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We propose a method to parameterize a coarse grained model for the hydrodynamic friction between nearly touching rough spheres in suspension flows. The frictional resistance due to surface roughness primarily alters the sliding and rolling…
Hydrodynamics calculations have been successfully used in studies of the bulk properties of the Quark-Gluon Plasma, particularly of elliptic flow and shear viscosity. However, there are areas (for instance event-by-event simulations for…
The abundance of data has given machine learning considerable momentum in natural sciences and engineering, though modeling of physical processes is often difficult. A particularly tough problem is the efficient representation of geometric…
Solving large complex partial differential equations (PDEs), such as those that arise in computational fluid dynamics (CFD), is a computationally expensive process. This has motivated the use of deep learning approaches to approximate the…
The last few years have witnessed an explosion of new numerical methods for filament hydrodynamics. Aside from their ubiquity in biology, physics, and engineering, filaments present unique challenges from an applied-mathematical point of…
We propose numerical simulations of viscoelastic fluids based on a hybrid algorithm combining Lattice-Boltzmann models (LBM) and Finite Differences (FD) schemes, the former used to model the macroscopic hydrodynamic equations, and the…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…
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…
We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA. The two parameters of the model, $T^*$ and $\nu$, are chosen to match its experimental force-extension…
Molecular dynamics simulations of a short-chain polymer melt between two brush-covered surfaces under shear have been performed. The end-grafted polymers which constitute the brush have the same chemical properties as the free chains in the…
We consider the depth-integrated non-hydrostatic system derived by Yamazaki et al. An efficient formally second-order well-balanced hybrid finite volume finite difference numerical scheme is proposed. The scheme consists of a two-step…
This study presents a GPU-accelerated, fully coupled fluid-solid-thermal Smoothed Particle Hydrodynamics (SPH) framework for high-fidelity analysis of splash-lubricated gearboxes. A series of thermo-fluid simulations of a bevel-helical gear…
A new parallel algorithm utilizing partitioned global address space (PGAS) programming model to achieve high scalability is reported for particle tracking in direct numerical simulations of turbulent flow. The work is motivated by the…
We study the dynamics of inertial active particles in a one-dimensional chain with harmonic nearest-neighbor interactions, highlighting the interplay of persistence, interaction, and inertial timescales. Using a Green's function approach,…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD)…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
In this paper we present a methodology for data accesses when solving batches of Tridiagonal and Pentadiagonal matrices that all share the same left-hand-side (LHS) matrix. The intended application is to the numerical solution of Partial…
We describe numerical simulations and analyses of a quasi-one-dimensional (Q1D) model of glassy dynamics. In this model, hard rods undergo Brownian dynamics through a series of narrow channels connected by $J$ intersections. We do not allow…
We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber…