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Molecular dynamics (MD) is a powerful tool for exploring the behavior of atomistic systems, but its reliance on sequential numerical integration limits simulation efficiency. We present a novel neural network architecture, MDtrajNet, and a…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
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…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the…
The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a models' dynamics over a large parameter space…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…
Quantum molecular dynamics is applied to study the ground state properties of nuclear matter at subsaturation densities. Clustering effects are observed as to soften the equation of state at these densities. The structure of nuclear matter…
Consider briefly the equations of fluid dynamics-they describe the enormous wealth of detail in all the interacting physical elements of a fluid flow-whereas in applications we want to deal with a description of just that which is…
This work addresses the problem of predicting the motion trajectories of dynamic objects in the environment. Recent advances in predicting motion patterns often rely on machine learning techniques to extrapolate motion patterns from…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Molecular clouds are the principle stellar nurseries of our universe, keeping them in the focus of both observational and theoretical studies. From observations, some of the key properties of molecular clouds are well known but many…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
I review recent results from numerical simulations on the structure and dynamics of the ISM, and attempt to put together a coherent dynamical scenario. In particular, I discuss results on 1) the spatial distribution of the gas components,…
In this work, we analytically examine the validity of molecular dynamics for a soft potential system by considering a simple one-dimensional system with a piecewise continuous linear repulsive potential wall having a constant slope $a$. We…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
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…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…