Related papers: A fast Monte Carlo algorithm for studying bottle-b…
We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we…
In this paper we present a Path Integral Monte Carlo (PIMC) simulation of the orthorhombic phase of crystalline polyethylene, using an explicit atom force field with unconstrained bond lengths and angles. This work represents a quantum…
We analyze correlations in step-edge fluctuations using the Bortz-Kalos-Lebowitz kinetic Monte Carlo algorithm, with a 2-parameter expression for energy barriers, and compare with our VT-STM line-scan experiments on spiral steps on Pb(111).…
Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…
Polydisperse brushes obtained by reversible radical chain polymerization reaction onto a solid substrate with surface-attached initiators, are studied by means of an off-lattice Monte Carlo algorithm of living polymers (LP). Various…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
The pivot algorithm is the most efficient known method for sampling polymer configurations for self-avoiding walks and related models. Here we introduce two recent improvements to an efficient binary tree implementation of the pivot…
We present a Monte Carlo algorithm that provides efficient and unbiased sampling of polymer melts consisting of two chains of equal length that jointly visit all the sites of a cubic lattice with rod geometry L x L x rL and non-periodic…
This paper presents an extended coarse-grained investigation of the elastic properties of polystyrene. In particular, we employ the well-known MARTINI force field and its modifications to perform extended molecular dynamics simulations at…
Global optimization is an active area of research in atomistic simulations, and many algorithms have been proposed to date. A prominent example is basin hopping Monte Carlo, which performs a modified Metropolis Monte Carlo search to explore…
We present a numerical solution of the Worm-Like Chain (WLC) model for semi-flexible polymers. We display graphs for the end-to-end distance distribution and the force-extension relation expected from the model. We predict the expected…
In molecular simulations, efficient methods for investigating equilibration and slow relaxation in dense systems are crucial yet challenging. This study focuses on the diffusional characteristics of monodisperse hard disk systems at…
When fluids are confined in nanopores, many of their properties deviate from bulk. These include bulk modulus, or compressibility, which determines the mechanical properties of fluid-saturated porous solids. Such properties are of…
Despite their exceptional flexibility and popularity, the Monte Carlo methods often suffer from slow mixing times for challenging statistical physics problems. We present a general strategy to overcome this difficulty by adopting ideas and…
This review gives an overview on the research of algorithms for dynamical fermions used in large scale lattice QCD simulations. First a short overview on the state-of-the-art of ensemble generation at the physical point is given. Followed…
We present a method which extends Monte Carlo studies to situations that require a large dynamic range in particle number. The underlying idea is that, in order to calculate the collisional evolution of a system, some particle interactions…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
In this paper, we extend our analysis of lattice systems using the wavelet transform to systems for which exact enumeration is impractical. For such systems, we illustrate a wavelet-accelerated Monte Carlo (WAMC) algorithm, which…
Strong and weak simulation relations have been proposed for Markov chains, while strong simulation and strong probabilistic simulation relations have been proposed for probabilistic automata. However, decision algorithms for strong and weak…