Related papers: Links between nonlinear dynamics and statistical m…
We generalize the method of obtaining the fundamental linear partial differential equations such as the diffusion and Schrodinger equation, Dirac and telegrapher's equation from a simple stochastic consideration to arrive at certain…
We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
Analytical solution of one dimensional hydrodynamical model is derived, where phase transition from the QGP state to the hadronic state is effectively taken into account. The single particle rapidity distribution of charged $\pi$ mesons…
The relation between thermodynamic phase transitions in classical systems and topological changes in their configuration space is discussed for two physical models and contains the first exact analytic computation of a topologic invariant…
A mathematical model of the heat process in one-dimensional domain governed by a cylindrical heat equation with a heat source on the axis $z=0$ and nonlinear thermal coefficients is considered. The developed model is particularly applicable…
The content of this contribution is based on the course on numerical analysis techniques for non-linear dynamics. After introducing basic concepts as the visual analysis of trajectories in phase space and the importance of the nature of…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
A non-equilibrium plasma was studied using classical electrodynamic field theory. Non-linear interaction terms contribute to a finite lifetime for the dressed electrodynamic field. The lifetime exhibits a $\sim n^{-1} T_{e}^{3/2}…
In traditional thermodynamical and statistical-mechanical approaches one has (some) detailed knowledge of the principles governing the microdynamics of a system. However in many instances we may not have a Hamiltonian or good information…
We study sporadic randomness by means of a non-extensive form of Lyapunov coefficient. We recover from a different perspective the same conclusion as that of an earlier work, namely, that the ordinary Pesin theorem applies (P.Gaspard and…
The quantum master equation obtained by generalizing the geometric formulation of nonequilibrium thermodynamics to dissipative quantum systems is seriously nonlinear. We argue that nonlinearity occurs naturally in the step from reversible…
A basic statistical mechanics analysis of many-body systems with non-reciprocal pair interactions is presented. Different non-reciprocity classes in two- and three-dimensional binary systems (relevant to real experimental situations) are…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
Extensive studies have investigated the transition mechanism of boundary layers initiated by a single primary instability. In a real-world scenario, however, multiple primary instabilities of different physical nature would coexist and…
We study the growth of a periodic pattern in one dimension for a model of spinodal decomposition, the Cahn-Hilliard equation. We particularly focus on the intermediate region, where the non-linearity cannot be negected anymore, and before…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…
Nonlinear dynamical systems are ubiquitous in nature and they are hard to forecast. Not only they may be sensitive to small perturbations in their initial conditions, but they are often composed of processes acting at multiple scales.…