arXiv subjects

Anirban Polley

Publications and source records attributed to Anirban Polley.

11 recordsLinked to original sources

arXiv2026

Pure FENE Bond Potential for Soft Matter and Biological Simulations: Theory, HOOMD-blue Implementation, and Applications to Polymer, Colloidal, and Membrane Systems

The finitely extensible nonlinear elastic (FENE) potential is widely used as a bonded interaction in coarse-grained simulations of polymers, soft matter, colloids, and biological systems. In the classical Kremer--Grest framework, FENE bonding is combined with a short-range Weeks--Chandler--Andersen (WCA) interaction to provide finite bond extensibility together with excluded-volume repulsion. Although this combination is highly successful, it intrinsically couples bonded elasticity to the nonbonded interaction, limiting the ability to independently control these two contributions. Here, we introduce a standalone FENE bond potential in HOOMD-blue in which finite bond extensibility is implemented independently of the choice of nonbonded interaction. This formulation allows the same FENE bond potential to be combined with WCA, Lennard--Jones, or other pair interactions without modifying the bonded interaction itself. We demonstrate the utility of the standalone formulation in coarse-grained polymer chains, colloidal networks, and mesh-based biological membrane models. Across these systems, Pure FENE bonding without short-range excluded-volume stabilization produces pronounced structural contraction, whereas the addition of WCA repulsion suppresses this collapse and preserves finite, spatially extended structures. These results demonstrate that separating finite bond extensibility from steric interactions provides independent control over local bond mechanics and collective structural organization. The standalone FENE formulation therefore provides a modular framework for coarse-grained simulations in which molecular connectivity and nonbonded interactions represent distinct physical mechanisms.

cond-mat.soft↗

arXiv2026

Concentration-Dependent Membrane Destabilization in DPPC Bilayers: Distinct Insertion Mechanisms and Stress Redistribution by Chloroform and Alkanols

How do solute concentration and molecular chemistry govern the transition from membrane saturation to destabilization? We address this using microsecond-scale molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) bilayers with chloroform (CHCl$_3$) and a homologous series of alkanols (methanol, ethanol, octanol) over $0-50\%$ concentrations. Although complete membrane melting is not observed within $1000\, ns$, all systems exhibit clear precursors of destabilization, including enhanced thickness fluctuations, reduced lipid order, and mechanical softening. Chloroform induces pronounced thinning and large fluctuations, consistent with deep, transient insertion. Methanol perturbs primarily the headgroup region, while ethanol shows intermediate behavior with partial insertion. Octanol preserves bilayer thickness at high concentrations due to lipid-like insertion but significantly increases fluctuations and interdigitation. Across all systems, increasing concentration decreases the area compressibility modulus and deuterium order parameter, accompanied by smoothing of lateral pressure profiles, indicating stress redistribution. Free energy analysis reveals increased membrane partitioning and reduced translocation barriers with concentration, strongest for octanol and weakest for methanol. These results demonstrate that membrane destabilization is governed by the interplay of insertion depth, interfacial crowding, and lipid packing disruption.

cond-mat.soft↗

arXiv2026

Chain-Length-Dependent Partitioning of 1-Alkanols in Raft-Like Lipid Membranes

Although 1-alkanols are widely used as anesthetics and membrane-active agents, the molecular basis of their chain-length-dependent cutoff behavior remains unclear. Here, we perform extensive atomistic molecular dynamics simulations to investigate the partitioning of 1-alkanols with varying chain lengths in a raft-like lipid bilayer composed of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol (Chol), which exhibits coexistence of liquid-ordered ($l_o$) and liquid-disordered ($l_d$) domains. We observe pronounced lateral heterogeneity in alkanol distribution, membrane thickness, number density, and lateral pressure profiles across coexisting phases. A distinct cutoff chain length, $n_{cutoff}=12$, is identified: alkanols with $n<n_{cutoff}$ preferentially partition into DOPC-rich $l_d$ domains, whereas alkanols with $n \ge n_{cutoff}$ preferentially localize within DPPC- and cholesterol-rich $l_o$ domains. This chain-length-dependent redistribution is accompanied by systematic reductions in the lateral pressure profile, membrane compressibility, and bending rigidity of the bilayer. The results provide a detailed molecular characterization of how alkanol chain length modulates membrane structure and mechanical response in laterally heterogeneous lipid membranes.

