Related papers: On the hierarchical parallelization of ab initio s…
We compare the longitudinal deposition of various conserved quantities in the initial condition models of a string based (SMASH) and a saturation based (McDipper) approach. SMASH has been shown to work reasonably well at lower collision…
Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
A computational fluid dynamics code is differentiated using algorithmic differentiation (AD) in both tangent and adjoint modes. The two novelties of the present approach are 1) the adjoint code is obtained by letting the AD tool Tapenade…
Heliospheric plasmas require multi-scale and multi-physics considerations. On one hand, MHD codes are widely used for global simulations of the solar-terrestrial environments, but do not provide the most elaborate physical description of…
Pipeline parallelism enables efficient training of Large Language Models (LLMs) on large-scale distributed accelerator clusters. Yet, pipeline bubbles during startup and tear-down reduce the utilization of accelerators. Although efficient…
Using the Gaussian-03 for ab initio calculations, interactions of various acid molecules with a single water molecule were studied. The molecular and supermolecular optimized structures were found with the Becke-3-Lee-Yang-Parr…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
The smoothed particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations with detailed physics…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
A parallel code has been written in FORTRAN90, C, and MPI for the analysis of biological simulation data. Using a master/slave algorithm, the software operates on AMBER generated trajectory data using either UNIX or MPI file IO, and it…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
Full Multiple Spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical…
We derive a new parallel-in-time approach for solving large-scale optimization problems constrained by time-dependent partial differential equations arising from fluid dynamics. The solver involves the use of a block circulant approximation…
An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD) [J. Chem.…
Computational Fluid Dynamics (CFD) simulations are often constrained by the memory-bound nature of sparse matrix-vector operations, which eventually limits performance on modern high-performance computing (HPC) systems. This work introduces…
The simulation of chemical reactions is an anticipated application of quantum computers. Using a Diels-Alder reaction as a test case, in this study we explore the potential applications of quantum algorithms and hardware in investigating…
Finite temperature calculations, based on ab initio molecular dynamics (AIMD) simulations, are a powerful tool able to predict material properties that cannot be deduced from ground state calculations. However, the high computational cost…
BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…