Related papers: A Stochastic Finite Element Model for the Dynamics…
We consider systematic numerical approximation of a viscoelastic phase separation model that describes the demixing of a polymer solvent mixture. An unconditionally stable discretisation method is proposed based on a finite element…
We investigate by analytical means the stochastic equations of motion of a linear molecular motor model based on the concept of protein friction. Solving the coupled Langevin equations originally proposed by Mogilner et al. (A. Mogilner et…
Living soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set-point. This phenomenon is often referred to as mechanical homeostasis. In contradiction…
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…
Energy-Based Models (EBMs) have proven to be a highly effective approach for modelling densities on finite-dimensional spaces. Their ability to incorporate domain-specific choices and constraints into the structure of the model through…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
We propose a finite element method for simulating one-dimensional solid models moving and experiencing large deformations while immersed in generalized Newtonian fluids. The method is oriented towards applications involving microscopic…
We present a general formalism for the construction of thermodynamically consistent stochastic models of non-linear electronic circuits. The devices constituting the circuit can have arbitrary I-V curves and may include tunnel junctions,…
A stochastic treatment yielding to the derivation of a general Fokker-Planck equation is presented to model the slow convergence towards equilibrium of mean-field systems due to finite-N effects. The thermalization process involves notably…
Using a realistic flexible molecule model of the fragile glass former orthoterphenyl, we calculate via molecular dynamics simulation the collective dynamic structure factor, recently measured in this system by Inelastic X-ray Scattering.…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
This paper concerns with finite element approximations of a quasi-static poroelasticity model in displacement-pressure formulation which describes the dynamics of poro-elastic materials under an applied mechanical force on the boundary. To…
I formulate a general finite element method (FEM) for self-gravitating stellar systems. I split the configuration space to finite elements, and express the potential and density functions over each element in terms of their nodal values and…
We investigate the behavior of energy fluctuations in several models of granular gases maintained in a non-equilibrium steady state. In the case of a gas heated from a boundary, the inhomogeneities of the system play a predominant role.…
In conventional formulations of poroelasticity, when the porosity approaches zero or vanishes in some parts of the poroelastic domain, if only temporarily, the governing equations degenerate to those for the solid phase thereby inhibiting a…
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
Novel physical mechanism is proposed for explanation of temperature-independent transition reactions in molecular systems. The mechanism becomes effective in the case of conformation transitions between quasi-isoenergetic molecular states.…
A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…
We present a mesoscopic approach to granular crystal dynamics, which comprises a three-dimensional finite-element model and a one-dimensional regularized contact model. The approach investigates the role of vibrational-energy trapping…