Related papers: New alphabet-dependent morphological transition in…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
The nucleation of crystals from the liquid melt is often characterized by a competition between different crystalline structures or polymorphs, and can result in nuclei with heterogeneous compositions. These mixed-phase nuclei can display…
We study different scenarios of topological phase transitions in the vicinity of the \pi^0 condensation point in neutron matter. The transitions occur between the Fermi-liquid state and a topologically different one with two sheets of the…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
The effect of short chain grafting on the liquid crystalline (LC) ordering of nano-crystals is investigated using molecular dynamics simulations of a coarse-grained grafted nano-rod model. Monodisperse nano-rods, with aspect ratios typical…
Models for viral populations with high replication error rates (such as RNA viruses) rely on the quasispecies concept, in which mutational pressure beyond the so-called "Error Threshold" leads to a loss of essential genetic information and…
The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…
We study biological evolution on a random fitness landscape where correlations are introduced through a linear fitness gradient of strength $c$. When selection is strong and mutations rare the dynamics is a directed uphill walk that…
We study a system involving a single quantum degree of freedom per site of the lattice interacting with a few neighbors (up to second neighbors), with the interactions chosen as to produce frustration. At zero temperature, this system…
In the critical beta-splitting model of a random $n$-leaf rooted tree, clades are recursively (from the root) split into sub-clades, and a clade of $m$ leaves is split into sub-clades containing $i$ and $m-i$ leaves with probabilities…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations.…
We investigate the phase diagram of a quantum many-body system constructed via the strange correlator approach, based on the non-Abelian $SU(2)_4$ fusion category, to probe topological phase transitions. Using tensor network methods, we…
We consider discrete-time random perturbations of monotone cellular automata (CA) in two dimensions. Under general conditions, we prove the existence of half-space velocities, and then establish the validity of the Wulff construction for…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
We numerically study structural properties of mechanically stable packings of hard spheres (HS), in a wide range of packing fractions $0.53 \le \phi \le 0.72$. Detailed structural information is obtained from the analysis of orientational…
Angular perturbations modify the band structure of armchair (and other metallic) carbon nanotubes by breaking the tube symmetry and may induce a metal-semiconductor transition when certain selection rules are satisfied. The symmetry…
In this paper we study the distribution of stacks in $k$-noncrossing, $\tau$-canonical RNA pseudoknot structures ($<k,\tau> $-structures). An RNA structure is called $k$-noncrossing if it has no more than $k-1$ mutually crossing arcs and…
A phase-separation front will leave in its wake a phase-separated morphology that differs markedly from homogeneous phase-separation morphologies. For a purely diffusive system such a front, moving with constant velocity, will generate very…
We propose a new analytic approach to study the phase diagram of random heteropolymers, based on the cavity method. For copolymers we analyze the nature and phenomenology of the glass transition as a function of sequence correlations.…