Biomedical subjects

P B Sunil Kumar

Publications and source records attributed to P B Sunil Kumar.

12 recordsLinked to original sources

PubMed2006

Self-propulsion of nematic drops: novel phase separation dynamics in impurity-doped nematogens.

We report a novel phase separation dynamics, mediated by self-propelled motion of the nucleated drops, in a mixture of a nematogen and an isotropic dopant. We show that surface flow, induced by the gradient in the concentration of the dopant expelled by the growing drops, provides the driving force for the propulsion of nematic droplets. While the liquid crystal-isotropic transition is used here to demonstrate the phenomenon, self-propulsion should be observable in many other systems in which the dynamics of a conserved order parameter is coupled to a nonconserved order parameter.

Journal Article↗

PubMed2006

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 their 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.

Algorithms↗

PubMed2006

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. 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 toward full phase separation.

Anisotropy↗

PubMed2005

Domain growth, budding, and fission in phase-separating self-assembled fluid bilayers.

A systematic investigation of the phase-separation dynamics in self-assembled binary 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.

Algorithms↗

PubMed2005

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 heterogeneous chains, we demonstrate a strong dependence of loop formation probabilities on sequence.

DNA↗

PubMed2004

Dynamics of domain growth in self-assembled fluid vesicles.

The dynamics of phase separation in multicomponent 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.

Cytoplasmic Vesicles↗

PubMed2004

Self-organized pattern formation in motor-microtubule mixtures.

We model the stable self-organized patterns obtained in the nonequilibrium steady states of mixtures of molecular motors and microtubules. In experiments [Nédélec et al., Nature (London) 389, 305 (1997); Surrey et al., Science 292, 1167 (2001)] performed in a quasi-two-dimensional geometry, microtubules are oriented by complexes of motor proteins. This interaction yields a variety of patterns, including arrangements 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. For systems in which the effects of confinement can be neglected, we present a map of nonequilibrium steady states, which includes arrangements of asters and vortices separately as well as aster-vortex mixtures and fully disordered states. 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 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. We also comment on the implications of our results for experiments.

Animals↗

PubMed2003

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.

Journal Article↗

PubMed2002

Two-component fluid membranes near repulsive walls: Linearized hydrodynamics of equilibrium and nonequilibrium states.

We study the linearized hydrodynamics of a two-component fluid membrane near a repulsive wall, using a model that 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 nonequilibrium force centers embedded in fluid membranes, such as light-activated bacteriorhodopsin pumps incorporated in phospholipid egg phosphatidyl choline (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. These results should apply, more generally, to equilibrium fluid membranes comprised of two components, in which the effects of curvature-concentration coupling are significant, above the threshold for phase separation. We then discuss the fluctuations and mode structure in the 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 nonequilibrium result is a consequence of the incorporation of curvature-concentration coupling in our hydrodynamic treatment. This result also indicates that earlier scaling arguments which obtained an increase in the roughness of active membranes near repulsive walls upon neglecting the role played by such couplings may need to be reevaluated.

Journal Article↗

PubMed2002

Dynamics of folding in semiflexible filaments.

The dynamics of a single semiflexible filament under the action of a compressing force is simulated. We find that the filament folds asymmetrically with a folding length which depends only on the bending stiffness kappa and the applied force f. It is shown that this behavior can be attributed to the exponentially falling tension profile in the filament. While the folding time tau(0) depends on the initial configuration, the distance moved by the terminal point of the filament and the length of the fold scales as tau(1/2) at tau>>tau(0) and is independent of the initial configuration.

Actins↗

PubMed2001

Budding dynamics of multicomponent membranes.

The budding of multicomponent membranes is studied by computer simulations and scaling arguments. The simulation algorithm combines dynamic triangulation with Kawasaki exchange dynamics. The budding process exhibits three distinct time regimes: (i) formation and growth of intramembrane domains; (ii) formation of many buds; and (iii) coalescence of small buds into larger ones. The coalescence regime (iii) is characterized by scaling laws which describe the long-time behavior. Thus, the number of buds, N(bud), decays as N(bud) approximately 1/t(theta) for large time t with theta = 1/2 and theta = 2/3 in the absence and the presence of hydrodynamic interactions, respectively.

Journal Article↗

PubMed1999

Modulated phases in multicomponent fluid membranes.

We investigate the behavior of flexible two-component bilayer and three-component monolayer membranes. The components are assumed to have different spontaneous curvatures, and to mutually phase separate in planar membranes. As a function of temperature, lateral tension and bending rigidity, a rich phase behavior is obtained. In particular, we find three different types of modulated phases. In symmetric bilayers, the excess component assembles at the boundary between oppositely curved domains; in sufficiently asymmetric bilayers, the excess component is found to preferentially assemble in a single layer, with no tendency for segregation to the domain boundaries. We show that the phase behavior of three-component monolayer strongly resembles the behavior of two-component bilayers. In fact, in a certain, restricted region of parameter space, the two models can be shown to be equivalent.

Cell Membrane↗