Related papers: An exactly solvable model for a beta-hairpin with …

We contemplate the pair of the purely imaginary delta-function potentials on a finite interval with Dirichlet boundary conditions. The two parameter model exhibits nicely the expected quantitative features of the unavoided level crossing…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

Recently we introduced a new technique for computing the average free energy of a system with quenched randomness. The basic tool of this technique is a distributional zeta-function. The distributional zeta-function is a complex function…

The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…

We develop an analytical expression for the self-energy of the infinite-dimensional Hubbard model that is correct in a number of different limits. The approach represents a generalization of the iterative perturbation theory to arbitrary…

We analyze the gapped phase of the Kitaev honeycomb model perturbatively in the isolated-dimer limit. Our analysis is based on the continuous unitary transformations method which allows one to compute the spectrum as well as matrix elements…

We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for…

Optimal structure of proteins is described by linear stochastic differential equation with mean decrease of free energy and volatility. Structure determining strategy is given by a twin of stochastic variables for which empirical conditions…

We define and study a model of winding for non-colliding particles in finite trees. We prove that the asymptotic behavior of this statistic satisfies a central limiting theorem, analogous to similar results on winding of bounded particles…

We propose a hybrid model governed by the Blume-Emery-Griffiths (BEG) Hamiltonian with a mean-field-like interaction, where the spins are randomly quenched such that some of them are "pure" Ising and the others admit the BEG set of states.…

The relationship between the spectral density and free energy of a spin system is considered. The analytical expressions allowing for the calculation of the spectral density for solvable models are determined. A linear Ising model is taken…

We consider two versions of a simple evolutionary algorithm model for protein folding at temperature zero: the (1+1)-EA on the LeadingOnes problem. In this schematic model, the structure of the protein, which is encoded as a bit-string of…

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…

We consider a general discrete model for heterogeneous semiflexible polymer chains. Both the thermal noise and the inhomogeneous character of the chain (the disorder) are modeled in terms of random rotations. We focus on the quenched…

Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…

The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…

We study the dynamic and metastable properties of the fully connected Ising $p$-spin model with finite number of variables. We define trapping energies, trapping times and self correlation functions and we analyse their statistical…

In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…

Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…

We investigate a discrete model consisting of self-propelled particles that obey simple interaction rules. We show that this model can self-organize and exhibit coherent localized solutions in one- and in two-dimensions.In one-dimension,…