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9 papers · 1 filter
Thermodynamics of a subensemble of a canonical ensemble
M. F. Gelin, M. Thoss
Two approaches to describe the thermodynamics of a subsystem that interacts with a thermal bath are considered. Within the first approach, the mean system energy is identif…
Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach
Pinaki Chaudhury, Ralf Metzler, Suman K Banik
We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathi…
Microscopic origin of the jump diffusion model
M. F. Gelin, D. S. Kosov
The present paper is aimed at studying the microscopic origin of the jump diffusion. Starting from the -body Liouville equation and making only the assumption that molecular reo…
Asymptotic non-equilibrium steady state operators
M. F. Gelin, D. S. Kosov
We present a method for the calculation of asymptotic operators for nonequilibrium steady-state quantum systems. The asymptotic steady-state operator is obtained by averaging the c…
Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem
Hans C. Fogedby, Ralf Metzler
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We show that long time distributions for the survival of DNA bubbles…
Subdiffusion and weak ergodicity breaking in the presence of a reactive boundary
Michael A. Lomholt, Irwin M. Zaid, Ralf Metzler
We derive the boundary condition for a subdiffusive particle interacting with a reactive boundary with finite reaction rate. Molecular crowding conditions, that are found to cause…