arXiv subjects

P. B. Sunil Kumar

Publications and source records attributed to P. B. Sunil Kumar.

At least 37 records · Page 2Linked to original sources

arXiv2011

Modeling anisotropic elasticity of fluid membranes

The biological membrane, which compartmentalizes the cell and its organelles, exhibit wide variety of macroscopic shapes of varying morphology and topology. A systematic understanding of the relation of membrane shapes to composition, external field, environmental conditions etc. have important biological relevance. Here we review the triangulated surface model, used in the macroscopic simulation of membranes and the associated Monte Carlo (DTMC) methods. New techniques to calculate surface quantifiers, that will facilitate the study of additional in-plane orientational degrees of freedom, has been introduced. The mere presence of a polar and nematic fields in the ordered phase drives the ground state conformations of the membrane to a cylinder and tetrahedron respectively.

physics.bio-ph↗

arXiv2010

Monte Carlo simulations of fluid vesicles with in plane orientational ordering

We present a method for simulating fluid vesicles with in-plane orientational ordering. The method involves computation of local curvature tensor and parallel transport of the orientational field on a randomly triangulated surface. It is shown that the model reproduces the known equilibrium conformation of fluid membranes and work well for a large range of bending rigidities. Introduction of nematic ordering leads to stiffening of the membrane. Nematic ordering can also result in anisotropic rigidity on the surface leading to formation of membrane tubes.

physics.bio-ph↗

arXiv2008

Equilibrium properties of a grafted polyelectrolyte with explicit counterions

We study the equilibrium conformations of a grafted polyelectrolyte (PE) in the presence of explicit counterions (CI) using Monte Carlo simulations. The interplay between attractive Lennard-Jones interactions (parametrized by epsilon), and electrostatics (parametrized by A = q^2l_B/a, where q =counterion valency, l_B = Bjerrum length and a = monomer diameter), results in a variety of conformations, characterized as extended (E), pearls with m beads (P_m), sausage (S) and globular (G). For large epsilon, we observe a transition from G -> P_2 -> P_3 -> . . . -> S -> G with increasing A, i.e., a change from poor to good, to reentrant poor solvent, whereas, at lower epsilon, the sequence of transitions is, E -> S -> G. The conformation changes are directly related to the nature of binding of CI onto the PE. The transition between S -> G is continuous and associated with critical fluctuations in the shape driven by fluctuations in the fraction of condensed CI.

cond-mat.soft↗

arXiv2008

Lipid Flip-Flop Driven Mechanical and Morphological Changes in Model Membranes

We study, using dissipative particle dynamics simulations, the effect of active lipid flip-flop on model fluid bilayer membranes. We consider both cases of symmetric as well as asymmetric flip-flops. Symmetric flip-flop leads to a steady state of the membrane with an effective temperature higher than that of the equilibrium membrane and an effective surface tension lower than that of the equilibrium membrane. Asymmetric flip-flop leads to transient conformational changes of the membrane in the form of bud or blister formation, depending on the flip rate.

cond-mat.soft↗

arXiv2006

Anomalously Slow Domain Growth in Fluid Membranes with Asymmetric Transbilayer Lipid Distribution

The effect of asymmetry in the transbilayer lipid distribution on the dynamics of phase separation in fluid vesicles is investigated numerically for the first time. This asymmetry is shown to set a spontaneous curvature for the domains that alter the morphology and dynamics considerably. For moderate tension, the domains are capped and the spontaneous curvature leads to anomalously slow dynamics, as compared to the case of symmetric bilayers. In contrast, in the limiting cases of high and low tensions, the dynamics proceeds towards full phase separation.

cond-mat.soft↗

arXiv2006

Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers

A systematic investigation of the phase separation dynamics in self-assembled multi-component bilayer fluid vesicles and open membranes is presented. We use large-scale dissipative particle dynamics to explicitly account for solvent, thereby allowing for numerical investigation of the effects of hydrodynamics and area-to-volume constraints. In the case of asymmetric lipid composition, we observed regimes corresponding to coalescence of flat patches, budding, vesiculation and coalescence of caps. The area-to-volume constraint and hydrodynamics have a strong influence on these regimes and the crossovers between them. In the case of symmetric mixtures, irrespective of the area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The same exponent is also found in the case of open membranes with symmetric composition.

