Related papers: Coupled dynamics of sequence selection and compact…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
A mean field rate theory description of the homo- and co-polymerization of $f$-functional molecules is developed, which contains the formation of short cyclic structures inside the network. The predictions of this model are compared with…
Using the Gaussian Ansatz for the monomer-monomer correlation functions we derive a set of the self-consistent equations for determination of the conformational state in the bead-and-spring copolymer model. The latter is based on the…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
In this paper we analyse both the dynamics and the high density physics of the infinite dimensional lattice gas model for random heteropolymers recently introduced in \cite{jort}. Restricting ourselves to site-disordered heteropolymers, we…
This contribution is concerned with mathematical models for the dynamics of the genetic composition of populations evolving under recombination. Recombination is the genetic mechanism by which two parent individuals create the mixed type of…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
Using a mapping of compact polymers on the Manhattan lattice to spanning trees, we calculate exactly the average number of bends at infinite temperature. We then find, in a high temperature approximation, the energy of the system as a…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
A fundamental problem in protobiological dynamics is to understand how chemically generated polymers can form persistent sequence distributions before the emergence of replication. We study deterministic polymer growth in which each finite…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…