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A. Usheva

Publications and source records attributed to A. Usheva.

4 recordsLinked to original sources
arXiv2009

DNA Breathing Dynamics in the Presence of a Terahertz Field

We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to dynamic dimerization, while true local strand separations require a threshold amplitude mechanism. Based on our results we argue that a specific terahertz radiation exposure may significantly affect the natural dynamics of DNA, and thereby influence intricate molecular processes involved in gene expression and DNA replication.

physics.bio-ph↗
arXiv2006

Healing Length and Bubble Formation in DNA

We have recently suggested that the probability for the formation of thermally activated DNA bubbles is, to a very good approximation, proportional to the number of soft AT pairs over a length L(n) that depend on the size $n$ of the bubble and on the temperature of the DNA. Here we clarify the physical interpretation of this length by relating it to the (healing) length that is required for the effect of a base-pair defect to become neligible. This provides a simple criteria to calculate L(n) for bubbles of arbitrary size and for any temperature of the DNA. We verify our findings by exact calculations of the equilibrium statistical properties of the Peyrard-Bishop-Dauxois model. Our method permits calculations of equilibrium thermal openings with several order of magnitude less numerical expense as compared with direct evaluations.

cond-mat.soft↗
arXiv2003

Structurally specific thermal fluctuations identify functional sites for DNA transcription

We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that the most probable opening occurs at the transcription start site. Minor openings appear to be related to other regulatory sites. Our results suggest that coherent thermal fluctuations play an important role in the initiation of transcription. Essential elements of the dynamics, in addition to sequence specificity, are nonlinearity and entropy, provided by local base-pair constraints.

cond-mat.soft↗