Related papers: Long Range Moves for High Density Polymer Simulati…
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…
We show how the thermodynamic properties of large many-body localized systems can be studied using quantum Monte Carlo simulations. To this end we devise a heuristic way of constructing local integrals of motion of very high quality, which…
We consider dynamically constrained Monte-Carlo dynamics and show that this leads to the generation of long ranged effective interactions. This allows us to construct a local algorithm for the simulation of charged systems without ever…
A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte…
Markov chain Monte Carlo (MCMC) sampling of densities restricted to linearly constrained domains is an important task arising in Bayesian treatment of inverse problems in the natural sciences. While efficient algorithms for uniform polytope…
We study the diffusion process through an ideal polymer network, using numerical methods. Polymers are modeled by random walks on the bonds of a two-dimensional square lattice. Molecules occupy the lattice cells and may jump to the…
The osmotic equation of state for the athermal bond fluctuation model on the simple cubic lattice is obtained from extensive Monte Carlo simulations. For short macromolecules (chain length N=20) we study the influence of various choices for…
Long chains of the HP lattice protein model are studied by the Multi-Self-Overlap Ensemble(MSOE) Monte Carlo method, which was developed recently by the authors. MSOE successfully finds the lowest energy states reported before for sequences…
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…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
In this work we illustrate our novel quantitative simulation approach for dense amorphous polymer systems, as discussed in our previous work[Kulkarni et al., A Novel Approach for Lattice Simulations of Polymer Chains in Dense Amorphous…
We recently demonstrated that standard fixed-time lattice random-walk models cannot be modified to properly represent biased diffusion processes in more than two dimensions. The origin of this fundamental limitation appears to be the fact…
A path integral ground state approach has been used to estimate the ground-state energy and structural properties of hydrogen fluoride molecules pinned to a one-dimensional lattice. In the simulations, the molecules are assumed to be rigid,…
The extended Hubbard model on a two-dimensional lattice captures key physical phenomena, but is challenging to simulate due to the presence of long-range interactions. In this work, we present an efficient quantum algorithm for simulating…
We study random heteropolymer chain with gaussian distribution of kinds of monomers. The long-range correlations between kinds of monomers were introduce. The mean-field analysis of such heteropolymer indicates the existence of infinite…
We present in detail two variants of the lattice Monte Carlo method aimed at tackling systems in external trapping potentials: a uniform-lattice approach with hard-wall boundary conditions, and a non-uniform Gauss-Hermite lattice approach.…
We investigated the spinning process of a polymeric material by using a multiscale simulation method which connects the macroscopic and microscopic states through the stress and strain-rate tensor fields, by using Lagrangian particles…
An overview is given over the recently developed and now widely used Monte Carlo algorithms with reduced or eliminated critical slowing down. The basic techniques are overrelaxation, cluster algorithms and multigrid methods. With these…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
We perform equilibrium computer simulations of a two-dimensional pinned flexible polymer exposed to a quenched disorder potential consisting of hard disks. We are especially interested in the high-density regime of the disorder, where…