Related papers: Exploring molecular dynamics with forces from n-bo…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
We introduce a method of exploring potential energy contours in complex dynamical systems based on potentiostatic kinematics wherein the systems are evolved with minimal changes to their potential energy. We construct a simple iterative…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…
Nonperturbative lattice methods are applied to the investigation of strong, electroweak, and gravitational interactions. Selected models of new physics (expected at the TeV scale) are discussed.
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
Recent experimental results in three-body systems have unambiguously shown that calculations based on nucleon-nucleon forces fail to accurately describe many experimental observables and one needs to include effects which are beyond the…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
This study introduces a novel approach for deriving the governing equations of the musculoskeletal system in the human body. The proposed formalism offers a framework to effectively incorporate the kinematic characteristics of biological…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Models on logarithmic lattices have recently been proposed as an alternative approach to the study of multi-scale nonlinear physics. Here, we introduce LogLatt, an efficient MATLAB library for the calculus between functions on…
Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…
We present a simple, experimentally realizable method to make coherent three-body interactions dominate the physics of an ultracold lattice gas. Our scheme employs either lattice modulation or laser-induced tunneling to reduce or turn off…
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…
We propose a new model suitable for a nonequilibrium molecular dynamics (MD) simulation of electrical conductors. The model consists of classical electrons and atoms. The atoms compose a lattice vibration system. The electrons are scattered…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
New technologies, such as MOOCs, provide innovative methods to tackle new challenges in teaching and learning, such as globalization and changing contemporary culture and to remove the limits of conventional classrooms. However, they also…