Report
In search of the origin of long-time power-law decay in DNA solvation dynamics
| العنوان: | In search of the origin of long-time power-law decay in DNA solvation dynamics |
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| المؤلفون: | Mukherjee, Saumyak, Mondal, Sayantan, Acharya, Subhajit, Bagchi, Biman |
| سنة النشر: | 2018 |
| المجموعة: | Condensed Matter Quantitative Biology |
| مصطلحات موضوعية: | Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter, Quantitative Biology - Biomolecules |
| الوصف: | Experiments reveal that DNA solvation dynamics (SD) is characterized by multiple time scales ranging from a few ps to hundreds of ns and in some cases even up to microseconds. The last part of decay is slow and is characterized by a power law (PL). The microscopic origin of this PL is not yet clearly understood. Here we present a theoretical study based on time dependent statistical mechanics and computer simulations. Our investigations show that the primary candidates responsible for this exotic nature of SD are the counterions and ions from the buffer solution. We employ the model developed by Oosawa for polyelectrolyte solution that includes effects of counterion fluctuations to construct a frequency dependent dielectric function. We use it in the continuum model of Bagchi, Fleming and Oxtoby only to find that it fails to explain the slow PL decay of DNA solvation dynamics. We then extend the model by employing the continuous time random walk technique developed by Scher-Montroll-Lax. This approach can explain the long time PL decay, in terms of the collective response of the counter ions. From MD simulations we find frequent occurrence of random walk of tagged counter ions along the phosphate backbone. We propose a generalized random walk model for counterion hopping and carry out kinetic Monte Carlo simulations to show that the nonexponential contribution to solvation dynamics can indeed arise from dynamics of such ions. We also employ a Mode Coupling Theory analysis to understand the slow relaxation that originates from ions in solution. Explicit evaluation suggests that buffer ion contribution could explain logarithmic time dependence in the ns time scale, but not a power law. From MD simulations we find log-normal distributions of relaxation times of water dynamics inside the grooves. This is responsible for the initial faster multiexponential decay of SD. Comment: 60 pages, 15 figures, 6 tables |
| نوع الوثيقة: | Working Paper |
| URL الوصول: | http://arxiv.org/abs/1808.10471 |
| رقم الانضمام: | edsarx.1808.10471 |
| قاعدة البيانات: | arXiv |
| الوصف غير متاح. |