Related papers: tinyMD: A Portable and Scalable Implementation for…
We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…
It is shown in this work how the Wang-Landau algorithm can be parallelized through the concept of the micromagnetic ensemble, when the Hamiltonian contains both spin interaction and the external field terms, and thus energy-magnetization…
Tiny Machine Learning (TinyML) systems, which enable machine learning inference on highly resource-constrained devices, are transforming edge computing but encounter unique security challenges. These devices, restricted by RAM and CPU…
Deployment of solutions based on TinyML requires meeting several challenges. These include hardware heterogeneity, microprocessor (MCU) architectures, and resource availability constraints. Another challenge is the variety of operating…
We present GSPMD, an automatic, compiler-based parallelization system for common machine learning computations. It allows users to write programs in the same way as for a single device, then give hints through a few annotations on how to…
Design of robots at the small scale is a trial-and-error based process, which is costly and time-consuming. There are few dynamic simulation tools available to accurately predict the motion or performance of untethered microrobots as they…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
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…
High-density microfluidics is becoming an important experimental platform for studying complex biological systems such as synthetic gene regulatory networks, molecular biocomputating of engineered cells, distributing rapid point-of-care…
We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified interface. Our framework is intrinsically parallel, and conveniently separates all component numerical modules in…
Effective mixing is essential for biochemical reactions. In droplet-based microfluidics, immediate mixing of substances upon contact in the droplet formation stage can greatly enhance the uniformity of chemical reactions. Furthermore, it…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Cross-reactions and other systematic issues generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key…
We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields.…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…
Currently, the potential of microsimulation in space time trellis code has not been thoroughly ascertained. Therefore, this letter explores the possibility of using microsimulation in performing a pairwise comparison between competing…
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…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…