Related papers: Simulating flexible polymers in a potential of ran…
In simulations of crystals, unlike liquids or gases, it may happen that the properties of the studied system depend not only on the volume of the simulation cell but also on its shape. For such cases it is desirable to change the shape of…
We report the results of extensive Dynamic Monte Carlo simulations of systems of self-assembled Equilibrium Polymers without rings in good solvent. Confirming recent theoretical predictions, the mean-chain length is found to scale as $\Lav…
Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
We consider the growth of a polymer layer on a flat surface in a good solvent by in-situ polymerization. This is viewed as a modified form of diffusion-limited aggregation without branching. We predict theoretically the formation of a…
Sampling equilibrium ensembles of dense polymer mixtures is a paradigmatically hard problem in computational physics, even in lattice-based models. Here, we develop a formalism based on interacting binary tensors that allows for tackling…
A computational framework that leverages data from self-consistent field theory simulations with deep learning to accelerate the exploration of parameter space for block copolymers is presented. This is a substantial two-dimensional…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
We analyze, via Imry-Ma scaling arguments, the strong disorder phases that exist in low dimensions at all temperatures for directed polymers and interfaces in random media. For the uncorrelated Gaussian disorder, we obtain that the optimal…
Nano-scale confinement of polymer in cone-shaped geometries occurs in many experimental situations. A flexible polymer confined in a cone-shaped nano-channel is studied theoretically and using molecular dynamics simulations. Distribution of…
The basic idea of fast Monte Carlo (MC) simulations is to perform particle-based MC simulations with the excluded-volume interactions modeled by "soft" repulsive potentials that allow particle overlapping. This gives much faster system…
We use an off - lattice bead - spring model of a self - avoiding polymer chain immersed in a 3-dimensional quenched random medium to study chain dynamics by means of a Monte - Carlo (MC) simulation. The chain center of mass mean-squared…
Computer simulations are used to characterize the entropic force of one or more polymers tethered to the tip of a hard conical object that interact with a nearby hard flat surface. Pruned-enriched-Rosenbluth-method (PERM) Monte Carlo…
We model the behaviour of a single colloid embedded in a cross-linked polymer gel, immersed in a viscous background fluid. External fields actuate the particle into a periodic motion, which deforms the embedding matrix and creates a local…
We present an exactly solvable model of a Gaussian (flexible) polymer chain in a quenched random medium. This is the case when the random medium obeys very long range quadratic correlations. The model is solved in $d$ spatial dimensions…
Monte Carlo simulations of proteins are hindered by the system's high density which often makes local moves ineffective. Here we devise and test a set of long range moves that work well even when all sites of a lattice simulation are…
Widely used closed product-form networks have emerged recently as a primary model of stochastic growth of sub-cellular structures, e.g., cellular filaments. In the baseline model, homogeneous monomers attach and detach stochastically to…
Recent experiments have imposed controlled swelling patterns on thin polymer films, which subsequently buckle into three-dimensional shapes. We develop a solution to the design problem suggested by such systems, namely, if and how one can…
We study surface effects in amorphous polymer systems by means of computer simulation. In the framework of molecular dynamics, we present two different methods to prepare such surfaces. {\em Free} surfaces are stabilized solely by…
We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system…