cond-mat.soft↗

arXiv2025

The understanding of the penetration and clusterization of 1-alkanol in bilayer membrane: An open outlook based on atomistic molecular dynamics simulation

1-alkanols are well known to have anesthetic and penetration properties, though the mode of operation remains enigmatic. We perform extensive atomistic molecular dynamics simulation to study the penetration of 1-alkanols of different chain lengths in the dioleoyl-phosphatidylcholine (DOPC) bilayer model membrane. Our simulations show that the depth of penetration of 1-alkanol increases with chain length, n, and the deuterium order of the DOPC tail increases with the chain length of the acyl-chain of the 1-alkanol. We find a cut-off value for the length of the acyl-chain of 1-alkanol, n = 12, where 1-alkanol with a chain length greater than the cut-off value takes longer to penetrate the membrane. Our simulation study also demonstrates that the membrane exhibits clusters of 1-alkanols with acyl chains longer than the cut-off value, whereas 1-alkanols with acyl-chain shorter than the cut-off value are distributed homogeneously in the membrane and penetrate the membrane in a shorter time than longer-acyl-chain 1-alkanols. These findings add to our understanding of the anomalies in anesthetic molecule partitioning in the cell membrane and may have implications for general anesthesia.

cond-mat.soft↗

arXiv2022

Clustering of lipids driven by integrin

Integrin is an important transmembrane receptor protein which remodels the actin network and anchors the cell membrane towards the extracellular matrix via mechanochemical pathways. The clustering of specific lipids and lipid-anchored proteins, which is essential for a certain type of endocytosis process, is facilitated at integrin-mediated active regions. To study this, we propose a minimal exactly solvable model which includes the interplay of stochastic shuttling between integrin on and off states with the intrinsic dynamics of the membrane. We obtain an analytic expression for the deformation and local membrane velocity, and thereby the evolution of clustering mediated by a single integrin. The deformation, velocity and lipid clustering evolve nonmonotonically and their dependences on the stochastic shuttling timescales and membrane properties are elucidated.

physics.bio-ph↗

arXiv2018

Partitioning of 1-alkanols in composite raft-like lipid membrane

Though 1-alkanols are well known to have anesthetic properties, the mode of operation remains enigmatic. We perform extensive atomistic molecular dynamics simulation to study the partitioning of 1- alkanols of different chain-lengths in raft-like model membrane made up of mixture of unsaturated dioleoyl-phosphatidylcholine (DOPC) and saturated dipalmitoyl-phosphatidylcholine (DPPC) and choles- terol (Chol) exhibiting phase coexistence of liquid-ordered (lo) - liquid disordered (ld) phase domains. Our simulation shows that the effect of 1-alkanols on the mechanical properties of the membrane has been pronounced with the chain-length of it. In particular, the 1-alkanols prefer to partition in the ld phase domain. The penetration of the 1-alkanols in the membrane increases significantly for the long-chain alkanol. We also have found the dependency of the order of chains of the lipids and rigidity of the membrane on the 1-alkanols.

physics.bio-ph↗

arXiv2018

Common anesthetic molecules prefer to partition in liquid disorder phase domain in a composite multicomponent membrane

Despite a vast clinical application of anesthetics, the molecular level of understanding of general anesthesia is far from our reach. Using atomistic molecular dynamics simulation, we study the effects of common anesthetics: ethanol, chloroform and methanol in the fully hydrated symmetric multicomponent lipid bilayer membrane comprising of an unsaturated palmitoyl-oleoyl-phosphatidyl-choline (POPC), a saturated palmitoyl-sphingomyelin (PSM) and cholesterol (Chol) which exhibits phase coexistence of liquid-ordered (lo) - liquid disordered (ld) phase domains. We find that the mechanical and physical properties such as the thickness and rigidity of the membrane are reduced while the lateral expansion of the membrane is exhibited in presence of anesthetic molecules. Our simulation shows both lateral and transverse heterogeneity of the anesthetics in the composite multicomponent lipid membrane. Both ethanol and chloroform partition in the POPC-rich ld phase domain, while methanol is distributed in both lo-ld phase domains. Chloroform can penetrate deep into the membrane, while methanol partitions mostly at the water layer closed to the head-group and ethanol at the neck of the lipids in the membrane.

