相关论文: Secondary Structures in Long Compact Polymers

The persistence length of macromolecules is one of their basic characteristics, describing their intrinsic local stiffness. However, it is difficult to extract this length from physical properties of the polymers, different recipes may give…

Lattice models are valuable tools to gain insight into the statistical physics of heteropolymers. We rigorously map the partition function of these models into a vacuum expectation value of a $\mathbb{Z}_2$ lattice gauge theory (LGT), with…

We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…

We propose here a method to generate random networked amorphous structure using only readily available short-range properties like bond lengths, bond angles and connectivity of the constituents. This method is a variant of Monte-Carlo (MC)…

The behaviour of the one--dimensional random--forced Burgers equation is investigated in the path integral formalism, using a discrete space--time lattice. We show that by means of Monte Carlo methods one may evaluate observables, such as…

The triangular lattice model with nearest-neighbor attraction and third-neighbor repulsion, introduced in [J. Pekalski, A. Ciach and N. G. Almarza, arXiv:1401.0801 [cond-mat.soft]] is studied by Monte Carlo simulation. Introduction of…

Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…

Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present…

We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations…

The advances in materials and biological sciences have necessitated the use of molecular simulations to study polymers. The Markov chain Monte Carlo simulations enable the sampling of relevant microstates of polymeric systems by traversing…

Multiblock copolymer chains in implicit nonselective solvents are studied by Monte Carlo method which employs a parallel tempering algorithm. Chains consisting of 120 $A$ and 120 $B$ monomers, arranged in three distinct microarchitectures:…

We study the localisation of lattice polymer models near a permeable interface in two dimensions. Localisation can arise due to an interaction between the polymer and the interface, and can be altered by a preference for the bulk solvent on…

A simple lattice model is used to study compaction in granular media. As in real experiments, we consider a series of taps separated by large enough waiting times. The relaxation of the density exhibits the characteristic inverse…

Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…

Aggregation of amphiphiles through the action of hydrophobic interactions is a common feature in soft condensed matter systems and is of particular importance in the context of biophysics as it underlies both the generation of functional…

There have been separate studies of the polymer collapse transition, where the collapse was induced by two different types of attraction. In each case, the configurations of the polymer were given by the same subset of random walks being…

In the design and analysis of political redistricting maps, it is often useful to be able to sample from the space of all partitions of the graph of census blocks into connected subgraphs of equal population. There are influential Markov…

Pour modeliser le repliement compact d'un polymere, on etudie la statistique des meandres, definis comme configurations d'un circuit automobile traversant n fois une riviere. Grace a une methode Monte-Carlo adaptee a un ordinateur…

We study uniform 3-star polymers with one branch tethered to an attractive surface and another branch pulled by a force away from the surface. Each branch of the 3-star lattice is modelled as a self-avoiding walk on the simple cubic lattice…

A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…