Related papers: FOSS solution for Molecular Dynamics Simulation Au…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
With FPGAs now being deployed in the cloud and at the edge, there is a need for scalable design methods which can incorporate the heterogeneity present in the hardware and software components of FPGA systems. Moreover, these FPGA systems…
Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bottleneck lies not only in software…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified…
Search-based software testing (SBT) is an effective and efficient approach for testing automated driving systems (ADS). However, testing pipelines for ADS testing are particularly challenging as they involve integrating complex driving…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
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…
Various works have utilized deep learning to address the query optimization problem in database system. They either learn to construct plans from scratch in a bottom-up manner or steer the plan generation behavior of traditional optimizer…
We introduce MOS, a software application designed to facilitate the deployment, integration, management, and analysis of mathematical optimization models. MOS approaches mathematical optimization at a higher level of abstraction than…
XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
Combining machine learning (ML) with computational fluid dynamics (CFD) opens many possibilities for improving simulations of technical and natural systems. However, CFD+ML algorithms require exchange of data, synchronization, and…
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations provide a rigorous physical basis for studying these dynamics,…
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…
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…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…