Related papers: Folding dynamics of the helical structures in a mi…
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.
Force-induced reversible transformations between coiled and normal polymorphs of bacterial flagella have been observed in recent optical-tweezer experiment. We introduce a discrete elastic rod model with two competing helical states…
Molecular dynamics simulation has been used to model pattern formation in three-dimensional Rayleigh--Benard convection at the discrete-particle level. Two examples are considered, one in which an almost perfect array of hexagonally-shaped…
Model chains are studied via Monte Carlo simulations which are deposited with a fixed flux on a substrate. They may represent, e.g., stiff lipophilic chains with an head group and tail groups mimicking the alkyl chain. After some subsequent…
Dynamics of spreading of viscous non - volatile fluid droplets on surfaces is modelled using a solid - on - solid model, which is studied with Monte Carlo simulations. Tendency for dynamical layering and surface attraction are in part…
Colloidal gels are prime examples of functional materials exhibiting disordered, amorphous, yet meta-stable forms. They maintain stability through short-range attractive forces and their material properties are tunable by external forces.…
Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…
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 protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Soft colloids allow to explore high density states well beyond random close packing. An important open question is whether softness controls the dynamics under these dense conditions. While experimental works reported conflicting results,…
Using continuum elasticity theory, we describe the elastic behavior of helical coils with an asymmetric double-helix structure and identify conditions, under which they become very rigid. Theoretical insight gained for macro-structures…
We investigate the slow dynamics in gelling systems by means of MonteCarlo simulations on the cubic lattice of a minimal statistical mechanics model. By opportunely varying some model parameter we are able to describe a crossover from the…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
In this work we present the general phase behavior of short tubelike flexible polymers. The geometric thickness constraint is implemented through the concept of the global radius of curvature. We use sophisticated Monte Carlo sampling…