TY - JOUR AU - Sun, Tiedong AU - Minhas, Vishal AU - Korolev, Nikolay AU - Mirzoev, Alexander AU - Lyubartsev, Alexander P. AU - Nordenskiöld, Lars PY - 2021 M3 - Review TI - Bottom-Up Coarse-Grained Modeling of DNA JO - Frontiers in Molecular Biosciences UR - https://www.frontiersin.org/articles/10.3389/fmolb.2021.645527 VL - 8 SN - 2296-889X N2 - 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. ER -