Related papers: Folding dynamics of the helical structures in a mi…
Many biological and synthetic materials self-assemble into helical or twisted aggregates. The shape is determined by a complex interplay between elastic forces and the orientation and chirality of the constituent molecules. We study this…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
We consider the relation between the microscopic and effective descriptions of the unfolding experiment on a model polypeptide. We evaluate the probability distribution function of the performed work by Monte Carlo simulations and compare…
We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential, and a sideways constant…
We investigate the effect of fragmentation on the homogeneous free cooling of inelastic hard spheres, using Boltzmann kinetic theory and Direct Monte Carlo simulations. We analyze in detail a model where dissipative collisions may…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes…
By means of sophisticated Monte Carlo methods, we investigate the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness constraint, which is introduced geometrically via the global…
We propose a potential for wormlike polymer chains which can be used to model the low-temperature conformational structures. We successfully reproduced helix ground states up to 6.5 helical loops, using the multicanonical Monte Carlo…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
The physical mechanisms that bring about the propulsion of a rotating helix in a granular medium are considered. A propulsive motion along the axis of the rotating helix is induced by both symmetry breaking due to the helical shape, and the…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
Helically coiled filaments are a frequent motif in nature. In situations commonly encountered in experiments coiled helices are squeezed flat onto two dimensional surfaces. Under such 2-D confinement helices form "squeelices" - peculiar…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…