Related papers: Tree-hierarchy of DNA and distribution of Holliday…
We define a DNA as a sequence of $1, 2$'s and embed it on a path of Cayley tree in such a way that each vertex of the Cayley tree belongs only to one of DNA and each DNA has its own countably many set of neighboring DNAs. The Hamiltonian of…
Kittel's 1D model represents a natural DNA with two strands as a (molecular) zipper, which may separated as the temperature is varied. We define multidimensional version of this model on a Cayley tree and study the set of Gibbs measures. We…
In this paper, we study the HC-model with a countable set $\mathbb Z$ of spin values on a Cayley tree of order $k\geq 2$. This model is defined by a countable set of parameters (that is, the activity function $\lambda_i>0$, $i\in \mathbb…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
In this paper, we investigate tree-indexed Markov chains (Gibbs measures) defined by a Hamiltonian that couples two Ising layers: hidden spins \(s(x) \in \{\pm 1\}\) and observed spins \(\sigma(x) \in \{\pm 1\}\) on a Cayley tree. The…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
In this paper, we study the Hard Core (HC) model with a countable set $\mathbb Z$ of spin values on a Cayley tree of order $k=2$. This model is defined by a countable set of parameters (that is, the activity function $\lambda_i>0$, $i\in…
For the $q$-state Potts model on a Cayley tree of order $k\geq 2$ it is well-known that at sufficiently low temperatures there are at least $q+1$ translation-invariant Gibbs measures which are also tree-indexed Markov chains. Such measures…
We consider an Ising model on the Cayley tree $\Gamma_k$ of arbitrary order $k\ge1$ with three spin species of values $(\tfrac12,1,\tfrac32)$ distributed deterministically with period three along the generations. Within the framework of…
We consider a nearest-neighbor SOS model, spin values $0,1,..., m$, $m\geq 2$, on a Cayley tree of order $k$ . We mainly assume that $m=2$ and study translation-invariant (TI) and `splitting' (S) Gibbs measures (GMs). For $m=2$, in the…
An exact analytical derivation is presented, showing that the Ising model on the Cayley tree exhibits a line of third order phase transition points, between temperatures $T_2=2k_B^{-1}J\ln ({\sqrt 2}+1) $ and $T_{BP}=k_B^{-1}J\ln (3)$, and…
Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal…
In this paper we investigate generalized Gibbs measure (GGM) for $p$-adic Hard-Core(HC) model with a countable set of spin values on a Cayley tree of order $k\geq 2$. This model is defined by $p$-adic parameters $\lambda_i$, $i\in \mathbb…
We consider a hard core (HC) model with a countable set $\mathbb{Z}$ of spin values on the Cayley tree. This model is defined by a countable set of parameters $\lambda_{i}>0, i \in \mathbb{Z}\setminus\{0\}$. For all possible values of…
In this paper, we focus on studying non-probability Gibbs measures for a Hard Core (HC) model on a Cayley tree of order $k\geq 2$, where the set of integers $\mathbb Z$ is the set of spin values. It is well-known that each Gibbs measure,…
We continue our study of the full set of translation-invariant splitting Gibbs measures (TISGMs, translation-invariant tree-indexed Markov chains) for the $q$-state Potts model on a Cayley tree. In our previous work \cite{KRK} we gave a…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
In this paper we consider a model with nearest-neighbor interactions and with the set $[0,1]$ of spin values, on a Cayley tree of order $k \geq 2$. To study translation-invariant Gibbs measures of the model we drive an nonlinear functional…
We consider a new model which consists of a DNA together with a RNA. Here we assume that DNA is from a mammal or bird but RNA comes from a virus. To study thermodynamic properties of this model we use methods of statistical mechanics,…
Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate…