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Title: Bottom-up coarse-grained modeling of DNA
Authors: Sun, Tiedong
Minhas, Vishal
Korolev, Nikolay
Mirzoev, Alexander
Lyubartsev, Alexander P.
Nordenskiöld, Lars
Keywords: Science::Biological sciences::Biophysics
Issue Date: 2021
Source: Sun, T., Minhas, V., Korolev, N., Mirzoev, A., Lyubartsev, A. P. & Nordenskiöld, L. (2021). Bottom-up coarse-grained modeling of DNA. Frontiers in Molecular Biosciences, 8.
Project: MOE2019-T3-1-012
Journal: Frontiers in Molecular Biosciences
Abstract: Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, “melting,” and DNA condensation.
ISSN: 2296-889X
DOI: 10.3389/fmolb.2021.645527
Rights: © 2021 Sun, Minhas, Korolev, Mirzoev, Lyubartsev and Nordenskiöld. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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