cond-mat.soft↗

arXiv2016

Phase segregation of passive advective particles in an active medium

Localized contractile configurations or asters spontaneously appear and disappear as emergent structures in the collective stochastic dynamics of active polar actomyosin filaments. Passive parti- cles which (un)bind to the active filaments get advected into the asters, forming transient clusters. We study the phase segregation of such passive advective scalars in a medium of dynamic asters, as a function of the aster density and the ratio of the rates of aster remodeling to particle diffusion. The dynamics of coarsening shows strong violation of Porod behaviour, suggesting diffuse interfaces. The phase segregated steady state shows strongly fluctuations characterized by multiscaling and in- termittency. We expect these unique nonequilibrium features to manifest in the actin-dependent molecular clustering at the cell surface.

cond-mat.soft↗

arXiv2013

Bilayer registry in a multicomponent asymmetric membrane : dependence on lipid composition and chain length

A question of considerable interest to cell membrane biology is whether phase segregated domains across an asymmetric bilayer are strongly correlated with each other and whether phase segregation in one leaflet can induce segregation in the other. We answer both these questions in the affirmative, using an atomistic molecular dynamics simulation to study the equilibrium statistical properties of a 3-component {\em asymmetric} lipid bilayer comprising an unsaturated POPC (palmitoyl-oleoyl-phosphatidyl-choline), a saturated SM (sphingomyelin) and cholesterol with different composition ratios. Our simulations are done by fixing the composition of the upper leaflet to be at the coexistence of the liquid ordered ($l_o$) - liquid disordered ($l_d$) phases, while the composition of the lower leaflet is varied from the phase coexistence regime to the mixed $l_d$ phase, across a first-order phase boundary. In the regime of phase coexistence in each leaflet, we find strong transbilayer correlations of the $l_o$ domains across the two leaflets, resulting in {\it bilayer registry}. This transbilayer correlation depends sensitively upon the chain length of the participating lipids and possibly other features of lipid chemistry, such as degree of saturation. We find that the $l_o$ domains in the upper leaflet can {\em induce} phase segregation in the lower leaflet, when the latter is nominally in the mixed ($l_d$) phase.

physics.bio-ph↗

arXiv2013

Bending elasticity of macromolecules: analytic predictions from the wormlike chain model

We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our results go beyond the Hookean regime and explore the nonlinear elastic behaviour of a single molecule. We present analytical formulae for the bend angle distribution and for the moment-angle relation. Our analytical study is compared against numerical Monte Carlo simulations. The functional forms derived here can be applied to fluorescence microscopic studies on actin and DNA. Our results are relevant to recent studies in "kinks" and cyclization in short and intermediate length DNA strands.

cond-mat.soft↗

arXiv2012

Atomistic simulations of a multicomponent asymmetric lipid bilayer

The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid bilayer system comprising of an unsaturated POPC (palmitoyl-oleoyl-phosphatidyl-choline), a saturated SM (sphingomyelin) and cholesterol are investigated. In these simulations, the initial stages of liquid ordered, $l_o$, domain formation are observed and such domains are found to be highly enriched in cholesterol and SM. The current simulations also suggest that the cholesterol molecules may partition into these SM-dominated regions in the ratio of $3:1$ when compared to POPC-dominated regions. SM molecules exhibit a measurable tilt and long range tilt correlations are observed within the $l_o$ domain as a consequence of the asymmetry of the bilayer, with implications to local membrane deformation and budding. Tagged particle diffusion for SM and cholesterol molecules, which reflects spatial variations in the physical environment encountered by the tagged particle, is computed and compared with recent experimental results obtained from high resolution microscopy.

cond-mat.soft↗