arXiv subjects

P. B. Sunil Kumar

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

At least 19 recordsLinked to original sources

arXiv2026

Active Hydrodynamics Couples Polymer Organization, Shape Fluctuations, and Motility in Deformable Droplets

We study semiflexible active polymers confined within a soft, deformable droplet suspended in a fluid using dissipative particle dynamics (DPD) simulations. Extensile and contractile force dipoles along the polymer backbone generate distinct hydrodynamic flow fields that mediate effective interactions between polymer segments. Extensile activity promotes parallel alignment and lateral attraction, whereas contractile activity favors predominantly perpendicular organization, leading to qualitatively different collective behavior. The activity-generated flows couple strongly to the deformable interface, selectively enhancing low-order spherical-harmonic modes associated with long-wavelength droplet deformations. Activity also drives the interfacial relaxation away from passive capillary behavior, with extensile and contractile droplets exhibiting distinct mode-dependent dynamics. These differences in internal organization and interfacial fluctuations strongly influence droplet motility. Extensile activity produces increasingly persistent droplet motion with increasing polymer number, whereas contractile activity can sustain long-lived near-ballistic motion whose duration depends sensitively on polymer number and activity strength. Our results demonstrate how active hydrodynamics governs the interplay between internal structure, interfacial fluctuations, and emergent motility in confined active matter systems.

cond-mat.soft↗

arXiv2026

Stress-Boundary-Memory Feedback Drives Vortical-Polar Transitions in Softly Confined Active Matter

We computationally investigate how environmental sensitivity of active matter interacts with soft confinement to shape collective dynamics. In our model, the active constituents are represented as self-propelled particles (SPPs), implemented as nematic, disjoint ring polymers whose direction of motion can reverse without tumbling. Coarse-grained molecular dynamics simulations reveal that collective dynamics arise from a three-way feedback between active stresses, boundary elasticity, and particle-level memory. With increasing driving force, FD, this feedback generates a sequence of collective dynamical regimes. At low FD, SPP motion is dominated by thermal fluctuations. At intermediate FD, coherent vortical motion emerges with intermittent, noise-driven reversals. With further increase in FD, reversals are suppressed, yielding sustained unidirectional vortical motion. At sufficiently high FD, the system transitions to a polar state characterized by strong nematic ordering of the SPPs, symmetry breaking of the enclosure shape, and persistent polar collective motion. In this regime, the SPPs accumulate at the leading edge of the enclosure, driving sustained ballistic propulsion. These results demonstrate how environmental sensitivity and soft confinement jointly regulate emergent collective states and identify boundary elasticity as a control parameter governing the balance between vortical and ballistic dynamics.

cond-mat.soft↗

arXiv2023

Collective Vortical Motion and Vorticity Reversals of Self-Propelled Particles on Circularly Patterned Substrates

The collective behavior of self-propelled particles (SPPs) under the combined effects of a circularly patterned substrate and circular confinement is investigated through coarse-grained molecular dynamics simulations of polarized and disjoint ring polymers. The study is performed over a wide range of values of the SPPs packing fraction $\barϕ$, motility force $F_D$, and area fraction of the patterned region. At low packing fractions, the SPPs are excluded from the system's center and exhibit a vortical motion that is dominated by the substrate at intermediate values of $F_D$. This exclusion zone is due to the coupling between the driving force and torque induced by the substrate, which induces an outward spiral motion of the SPPs. For high values of $F_D$, the SPPs exclusion from the center is dominated by the confining boundary. At high values of $\barϕ$, the substrate pattern leads to reversals in the vorticity, which become quasi-periodic with increasing $\barϕ$. We also found that the substrate pattern is able to separate SPPs based on their motilities.

