Related papers: Modeling the interaction of DNA with alternating f…
The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to…
Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition --…
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores…
The phase transition patterns displayed by a model of two coupled complex scalar fields are studied at finite temperature and chemical potential. Possible phenomena like symmetry persistence and inverse symmetry breaking at high…
A scalar model is built, as a quantum field theory defined on toroidal topologies, to describe phase transition in films subjected to periodic boundary conditions and influenced by an external and constant magnetic field. Criticality is…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
In the paper a study of a model magnetoelastic solid system is presented. The system of interest is a mean-field magnet with nearest-neighbour ferromagnetic interactions and the underlying s.c. crystalline lattice with the long-range Morse…
Proteins can be regarded as thermal nanosensors in an intra-body network. Upon being stimulated by Terahertz (THz) frequencies that match their vibrational modes, protein molecules experience resonant absorption and dissipate their energy…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aromatic nucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between the two, a phenomenon related to…
The thermal entanglement is investigated in a two-qubit Heisenberg XXZ system with Dzyaloshinskii-Moriya (DM) interaction. It is shown that the entanglement can be efficiently controlled by the DM interaction parameter and coupling…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
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 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…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
The thermodynamics of an electrically charged, multicomponent fluid with spontaneous electric dipoles and magnetic moments is analysed in the presence of electromagnetic fields. Taking into account the chemical composition of the current…
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…
The study of critical phenomena and phase transitions is an important part of modern condensed matter physics. In this regard, the phenomenological Landau theory has been extraordinarily useful. Hereby we present an alternative theoretical…
In this paper, we investigate the dynamics of the Bloch vector of a single two-level atom which interacts with a single quantized electromagnetic field mode according to the Jaynes-Cummings model, where the field is initially prepared in a…