Related papers: ACEMD: Accelerating bio-molecular dynamics in the …
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
With high computation power and memory bandwidth, graphics processing units (GPUs) lend themselves to accelerate data-intensive analytics, especially when such applications fit the single instruction multiple data (SIMD) model. However,…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
A class of analog computers built from large numbers of microscopic probabilistic machines is discussed. It is postulated that such computers are implemented in biological systems as ensembles of protein molecules. The formalism is based on…
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the…
The design of microfluidic devices is a cumbersome and tedious process that can be significantly improved by simulation. Methods based on Computational Fluid Dynamics (CFD) are considered state-of-the-art, but require extensive compute time…
Integrating population genetics into community ecology theory is a major goal in ecology and evolution, but analyzing the resulting models is computationally daunting. Here we describe sPEGG ($\underline{\textrm{s}}\textrm{imulating}$…
The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…
Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…
Molecular dynamics (MD) simulations provide considerable benefits for the investigation and experimentation of systems at atomic level. Their usage is widespread into several research fields, but their system size and timescale are also…
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
The numerical simulation of cardiac electrophysiology is a highly challenging problem in scientific computing. The Bidomain system is the most complete mathematical model of cardiac bioelectrical activity. It consists of an elliptic and a…
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…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
Molecular dynamics (MD) simulations play an important role in understanding and engineering heat transport properties of complex materials. An essential requirement for reliably predicting heat transport properties is the use of accurate…
Edge computing is a popular target for accelerating machine learning algorithms supporting mobile devices without requiring the communication latencies to handle them in the cloud. Edge deployments of machine learning primarily consider…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Modern multi GPU HPC systems expose substantial computational capacity, yet inefficient GPU allocation often leads to wasted energy and underutilization. In practice, GPU applications exhibit heterogeneous and nonlinear scaling, making it…