Related papers: Kinetic Selection of Template Polymer with Complex…
We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and…
We study theoretically the dynamics of living polymers which can add and subtract monomer units at their live chain ends. The classic example is ionic living polymerization. In equilibrium, a delicate balance is maintained in which each…
We develop a formal model of the emergence of self-constructing objects (e.g. heteropolymers with autocatalytic capability) in an open system, which don't contain such objects initially. The objects are constructed from subunits (e.g.…
In this work we used dissipative particle dynamics simulations to study the copolymerization process in the presence of spatial heterogeneities caused by incompatibility between polymerizing monomers. The polymer sequence details as well as…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
We study the diffusion process through an ideal polymer network, using numerical methods. Polymers are modeled by random walks on the bonds of a two-dimensional square lattice. Molecules occupy the lattice cells and may jump to the…
The poly-tRNA model was recently presented for the origin and evolution of genetic coding. This model has led to a rather precise description of what might have occurred at the beginning of protein synthesis in the first life form. Here, we…
Natural supports of information are given by random copolymers such as DNA or RNA where information is coded in the sequence of covalent bonds. At the molecular scale, the stochastic growth of a single copolymer with or without a template…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
When a population inhabits an inhomogeneous environment, the fitness value of traits can vary with the position in the environment. Gene flow caused by random mating can nevertheless prevent that a sexually reproducing population splits…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
In this chapter we review concepts and theories of polymer dynamics. We think of it as an introduction to the topic for scientists specializing in other subfields of statistical mechanics and condensed matter theory, so, for the readers…
The non-stretching approximation of polymer rheology simplifies a constitutive equation but fundamentally changes its behavior in fast flows, and the circumstances under which fast flows emerge cannot always be predicted a-priori. In this…
The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclisation. Using a…
Chemically-responsive polymers are macromolecules that respond to local variations of the chemical composition of the solution by changing their conformation, with notable examples including polyelectrolytes, proteins and DNA. The polymer…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
Polymer melts represent the flow-history-dependent behavior. To clearly show this behavior, we have investigated flow behavior of an entangled polymer melt around two cylinders placed in tandem along the flow direction in a two dimensional…
To introduce selection into a model of coalescence, I explore the use of modified integer partitions that allow the identification of a preferred lineage. I show that a partition-partition transition matrix, along with Monte Carlo discrete…
Although the behavior of entangled polymers in startup shear flows with constant shear rates has been thoroughly investigated, the response under creep has not been frequently considered. In this study, primitive chain network simulations,…
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…