Related papers: Assessing numerical methods for molecular and part…
Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
We propose in this paper a Proper Generalized Decomposition (PGD) approach for the solution of problems in linear elastodynamics. The novelty of the work lies in the development of weak formulations of the PGD problems based on the…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
Despite their ubiquity throughout science and engineering, only a handful of partial differential equations (PDEs) have analytical, or closed-form solutions. This motivates a vast amount of classical work on numerical simulation of PDEs and…
In the last decade, the perfectly matched layer (PML) approach has proved a flexible and accurate method for the simulation of waves in unbounded media. Most PML formulations, however, usually require wave equations stated in their standard…
Stochastic gradient Langevin dynamics and its variants approximate the likelihood of an entire dataset, via random (and typically much smaller) subsets, in the setting of Bayesian sampling. Due to the (often substantial) improvement of the…
Recently it has been questioned, notably in the context of the scalar singlet dark matter model with $m_\varphi^{ }\simeq 60$ GeV, how efficiently kinetic equilibrium is maintained if freeze-out dynamics is pushed down to low temperatures…
Flexible elastic structures, such as beams, rods, ribbons, plates, and shells, exhibit complex nonlinear dynamical behaviors that are central to a wide range of engineering and scientific applications, including soft robotics, deployable…
Electronic friction and Langevin dynamics is a popular mixed quantum-classical method for simulating the nonadiabatic dynamics of molecules interacting with metal surfaces, as it can be computationally more efficient than fully quantum…
We present a novel convex formulation that weakly couples the Material Point Method (MPM) with rigid body dynamics through frictional contact, optimized for efficient GPU parallelization. Our approach features an asynchronous time-splitting…
Taking advantage of the flexibility of the variational method with coordinate transformations, we derive a self-consistent set of equations of motion from a discretized Lagrangian to study kinetic plasmas using a Fourier decomposed…
We introduce a scheme for deriving an optimally-parametrised Langevin dynamics of few collective variables from data generated in molecular dynamics simulations. The drift and the position-dependent diffusion profiles governing the Langevin…
In this paper, a three-dimensional numerical solver is developed for suspensions of rigid and soft particles and droplets in viscoelastic and elastoviscoplastic (EVP) fluids. The presented algorithm is designed to allow for the first time…
We examine a variety of numerical methods that arise when considering dynamical systems in the context of physics-based simulations of deformable objects. Such problems arise in various applications, including animation, robotics, control…
There are two usual computational methods for linear (waves and instabilities) problem: eigenvalue (dispersion relation) solver and initial value solver. In fact, we can introduce an idea of the combination of them, i.e., we keep time…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
The dynamics of dissipative soft-sphere gases obeys Newton's equation of motion which are commonly solved numerically by (force-based) Molecular Dynamics schemes. With the assumption of instantaneous, pairwise collisions, the simulation can…