Related papers: Molecular dynamics simulations of complex shaped p…
The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
The second-order formula of Minkowski functionals in weakly non-Gaussian fields is compared with the numerical $N$-body simulations. Recently, weakly non-Gaussian formula of Minkowski functionals is extended to include the second-order…
Quantum computers hold promise to enable efficient simulations of the properties of molecules and materials; however, at present they only permit ab initio calculations of a few atoms, due to a limited number of qubits. In order to harness…
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,…
We provide a two dimensional deformation model to describe how soft squishy circular particles respond to external forces and collisions. This model involves formulating mathematical equations and algorithms for the shape of a deformed…
A system of reduced equations is proposed for the electron motion in the strongly-radiation dominated regime for an arbitrary electromagnetic field configuration. The developed approach is used to analyze various scenarios of an electron…
We propose a method for efficiently coupling the finite element method with atomistic simulations, while using molecular dynamics or kinetic Monte Carlo techniques. Our method can dynamically build an optimized unstructured mesh that…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
When the Standard Model is interpreted as the renormalizable sector of a low-energy effective theory, the effects of new physics are encoded into a set of higher dimensional operators. These operators potentially deform the shapes of…
For large scale electronic structure calculation, the Krylov subspace method is introduced to calculate the one-body density matrix instead of the eigenstates of given Hamiltonian. This method provides an efficient way to extract the…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
In this article, we propose a numerical method to solve semi-discrete optimal transport problems for gigantic pointsets (108 points and more). By pushing the limits by several orders of magnitude, it opens the path to new applications in…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…
We define morphological operators and filters for directional images whose pixel values are unit vectors. This requires an ordering relation for unit vectors which is obtained by using depth functions. They provide a centre-outward ordering…
This is our current research perspective on models providing insight into statistical mechanics. It is necessarily personal, emphasizing our own interest in simulation as it developed from the National Laboratories' work to the worldwide…
We introduce a variational hybrid classical-quantum algorithm to simulate the Lindblad master equation and its adjoint for time-evolving Markovian open quantum systems and quantum observables. Our method is based on a direct representation…