Coarse-Grained Models of Nucleic Acids and Their Applications

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Background

The first computer simulations of biological systems were performed more than 40 years ago. Since then one can observe tremendous improvement in both the methodology of simulations and the efficiency of computer hardware. Recent implementation of molecular dynamics software on GPU’s allowed millisecond-long all-atom simulations of small systems containing proteins or nucleic acids. Although the time scale of biological processes accessible for all-atom molecular dynamics simulations has increased by six orders of magnitude in the last twenty years, many long time-scale processes are still inaccessible for this methodology. Therefore many so-called coarse-grained models were developed. In these models groups of atoms are replaced by smaller numbers of interaction centers leading to a reduction of the computational cost of simulations. This is due to three main reasons: the number of interactions which must be computed at each simulations step is severely reduced; the time-step applied in the integration algorithm can be increased because fast vibrations in the system are removed; the potential energy surface is smoother in coarse-grained models leading to faster progress of observed processes.

The diversity of available coarse-grained models for nucleic acids make it difficult to select the most appropriate for users with an average molecular-modeling background. There are models which predict thermodynamic properties or flexibility accurately but need the experimental structure to work. On the other hand, a number of knowledge- and physics-based models can work in the ab initio mode, but reproduce properties less accurately. Furthermore, more detailed models are usually more accurate, but also need more computer time. The goal of this Research Topic is to trigger some progress in the development of coarse-grained models of nucleic acids and highlight their importance for description of large-scale biomolecular systems.

We aim to collect papers describing new coarse-grained models of nucleic acids as well as improvements of already established models, both knowledge- and physics-based or mixed. We also ask for publications which utilize coarse-grained models of nucleic acids for the description of important biological phenomena, such as RNA-folding or protein-nucleic acid association. Review papers comparing various coarse-grained models and pointing out their strengths and weaknesses are also welcomed. We hope that by collecting these publications we will enable scientists to choose the model most suitable for their research objectives, and the collection will also be useful for developers to determine the direction of future research on the coarse-grained models of nucleic acids.

Original papers or up-to-date reviews/perspective investigating/focusing on topics presented below are welcome:

• New coarse-grained models of nucleic acids
• Development of already established models of nucleic acids
• Application of coarse-grained models of nucleic acids to study biological phenomena: DNA and RNA folding, DNA nanostructure assembly etc.
• Nucleic acid – protein association with coarse-grained models
• Description of interactions of nucleic acids with ions

Keywords: DNA, RNA, coarse-grained model, folding

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