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Recent progress in the development of quantum technologies has enabled the direct investigation of dynamics of increasingly complex quantum many-body systems. This motivates the study of the complexity of classical algorithms for this…
We developed a semiclassical approximation method in combination with an adaptive moment estimation optimizer (SCA + ADAM) approach based on the PyTorch plus CUDA library on a the graphics processing unit (GPU). This method was employed to…
Lattice Boltzmann method models offer a novel framework for the simulation of high Reynolds number dilute gravity currents. The numerical algorithm is well suited to acceleration via implementation on massively parallel computer…
Within the nuclear-electronic orbital (NEO) framework, the real-time NEO time-dependent density functional theory (RT-NEO-TDDFT) approach enables the simulation of coupled electronic-nuclear dynamics. In this approach, the electrons and…
A controlled hybridization between full quantum dynamics and semiclassical approaches (mean-field and truncated Wigner) is implemented for interacting many-boson systems. It is then demonstrated how simulating the resulting hybrid evolution…
Path Integral Molecular Dynamics (PIMD) is a well established simulation technique to compute exact equilibrium properties for a quantum system using classical trajectories in an extended phase space. Standard PIMD simulations are…
In this article we propose and numerically implement a mathematical model for the simulation of three-dimensional semiconductor devices characterized by an heterogeneous material structure. The model consists of a system of nonlinearly…
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…
The use of ring polymer molecular dynamics (RPMD) for the direct simulation of electron transfer (ET) reaction dynamics is analyzed in the context of Marcus theory, semiclassical instanton theory, and exact quantum dynamics approaches. For…
This paper validates 3D simulation results of electron beam melting (EBM) processes comparing experimental and numerical data. The physical setup is presented which is discretized by a three dimensional (3D) thermal lattice Boltzmann method…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
An efficient numerical method is developed using the matrix product formalism for computing the properties at finite energy densities in one-dimensional (1D) many-body localized (MBL) systems. Arguing that any efficient (possibly quantum)…
The combined quantum electron-nuclear dynamics is often associated with the Born-Huang expansion of the molecular wave function and the appearance of nonadiabatic effects as a perturbation. On the other hand, native multicomponent…
We present a general framework for obtaining robust bounds on the nature of dark matter using cosmological $N$-body simulations and Lyman-alpha forest data. We construct an emulator of hydrodynamical simulations, which is a flexible,…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
The Spinsim python package simulates spin-half and spin-one quantum mechanical systems following a time dependent Shroedinger equation. It makes use of numba.cuda, which is an LLVM (Low Level Virtual Machine) compiler for Nvidia Cuda…
We introduce EChemDID, a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…