相关论文: Topological complexity, contact order and protein …

We study correlations on the euclidean spacetimes generated in Monte Carlo simulations of the model. In the elongated phase, curvature correlations appear to fall off like a fractional power. Near the transition to the crumpled phase this…

We investigate the momentum-resolved spin and charge susceptibilities, as well as the chemical potential and double occupancy in the two-dimensional Hubbard model as functions of doping, temperature and interaction strength. Through these…

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…

Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…

Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…

We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the…

The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…

Long chains of the HP lattice protein model are studied by the Multi-Self-Overlap Ensemble(MSOE) Monte Carlo method, which was developed recently by the authors. MSOE successfully finds the lowest energy states reported before for sequences…

Residue-wise contact order (RWCO) is a new kind of one-dimensional protein structures which represents the extent of long-range contacts. We have recently shown that a set of three types of one-dimensional structures (secondary structure,…

In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…

We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…

Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…

In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…

Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…

The d-wave pairing correlations along with spin correlation are calculated with quantum Monte Carlo method for the two-dimensional Hubbard model on lattice structures representing organic superconductors $\kappa$-(BEDT-TTF)$_2$X and…

We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…

A $\theta$ term, which couples to topological charge, is added to the two-dimensional lattice CP^3 model and U(1) gauge theory. Monte Carlo simulations are performed and compared to strong-coupling character expansions. In certain…

The lowest energy configurations of close-packed clusters up to N=110 atoms with stacking faults are studied using the Monte Carlo method with Metropolis algorithm. Two types of contact interactions, a pair-potential and a many-atom…

The interplay between electrostatic interactions and orientational correlations is studied for a model system of charged rods positioned on a chain, using Monte Carlo simulation techniques. It is shown that the coupling brings about the…