کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
11006450 1503030 2018 8 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Coarse-grained models of double-stranded DNA based on experimentally determined knotting probabilities
موضوعات مرتبط
مهندسی و علوم پایه شیمی شیمی آلی
پیش نمایش صفحه اول مقاله
Coarse-grained models of double-stranded DNA based on experimentally determined knotting probabilities
چکیده انگلیسی
To accurately model double-stranded DNA in a manner that is computationally efficient, coarse-grained models of DNA are introduced, where model parameters are selected by fitting the spectrum of observable DNA knots: We develop a general method to fit free parameters of coarse-grained chain models by comparing experimentally obtained knotting probabilities of short DNA chains to knotting probabilities that are computed in Monte Carlo simulations, resulting in coarse-grained DNA models which are tailored to reflect DNA topology in the best possible way. The method is exemplified by fitting ideal chain models as well as a bead-spring model with excluded volume interactions, to model double-stranded DNA for physiological as well as for high salt concentrations. The resulting coarse-grained DNA models predict the correct persistence length and effective diameter of double-stranded DNA, and can in principle be used for dynamical investigations using Molecular Dynamics. Our modelling ansatz thus provides a blueprint for building coarse-grained models of polymers, which are solely based on knotting spectra.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Reactive and Functional Polymers - Volume 131, October 2018, Pages 243-250
نویسندگان
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