oxDNA3 - Introducing Sequence-Specific Curvature And Elasticity Into A Coarse-Grained DNA Model

我们建议开发和应用下一代oxDNA3粗粒度DNA模型，该模型具有当前版本oxDNA2中被忽略的基本重要特性。OxDNA2是领先的DNA粗粒度模型，在学术和工业背景下都支持对DNA生物物理、材料科学和纳米技术的研究。这是迄今为止唯一的CG模型，它结合了DNA双链形成的热力学，并很好地表示了单链和双链DNA的平均结构和力学性质。然而，它目前忽略了依赖于序列的机械和结构特性，禁止它应用于重要的开放问题，这些问题支撑着DNA在生命和工程系统中的作用，包括DNA与蛋白质的相互作用。为了迎接这一挑战，我们将利用oxDNA2模型开发人员、高性能计算专家以及DNA结构和力学序列相关性专家的综合专业知识。这一综合使我们处于进行这项研究的独特地位。OxDNA3将通过两种途径发布，即流行的LAMMPS分子动力学代码和oxDNA独立代码，加速其在学术界和目前使用oxDNA的生物技术公司中的影响。

We propose to develop and apply the next-generation oxDNA3 coarse-grained model of DNA, featuring fundamentally important properties that are neglected in the current version oxDNA2. oxDNA2 is the leading coarse-grained model of DNA, underpinning research into DNA bio- physics, materials science and nanotechnology in both academic and industrial contexts. It is the only CG model to date that combines the thermodynamics of DNA duplex formation with a good represen- tation of its average structural and mechanical properties in both single- and double-stranded DNA. However, it currently neglects sequence-dependent mechanical and structural properties, prohibiting its application to important open questions that underpin the role of DNA in living and engineered systems, including DNA-protein interactions. To meet this challenge, we will leverage the combined expertise of the developers of the oxDNA2 model, specialists in high-performance computing, and experts in the sequence-dependence of DNA structure and mechanics. This synthesis puts us in a unique position to conduct this research. oxDNA3 will be released through both avenues, the popular LAMMPS molecular dynamics code and the oxDNA standalone code, accelerating its impact in both academia and biotechnology companies that are now using oxDNA.