相关论文: Streaming Molecular Dynamics Simulation Data for O…

This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…

Some of the most relevant document schemas used online, such as XML and JSON, have a nested format. In the last decade, the task of extracting data from nested documents over streams has become especially relevant. We focus on the streaming…

Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…

Devices and sensors generate streams of data across a diversity of locations and protocols. That data usually reaches a central platform that is used to store and process the streams. Processing can be done in real time, with…

Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…

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…

Predictive modeling of the phonon/thermal transport properties of materials is vital to rational design for a diverse spectrum of engineering applications. Classical Molecular Dynamics (MD) simulations serve as a tool to simulate the time…

Exa-scale simulations are on the horizon but almost no new design for the output has been proposed in recent years. In simulations using individual time steps, the traditional snapshots are over resolving particles/cells with large time…

Constructing photo-realistic Free-Viewpoint Videos (FVVs) of dynamic scenes from multi-view videos remains a challenging endeavor. Despite the remarkable advancements achieved by current neural rendering techniques, these methods generally…

Cosmological $N$-body simulations play a vital role in studying models for the evolution of the Universe. To compare to observations and make a scientific inference, statistic analysis on large simulation datasets, e.g., finding halos,…

Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…

Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…

High-dimensional data are often assumed to lie on lower-dimensional manifolds. We study how to construct diffusion processes on this data manifold using only point cloud samples and without access to charts, projections, or other geometric…

In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane, and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute…

RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…

Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…

Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…

In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD).…

3D multi-object tracking and trajectory prediction are two crucial modules in autonomous driving systems. Generally, the two tasks are handled separately in traditional paradigms and a few methods have started to explore modeling these two…

Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…