Related papers: An exactly solvable model for a beta-hairpin with …
We introduce a class of damage models on regular lattices with isotropic interactions, as e.g. quasistatic fiber bundles. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated…
A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of approximately 3A to the experimentally determined structure (Protein Data Bank…
The Haldane-Shastry model is one of the most studied interacting spin systems. The Yangian symmetry makes it exactly solvable, and the model has semionic excitations. We introduce disorder into the Haldane-Shastry model by allowing the…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
The model considered is a d=2 layered random Ising system on a square lattice with nearest neighbours interaction. It is assumed that all the vertical couplings are equal and take the positive value J while the horizontal couplings are…
Although most studies of strongly correlated systems away from equilibrium have focused on clean systems, it is well known that disorder may significantly modify observed properties in various nontrivial ways. The nonequilibrium interplay…
We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…
I address here the question of the mutual interplay of strong correlations and disorder in the system. I consider random version of the Hubbard model. Diagonal randomness is introduced {\it via} random on-site energies and treated by the…
In this paper we study the exact solution of a one-dimensional model of spin-$\frac{1}{2}$ electrons composed by a nearest-neighbor triplet pairing term and the on-site Hubbard interaction. We argue that this model admits a Bethe ansatz…
This study investigates the entanglement properties of disordered free fermion systems undergoing an Anderson phase transition from a delocalized to a localized phase. The entanglement entropy is employed to quantify the degree of…
The problem of quasistatic and rate-independent evolution of elastic-plastic-brittle delamination at small strains is considered. Delamination processes for linear elastic bodies glued by an adhesive to each other or to a rigid outer…
The exactly solvable model of two indistinguishable quantum particles (bosons or fermions) confined in a one-dimensional harmonic trap and interacting via finite-range soft-core interaction is presented and many properties of the system are…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…