cond-mat.soft↗

arXiv2019

Models for membrane curvature sensing of curvature generating proteins

The curvature sensitive localization of proteins on membranes is vital for many cell biological processes. Coarse-grained models are routinely employed to study the curvature sensing phenomena and membrane morphology at the length scale of few micrometers. Two prevalent phenomenological models exist for modeling experimental observations of curvature sensing, (1) the spontaneous curvature model and (2) the curvature mismatch model, which differ in their treatment of the change in elastic energy due to the binding of proteins on the membrane. In this work, the prediction of sensing and generation behaviour, by these two models, are investigated using analytical calculations as well as Dynamic Triangulation Monte Carlo simulations of quasi-spherical vesicles. While the spontaneous curvature model yields a monotonically decreasing sensing curve as a function of vesicle radius, the curvature mismatch model results in a non-monotonic sensing curve. We highlight the main differences in the interpretation of the protein-related parameters in the two models. We further propose that the spontaneous curvature model is appropriate for modeling peripheral proteins employing the hydrophobic insertion mechanism, with minimal modification of membrane rigidity, while the curvature mismatch model is appropriate for modeling curvature generation using scaffolding mechanism where there is significant stiffening of the membrane due to protein binding.

cond-mat.soft↗

arXiv2018

Kosmotropic effect leads to LCST decrease in thermoresponsive polymer solutions

We study the phenomena of decrease in lower critical solution temperature (LCST) with addition of kosmotropic (order-making) cosolvents in thermoresponsive polymer solutions. A combination of explicit solvent coarse-grained simulations and mean-field theory has been employed. The polymer-solvent LCST behavior in the theoretical models have been incorporated through the Kolomeisky-Widom solvophobic potential. Our results illustrate how the decrease in the LCST can be achieved by the reduction in the bulk solvent energy with addition of cosolvent. It is shown that this effect of cosolvent is weaker with increase in polymer hydrophilicity which can explain the absence of LCST decrease in PDEA, water and methanol systems. The coarse-grained nature of the models indicates that a mean energetic representation of the system is sufficient to understand the phenomena of LCST decrease.

cond-mat.soft↗

arXiv2018

Lipid-protein interaction induced domains: kinetics and conformational changes in multicomponent vesicles

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated in the past. We show, using Monte Carlo simulations, that the affinity of proteins for specific lipids can hasten its aggregation kinetics. The lipid membrane is modeled as a dynamically triangulated surface with the proteins defined as in-plane fields at the vertices. We show that, even at low protein concentrations, strong lipid-protein interactions can result in large protein clusters indicating a route to lipid mediated signal amplification. At high protein concentrations the domains form buds similar to that seen in lipid-lipid interaction induced phase separation. Protein interaction induced domain budding is suppressed when proteins act as anisotropic inclusions and exhibit nematic orientational order. The kinetics of protein clustering and resulting conformational changes are shown to be significantly different for the isotropic and anisotropic curvature inducing proteins.

physics.bio-ph↗

arXiv2017

Molecular Structuring and Percolation Transition in Hydrated Sulfonated Poly(ether ether ketone) Membranes

The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether ketone), sPEEK, membrane is investigated using atomistic molecular dynamics (MD) simulation at various hydration levels (λ: number of water molecules per sulfonate group) between 4 and 15. At the molecular level, the evolution of local morphology is investigated in terms of structural pair correlations and minimum pair distances, and the transport properties are studied in terms of mean squared displacements (MSDs) and diffusion coefficients. The water-sulfur interaction in sPEEK is found to be stronger than that in Nafion, as observed in experiments. As opposed to Nafion, a weaker interaction of hydronium, with sulfonate, than water is observed. The behavior of water in sPEEK membrane is found to remain far from bulk as indicated by its diffusion coefficient. Analysis of simulation data indicate that at low λ, the largest water cluster forms a narrow connected path of water molecules and hydronium ions. With increasing λ, larger water domains appear, spanning more than half of the simulation box at λ = 15. Small isolated clusters are present at all hydration levels, demonstrating the extent of phase separation in sPEEK to be lesser than that in Nafion. Various analyses, both at molecular and collective level, suggest the occurrence of a percolation transition between λ = 8 and 10, which leads to a connected network of water channels in the membrane, thereby boosting the mobility of hydronium ions.

