Related papers: Numerical methods for unraveling inter-particle po…
The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The…
Probabilistic inversion methods based on Markov chain Monte Carlo (MCMC) simulation are well suited to quantify parameter and model uncertainty of nonlinear inverse problems. Yet, application of such methods to CPU-intensive forward models…
Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning…
The so-called 'raspberry' model refers to the hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of colloidal particles, originally developed by [V. Lobaskin and B. D\"unweg, New J.…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
This paper presents a two-phase method for learning interaction kernels of stochastic many-particle systems. After transforming stochastic trajectories of every particle into the particle density function by the kernel density estimation…
We present a progress report on our work on lattice Boltzmann methods for colloidal suspensions. We focus on the treatment of colloidal particles in binary solvents and on the inclusion of thermal noise. For a benchmark problem of colloids…
Compact analytical forms are derived for the interactions involving thin disks in two dimensions using an integration approach. These include interactions between a disk and a material point, between two disks, and between a disk and a…
In computational mechanics, multiple models are often present to describe a physical system. While Bayesian model selection is a helpful tool to compare these models using measurement data, it requires the computationally expensive…
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI calculations are computationally expensive and typically…
Suspensions with fiber-like particles in the low Reynolds number regime are modeled by two different approaches that both use a Lagrangian representation of individual particles. The first method is the well-established formulation based on…
The central approximation made in classical molecular dynamics simulation of materials is the interatomic potential used to calculate the forces on the atoms. Great effort and ingenuity is required to construct viable functional forms and…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the…
We study collective modes in a classical system of particles with repulsive inverse-power-law (IPL) interactions in the fluid phase, near the fluid-solid coexistence (IPL melts). The IPL exponent is varied from $n=10$ to $n=100$ to mimic…
The Gibbs-Boltzmann distribution offers a physically interpretable way to massively reduce the dimensionality of high dimensional probability distributions where the extensive variables are `features' and the intensive variables are…
In this paper, we study a one-dimensional boson system in a superlattice potential.This system is experimentally feasible by using ultracold atomic gases,and attracts much attention these days. It is expected that the system has a…
We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the…
This mini-review discusses the recent contribution of theoretical and computational physics as well as experimental efforts to the understanding of the behavior of colloidal particles in confined geometries and at liquid crystalline…
Probabilistic and set-based methods are two approaches for model invalidation, parameter and state estimation. Both classes of methods use different types of data, i.e. deterministic or probabilistic data, which allow different statements…