相关论文: Argon Simulations with EM3, a New Modular Molecula…

Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…

In this work, molecular mechanics simulations were performed using a modified embedded-atom method (MEAM) potential to generate the stress-strain responses of a series of n-alkane molecules from ethane (C$_2$H$_6$) to undecane…

Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D…

In high-energy physics, Monte Carlo event generators (MCEGs) are used to simulate the interactions of high energy particles. MCEG event records store the information on the simulated particles and their relationships, and thus reflects the…

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…

The molecular dynamics (MD) approach is an effective tool for investigating atomistic dynamical phenomena at the surface of materials under strong laser irradiation. Therefore, numerous laser ablation MD simulation studies have been…

Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded…

Monte Carlo (MC) simulations are powerful computational tools for investigating thermodynamic behavior and validating analytical approaches in complex physical systems. Here we present ETHER (Efficient Tool for THermodynamics Exploration…

Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…

We present a foundation model for exascale molecular dynamics simulations by leveraging an E(3) equivariant network architecture (Allegro) and a set of large-scale organic and inorganic materials datasets merged by Total Energy Alignment…

Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…

The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…

Molecular dynamics (MD) simulation, a computationally intensive method that provides invaluable insights into the behavior of biomolecules, typically requires large-scale parallelization. Implementation of fast parallel MD simulation…

This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…

A variety of optimization algorithms have been developed to solve engineering design problems in which the solution space is too large to manually determine the optimal solution. The Modular Optimization Framework (MOF) was developed to…

Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…

This paper introduces the Modular Neural Computer (MNC), a memory-augmented neural architecture for exact algorithmic computation on variable-length inputs. The model combines an external associative memory of scalar cells, explicit read…

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus…

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…