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Machine learning force fields have emerged as promising tools for molecular dynamics (MD) simulations, potentially offering quantum-mechanical accuracy with the efficiency of classical MD. Inspired by foundational large language models,…
The goal of the present article is to review the major developments that have led to the current understanding of molecule-field interactions and experimental methods for manipulating molecules with electromagnetic fields. Molecule-field…
We have studied the dependence of metal oxide properties in molecular dynamics (MD) simulations on the polarizability of oxygen ions. We present studies of both liquid and crystalline structures of silica (SiO2), magnesia (MgO) and alumina…
An accurate force field is the key to the success of all molecular mechanics simulations on organic polymers and biomolecules. Accuracy beyond density functional theory is often needed to describe the intermolecular interactions, while most…
Assuming the charged particle to be a two-dimensional oscillator that scatters the classical background of zero-point field one can deduce the Coulomb force of the two interacting particles. The correct deduction of the force is conditioned…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
A simple formula is obtained for coupling electrons in a complex system to the electromagnetic field. It includes the effect of intra-atomic excitations and nuclear motion, and can be applied in. e.g., first-principles-based simulations of…
The possibility to construct and parametrize the nonbonded interactions in atomistic force fields based on the valence electron structure of molecules is explored in this paper. Three different charge distribution models using simple…
We report a computational strategy to obtain the charges of individual dielectric particles from experimental observation of their interactions as a function of time. This strategy uses evolutionary optimization to minimize the difference…
In this brief contribution to the Proceedings of the NATO-ASI on ``Electrostatic Effects in Soft Matter and Biophysics'', which took place in Les Houches from Oct. 1-13, 2000, we summarize in short aspects of the simulations methods to…
The interaction of partially ionized plasmas with an electromagnetic field is investigated using quantum statistical methods. A general statistical expression for the current density of a plasma in an electromagnetic field is presented and…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
Electrodynamics is usually written with a polarization vector field to describe the response of matter to electric fields, or more specifically, to describe changes in distribution of charge as an electric field is changed. This approach…
The correct description of the ionic interaction and stable equilibrium of the simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model of the monovalent ions is very important. The force field…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Line-by-line calculations are becoming the standard procedure for carrying spectral simulations. However, it is important to insure the accuracy of such spectral simulations through the choice of adapted models for the simulation of key…
The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, has revolutionized the fields of computational chemistry and materials discovery. In this domain, rigorous…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…