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

DNA动力学和自组装的千万亿次模拟PI, Rajiv K. Kalia, Aiichiro Nakano（南加州大学）Ananth Grama（普渡大学）通过固态纳米孔和纳米流体通道的DNA易位是芯片实验室的基础？技术与固态纳米孔显微镜？用于分子结构和高速测序。DNA定向自组装的高效方法为新基因的合成、染色体定位、生物传感器、分子机器、纳米电子学和纳米力学系统，以及作为新兴的由DNA组成的周期性和非周期性纳米结构的构建块的介观结构基序的制定提供了前所未有的机会。该项目涉及通过纳米级二氧化硅和氮化硅膜的孔隙研究DNA自组装和易位，使用预测性分层千万亿级模拟框架，包括：(1)高度精确的量子力学（QM）模拟来描述DNA易位和连接的化学过程；(2)数十亿原子分子动力学（MD）模拟了dna在受限流体环境中的结构特性和动力学过程，并通过量子力学计算和关键实验验证了原子间的相互作用；(3)混合MD和自适应晶格玻尔兹曼（LB）模拟，其中MD嵌入在移位/连接区域，LB嵌入在流体的其余部分；(4)加速动力学方法达到宏观时间尺度，与实验数据直接比较；(5)元可扩展、自调优、多核并行仿真算法；(6)自动模型转换，在控制误差传播的情况下，根据需要将更高保真度的仿真嵌入到较粗的仿真中。元可伸缩(或？设计一次，在新架构上扩展？)并行应用程序开发框架也正在开发用于定向DNA自组装的第一性原理模拟。

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.