cond-mat.soft↗

arXiv2016

Colloidal transport by active filaments

Enhanced colloidal transport beyond the limit imposed by diffusion is usually achieved through external fields. Here, we demonstrate the ballistic transport of a colloidal sphere using internal sources of energy provided by an attached active filament. The latter is modeled as a chain of chemo-mechanically active beads connected by potentials that enforce semi-flexibility and self-avoidance. The fluid flow produced by the active beads and the forces they mediate are explicitly taken into account in the overdamped equations of motion describing the colloid-filament assembly. The speed and efficiency of transport depend on the dynamical conformational states of the filament. We characterize these states using filament writhe as an order parameter and identify ones yielding maxima in speed and efficiency of transport. The transport mechanism reported here has a remarkable resemblance to the flagellar propulsion of microorganisms which suggests its utility in biomimetic systems.

cond-mat.soft↗

arXiv2016

Spherically symmetric solvent is sufficient to explain lower critical solution temperature in polymer solutions

We study the lower critical solution temperature (LCST) in thermoresponsive polymer solutions by means of a coarse grained single polymer chain simulation and a theoretical approach. The simulation model includes solvent explicitly and thus accounts for solvent interactions and entropy directly. The theoretical model consists of a single chain polymer in an implicit solvent where the effect of solvent is included through the intra-polymer solvophobic potential proposed by Kolomeisky and Widom. Our results indicate that the LCST behavior is determined by the competition between the mean energy difference between the bulk and bound solvent, and the entropy loss due to the bound solvent. At low temperatures, solvent molecules are bound to the polymer and the solvophobicity of the polymer is screened, resulting in a coiled state. At high temperatures the entropy loss due to bound solvent offsets the energy gain due to binding which causes the solvent molecules to unbind, leading to the collapse of the polymer chain to a globular state. Furthermore, the coarse grained nature of these models indicates that mean interaction energies are sufficient to explain LCST in comparison to specific solvent structural arrangements.

cond-mat.soft↗

arXiv2015

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.

physics.bio-ph↗

arXiv2015

Active remodeling of chromatin and implications for in-vivo folding

Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to such specific statistical conformations. Here, we show that an active chromatin model of in-vivo folding, based on the interplay between polymer elasticity, confinement, topological constraints and active stresses arising from the (un)binding of ATP-dependent chromatin-remodeling proteins gives rise to steady state conformations consistent with these experiments. Our results lead us to conjecture that the chromatin conformation resulting from this active folding optimizes information storage by co-locating gene loci which share transcription resources.

physics.bio-ph↗

arXiv2015

Flow-induced nonequilibrium self-assembly in suspensions of stiff, apolar, active filaments

Active bodies in viscous fluids interact hydrodynamically through self-generated flows. Here we study spontaneous aggregation induced by hydrodynamic flow in a suspension of stiff, apolar, active filaments. Lateral hydrodynamic attractions in extensile filaments lead, independent of volume fraction, to anisotropic aggregates which translate and rotate ballistically. Lateral hydrodynamic repulsion in contractile filaments lead, with increasing volume fractions, to microstructured states of asters, clusters, and incipient gels where, in each case, filament motion is diffusive. Our results demonstrate that the interplay of active hydrodynamic flows and anisotropic excluded volume interactions provides a generic nonequilibrium mechanism for hierarchical self-assembly of active soft matter.

cond-mat.soft↗

arXiv2014

Organelle morphogenesis by active remodeling

Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both sense and generate local membrane curvature. Here we investigate through Dynamical Triangulation Monte Carlo simulations, the role that these active processes play in determining the morphology and compositional segregation in closed membranes. Our results suggest that the ramified morphologies of organelles observed in-vivo are a consequence of driven nonequilibrium processes rather than equilibrium forces.

physics.bio-ph↗

arXiv2013

Hydrodynamic Instabilities Provide A Generic Route To Spontaneous Biomimetic Oscillations In Chemomechanically Active Filaments

