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

The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper,…

Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…

Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…

A system of replicators with Hebbian random couplings is studied using dynamical methods. The self-reproducing species are here characterized by a set of binary traits and interact based on complementarity. In the case of an extensive…

Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…

We discuss uniform sampling algorithms that are based on stochastic growth methods, using sampling of extreme configurations of polymers in simple lattice models as a motivation. We shall show how a series of clever enhancements to a…

We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…

There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is…

We propose a field-theoretical approach to a polymer system immersed in an ideal mixture of clustering centers. The system contains several species of these clustering centers with different functionality, each of which connects a fixed…

We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…

We study a continuous-time dynamical system that models the evolving distribution of genotypes in an infinite population where genomes may have infinitely many or even a continuum of loci, mutations accumulate along lineages without…

Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…

We explore a generalized Seceder Model with variable size selection groups and higher dimensional genotypes, uncovering its well-defined mean-field limiting behavior. Mapping to a discrete, deterministic version, we pin down the upper…

A dynamical model of an ecological community is analyzed within a "mean-field approximation" in which one of the species interacts with the combination of all of the other species in the community. Within this approximation the model may be…

We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…

We investigate a continuous time, probability measure-valued dynamical system that describes the process of mutation-selection balance in a context where the population is infinite, there may be infinitely many loci, and there are weak…

We seek models for the genotype evolution of agricultural animals, animals involved in primary production processes. Classical models for genotype evolution have tended to be very simple in order that analytic methods may be employed in…

The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…

Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…