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Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Despite the fact that computational fluid dynamics (CFD) software is now (relatively) fast and freely available, it is still amazingly difficult to use. Inaccessible software imposes a significant entry barrier on students and junior…
The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an…
We develop a general hydrodynamic theory describing a system of interacting actively propelling particles of arbitrary shape suspended in a viscous fluid. We model the active part of the particle motion using a slip velocity prescribed on…
The immersed boundary method (IB) is an elegant way to fully couple the motion of a fluid and deformations of an immersed elastic structure. In that vein, the IB2d software allows for expedited explorations of fluid-structure interaction…
In conventional fluid mechanics, the chemical composition and thermodynamic state of a fluid-solid interface are not considered when establishing velocity-field boundary conditions. As a consequence, fluid simulations are usually not able…
We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from…
Creating realistic droplet simulations and animations has long been a formidable challenge for researchers and developers due to the inherent complexity of fluid dynamics. Achieving lifelike droplet splash simulations while managing…
We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids $A$ and $B$ of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the…
One of the current challenges in physically-based simulations, and, more specifically, fluid simulations, is to produce visually appealing results at interactive rates, capable of being used in multiple forms of media. In recent times, a…
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows…
We describe the large-scale collective behavior of solutions of polar biofilaments and both stationary and mobile crosslinkers. Both mobile and stationary crosslinkers induce filament alignment promoting either polar or nematic order. In…
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…
Graphics research on Smoothed Particle Hydrodynamics (SPH) has produced fantastic visual results that are unique across the board of research communities concerned with SPH simulations. Generally, the SPH formalism serves as a spatial…
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…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
The smoothed particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations with detailed physics…
The Lattice Boltzmann Method (LBM) is a computational technique of Computational Fluid Dynamics (CFD) that has gained popularity due to its high parallelism and ability to handle complex geometries with minimal effort. Although LBM…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
Collective motion is often modeled within the framework of active fluids, where the constituent active particles, when interactions with other particles are switched off, perform normal diffusion at long times. However, in biology,…