Related papers: Coupled dynamics of sequence selection and compact…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
The adoption of agroecological practices will be crucial to address the challenges of climate change and biodiversity loss. Such practices favor the cultivation of plants in complex mixtures with layouts differing from the monoculture…
The phase separation of a simple binary mixture of incompatible linear polymers in solution is investigated using an extension of the sedimentation equilibrium method, whereby the osmotic pressure of the mixture is extracted from the…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
We study the influence of some quenched disorder in the sequence of monomers on the entropic elasticity of long polymeric chains. Starting from the Kratky-Porod model, we show numerically that some randomness in the favoured angles between…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
We investigate an simple evolutionary game of sequences and demonstrate on this example the structure of fitness landscapes in discrete problems. We show the smoothing action of the genotype-phenotype mapping which still makes it feasible…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
We study a stochastic model of a copolymerization process that has been extensively investigated in the physics literature. The main questions of interest include: (i) what are the criteria for transience, null recurrence, and positive…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
A recent dynamic mean-field theory for sequence processing in fully connected neural networks of Hopfield-type (During, Coolen and Sherrington, 1998) is extended and analized here for a symmetrically diluted network with finite connectivity…