Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium Export

@article{citeulike:3879574, abstract = {We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous medium. The nonlinear dynamics of the above molecular system in general is governed by a perturbed nonlinear Schr\"{o}dinger equation. In the non-viscous limit, the equation reduces to the completely integrable nonlinear Schr\"{o}dinger (NLS) equation which admits N-soliton solutions. The soliton excitations of the DNA bases make localized base pair opening and travel along the DNA chain in the form of a bubble. This may represent the bubble generated during the transcription process when an RNA-polymerase binds to a promoter site in the DNA double helical chain. The perturbed NLS equation is solved using a perturbation theory by treating the viscous effect due to surrounding as a weak perturbation and the results show that the viscosity of the solvent in the surrounding damps out the amplitude of the soliton.}, archivePrefix = {arXiv}, author = {Vasumathi, V. and Daniel, M.}, citeulike-article-id = {3879574}, citeulike-linkout-0 = {http://arxiv.org/abs/0812.4538}, citeulike-linkout-1 = {http://arxiv.org/pdf/0812.4538}, day = {24}, eprint = {0812.4538}, keywords = {th\_ibg}, month = {Dec}, posted-at = {2009-01-13 01:02:50}, priority = {2}, title = {Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium}, url = {http://arxiv.org/abs/0812.4538}, year = {2008} }

TY - JOUR ID - citeulike:3879574 L3 - citeulike-article-id:3879574 N2 - We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous medium. The nonlinear dynamics of the above molecular system in general is governed by a perturbed nonlinear Schr\"{o}dinger equation. In the non-viscous limit, the equation reduces to the completely integrable nonlinear Schr\"{o}dinger (NLS) equation which admits N-soliton solutions. The soliton excitations of the DNA bases make localized base pair opening and travel along the DNA chain in the form of a bubble. This may represent the bubble generated during the transcription process when an RNA-polymerase binds to a promoter site in the DNA double helical chain. The perturbed NLS equation is solved using a perturbation theory by treating the viscous effect due to surrounding as a weak perturbation and the results show that the viscosity of the solvent in the surrounding damps out the amplitude of the soliton. TI - Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium KW - th_ibg AU - Vasumathi, V AU - Daniel, M PY - 2008/Dec/24/ UR - http://arxiv.org/abs/0812.4538 ER -