Related papers: Exploring molecular dynamics with forces from n-bo…
Nonadiabatic molecular dynamics simulations aim to describe the coupled electron-nuclear dynamics of molecules in excited electronic states. These simulations have been applied to understand a plethora of photochemical and photophysical…
The evaluation of Coulomb forces is a difficult task. The summations that are involved converge only conditionally and care has to be taken in selecting the appropriate procedure to define the limits. The Ewald method is a standard method…
In the past decades, it has been shown that the three-body force is necessary for a fully microscopic understanding of nuclear many-body systems, and thus efficient schemes for storing and utilizing three-body matrix elements have been…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
We performed bound state calculations to obtain the first few vibrational states for the Ar_3 molecular system. The equations used are of Faddeev-type and are solved directly as three-dimensional equations in configuration space, i.e.…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
The description of quantum many-body dynamics is extremely challenging on classical computers, as it can involve many degrees of freedom. On the other hand, the time evolution of quantum states is a natural application for quantum computers…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
The study of molecular physics using ultracold gases has provided a unique probe into the fundamental properties of nature and offers new tools for quantum technologies. In this article we outline how the use of a space environment to study…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
In this paper, we present a novel general framework grounded in the factor graph theory to solve kinematic and dynamic problems for multi-body systems. Although the motion of multi-body systems is considered to be a well-studied problem and…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
In this paper, we present an efficient form of Volterra's equations of motion for both unconstrained and constrained multibody dynamical systems that include ignorable coordinates. The proposed method is applicable for systems with both…
The traditional nuclear shell model approach is extended to include many-body forces. The empirical Hamiltonian with a three-body force is constructed for the identical nucleons on the 0f7/2 shell. Manifestations of the three-body force in…
Differential equations are fundamental to modeling dynamic systems in physics, engineering, biology, and economics. While analytical solutions are ideal, most real-world problems necessitate numerical approaches. This study conducts a…
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
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…
We demonstrate that the multicanonical approach is not restricted to Monte Carlo simulations, but can also be applied to simulation techniques such as molecular dynamics, Langevin, and hybrid Monte Carlo algorithms. The effectiveness of the…