Related papers: ACEMD: Accelerating bio-molecular dynamics in the …
A finite-difference Micromagnetic solver is presented utilizing the C++ Accelerated Massive Parallelism (C++ AMP). The high speed performance of a single Graphics Processing Unit (GPU) is demonstrated compared to a typical CPU-based solver.…
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.…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Molecular dynamics (MD) simulations remain the gold standard for studying protein dynamics, but their computational cost limits access to biologically relevant timescales. Recent generative models have shown promise in accelerating…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging…
One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…
Argon molecular dynamics (MD) simulations are performed with a newly developed MD program, Easy M(1)odular M(2)olecular M(3)echanics (EM3). The program was developed in an object-oriented fashion containing classes for each critical part of…
Magnetohydrodynamic (MHD) simulations based on the ideal MHD equations have become a powerful tool for modeling phenomena in a wide range of applications including laboratory, astrophysical, and space plasmas. In general, high-resolution…
Computational fluid dynamics (CFD) can be used to simulate vascular haemodynamics and analyse potential treatment options. CFD has shown to be beneficial in improving patient outcomes. However, the implementation of CFD for routine clinical…
Temporal Interaction Graphs (TIGs) are widely employed to model intricate real-world systems such as financial systems and social networks. To capture the dynamism and interdependencies of nodes, existing TIG embedding models need to…
Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…
We present eACGM, a full-stack AI/ML system monitoring framework based on eBPF. eACGM collects real-time performance data from key hardware components, including the GPU and network communication layer, as well as from key software stacks…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
We previously introduced a conformational sampling method, a multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD), to enhance conformational sampling of a biomolecular system by computer simulations. Here, we present a new…
The new Cell processor represents a turning point for computing intensive applications. Here, I show that for molecular dynamics it is possible to reach an impressive sustained performance in excess of 30 Gflops with a peak of 45 Gflops for…
In studying solidification process by simulations on the atomic scale, the modeling of crystal nucleation or amorphisation requires the construction of interatomic interactions that are able to reproduce the properties of both the solid and…
Graphics processing units (GPUs) excel at parallel processing, but remain largely unexplored in ultra-low-power edge devices (TinyAI) due to their power and area limitations, as well as the lack of suitable programming frameworks. To…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…