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

EMT/BSSE：DNA 动力学和自组装的千万亿次模拟

• 批准号: 0829815
• 负责人: Priya Vashishta
• 金额: $ 45万
• 依托单位: University of Southern California
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-15 至 2012-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0829815&HistoricalAwards=false
• 关键词: EMT; BSSE; Petascale; Simulations; DNA

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.

DNA双链体和自组装BLYPriya Vashishta？拉吉夫·PI卡利亚，Aiichiro中野（南加州大学）Ananth Grama（普渡大学）DNA易位通过固态纳米孔和纳米流体通道的基础？芯片实验室？技术和固态纳米孔？显微镜吗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、染色体作图、生物传感器、分子机器、纳米电子学和纳米机械系统提供了前所未有的机会，以及介观结构基序的配方，作为由DNA组成的新兴周期性和非周期性纳米结构的构建块。该项目涉及DNA通过纳米结构的自组装和移位的研究。使用预测性分级千万亿次模拟框架在二氧化硅和氮化硅膜中缩放孔，该框架由以下组成：（1）描述DNA移位和连接中的化学过程的高度精确的量子力学（QM）模拟;（2）对DNA在受限流体环境中的结构性质和动力学过程的数十亿原子分子动力学（MD）模拟，（3）混合MD和自适应格子Boltzmann（LB）模拟，其中MD嵌入在易位/级联区域中，LB嵌入在流体的其余部分中;（4）加速动力学方法，以达到宏观时间尺度，用于与实验数据直接比较;（5）元可缩放、自调整、多核并行仿真算法;以及（6）自动化模型转换，以在受控误差传播的情况下按需将更高保真度的仿真嵌入到更粗糙的仿真中。 一个元可伸缩（或？设计一次，在新架构上扩展？）还正在为定向DNA自组装的第一原理模拟开发一个并行应用开发框架。