Related papers: Crowding effects on the structural transitions in …
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the…
We report the results of Monte Carlo simulations investigating the effect of a spherical confinement within a simple model for a flexible homopolymer. We use the parallel tempering method combined with multi-histogram reweighting analysis…
The quasi-equilibrium evolution of the helical fraction occurring in a biopolymer network (gelatin gel) under an applied stress has been investigated by observing modulation in its optical activity. Its variation with the imposed chain…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
We study the evaporation-induced stratification of a mixture of short and long polymer chains in a drying droplet using molecular simulations. We systematically investigate the effects of hydrodynamic interactions (HI) on this process by…
In a freely cooling granular material fluctuations in density and temperature cause position dependent energy loss. Due to strong local dissipation, pressure and energy drop rapidly and material moves from `hot' to `cold' regions, leading…
Transitions between solid-like and fluid-like states in living tissues have been found in steps of embryonic development and in stages of disease progression. Our current understanding of these transitions has been guided by experimental…
We discuss a simple model of particles hopping in one dimension with attractive interactions. Taking a hydrodynamic limit in which the interaction strength increases with the system size, we observe the formation of multiple clusters of…
Extensive coarse grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowded densities, the polymer…
The spatial distribution of structural relaxation in a supercooled liquid is studied using molecular dynamics simulations of a 2D binary mixture. It is shown that the spatial heterogeneity of the relaxation along with the time scale of the…
Collective cell motility plays central roles in various biological phenomena such as inflammatory response, wound healing, cancer metastasis and embryogenesis. These are biological demonstrations of the unjamming transition. However,…
We study the clustering properties of inertial particles in a turbulent viscoelastic fluid. The investigation is carried out by means of direct numerical simulations of turbulence in the Oldroyd-B model. The effects of polymers on the small…
A mixture of solvent particles with short-range, directional interactions and solute particles with short-range, isotropic interactions that can bond multiple times is of fundamental interest in understanding liquids and colloidal mixtures.…
We study multicomponent liquids by increasing the mass of $15\%$ of the particles in a binary Kob-Andersen model. We find that the heavy particles have dual effects on the lighter particles. At higher temperatures, there is a significant…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the…
Coherent collective motion is a widely observed phenomenon in active matter systems. Here, we report a flocking transition mechanism in a system of chemically interacting active colloidal particles sustained purely by chemo-repulsive…
Acid-base equilibria directly influence the functionality and behavior of particles in a system. Due to the ionizing effects of acid-base functional groups, particles will undergo charge exchange. The degree of ionization and their…
A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139…
We investigate the effects of atmospheric circulation on the chemistry of the hot Jupiter HD 209458b. We use a simplified dynamical model and a robust chemical network, as opposed to previous studies which have used a three dimensional…