Non-equilibrium processes which convert chemical energy into mechanical motion enable the motility of organisms. Bundles of inextensible filaments driven by energy transduction of molecular motors form essential components of micron-scale motility engines like cilia and flagella. The mimicry of cilia-like motion in recent experiments on synthetic active filaments supports the idea that generic physical mechanisms may be sufficient to generate such motion. Here we show, theoretically, that the competition between the destabilising effect of hydrodynamic interactions induced by force-free and torque-free chemomechanically active flows, and the stabilising effect of nonlinear elasticity, provides a generic route to spontaneous oscillations in active filaments. These oscillations, reminiscent of prokaryotic and eukaryotic flagellar motion, are obtained without having to invoke structural complexity or biochemical regulation. This minimality implies that biomimetic oscillations, previously observed only in complex bundles of active filaments, can be replicated in simple chains of generic chemomechanically active beads.

cond-mat.soft↗

arXiv2013

Membrane mediated aggregation of curvature inducing nematogens and membrane tubulation

The shapes of cell membranes are largely regulated by membrane associated, curvature active, proteins. We use a numerical model of the membrane with elongated membrane inclusions, recently developed by us, which posses spontaneous directional curvatures that could be different along and perpendicular to its long axis. We show that, due to membrane mediated interactions these curvature inducing membrane nematogens can oligomerize spontaneously, even at low concentrations, and change the local shape of the membrane. We demonstrate that for a large group of such inclusions, where the two spontaneous curvatures have equal sign, the tubular conformation and sometime the sheet conformation of the membrane are the common equilibrium shapes. We elucidate the factors necessary for the formation of these {\it protein lattices}. Furthermore, the elastic properties of the tubes, like their compressional stiffness and persistence length are calculated. Finally, we discuss the possible role of nematic disclination in capping and branching of the tubular membranes.

physics.bio-ph↗

arXiv2012

Autonomous Motility of Active Filaments due to Spontaneous Flow-Symmetry Breaking

We simulate the nonlocal Stokesian hydrodynamics of an elastic filament which is active due a permanent distribution of stresslets along its contour. A bending instability of an initially straight filament spontaneously breaks flow symmetry and leads to autonomous filament motion which, depending on conformational symmetry, can be translational or rotational. At high ratios of activity to elasticity, the linear instability develops into nonlinear fluctuating states with large amplitude deformations. The dynamics of these states can be qualitatively understood as a superposition of translational and rotational motion associated with filament conformational modes of opposite symmetry. Our results can be tested in molecular-motor filament mixtures, synthetic chains of autocatalytic particles, or other linearly connected systems where chemical energy is converted to mechanical energy in a fluid environment.

cond-mat.soft↗

arXiv2012

Role of disclinations in determining the morphology of deformable fluid interfaces

We study the equilibrium shapes of vesicles, with an in-plane nematic order, using a Monte-Carlo scheme and show that highly curved shapes, like tubes and discs, with a striking similarity to the structures engendered by certain curvature sensing peripheral membrane proteins, can be spontaneously generated by anisotropic directional curvature with nematic disclinations playing and important role. We show that the coupling between nematic order and local curvature could lead to like defects moving towards each other and unlike defects moving away, in turn leading to tube formation. Thermally induced defect pair production lead to branched tubular structures. It is also shown that helical arrangement of the membrane tubes, with nematic field spiraling around it, is a dominant soft mode of the system.

physics.bio-ph↗

arXiv2011

Computer Simulation of Cytoskeleton-Induced Blebbing in Lipid Membranes

Blebs are balloon-shaped membrane protrusions that form during many physiological processes. Using computer simulation of a particle-based model for self-assembled lipid bilayers coupled to an elastic meshwork, we investigated the phase behavior and kinetics of blebbing. We found that blebs form for large values of the ratio between the areas of the bilayer and the cytoskeleton. We also found that blebbing can be induced when the cytoskeleton is subject to a localized ablation or a uniform compression. The results obtained are qualitatively in agreement with the experimental evidence and the model opens up the possibility to study the kinetics of bleb formation in detail.

physics.bio-ph↗