Related papers: Huge-scale Molecular Dynamics Simulation of Multib…
We utilize the Open Accelerator (OpenACC) approach for graphics processing unit (GPU) accelerated particle-resolved thermal lattice Boltzmann (LB) simulation. We adopt the momentum-exchange method to calculate fluid-particle interactions to…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale…
Quantum-mechanically accurate reactive molecular dynamics (MD) at the scale of billions of atoms has been achieved for the heterogeneous catalytic system of H$_2$/Pt(111) using the FLARE Bayesian force field. This achievement provides…
In the quest for highest performance in scientific computing, we present a novel framework that relies on high-bandwidth communication between GPUs in a compute cluster. The framework offers linear scaling of performance for explicit…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
Molecular Dynamic (MD) approach is applied to study the converging cylindrical shock waves in a dense Lennard-Jones (LJ) fluid. MD method is based on tracking of the atom motions and hence it has an fundamental advantages over hydrodynamic…
RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…
Recent developments dedicated to the building of multiscale mechanical and chemical constitutive laws for energetic molecular crystals are presented and discussed. In particular, various tools have been specifically incorporated in…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics…
We use machine learning to enable large-scale molecular dynamics (MD) of a correlated electron model under the Gutzwiller approximation scheme. This model exhibits a Mott transition as a function of on-site Coulomb repulsion $U$. The…
The non-orthogonal local submatrix method applied to electronic-structure based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32 mixed floating-point arithmetic when using 4,400 NVIDIA A100 GPUs of the Perlmutter…
By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semi-local density functional theory (DFT), and thereby furnish a more accurate and reliable description of the electronic structure in…
A 3D Cellular Automaton model developed by the authors to deal with the dynamics of N-body interactions has been adapted to investigate the head-on collision of two identical bound clusters of particles, and the ensuing process of…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…