Related papers: Efficient simulation of semiflexible polymers
Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a…
The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…
We study the theoretical complexity of simulated tempering for sampling from mixtures of log-concave components differing only by location shifts. The main result establishes the first polynomial-time guarantee for simulated tempering…
In the present work, crystallization in melts and poor-solvent solutions of semiflexible polymers with different concentration was studied by means of dissipative particle dynamics simulation technique. We use a coarse-grained polymer model…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
An elementary algorithm is used to simulate the industrial production of a fiber of a 3-dimensional nonwoven fabric. The algorithm simulates the fiber as a polyline where the direction of each segment is stochastically drawn based on a…
DNA minicircles are closed double-stranded DNA (dsDNA) fragments that have been demonstrated to be an important experimental tool to understand supercoiled, or stressed, DNA mechanics, such as nucleosome positioning and DNA-protein…
Using Langevin dynamics complemented by Wang-Landau Monte Carlo simulations, we study the phase behavior of single and multiple semiflexible polymer chains in solution under poor-solvent conditions. In the case of a single chain, we obtain…
The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics…
We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients…
Monte Carlo simulations have been performed to analyze the sub-diffusion dynamics of a tagged monomer in self-avoiding polymerized membranes in the flat phase. By decomposing the mean square displacement into the out-of-plane ($\parallel$)…
This work introduces a Bayesian methodology for fitting large discrete graphical models with spike-and-slab priors to encode sparsity. We consider a quasi-likelihood approach that enables node-wise parallel computation resulting in reduced…
Direct numerical simulations (DNS) are accurate but computationally expensive for predicting materials evolution across timescales, due to the complexity of the underlying evolution equations, the nature of multiscale spatio-temporal…
In this paper, we propose a Generalized Langevin Equation (GLE)-based model to describe the lateral diffusion of a protein in a lipid bilayer. The memory kernel is represented in terms of a viscous (instantaneous) and an elastic (non…
Given nonstationary data from molecular dynamics simulations, a Markovian Langevin model is constructed that aims to reproduce the time evolution of the underlying process. While at equilibrium the free energy landscape is sampled,…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
The linear viscoelastic response of flexible polymer solutions in the dilute and semidilute unentangled regimes is investigated using Brownian dynamics simulations. The relaxation modulus and dynamic moduli are computed over a wide range of…
We present a stable discontinuous Galerkin (DG) method with a perfectly matched layer (PML) for three and two space dimensional linear elastodynamics, in velocity-stress formulation, subject to well-posed linear boundary conditions. First,…
We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structures out of patchy particles, and investigate it with Brownian Dynamics (BD) simulations. Its first element is the use of specific patch-patch and…
The dynamic structure factor of semiflexible polymers in solution is derived from the wormlike chain model. Special attention is paid to the rigid constraint of an inextensible contour and to the hydrodynamic interactions. For the cases of…