Related papers: An exactly solvable model for a beta-hairpin with …
We use the Dominant Reaction Pathway (DRP) approach to study the dynamics of the folding of a beta-hairpin, within a model which accounts for both native and non-native interactions. We compare the most probable folding pathways calculated…
We introduce an individual-based model for fiber elements having the ability to cross-link or unlink each other and to align with each other at the cross links. We first formally derive a kinetic model for the fiber and cross-links…
Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…
We briefly review the Ising model with uncorrelated, quenched random-site or random-bond disorder, which has been controversial in both two and four dimensions. In these dimensions, the leading exponent alpha, which characterizes the…
We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head- and two tail-beads. By means of simple pair potentials these robustly self-assemble to a fluid bilayer state over a…
We present an extension of the Hamiltonian of the two dimensional limit of the vibron model encompassing all possible interactions up to four-body operators. We apply this Hamiltonian to the modeling of the experimental bending spectrum of…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
An exactly solvable model based on the topology of a protein native state is applied to identify bottlenecks and key-sites for the folding of HIV-1 Protease. The predicted sites are found to correlate well with clinical data on resistance…
Motivated by the problem of N coupled Hubbard chains, we investigate a generalisation of the Schulz-Shastry model containing two species of one-dimensional fermions interacting via a gauge field that depends on the positions of all the…
We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest…
We develop a recently-proposed mapping of the two-dimensional Ising model with random exchange (RBIM), via the transfer matrix, to a network model for a disordered system of non-interacting fermions. The RBIM transforms in this way to a…
We propose a model that accounts for budding behavior of domains in lipid bilayers, where each of the bilayer leaflets has a coupling between its local curvature and local lipid composition. The compositional asymmetry between the two…
We consider the $\pm J$ Ising model on a cubic lattice with a gauge-invariant disorder distribution. Disorder depends on a parameter $\beta_G$ that plays the role of a chemical potential for the amount of frustration. We study the model at…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
Several recent experiments in biology study systems composed of several interacting elements, for example neuron networks. Normally, measurements describe only the collective behavior of the system, even if in most cases we would like to…
The effect of quenched disorder on the low-energy and low-temperature properties of various two- and three-dimensional Heisenberg models is studied by a numerical strong disorder renormalization group method. For strong enough disorder we…
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of…
Network equilibrium models represent a versatile tool for the analysis of interconnected objects and their relationships. They have been widely employed in both science and engineering to study the behavior of complex systems under various…
We develop a continuum theory for equilibrium elasticity of a network of crosslinked semiflexible filaments, spanning the full range between flexible entropy-driven chains to stiff athermal rods. We choose the 3-chain constitutive model…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…