Related papers: Analysis of PIN1 WW domain through a simple Statis…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein…
We study the thermodynamical properties of a topology-based model proposed by Galzitskaya and Finkelstein for the description of protein folding. We devise and test three different mean-field approaches for the model, that simplify the…
The WW domain of the human Pin1 protein for its simple topology and the large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of the present work is to compare the…
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…
Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central…
Along with experiments, numerical simulations are key to gaining insight into the underlying mechanisms governing domain wall motion in thin ferromagnetic systems. However, a direct comparison between numerical simulation of model systems…
Motion of ferroelectric domain walls greatly contributes to the macroscopic dielectric and piezoelectric response of ferroelectric materials. The domain wall motion through the ferroelectric material is however hindered by pinning on…
Domain-wall dynamics in ferroelectric materials are strongly position-dependent since each polar interface is locked into a unique local microstructure. This necessitates spatially resolved studies of the wall-pinning using scanning-probe…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
We report studies of the behaviour of a single driven domain wall in the 2-dimensional non-equilibrium zero temperature random-field Ising model, closely above the depinning threshold. It is found that even for very weak disorder, the…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Using the quantum Monte Carlo Loop algorithm, we calculate the temperature dependence of the uniform susceptibility, the specific heat, the correlation length, the generalized staggered susceptibility and magnetization of a spin-1/2 chain…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
We study the interplay of interactions and topology in a pseudo-spin Weyl system, obtained from a minimally modified Hubbard model, using the numerically exact auxiliary-field quantum Monte Carlo method complemented by mean-field theory. We…
We report first principle numerical study of domain wall (DW) depinning in two-dimensional magnetic film, which is modeled by 2D random-field Ising system with the dipole-dipole interaction. We observe nonconventional activation-type motion…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
The spin dynamics of a single bi-layer ferromagnetic model, as proposed for a manganite system $La_{1.2}Sr_{1.8}Mn_{2}O_{7}$ as an approximate minimal model, is studied both below and above the bulk magnetic transition temperature using the…
We employ the domain wall fermion (DWF) formulation of the Thirring model on a lattice in 2+1+1 dimensions and perform $N=1$ flavor Monte Carlo simulations. At a critical interaction strength the model features a spontaneous…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…