Related papers: Exploring molecular dynamics with forces from n-bo…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
In this review chapter we focus on the many-body dynamics of cold polar molecules in the strongly interacting regime. In particular, we discuss a toolbox for engineering many-body Hamiltonians based on the manipulation of the electric…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
We investigate the coupling of different quantum-embedding approaches with a third molecular-mechanics layer, which can be either polarizable or non-polarizable. In particular, such a coupling is discussed for the multilevel families of…
Mixed-quantum classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
Force matching is an established technique to generate effective potentials for molecular dynamics simulations from first-principles data. This method has been implemented in the open source code potfit. Here, we present a review of the…
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…
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…
In this paper we propose an ab initio method to solve quantum many-body problems of molecular dynamics where both the electronic and the nuclear degrees are represented by ensembles of trajectories and guiding waves in physical space. Both…
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…
Analyzing the motion of multiple biological agents, be it cells or individual animals, is pivotal for the understanding of complex collective behaviors. With the advent of advanced microscopy, detailed images of complex tissue formations…
We present a new formulation for the mean-field propagation part of the relativistic quantum molecular dynamics, simulating an $N$-body system of interacting Gaussian wave packets via Lorentz scalar and vector potentials. Covariant…
Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting…
We present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple…
Polynomial dynamical systems describing interacting particles in the plane are studied. A method replacing integration of a polynomial multi--particle dynamical system by finding polynomial solutions of a partial differential equations is…
Machine learned interaction potentials (MLIPs) have become a critical component of large-scale, high-quality simulations for a range of chemical and biochemical systems. Yet, despite their in-distribution accuracy, molecular dynamics…
WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt with quantum…
We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order $O(N)$, where $N$ is the number of particles. The algorithm works very effectively when the…
The possibility of interaction between Maple and numeric compiled languages in performing extensive numeric calculations is exemplified by the Ndynamics package, a tool for studying the (chaotic) behavior of dynamical systems. Programming…