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中被忽视的重要特性。oxDNA2是领先的DNA粗粒度模型，在学术和工业背景下支持DNA生物物理学，材料科学和纳米技术的研究。这是迄今为止唯一的CG模型，结合了DNA双链形成的热力学和单链和双链DNA的平均结构和力学性能的良好表现。然而，它目前忽略了序列依赖的机械和结构特性，禁止其应用于重要的开放性问题，这些问题支持DNA在生活和工程系统中的作用，包括DNA-蛋白质相互作用。为了应对这一挑战，我们将利用oxDNA2模型开发人员、高性能计算专家以及DNA结构和力学序列依赖性专家的综合专业知识。这种合成使我们处于一个独特的位置来进行这项研究。oxDNA3将通过两种途径发布，流行的LAMMPS分子动力学代码和oxDNA独立代码，加速其对目前使用oxDNA的学术界和生物技术公司的影响。

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.