Related papers: Long range correlations and folding angle in polym…
The aim of this paper is to investigate the distribution of a continuous polymer in the presence of an attractive finitely supported potential. The most intricate behavior can be observed if we simultaneously and independently vary two…
A continuum density-field formulation with particle-scale resolution is constructed to simultaneously incorporate the orientation dependence of interparticle interactions and the rotational invariance of the system, a fundamental but…
We consider the simplest representative of the class of multiply branched polymer macromolecules, known as a pom-pom structure. The molecule consists of a backbone linear chain terminated by two branching points with functionalities…
Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments displays two phase transitions, a theta-like collapse between swollen polymers and a globular state and another between the…
We introduce a class of models of semiflexible polymers. The latter are characterized by a strong rigidity, the correlation length associated to the gradient-gradient correlations, called the persistence length, being of the same order as…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
We consider self-avoiding polymers attached to the tip of an impenetrable probe. The scaling exponents $\gamma_1$ and $\gamma_2$, characterizing the number of configurations for the attachment of the polymer by one end, or at its midpoint,…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
We calculated the polarization degree of hydrogen Balmer broad emission lines from a number of active galactic nuclei (AGNs) with determined virial factors. The objects were selected from the sample presented by Decarli et al.(2008). In our…
We study the thermodynamic behavior of branched polymers. We first study random walks in order to clarify the thermodynamic relation between the canonical ensemble and the grand canonical ensemble. We then show that correlation functions…
The adhesion between a polymer melt and substrate is studied in the presence of chemically attached chains on the substrate surface. Extensive molecular dynamics simulations have been carried out to study the effect of temperature, tethered…
Monte Carlo simulations of proteins are hindered by the system's high density which often makes local moves ineffective. Here we devise and test a set of long range moves that work well even when all sites of a lattice simulation are…
In this paper we study the shape characteristics of star-like polymers in various solvent quality using a mesoscopic level of modeling. The dissipative particle dynamics simulations are performed for the homogeneous and four different…
Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…