Related papers: MIST: A Simple and Efficient Molecular Dynamics Ab…
The Image Source Method (ISM) is one of the most employed techniques to calculate acoustic Room Impulse Responses (RIRs), however, its computational complexity grows fast with the reverberation time of the room and its computation time can…
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Recently DRAM-based PIMs (processing-in-memories) with unmodified cell arrays have demonstrated impressive performance for accelerating AI applications. However, due to the very restrictive hardware constraints, PIM remains an accelerator…
Simulation of reasonable timescales for any long physical process using molecular dynamics (MD) is a major challenge in computational physics. In this study, we have implemented an approach based on multi-fidelity physics informed neural…
Non-adiabatic molecular dynamics (NAMD) simulations have become an indispensable tool for investigating excited-state dynamics in solids. In this work, we propose a general framework, N$^2$AMD which employs an E(3)-equivariant deep neural…
The correctness of complex software depends on the correctness of both the source code and the compilers that generate corresponding binary code. Compilers must do more than preserve the semantics of a single source file: they must ensure…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
MFEM is an open-source, lightweight, flexible and scalable C++ library for modular finite element methods that features arbitrary high-order finite element meshes and spaces, support for a wide variety of discretization approaches and…
Recent efforts in open-source GPU research are opening new avenues in a domain that has long been tightly coupled with a few commercial vendors. Emerging open GPU architectures define SIMT functionality through their own ISAs, but executing…
Molecular dynamics simulations have emerged as a fundamental instrument for studying biomolecules. At the same time, it is desirable to perform simulations of a collection of particles under various conditions in which the molecules can…
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…
Atomistic simulations of heat transport in complex materials are costly and hard to converge. This has led to the development of several noise-reduction techniques applicable to equilibrium molecular-dynamics (MD) simulations. We analyze…
We propose Multiplier-less INTeger (MINT) quantization, a uniform quantization scheme that efficiently compresses weights and membrane potentials in spiking neural networks (SNNs). Unlike previous SNN quantization methods, MINT quantizes…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
The need to use a short time step is a key limit on the speed of molecular dynamics (MD) simulations. Simulations governed by classical potentials are often accelerated by using a multiple-time-step (MTS) integrator that evaluates certain…
Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant…
Machine-learned interatomic potentials can offer near first-principles accuracy but are computationally expensive, limiting their application to large-scale molecular dynamics simulations. Inspired by quantum mechanics/molecular mechanics…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…