Related papers: Thermodynamics of G.A mispairs in DNA: continuum e…
The present work is devoted to the study of the thermostability of native DNA during binding to TiO$_{2}$ nanoparticles (NPs) at various concentrations under conditions close to physiological (0.1 M Na $^+$, pH 7) using thermal denaturation…
RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of…
We study the electric properties of single-stranded DNA molecules with hairpin-like shapes in the presence of a magnetic flux. It is shown that the current amplitude can be modulated by the applied field. The details of the electric…
We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…
A simple description of thermodynamics of DMAAS and DMAGaS ferroelectric crystals by means of Landau expansion is proposed. Conditions of occurrence of phase transitions are established and their temperatures are obtained. The influence of…
In many organisms, homologous (or repetitive) chromosomal regions can associate or/and undergo concerted epigenetic changes in the absence of DNA breakage and recombination. The direct specific pairing of DNA duplexes with similar…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
One-particle spectral properties in the normal phase of the two-dimensional attractive Hubbard model are investigated in the weak coupling regime using the non-selfconsistent T-matrix approximation. The corresponding equations are evaluated…
The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5$) by using exact real space renormalization group (RG)…
We study the role of cations on the stability of double stranded DNA (dsDNA) molecules.It is known that the two strands of double stranded DNA(dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution,…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
In a recent companion paper, we observed that the rules of ordinary thermodynamics generally fail to respect thermal duality, a symmetry of string theory under which the physics at temperature T is related to the physics at the inverse…
A combination of classical density-functional theory and thermodynamic perturbation theory is applied to a survey of finite-temperature trends in the relative stabilities of one-component crystals and quasicrystals interacting via effective…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
We address two issues in the thermodynamic model for nuclear disassembly. Surprisingly large differences in results for specific heat were seen in predictions from the canonical and grand canonical ensembles when the nuclear system passes…
Gluodynamics and two-flavor QCD at non-zero temperature are studied with the so-called overimproved cooling technique under which caloron solutions may remain stable. We consider topological configurations either at the first occuring…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…