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We consider polynomial long-range Ising models in one dimension, with ferromagnetic pair interactions decaying with power $2-\alpha$ (for $0 \leq \alpha < 1$), and prepared with randomly chosen boundary conditions. We show that at low…
We study increasing subsequences (IS) for an ensemble of sequences given by permutation of numbers {1,2,...,n}. We consider a Boltzmann ensemble at temperature T. Thus each IS appears with the corresponding Boltzmann probability where the…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
Topological entanglement entropy has been regarded as a smoking-gun signature of topological order in two dimensions, capturing the total quantum dimension of the topological particle content. An extrapolation method on cylinders has been…
We study evolutionary canalization using a spin-glass model with replica theory, where spins and their interactions are dynamic variables whose configurations correspond to phenotypes and genotypes, respectively. The spins are updated under…
We start with a rather detailed, general discussion of recent results of the replica approach to statistical mechanics of a single classical particle placed in a random $N (\gg 1)$-dimensional Gaussian landscape and confined by a…
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…
The phenomenon of PT (parity- and time-reversal) symmetry breaking is conventionally associated with a change in the complex mode spectrum of a non-Hermitian system that marks a transition from a purely oscillatory to an exponentially…
In the area of topological and geometric treatment of phase transitions and symmetry breaking in Hamiltonian systems, in a recent paper some general sufficient conditions for these phenomena in $\mathbb{Z}_2$-symmetric systems (i.e.…
Spin-glass theory is one of the leading paradigms of complex physics and describes condensed matter, neural networks and biological systems, ultracold atoms, random photonics, and many other research fields. According to this theory,…
In this work the spontaneous symmetry breaking in certain nonlinear theories with second-class constraints is explored. Using the Dirac's method we perform an analysis of the constraints and the counting of the degrees of freedom. The…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
We perform an extensive numerical study of the disordered Poland-Scheraga (PS) model for DNA denaturation in which self-avoidance is completely taken into account. In complement to our previous work, we focus here on the finite size scaling…
We present a numerical study of the ultrametric properties of the set of RNA secondary structures with the maximum number of base pairs (energetically degenerate minima) within the maximum matching model (Nussinov algorithm). Using 18…
In this article, we study an elastic manifold in quenched disorder in the limit of zero temperature. Naively it is equivalent to a free theory with elasticity in Fourier-space proportional to k^4 instead of k^2, i.e. a model without…
We present experimental study of magnetization in $\lambda$-DNA in conjunction with structural measurements. The results show the surprising interplay between the molecular structures and their magnetic property. In the B-DNA state,…
We study a matrix model of RNA in which an external perturbation acts on n nucleotides of the polymer chain. The effect of the perturbation appears in the exponential generating function of the partition function as a factor…
Using Monte Carlo simulations, we study in detail the overlap distribution for individual samples for several spin-glass models including the infinite-range Sherrington-Kirkpatrick model, short-range Edwards-Anderson models in three and…