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We consider a model for random hypergraphs with identifiability, an analogue of connectedness. This model has a phase transition in the proportion of identifiable vertices when the underlying random graph becomes critical. The phase…
The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting…
We study the effect of freezing the positions of a fraction $c$ of particles from an equilibrium configuration of a supercooled liquid at a temperature $T$. We show that within the Random First-Order Transition theory pinning particles…
We have discovered a novel transition rule for binary cellular automata (CA) that yields self-replicating structures across two spatial and temporal scales from sparsely populated random initial conditions. Lower-level, shapeshifting…
Nanoprecipitates form during nucleation of multiphase equilibria in phase segregating multicomponent systems. In spite of their ubiquity, their size-dependent physical chemistry, in particular at the boundary between phases with…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Linear binary fragmentation of synthetic fractal-like agglomerates composed of spherical, equal-size, touching monomers is numerically investigated. Agglomerates of different morphologies are fragmented via random bond removal. The…
Topological phase transition is accompanied with a change of topological numbers. It has been believed that the gap closing and the breakdown of the adiabaticity at the transition point is necessary in general. However, the gap closing is…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…
Biological systems exhibit remarkable morphogenetic plasticity, where a single genome can encode various specialized cellular structures triggered by local chemical signals. In the domain of Deep Learning, Differentiable Neural Cellular…
The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput…
We report on various nanocarbons formed from a unique structural pattern containing two pentagons, three hexagons and two heptagons, resulting from local rearrange- ments around a divacancy in pristine graphene or nanotubes. This defect can…
In studying the dynamics of large N_c, SU(N_c) gauge theory at finite temperature with fundamental quark flavours in the quenched approximation, we observe a first order phase transition. A quark condensate forms at finite quark mass, and…
We give a physical description in terms of percolation theory of the phase transition that occurs when the disorder increases in the random antiferromagnetic spin-1 chain between a gapless phase with topological order and a random singlet…
In this paper we study $k$-noncrossing, canonical RNA pseudoknot structures with minimum arc-length $\ge 4$. Let ${\sf T}_{k,\sigma}^{[4]} (n)$ denote the number of these structures. We derive exact enumeration results by computing the…
We provide information about the asymptotic regimes for a homogeneous fragmentation of a finite set. We establish a phase transition for the asymptotic behaviours of the shattering times, defined as the first instants when all the blocks of…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…