Related papers: Thermodynamics of DNA loops with long-range correl…
We analyse the thermal properties of a harmonic chain with weak correlated disorder. With the use of a perturbative approach we derive analytical expressions for the time-evolution of the chain temperature and of the heat flow when both…
Highlights: \begin{itemize} \item Relativistic effect of crystal dynamics "freezing". \item Non-statistical model of thermodynamic equilibration. \end{itemize} The dynamics of oscillations of a one-dimensional atomic chain is investigated…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
The article presents results of discrete thermodynamics (DTD) basic application to electrochemical systems. Consistent treatment of the electrochemical system as comprising two interacting subsystems - the chemical and the electrical…
Random walks are studied on disordered cellular networks in 2-and 3-dimensional spaces with arbitrary curvature. The coefficients of the evolution equation are calculated in term of the structural properties of the cellular system. The…
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…
At very small scales, thermodynamic energy exchanges like work and heat become comparable to thermal energy of the system, which leads to unusual phenomena like the transient violations of Second Law. We explore the generic characters of…
We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional traps across the thermal crossover from an amorphous solid- to liquid-like behaviors. While static correlations, that…
Understanding the roles of disorder and superconducting phase fluctuation in superconductivity has been a long-standing challenge. For example, while the phase fluctuation is expected to destroy the superconductivity of intrinsically…
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…
Loops are abundant in native RNA structures and proliferate close to the unfolding transition. By including a statistical weight ~ l^{-c} for loops of length l in the recursion relation for the partition function, we show that the…
It has become increasingly clear that a full understanding of the physics of electrons in disordered systems requires an approach in which both disorder and interactions are taken into account. Work on small numbers of electrons has…
We review recent rigorous mathematical results about the macroscopic behaviour of harmonic chains with the dynamics perturbed by a random exchange of velocities between nearest neighbor particles. The random exchange models the effects of…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
Systems with long-range interactions when quenced into a metastable state near the pseudo-spinodal exhibit nucleation processes that are quite different from the classical nucleation seen near the coexistence curve. In systems with…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
This study proposes and explores a linear hydrodynamic thermo-elasticity system within mixture models, comprising fluid and solid phases, with a focus on biological tissues, particularly tumor-related phenomena. Although tumor growth is not…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
When liquid-crystal elastomers are prepared without any alignment, disordered polydomain structures emerge as the materials are cooled into the nematic phase. These polydomain structures have been attributed to quenched disorder in the…