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

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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.