Related papers: Optimizing Replica Exchange Moves For Molecular Dy…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
Computational methods in drug repositioning can help to conserve resources. In particular, methods based on biological networks are showing promise. Considering only the network topology and knowledge on drug target genes is not sufficient…
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To address this, we have developed a novel method termed…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
Since its development, Stokesian Dynamics has been a leading approach for the dynamic simulation of suspensions of particles at arbitrary concentrations with full hydrodynamic interactions. Although originally developed for the simulation…
A reaction--diffusion replicator equation is studied. A novel method to apply the principle of global regulation is used to write down the model with explicit spatial structure. Properties of stationary solutions together with their…
We construct a generalized dynamics for particles moving in a symmetric space-time, i.e. a space-time admitting one or more Killing vectors. The generalization implies that the effective mass of particles becomes dynamical. We apply this…
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we…
Distributed optimization finds many applications in machine learning, signal processing, and control systems. In these real-world applications, the constraints of communication networks, particularly limited bandwidth, necessitate…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
This article proposes a new way to construct computationally efficient `wrappers' around fine scale, microscopic, detailed descriptions of dynamical systems, such as molecular dynamics, to make predictions at the macroscale `continuum'…
An improved real-time quantum Monte Carlo procedure is presented and applied to describe the electronic transfer dynamics along molecular chains. The model consists of discrete electronic sites coupled to a thermal environment which is…
We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
Generalized-ensemble algorithm and diffusion theory have been combined in order to compute the dynamical properties monitored by nuclear magnetic resonance experiments from efficient and reliable evaluation of statistical averages.…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…