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The function and lifetime of moving mechanical assemblies (MMAs) in space depend on the properties of lubricants. MMAs that experience high speeds or high cycles require liquid based lubricants due to their ability to reflow to the point of…
Accelerated coarse-graining (CG) algorithms for simulating heterogeneous chemical reactions on surface systems have recently gained much attention. In the present paper, we consider such an issue by investigating the oscillation behavior of…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
Computational fluid dynamics and aerodynamics, which complement more expensive empirical approaches, are critical for developing aerospace vehicles. During the past three decades, computational aerodynamics capability has improved…
Intracardiac flow patterns are shaped by the coupled motion of the cardiac chambers and heart valves and provide important information about cardiac function. However, clinical flow imaging remains limited by exam times, noise, resolution,…
This paper is concerned with the study of the embedding circulant matrix method to simulate stationary complex-valued Gaussian sequences. The method is, in particular, shown to be well-suited to generate circularly-symmetric stationary…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
With the continuous growth of processing power for scientific computing, first principles Born-Oppenheimer molecular dynamics (MD) simulations are becoming increasingly popular for the study of a wide range of problems in materials science,…
Machine-learned coarse-grained (MLCG) molecular dynamics is a promising option for modeling biomolecules. However, MLCG models currently require large amounts of data from reference atomistic molecular dynamics or substantial computation…
Molecular motors are in charge of almost every process in the life cycle of cells, such as protein synthesis, DNA replication, and cell locomotion, hence being of crucial importance for understanding the cellular dynamics. However, given…
Monte Carlo (MC) simulations of lattice models are a widely used way to compute thermodynamic properties of substitutional alloys. A limitation to their more widespread use is the difficulty of driving a MC simulation in order to obtain the…
We propose a defiltering method of turbulent flow fields for Lagrangian particle tracking using machine learning techniques. Numerical simulation of Lagrangian particle tracking is commonly used in various fields. In general, practical…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
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…
The parallel code NMAGIC is an implementation of a particle-based method to create made-to-measure models in agreement with observations of galaxies. It works by slowly correcting the particle weights of an evolving N-body system, until a…
Computational Fluid Dynamics (CFD) is a hugely important subject with applications in almost every engineering field, however, fluid simulations are extremely computationally and memory demanding. Towards this end, we present Lat-Net, a…
Background and Objective: Hemodynamic analysis of blood flow through arteries and veins is critical for diagnosing cardiovascular diseases, such as aneurysms and stenoses, and for investigating cardiovascular parameters, such as turbulence…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…