Related papers: Kinetic Selection of Template Polymer with Complex…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Polymers in nonuniform flows undergo strong deformation, which in the presence of persistent stretching can result in the coil-stretch transition. This phenomenon has been characterized by using the formalism of nonequilibrium statistical…
A simple one-dimensional model is constructed for polymer motion. It exhibits the crossover from reptation to Rouse dynamics through gradually allowing hernia creation and annihilation. The model is treated by the density matrix technique…
We study the effects of two kinds of interactions in tube-like polymers and demonstrate that they result in the formation of secondary motifs. The first has an entropic origin and is a measure of the effective space available to the…
Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as…
The cavitation flow of linear-polymer solutions around a cylinder is studied by performing a large-scale molecular dynamics simulation. The addition of polymer chains remarkably suppresses the cavitation. The polymers are stretched into a…
Recent work on the mechanism of polymer crystallization has led to a proposal for the mechanism of thickness selection which differs from those proposed by the surface nucleation theory of Lauritzen and Hoffman and the entropic barrier…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
The apparent difficulty of designing simple autocatalysts that grow exponentially in the absence of enzymes, external drives or ingenious internal mechanisms severely constrains scenarios for the emergence of evolution by natural selection…
The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by…
We investigate the effect of flow kinematics on the extensional viscosity of dilute polymer solutions by conducting dissipative particle dynamics simulations under uniaxial, planar, and biaxial extensional flows. At high extension rates,…
Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular…
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…
At an early stage in pre-biotic evolution, groups of replicating molecules must coordinate their reproduction to form aggregated units of selection. Mechanisms that enable this to occur are currently not well understood. In this paper we…
We construct a micromechanical version of an early model for topologically constrained polymers -- a 2D chain amongst point-like uncrossable obstacles -- which allows us to explicitly elucidate the role of topological forces beyond…
The process of force generation by the growth of biopolymers is simulated via a Langevin-dynamics approach. The interaction forces are taken to have simple forms that favor the growth of straight fibers from solution. The force-velocity…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Recent experimental evidence suggests that acute myeloid leukemias may originate from multiple clones of malignant cells. Nevertheless it is not known how the observed clones may differ with respect to cell properties such as proliferation…
Polymer materials have the characteristic feature that they are multiscale systems by definition. Already the description of a single molecules involves a multitude of different scales, and cooperative processes in polymer assemblies are…