Related papers: Lattice model for self-folding at the microscale
We present preliminary numerical results from a lattice study of the two-dimensional O(3) non-linear sigma model. In the continuum this model possesses N=2 supersymmetry. The lattice formulation we use retains an exact (twisted)…
We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders.
Curvature and mechanics are intimately connected for thin materials, and this coupling between geometry and physical properties is readily seen in folded structures from intestinal villi and pollen grains, to wrinkled membranes and…
The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion (SALR) potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk.…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
Motivated by the concept of geometrical frustration, we introduce a class of statistical mechanics lattice models for the glass transition. Monte Carlo simulations in three dimensions show that they display a dynamical glass transition…
We investigate theoretically the possibility to observe dynamical mode locking, in the form of Shapiro steps, when a time-periodic potential or force modulation is applied to a two-dimensional (2D) lattice of colloidal particles that are…
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
The result of 2-dimensional Gaussian lattice fit to a speckle intensity pattern based on a linear model that includes nearest-neighbor interactions is presented. We also include a Monte Carlo simulation of the same spatial speckle pattern…
We consider discrete dynamical systems and lattice models in statistical mechanics from the point of view of their symmetry groups. We describe a C program for symmetry analysis of discrete systems. Among other features, the program…
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…
There are three fundamental physical processes that gives rise to the morphology of a surface: deposition, surface diffusion and desorption. The characteristics of the interfaces generated by the combination of deposition and surface…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structures out of patchy particles, and investigate it with Brownian Dynamics (BD) simulations. Its first element is the use of specific patch-patch and…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
The self-assembly of hard polyhedral particles confined to a flat interface is studied using Monte Carlo simulations. The particles are pinned to the interface by restricting their movement in the direction perpendicular to it while…
A lattice Boltzmann model with interacting particles was developed in order to simulate the magneto-rheological characteristics of magnetic fluids. In the frame of this model, $6\, +\,1$ species of particles are allowed to move across a…
We study localized modes on the surface of a three-dimensional dynamical lattice. The stability of these structures on the surface is investigated and compared to that in the bulk of the lattice. Typically, the surface makes the stability…
Lipid membranes form the barrier between the inside and outside of cells and many of their subcompartments. As such, they bind to a wide variety of nano- and micrometer sized objects and, in the presence of strong adhesive forces, strongly…
We study the shape dynamics of a two-component fluid membrane, using a dynamical triangulation monte carlo simulation and a Langevin description. Phase separation induces morphology changes depending on the lateral mobility of the lipids.…