Bottom-up coarse-grained modeling of DNA

• Main Authors: Sun, Tiedong, Minhas, Vishal, Korolev, Nikolay, Mirzoev, Alexander, Lyubartsev, Alexander P., Nordenskiöld, Lars
• Other Authors: School of Biological Sciences
• Format: Article
• Language: English
• Published: 2021
• Subjects: Science::Biological sciences::Biophysics; DNA Condensation; Coarse-grained Model
• Online Access: https://hdl.handle.net/10356/147189
• Institution: Nanyang Technological University

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.