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Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
This paper describes an interdisciplinary approach to geometry modeling of geospatial boundaries. The objective is to extract surfaces from irregular spatial patterns using differential geometry and obtain coherent directional predictions…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
The most difficult aspect of the realistic modeling of granular materials is how to capture the real shape of the particles. Here we present a method to simulate granular materials with complex-shaped particles. The particle shape is…
Differentiable physics is a powerful approach to learning and control problems that involve physical objects and environments. While notable progress has been made, the capabilities of differentiable physics solvers remain limited. We…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
Low density plasmas are characterized by a large scale separation between the gyromotion of particles around local magnetic fields and the macroscopic scales of the system, often making global kinetic simulations computationally…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
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…
We present a computational framework for simulating filaments interacting with rigid bodies through contact. Filaments are challenging to simulate due to their codimensionality, i.e., they are one-dimensional structures embedded in…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
We describe a new electrostatic Particle-In-Cell (PIC) code in curvilinear geometry called Curvilinear PIC (CPIC). The code models the microscopic (kinetic) evolution of a plasma with the PIC method, coupled with an adaptive computational…
A common feature of wall-bounded turbulent particle-laden flows is enhanced particle concentrations in a thin layer near the wall due to a phenomenon known as turbophoresis. Even at relatively low bulk volume fractions, particle-particle…
The global topology of the Universe can affect long-range gravitational forces via boundary conditions. Detailed studies of non-trivial topologies require simulations that natively adopt such geometries. Cosmological $N$-body simulations…
Cosmic structure simulations have improved enormously over the past decade, both in terms of the resolution which can be achieved, and with the addition of hydrodynamic and other techniques to formerly purely gravitational methods. This is…
Discrete Element Methods (DEM), i.e.~the simulation of many rigid particles, suffer from very stiff differential equations plus multiscale challenges in space and time. The particles move smoothly through space until they interact almost…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
We provide a two dimensional deformation model to describe how soft squishy circular particles respond to external forces and collisions. This model involves formulating mathematical equations and algorithms for the shape of a deformed…
We present a collision model for phase-resolved Direct Numerical Simulations of sediment transport that couple the fluid and particles by the Immersed Boundary Method. Typically, a contact model for these types of simulations comprises a…