cond-mat.soft↗

arXiv2006

A Lattice-Boltzmann model for suspensions of self-propelling colloidal particles

We present a Lattice-Boltzmann method for simulating self-propelling (active) colloidal particles in two-dimensions. Active particles with symmetric and asymmetric force distribution on its surface are considered. The velocity field generated by a single active particle, changing its orientation randomly, and the different time scales involved are characterized in detail. The steady state speed distribution in the fluid, resulting from the activity, is shown to deviate considerably from the equilibrium distribution.

cond-mat.soft↗

arXiv2005

Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules

We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of ``bubbles'', localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in $P(R)$ and unusual force-extension curves. An analytic formula for the loop formation probability in the presence of bubbles is proposed. For short {\em heterogeneous} chains, we demonstrate a strong dependence of loop formation probabilities on sequence, as seen in recent experiments.

cond-mat.soft↗

arXiv2004

Dynamics of Domain Growth in Self-Assembled Fluid Vesicles

The dynamics of phase separation in multi-component bilayer fluid vesicles is investigated by means of large-scale dissipative particle dynamics. The model explicitly accounts for solvent particles, thereby allowing for the very first numerical investigation of the effects of hydrodynamics and area-to-volume constraints. We observed regimes corresponding to coalescence of flat patches, budding and vesiculation, and coalescence of caps. We point out that the area-to-volume constraint has a strong influence on crossovers between these regimes.

cond-mat.soft↗

arXiv2003

Asters, Spirals and Vortices in Mixtures of Motors and Microtubules: The Effects of Confining Geometries on Pattern Formation

We model the effects of confinement on the stable self-organized patterns obtained in the non-equilibrium steady states of mixtures of molecular motors and microtubules. In experiments [Nedelec et al. Nature, 389, 305 (1997); Surrey et al., Science, 292, 1167 (2001)] performed in a quasi-two-dimensional confined geometry, microtubules are oriented by complexes of motor proteins. This interaction yields a variety of patterns, including arangements of asters, vortices and disordered configurations. We model this system via a two-dimensional vector field describing the local coarse-grained microtubule orientation and two scalar density fields associated to molecular motors. These scalar fields describe motors which either attach to and move along microtubules or diffuse freely within the solvent. Transitions between single aster, spiral and vortex states are obtained as a consequence of confinement, as parameters in our model are varied. We also obtain other novel states, including ``outward asters'', distorted vortices and lattices of asters on confined systems. We calculate the steady state distribution of bound and free motors in aster and vortex configurations of microtubules and compare these to our simulation results, providing qualitative arguments for the stability of different patterns in various regimes of parameter space. We also study the role of crowding or ``saturation'' effects on the density profiles of motors in asters, discussing the role of such effects in stabilizing single asters.

cond-mat.stat-mech↗

arXiv2003

Self-organized Pattern Formation in Motor-Microtubule Mixtures

We propose and study a hydrodynamic model for pattern formation in mixtures of molecular motors and microtubules. The steady state patterns we obtain in different regimes of parameter space include arrangements of vortices and asters separately as well as aster-vortex mixtures and fully disordered states. Such stable steady states are observed in experiments in vitro. The sequence of patterns obtained in the experiments can be associated with smooth trajectories in a non-equilibrium phase diagram for our model.

cond-mat.stat-mech↗

arXiv2002

Two-Component Fluid Membranes Near Repulsive Walls: Linearized Hydrodynamics of Equilibrium and Non-equilibrium States

We study the linearized hydrodynamics of a two-component fluid membrane near a repulsive wall, via a model which incorporates curvature- concentration coupling as well as hydrodynamic interactions. This model is a simplified version of a recently proposed one [J.-B. Manneville et al. Phys. Rev. E, 64, 021908 (2001)] for non-equilibrium force-centres embedded in fluid membranes, such as light-activated bacteriorhodopsin pumps incorporated in phospholipid (EPC) bilayers. The pump/membrane system is modeled as an impermeable, two-component bilayer fluid membrane in the presence of an ambient solvent, in which one component, representing active pumps, is described in terms of force dipoles displaced with respect to the bilayer midpoint. We first discuss the case in which such pumps are rendered inactive, computing the mode structure in the bulk as well as the modification of hydrodynamic properties by the presence of a nearby wall. We then discuss the fluctuations and mode structure in steady state of active two-component membranes near a repulsive wall. We find that proximity to the wall smoothens membrane height fluctuations in the stable regime, resulting in a logarithmic scaling of the roughness even for initially tensionless membranes. This explicitly non-equilibrium result, a consequence of the incorporation of curvature-concentration coupling in our treatment, also indicates that earlier scaling arguments which obtained an increase in the roughness of active membranes near repulsive walls may need to be reevaluated.

