Healing length and bubble formation in DNA

Lengthscales and Cooperativity in DNA Bubble Formation

Z. Rapti, A. Smerzi, K. Ø. Rasmussen and A. R. Bishop 1 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and School of Mathematics, Institute for Advanced Study, Einstein Drive 1, Princeton, New Jersey 08540 2 Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 and 3 Istituto Nazionale di ...

Helix untwisting and bubble formation in circular DNA.

The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as ...

simulation and experimental studies for prediction mineral scale formation in oil field during mixing of injection and formation water

abstract: mineral scaling in oil and gas production equipment is one of the most important problem that occurs while water injection and it has been recognized to be a major operational problem. the incompatibility between injected and formation waters may result in inorganic scale precipitation in the equipment and reservoir and then reduction of oil production rate and water injection rate. ...

A Coarse-Grained DNA Model for Bubble Formation and Dynamics

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble c...