Related papers: Analysis of PIN1 WW domain through a simple Statis…
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
Quantum Monte Carlo method is used to study the coupled spin-pseudospin Hamiltonian in one-dimension (1D) that models the charge-ordering instability of the anisotropic Hubbard ladder at quarter filling. We calculate the temperature…
Using the Continuous Time Quantum Monte Carlo Loop algorithm, we calculate the temperature dependence of the uniform susceptibility, and the specific heat of a spin-1/2 chain with random antiferromagnetic and ferromagnetic couplings, down…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure…
The pinning phenomena of the domain wall in the presence of exchange bias is studied analytically. The analytic solution of the domain wall spin configuration is presented. Unlike the traditional solution which is symmetric, our new…
The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences,…
Magnetic domain wall motion is at the heart of new magneto-electronic technologies and hence the need for a deeper understanding of domain wall dynamics in magnetic systems. In this context, numerical simulations using simple models can…
We investigate the Monte Carlo approach to propagation of experimental uncertainties within the context of the established "MSTW 2008" global analysis of parton distribution functions (PDFs) of the proton at next-to-leading order in the…
Electrically manipulating domain wall (DW) is at central in the field of spintronics. Magnetic Weyl semimetal (WSM) offers an additional knob for electric manipulation of DW by utilizing the topological DW bound states. Using magnetic WSM…
One-dimensional Heisenberg spin 1/2 chains with random ferro- and antiferromagnetic bonds are realized in systems such as $Sr_3 CuPt_{1-x} Ir_x O_6$. We have investigated numerically the thermodynamic properties of a generic random bond…
A multi-chain mean-field theory is developed and applied to a two-dimensional system of weakly coupled S=1/2 Heisenberg chains. The environment of a chain C_0 is modeled by a number of neighbor chains C_d, d = +/-1,...,+/-n, with the edge…
Antiferromagnetic Heisenberg spin chains with various spin values ($S=1/2,1,3/2,2,5/2$) are studied numerically with the quantum Monte Carlo method. Effective spin $S$ chains are realized by ferromagnetically coupling $n=2S$…
The static critical behavior of the models of small magnetic particles of the real two sublattice antiferromagnet MnF2 is investigated by the Monte Carlo method taking into account the interaction of the second nearest neighbors. Systems…
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids,…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
We study a $U(1)\times U(1)$ system with two species of loops with mutual $\pi$-statistics in (2+1) dimensions. We are able to reformulate the model in a way that can be studied by Monte Carlo and we determine the phase diagram. In addition…
We introduce a parameter $W(\beta,L)= (\pi\,\langle |m| \rangle^2/\langle m^2 \rangle - 2)/(\pi-2)$ which like the kurtosis (Binder cumulant) is a phenomenological coupling characteristic of the shape of the distribution $p(m)$ of the order…