Related papers: Lattice model for self-folding at the microscale
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We investigate polymers pulled away from an interacting surface, where the force is applied to the untethered endpoint and at an angle $\theta$ to the surface. We use the canonical self-avoiding walk model of polymers and obtain the phase…
We consider a lattice model in which a tracer particle moves in the presence of randomly distributed immobile obstacles. The crowding effect due to the obstacles interplays with the quasi-confinement imposed by wrapping the lattice onto a…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native…
We determine the phase-diagram of a one-dimensional system of hard-core lattice bosons interacting via repulsive three-body interactions by analytic methods and extensive quantum Monte-Carlo simulations. Such three-body interactions can be…
A lattice-Boltzmann model for the study of the dynamics of oil-water-surfactant mixtures is constructed. The model, which is based on a Ginzburg-Landau theory of amphiphilic systems with a single, scalar order parameter, is then used to…
We investigate the behavior of colloidal suspensions with different volume fractions confined between parallel walls under a range of steady shears. We model the particles using molecular dynamics (MD) with full hydrodynamic interactions…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
Consider the macroscale modelling of microscale spatiotemporal dynamics. Here we develop a new approach to ensure coarse scale discrete models preserve important self-adjoint properties of the fine scale dynamics. The first part explores…
We consider a lattice model for amphiphiles in a solvent with molecules chemically similar to one part of the amphiphilic molecule. The dependence of the interaction potential on orientation of the amphiphilic molecules is taken into…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
We suggest a new mean field method for studying the thermodynamic competition between magnetic and superconducting phases in a two-dimensional square lattice. A partition function is constructed by writing microscopic interactions that…
We study the transverse cracking of the 90 degree ply in [0/90] cross-ply laminates by means of a discrete element method. To model the 90 degree ply a two-dimensional triangular lattice of springs is constructed where nodes of the lattice…
The understanding of thermodynamic glass transition has been hindered by the lack of proper models beyond mean-field theories. Here, we propose a three-dimensional lattice glass model on a simple cubic lattice that exhibits the typical…
Self-aggregation of tropical convection is a universal feature observed in a diverse range of atmospheric environments. Several preceding models conceptualized the self-aggregation of convection as a phase transition driven by collisions…
We consider self-avoiding lattice polygons, in the hypercubic lattice, as a model of a ring polymer adsorbed at a surface and either being desorbed by the action of a force, or pushed towards the surface. We show that, when there is no…
The goal of these lecture notes is to present in a unified way various models for the dynamics of aligning self-propelled rigid bodies at different scales and the links between them. The models and methods are inspired from [12,13], but, in…
We investigate the structural and thermodynamic properties of a model of particles with $2$ patches of type $A$ and $10$ patches of type $B$. Particles are placed on the sites of a face centered cubic lattice with the patches oriented along…