cond-mat.soft↗

arXiv2002

Scale invariance in coarsening of binary and ternary fluids

Phase separation in binary and ternary fluids is studied using a two dimensional Lattice Gas Automata. The lengths, given by the the first zero crossing point of the correlation function and the total interface length is shown to exhibit power law dependence on time. In binary mixtures, our data clearly indicate the existence of a regime having more than one length scale where the coarsening process proceeds through the rupture and reassociation of domains. In ternary fluids; in the case of symmetric mixtures there exists a regime with a single length scale having dynamic exponent 1/2, while in asymmetric mixtures our data establish the break down of scale invariance.

cond-mat.soft↗

arXiv2002

Dynamics of folding in Semiflexible filaments

We investigate the dynamics of a single semiflexible filament, under the action of a compressing force, using numerical simulations and scaling arguments. The force is applied along the end to end vector at one extremity of the filament, while the other end is held fixed. We find that, unlike in elastic rods the filament folds asymmetrically with a folding length which depends only on the bending stiffness and the applied force. It is shown that this behavior can be attributed to the exponentially falling tension profile in the filament. While the folding time depends on the initial configuration, at late time, the distance moved by the terminal point of the filament and the length of the fold shows a power law dependence on time with an exponent 1/2.

cond-mat.soft↗

arXiv1997

Shape Instabilities in the Dynamics of a Two-component Fluid Membrane

We study the shape dynamics of a two-component fluid membrane, using a dynamical triangulation monte carlo simulation and a Langevin description. Phase separation induces morphology changes depending on the lateral mobility of the lipids. When the mobility is large, the familiar labyrinthine spinodal pattern is linearly unstable to undulation fluctuations and breaks up into buds, which move towards each other and merge. For low mobilities, the membrane responds elastically at short times, preferring to buckle locally, resulting in a crinkled surface.

cond-mat.soft↗

arXiv1996

A Novel Monte Carlo Approach to the Dynamics of Fluids --- Single Particle Diffusion, Correlation Functions and Phase Ordering of Binary Fluids

We propose a new Monte Carlo scheme to study the late-time dynamics of a 2-dim hard sphere fluid, modeled by a tethered network of hard spheres. Fluidity is simulated by breaking and reattaching the flexible tethers. We study the diffusion of a tagged particle, and show that the velocity autocorrelation function has a long-time $t^{-1}$ tail. We investigate the dynamics of phase separation of a binary fluid at late times, and show that the domain size $R(t)$ grows as $t^{1/2}$ for high viscosity fluids with a crossover to $t^{2/3}$ for low viscosity fluids. Our scheme can accomodate particles interacting with a pair potential $V(r)$,and modified to study dynamics of fluids in three dimensions.

cond-mat↗

arXiv1996

Kinetics of Phase Ordering in a Two-Component Fluid Membrane

We present a novel Monte Carlo simulation of the phase separation dynamics of a model fluid membrane. Such a phase segregation induces shape changes of the membrane and results in local `budding' under favourable conditions. We present a preliminary investigation of the nucleation regime and compute a variety of growth laws. Our study indicates that membranes with high viscosity, buckle on account of phase segregation. We discuss the relation between this dynamical buckling and the phenomenon of `capping' seen in biological membranes.

cond-mat↗

arXiv1995

Imbibition: An Example of Nonconserved Cellular Automaton

We report an imbibition experiment in 2D random porous media in which height - height correlation function grows with a nonuniversal exponent. We find the exponent to depend on evaporation. A cellular automaton model for imbibition based on first principles is presented. A numerical study of the model gives results which are consistent with the experiment. The interface is shown to exhibit self-organised criticality (SOC).

cond-mat↗