Related papers: Fully Integrated On-FPGA Molecular Dynamics Simula…
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…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
FPGAs are quickly becoming available in the cloud as a one more heterogeneous processing element complementing CPUs and GPUs. There are many reports in the literature showing the potential for FPGAs to accelerate a wide variety of…
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…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
The paper presents investigations on the implementation and performance of the finite element numerical integration algorithm for first order approximations and three processor architectures, popular in scientific computing, classical CPU,…
Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
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 report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP,…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
This paper proposes a special-purpose system to achieve high-accuracy and high-efficiency machine learning (ML) molecular dynamics (MD) calculations. The system consists of field programmable gate array (FPGA) and application specific…
Recent researches on robotics have shown significant improvement, spanning from algorithms, mechanics to hardware architectures. Robotics, including manipulators, legged robots, drones, and autonomous vehicles, are now widely applied in…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
The edge computing paradigm has emerged to handle cloud computing issues such as scalability, security and low response time among others. This new computing trend heavily relies on ubiquitous embedded systems on the edge. Performance and…
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…
In-memory computing technology is used extensively in artificial intelligence devices due to lower power consumption and fast calculation of matrix-based functions. The development of such a device and its integration in a system takes a…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…