Related papers: Variational approximation method for the long-rang…
Efficient modeling of dispersive materials via time-domain simulations of the Maxwell equations relies on the technique of auxiliary differential equations. In this approach, a material's frequency-dependent permittivity is represented via…
We present a simulation study of colloidal particles having very short range attractions. In particular, we investigate the interplay between the effective attractive range and the viscoelastic properties of the gels that form when the…
We study two free energy approximations (Bethe and plaquette-CVM) for the Random Field Ising Model in two dimensions. We compare results obtained by these two methods in single instances of the model on the square grid, showing the…
This paper proposes and analyzes a class of new weak Galerkin (WG) finite element methods for 2- and 3-dimensional linear elasticity problems. The methods use discontinuous piecewise-polynomial approximations of degrees $k(\geq 0)$ for the…
As an effective method to deliver external materials into biological cells, microinjection has been widely applied in the biomedical field. However, the cognition of cell mechanical property is still inadequate, which greatly limits the…
Mean Field Variational Bayes (MFVB) is a popular posterior approximation method due to its fast runtime on large-scale data sets. However, it is well known that a major failing of MFVB is its (sometimes severe) underestimates of the…
We present and discuss a variance-reduced stochastic particle method for simulating the relaxation-time model of the Boltzmann transport equation. The present paper focuses on the dilute gas case, although the method is expected to directly…
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
This study presents a novel, versatile traction force microscopy framework for quantifying three-dimensional (3D) interfacial forces during bio-adhesion by integrating in situ stereo digital image correlation with finite element (FE)…
An introductory exposition of the virtual element method (VEM) is provided. The intent is to make this method more accessible to those unfamiliar with VEM. Familiarity with the finite element method for solving 2D linear elasticity problems…
We present a simple and \emph{non-invasive} experimental procedure to measure the linear viscoelastic properties of cells by passive video particle tracking microrheology. In order to do this, a generalised Langevin equation is adopted to…
In this paper a new approach is proposed to quantize mechanical systems whose equations of motion can not be put into Hamiltonian form. This approach is based on a new type of variational principle, which is adopted to a describe a…
A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and…
In this paper, we study applications of the virtual element method (VEM) for simulating the deformation of multiphase composites. The VEM is a Galerkin approach that is applicable to meshes that consist of arbitrarily-shaped polygonal and…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
In this paper, we develop a high-order adaptive virtual element method (VEM) to simulate the self-consistent field theory (SCFT) model in arbitrary domains. The VEM is very flexible in handling general polygon elements and can treat hanging…
A first principle micromagnetic and statistical calculation of viscous remanent magnetization (VRM) in an ensemble of cubic magnetite pseudo single-domain particles is presented. This is achieved by developing a fast relaxation algorithm…
Employing molecular dynamics simulations of jammed soft particles, we study microscopic responses of force-chain networks to quasi-static isotropic (de)compressions. We show that not only contacts but also interparticle gaps between the…
We extend our analysis on the Oldroyd-B model in Barrett and Boyaval [1] to consider the finite element approximation of the FENE-P system of equations, which models a dilute polymeric fluid, in a bounded domain $D $\subset$ R d , d = 2 or…
We study a model for a fluid showing viscoelastic and viscoplastic behavior, which describes the flow in terms of the fluid velocity and an internal stress. This stress tensor is transported via the Zaremba--Jaumann rate, and it is subject…