spatiotemporal heterogeneity. In wide channels, although the average flow profile remains plug like, at the underlying granular level, there is vigorous grain remodelling activity resulting from the velocity heterogeneity among the grains. As the channel width approaches typical grain size, the flowing polycrystalline state breaks up into a spatially heterogeneous mixture of flowing liquid like patches and chunks of nearly static grains. Despite these static grains, the average velocity still shows a parabolic profile, dominated by the moving liquid like patches. However, the solid-liquid front moves at nearly constant speed in the opposite direction of the external drive.

cond-mat.soft↗
arXiv2018

Tubulation pattern of membrane vesicles coated with bio filaments

Narrow membrane tubes are commonly pulled out from the surface of phospholipid vesicles using forces applied either through laser or magnetic tweezers or through the action of processive motor proteins. Recent examples have emerged where such tubes spontaneously grow from vesicles coated with bioactive cytoskeletal filaments (e.g. FtsZ, microtubule) in the presence GTP. We show how a soft vesicle deforms due to the interplay between its topology, local curvature and the forces due to the active filaments. We present results from Dynamically Triangulated Monte Carlo simulations of a spherical continuum membrane coated with a nematic field and show how the intrinsic curvature of the filaments and their ordering interactions drive membrane tubulation. We predict interesting patterns of nematic defects, on curved 2D membrane surfaces, which promote tube formation. Implication of our model for more dynamic cases where vesicles coated with an active mixture of microtubule and myosin show shape oscillation, are also discussed. All these cases point to a common theme that defect locations on 2D membrane surfaces are hot spots of membrane deformation activity.

physics.bio-ph↗
arXiv2013

Plastic flow in a sheared polycrystalline solid using phase field model

Plastic deformation in solids induced by external shear stress is of huge practical interest. Presence of local crystalline order in polycrystals, consisting of many grains, distinguishes its deformation pattern from that of amorphous materials. Despite strong anisotropy, induced by external stress, the plastic flow and the consequent deformation field show strong dynamical heterogeneity. The distribution $P(u)$ of particle displacements ($u$) shows three distinct regimes including a power law scaling regime at moderate displacements. Using a phase field simulation we show how polycrystals generate saddle and vortex like flow patterns, which hitherto have been termed as elementary plastic events in the context of amorphous materials. Interestingly, such events here find natural explanation in terms of the underlying dislocation dynamics. We also characterize the spatial distribution of the flow field using Okubo-Weiss measure.

cond-mat.soft↗
arXiv2012

Chemosensing in microorganisms to practical biosensors

Microorganisms like bacteria can sense concentration of chemo-attractants in its medium very accurately. They achieve this through interaction between the receptors on their cell surface and the chemo-attractant molecules (like sugar). But the physical processes like diffusion set some limits on the accuracy of detection which was discussed by Berg and Purcell in the late seventies. We have a re-look at their work in order to assess what insight it may offer towards making efficient, practical biosensors. We model the functioning of a typical biosensor as a reaction-diffusion process in a confined geometry. Using available data first we characterize the system by estimating the kinetic constants for the binding/unbinding reactions between the chemo-attractants and the receptors. Then we compute the binding flux for this system which Berg and Purcell had discussed. But unlike in microorganisms where the interval between successive measurements determines the efficiency of the nutrient searching process, it turns out that biosensors depend on long time properties like signal saturation time which we study in detail. We also develop a mean field description of the kinetics of the system.

cond-mat.soft↗
arXiv2012

Stuttering Min oscillations within E. coli bacteria: A stochastic polymerization model

We have developed a 3D off-lattice stochastic polymerization model to study subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding, and fragmentation of MinD filaments due to MinE. Each of processivity, protection, and fragmentation reduces stuttering, speeds oscillations, and reduces MinD filament lengths. Neither processivity or tip-protection were, on their own, sufficient to produce fast stutter-free oscillations. While filament fragmentation could, on its own, lead to fast oscillations with infrequent stuttering; high levels of fragmentation degraded oscillations. The infrequent stuttering observed in standard Min oscillations are consistent with short filaments of MinD, while we expect that mutants that exhibit higher stuttering frequencies will exhibit longer MinD filaments. Increased stuttering rate may be a useful diagnostic to find observable MinD polymerization in experimental conditions.

