Related papers: Long Range Moves for High Density Polymer Simulati…
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…
We present approximate algorithms for performing smoothing in a class of high-dimensional state-space models via sequential Monte Carlo methods ("particle filters"). In high dimensions, a prohibitively large number of Monte Carlo samples…
A multiscale model for real-time simulation of terrain dynamics is explored. To represent the dynamics on different scales the model combines the description of soil as a continuous solid, as distinct particles and as rigid multibodies. The…
A number of problems arise when long-range forces, such as those governed by Bessel functions, are used in particle-particle simulations. If a simple cut-off for the interaction is used, the system may find an equilibrium configuration at…
We present a Monte Carlo method that efficiently computes the density of states for spin models having any number of interaction per spin. By combining a random-walk in the energy space with collective updates controlled by the…
Monte Carlo simulation has been performed in one-dimensional Lebwohl-Lasher model and two dimensional XY-model using the Wang-Landau and the Wang-Landau-Transition-Matrix Monte Carlo methods. Random walk has been performed in the…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium.…
Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…
In this paper we present a new Monte Carlo Search (MCS) algorithm for finding the ground state energy of proteins in the HP-model. We also compare it briefly to other MCS algorithms not usually used on the HP-model and provide an overview…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
We discuss in detail a recently proposed hybrid particle-continuum scheme for complex fluids and evaluate it at the example of a confined homopolymer solution in slit geometry. The hybrid scheme treats polymer chains near the impenetrable…
Legged robots have the potential to traverse highly constrained environments with agile maneuvers. However, planning such motions requires solving a highly challenging optimization problem with a mixture of continuous and discrete decision…
We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…
The persistence length of macromolecules is one of their basic characteristics, describing their intrinsic local stiffness. However, it is difficult to extract this length from physical properties of the polymers, different recipes may give…
The densities of states are evaluated for very short chain molecules made up of overlapping monomers, using a model which has previously been shown to produce helical structure. The results of numerical calculations are presented for…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
We report results of extensive Dynamical Monte Carlo investigations on self-assembled Equilibrium Polymers (EP) without loops in good solvent. (This is thought to provide a good model of giant surfactant micelles.) Using a novel algorithm…