Related papers: A fast Monte Carlo algorithm for studying bottle-b…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
While recent work towards the development of tight-binding and ab-initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte…
Through extensive molecular simulations we determine a phase diagram of attractive, flexible polymer chains in two and three dimensions. A surprisingly rich collection of distinct crystal morphologies appear, which can be finely tuned…
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
Two coarse-grained models for polymer chains in dense glass-forming polymer melts are studied by computer simulation: the bond-fluctuation model on a simple cubic lattice, where a bond-length potential favors long bonds, is treated by…
We present Monte Carlo simulations of lattice models of polymers. These simulations are intended to demonstrate the strengths of a powerful new flat histogram algorithm which is obtained by adding microcanonical reweighting techniques to…
In this paper we present a classical Monte Carlo simulation of the orthorhombic phase of crystalline polyethylene, using an explicit atom force field with unconstrained bond lengths and angles and periodic boundary conditions. We used a…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
In this paper, a new progressive mesh algorithm is introduced in order to perform fast physical simulations by the use of a lattice Boltzmann method (LBM) on a single-node multi-GPU architecture. This algorithm is able to mesh automatically…
Some recent work pointed out the usefulness of taking a large-deviation perspective when trying to extract anything resembling a macroscopic order parameter from a computer simulation. In this paper we note that the end-to-end distance of…
On the base of a Feynman-Kac--type formula involving Poisson stochastic processes, recently a Monte Carlo algorithm has been introduced, which describes exactly the real- or imaginary-time evolution of many-body lattice quantum systems. We…
The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…
The effect of self-generated tension in the backbone of a bottle-brush (BB) macromolecule, adsorbed on an attractive surface, is studied by means of Molecular Dynamics simulations of a coarse-grained bead-spring model in the good solvent…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
We propose a novel combinatorial algorithm for efficient generation of Hamiltonian walks and cycles on a cubic lattice, modeling the conformations of lattice toy proteins. Through extensive tests on small lattices (allowing complete…
Monte Carlo simulations are widely employed to measure the physical properties of glass-forming liquids in thermal equilibrium. Combined with local Monte Carlo moves, the Metropolis algorithm can also be used to simulate the relaxation…
The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…