q-bio.SC↗
arXiv2012

Stretching force dependent transitions in single stranded DNA

Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living cell. Single stranded DNA (ssDNA), which, till recently was presumed to be an simple flexible polymer continues to spring surprises. Synthetic ssDNA, like polydA (polydeoxyadenosines) has revealed an intriguing force-extension (FX) behavior exhibiting two plateaus, absent in polydT (polydeoxythymidines) for example. Loop closing time in polydA had also been found to scale exponentially with inverse temperature, unexpected from generic models of homopolymers. Here we present a new model for polydA which incorporates both a helix-coil transition and a over-stretching transition, accounting for the two plateaus. Using transfer matrix calculation and Monte-Carlo simulation we show that the model reproduces different sets of experimental observations, quantitatively. It also predicts interesting reentrant behavior in the temperature-extension characteristics of polydA, which is yet to be verified experimentally.

cond-mat.soft↗
arXiv2009

Predicting the coherence resonance curve using a semi-analytical treatment

Emergence of noise induced regularity or Coherence Resonance in nonlinear excitable systems is well known. We explain theoretically why the normalized variance ($V_{N}$) of inter spike time intervals, which is a measure of regularity in such systems, has a unimodal profile. Our semi-analytic treatment of the associated spiking process produces a general yet simple formula for $V_{N}$, which we show is in very good agreement with numerics in two test cases, namely the FitzHugh-Nagumo model and the Chemical Oscillator model.

cond-mat.stat-mech↗
arXiv2009

Self-organization of the MinE ring in subcellular Min oscillations

We model the self-organization of the MinE ring that is observed during subcellular oscillations of the proteins MinD and MinE within the rod-shaped bacterium {\it Escherichia coli}. With a steady-state approximation, we can study the MinE-ring generically -- apart from the other details of the Min oscillation. Rebinding of MinE to depolymerizing MinD filament tips controls MinE ring formation through a scaled cell shape parameter $\tilde{r}$. We find two types of E-ring profiles near the filament tip: a strong plateau-like E-ring controlled by 1D diffusion of MinE along the bacterial length, or a weak cusp-like E-ring controlled by 3D diffusion near the filament tip. While the width of a strong E-ring depends on $\tilde{r}$, the occupation fraction of MinE at the MinD filament tip is saturated and hence the depolymerization speed do not depend strongly on $\tilde{r}$. Conversely, for weak E-rings both $\tilde{r}$ and the MinE to MinD stoichiometry strongly control the tip occupation and hence the depolymerization speed. MinE rings {\em in vivo} are close to the threshold between weak and strong, and so MinD-filament depolymerization speed should be sensitive to cell shape, stoichiometry, and the MinE-rebinding rate. We also find that the transient to MinE-ring formation is quite long in the appropriate open geometry for assays of ATPase activity {\it in vitro}, explaining the long delays of ATPase activity observed for smaller MinE concentrations in those assays without the need to invoke cooperative MinE activity.

q-bio.SC↗
arXiv2009

Effect of Intrinsic Curvature on Semiflexible Polymers

Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influence the conformational statistics of such polymers. We give exact results for the tangent-tangent spatial correlation function C(r) = t(s).t(s + r), both in two and three dimensions. Contrary to expectation, C(r) does not show any oscillatory behavior, rather decays exponentially and the effective persistence length has strong length dependence for short polymers. We also compute the distribution function P(R) of the end to end distance R and show how curved chains can be distinguihed from WLC using loop formation probability.

cond-mat.soft↗
arXiv2002

Brownian Motion in a Classical Ideal Gas: a Microscopic Approach to Langevin's Equation

We present an insightful ``derivation'' of the Langevin equation and the fluctuation dissipation theorem in the specific context of a heavier particle moving through an ideal gas of much lighter particles. The Newton's Law of motion ($m{\ddot x}=F$) for the heavy particle reduces to a Langevin equation (valid on a coarser time scale) with the assumption that the lighter gas particles follow a Boltzmann velocity distribution. Starting from the kinematics of the random collisions we show that (1) the average force $ \propto -{\dot x}$ and (2) the correlation function of the fluctuating force $η= F-< F>$ is related to the strength of the average force.

cond-mat.stat-mech↗
arXiv2000

Temporal correlation function in 3-D Turbulence

We observe oscillatory decay in the two-point, non-equal time, velocity correlation function of homogeneous, isotropic turbulence. We found this through a direct numerical simulation (DNS) of the three dimensional Navier-Stokes ($3-D$ NS) equation. We give an approximate analytic theory which explains this oscillatory behaviour. The wave-number and frequency dependent effective viscosity turns out to be complex; the imaginary part gives rise to the temporal oscillation. We find that, at least for the decay at short times, data collapse occur among the inertial range velocity wave-vector modes with the long time dynamic exponent $z=2/3$, but the time period of the temporal oscillation is not universal.

nlin.CD↗