Related papers: Molecular simulation from modern statistics: Conti…
Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Atomistic simulations with methods such as molecular dynamics are extremely powerful tools to understand nanoscale dynamical behavior. The resulting trajectories, by the virtue of being embedded in a high-dimensional configuration space,…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
Molecular science is governed by the dynamics of electrons, atomic nuclei, and their interaction with electromagnetic fields. A reliable physicochemical understanding of these processes is crucial for the design and synthesis of chemicals…
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…
Soliton models are used in elementary particle physics and nuclear physics to model extended objects such as nucleons, using effective field theories derived from more fundamental theories such as QCD. Computer simulation requires some sort…
We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
Continuous-time stochastic processes pervade everyday experience, and the simulation of models of these processes is of great utility. Classical models of systems operating in continuous-time must typically track an unbounded amount of…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…
As the most important solvent, water has been at the center of interest since the advent of computer simulations. While early molecular dynamics and Monte Carlo simulations had to make use of simple model potentials to describe the atomic…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Our computers today, from sophisticated servers to small smartphones, operate based on the same computing model, which requires running a sequence of discrete instructions, specified as an algorithm. This sequential computing paradigm has…
Over the past decades, atomistic simulations of chemical, biological and materials systems have become increasingly precise and predictive thanks to the development of accurate and efficient techniques that describe the quantum mechanical…
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…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…