相关论文: Thermodynamics of interacting system of DNAs

We define a DNA as a sequence of $\pm 1$'s and embed it on a path of Cayley tree. Using group representation of the Cayley tree, we give a hierarchy of a countable set of DNAs each of which 'lives' on the same Cayley tree. This hierarchy…

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,…

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…

The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…

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…

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…

A Hamiltonian dynamics is defined for the XY model by adding a kinetic energy term. Thermodynamical properties (total energy, magnetization, vorticity) derived from microcanonical simulations of this model are found to be in agreement with…

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…

The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…

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 show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…

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…

A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…

To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…

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…

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 a nearest-neighbor solid-on-solid (SOS) model, with several spin values $0,1,\ldots,m,$ $m\geq2,$ and nonzero external field, on a Cayley tree of degree $k$ (with $k+1$ neighbors). We are aiming to extend the results of…

The state of a thermodynamic system being characterized by its set of extensive variables $q^{i}(i=1,...,n) ,$ we write the associated intensive variables $\gamma_{i},$ the partial derivatives of the entropy $ S(q^{1},...,q^{n}) \equiv…

DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…