相关论文: Coupled dynamics of sequence selection and compact…

A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The…

An innovative method is proposed to generate configurations of coarse grained models for polymer melts. This method, largely inspired by chemical ``radical polymerization'', is divided in three stages: (i) nucleation of radicals (reacting…

We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…

We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated…

The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…

A computational framework that leverages data from self-consistent field theory simulations with deep learning to accelerate the exploration of parameter space for block copolymers is presented. This is a substantial two-dimensional…

The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…

We develop a statistical model for a confined chain molecule based on a monomer grand canonical ensemble. The molecule is subject to an external chemical potential, a backbone interaction, and an attractive interaction between all monomers.…

We study the phase transitions of a random copolymer chain with quenched disorder. We apply a replica variational approach based on a Gaussian trial Hamiltonian in terms of the correlation functions of monomer Fourier coordinates. This…

The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…

Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an…

Single-molecule force-extension experiments have allowed quantitative measurements of the mechanical responses of biomolecules to applied forces explaining their roles in key biological functions. Electrophoretic stretching of charged…

We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…

Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…

In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…

Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…

In this paper, we investigate a stochastic model describing the time evolution of a polymerization process. A polymer is a macro-molecule resulting from the aggregation of several elementary sub-units called monomers. Polymers can grow by…

The time for a DNA sequence to find its homologous depends on a long random search process inside the cell nucleus. Using polymer models, we model and compute here the mean first encounter time (MFET) between two sites located on two…

Conformations of a single semiflexible polymer chain dissolved in a low molecular weight liquid crystalline solvents (nematogens) are examined by using a mean field theory. We takes into account a stiffness and partial orientational…

The growth dynamics of rigid biopolymers, consisting of $N$ parallel protofilaments, is investigated theoretically using simple approximate models. In our approach, the structure of a polymer's growing end and lateral interactions between…