Collaborative Research: EMT/BSSE:Petascale Simulations of DNA Dynamics and Self-Assembly

DNA动力学和自我ASSEMBLYPriya Vashishta？Pi，Rajiv K.Kalia，Aiichiro Nakano(南加州大学)Ananth Grama(普渡大学)DNA通过固态纳米孔和纳米流体通道移位的Petscalale模拟？芯片实验室？技术和固态纳米孔？显微镜？用于分子结构和高速测序。高效的DNA定向自组装方法为新基因的合成、染色体作图、生物传感器、分子机器、纳米电子学和纳米机械系统以及介观结构基元的构建提供了前所未有的机会，这些结构基元是由DNA组成的新的周期性和非周期性纳米结构的构建块。本项目涉及利用预测的层次化Petascale模拟框架研究DNA在二氧化硅和氮化硅薄膜中通过纳米级孔的自组装和移位，该框架包括：(1)高精度的量子力学(QM)模拟以描述DNA移位和连接的化学过程；(2)对受限流体环境中DNA的结构性质和动力学过程进行数十亿原子分子动力学(MD)模拟，通过QM计算和关键实验验证原子间的相互作用；(3)混合MD和自适应格子Boltzmann(LB)模拟，其中MD嵌入到移位/级联区域，而LB嵌入流体的其余部分；(4)加速动力学方法，以达到宏观时间尺度，以便与实验数据直接比较；(5)可元缩放、自调整、多核并行模拟算法；以及(6)自动模型转换，以将高保真模拟嵌入到具有受控误差传播的按需模拟中。元可伸缩(或？设计一次，在新体系结构上伸缩？)并行应用开发框架也在为定向DNA自组装的第一性原理模拟而开发。

PETASCALE SIMULATIONS OF DNA DYNAMICS AND SELF-ASSEMBLYPriya Vashishta?PI, Rajiv K. Kalia, Aiichiro Nakano (University of Southern California)Ananth Grama (Purdue University)DNA translocation through solid-state nanopores and nanofluidic channels underlie ?lab-on-a-chip? technology and solid-state nanopore ?microscopy? for molecular structure and high-speed sequencing. Highly efficient methods for directed self-assembly of DNA offer unprecedented opportunities for the synthesis of novel genes, chromosome mapping, biosensors, molecular machines, nanoelectronics and nanomechanical systems, and formulations of mesoscopic structural motifs as building blocks of emerging periodic and aperiodic nanostructures consisting of DNAs.This project involves the study of DNA self-assembly and translocation through nanometer-scale pores in silica and silicon nitride membranes using a predictive hierarchical petascale simulation framework consisting of: (1) Highly accurate quantum mechanical (QM) simulations to describe chemical processes in DNA translocation and concatenation; (2) multibillion-atom molecular dynamics (MD) simulations for structural properties and dynamical processes of DNAs in confined fluidic environments, with interatomic interactions validated by QM calculations and key experiments; (3) hybrid MD and adaptive lattice Boltzmann (LB) simulations in which MD is embedded in translocation/concatenation regions, and LB in the rest of the fluid; (4) accelerated dynamics approaches to reach macroscopic time scales for direct comparison with experimental data; (5) metascalable, self-tuning, multicore parallel simulation algorithms; and (6) automated model transitioning to embed higher fidelity simulations inside coarser simulations on demand with controlled error propagation. A metascalable (or ?design once, scale on new architectures?) parallel application-development framework is also being developed for first-principles simulations of directed DNA self-assembly.