Collaborative Research: Petascale Hierarchical Simulations Of Biopolymer Translocation Through Silicon Nitride And Silica Nanopores And Nanofluidic Channels

技术摘要：该奖项是根据提交给PetaApps邀请函的一份提案而颁发的。数字基础设施办公室、材料研究司和数学和物理科学局、工程局以及计算机和信息科学和工程局的多学科活动办公室为这一奖项提供了资金。这个PetaApps项目专注于对离子在二氧化硅和氮化硅薄膜中通过纳米级孔和通道的离子传输和移位的混合量子力学-原子-介观模拟。PI的目标是开发一个预测的分级千万亿级模拟框架，用于：(1)高精度的量子力学模拟，以描述生物聚合物在转移过程中的化学过程；(2)对固态膜中受限流体环境中的生物聚合物的结构性质和动力学过程的数十亿原子分子动力学模拟，通过量子力学计算和关键实验验证原子间的相互作用；(3)混合分子动力学和自适应格子Boltzmann模拟，其中分子动力学嵌入到纳米孔/纳米通道表面和流体其余部分的晶格Boltzmann表面附近；(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)元可扩展、自调整的多核并行模拟算法；(6)自动模型转换以根据需要将更高逼真度的模拟嵌入到更粗略的模拟中，并控制误差传播以量化不确定性。经过验证，这个分层的千万亿级模拟框架将被用于研究：(1)DNA通过二氧化硅和氮化硅纳米孔的移位动力学和动力学；(2)用于顺序识别核苷酸的移位DNA的电子性质；(3)纳米孔/纳米通道中表面电荷的离子筛选；(4)单个二氧化硅纳米通道中压力驱动液体流动产生的流动电流，作为通道高度、压力梯度和盐浓度的函数；(5)压力驱动DNA在受限二氧化硅通道中的传输，用于新型诊断应用，如人工凝胶和熵陷阱阵列；以及(6)二氧化硅纳米管、纳米流体晶体管的表面功能化、极性转换和瞬时响应。该项目支持培训新一代研究生开发解决复杂系统水平问题所需的工具。他们将学习将理论、建模和高性能计算机模拟相结合。学生将参加一个双学位项目，在这个项目中，他们将在自己的学科范围内完成博士学位要求，并在计算机科学硕士S学位要求下，专门从事高性能计算和模拟。该奖项还支持为代表性不足群体举办的计算科学讲习班。来自历史上的黑人学院和大学以及少数族裔服务机构的本科生和教师导师参加了为期一周的并行计算和身临其境的交互式可视化的特殊的、密集的动手体验。非裔美国人、西班牙裔美国人和美国原住民学生将通过南加州大学S工程多样性中心招收，女性将通过南加州大学S女性理工科项目招生。非技术总结：该奖项是根据提交给PetaApps邀请函的一份提案而颁发的。数字基础设施办公室、数学和物理科学局、工程局以及计算机和信息科学与工程局为该奖项提供资金。该奖项支持为最先进的、？Petascale、？高性能的超级计算机将使模拟能够捕捉跨越一系列长度和时间尺度的现象。PI将专注于一个特别重要的问题，即生物分子如何通过二氧化硅和氮化硅等无机材料中的纳米大小的孔。该模拟可以捕捉到问题的详细物理过程，并可能阐明DNA和RNA分子测序的可能应用。PI还将更广泛地关注带电原子和分子如何通过纳米尺度尺度的通道。发展中的芯片实验室有潜在的应用吗？寻求将实验室分析功能微型化到电子设备芯片大小的技术。开发的软件将被分发，并可供广泛的研究人员在涉及材料研究、化学、工程、物理和纳米技术的各种学科和多学科研究中使用。该项目支持培训新一代研究生，以开发解决复杂系统级问题所需的工具。他们将学习将理论、建模和高性能计算机模拟相结合来解决复杂的问题。学生将参加一个双学位项目，在这个项目中，他们将在自己的学科范围内完成博士学位要求，并在计算机科学硕士S学位要求下，专门从事高性能计算和模拟。该奖项还支持为代表性不足群体举办的计算科学讲习班。来自历史上的黑人学院和大学以及少数族裔服务机构的本科生和教师导师参加了为期一周的并行计算和身临其境的交互式可视化的特殊的、密集的动手体验。

TECHNICAL SUMMARY:This award is made on a proposal submitted to the PetaApps Solicitation. The Office of Cyberinfrastructure, the Division of Materials Research and Office of Multidisciplinary activities in the Mathematical and Physical Sciences Directorate, the Engineering Directorate, and the Computer and Information Science and Engineering Directorate contribute funds to this award. This PetaApps project focuses on hybrid quantum mechanical-atomistic-mesoscale simulations of ion transport and translocation of biopolymers such as DNA and RNA through nanometer scale pores and channels in silica and silicon nitride membranes. The PIs aim to develop a predictive hierarchical petascale simulation framework for: (1) Highly accurate quantum mechanical simulations to describe chemical processes in translocating biopolymers; (2) multibillion-atom molecular dynamics simulations for structural properties and dynamical processes of biopolymers in confined fluidic environments in solid state membranes, with interatomic interactions validated by quantum mechanical calculations and key experiments; (3) hybrid molecular dynamics and adaptive lattice Boltzmann simulations in which molecular dynamics is embedded close to the surfaces of nanopores/nanochannels and lattice Boltzmann in the rest of the fluid; (4) accelerated dynamics approaches to reach macroscopic time scales for direct comparison with experimental data; (5) meta-scalable, 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 to quantify uncertainty.After validation, this hierarchical petascale simulation framework will be used to study: (1) Translocation kinetics and dynamics of DNA through silica and silicon nitride nanopores; (2) electronic properties of translocating DNAs for sequential identification of nucleotides; (3) ionic screening of surface charges in nanopores/nanochannels; (4) streaming electrical current generated by pressure-driven liquid flow in individual silica nanochannels as a function of channel height, pressure gradient, and salt concentration; (5) pressure-driven DNA transport in confined silica channels for novel diagnostic applications such as artificial gels and entropic trap arrays; and (6) surface functionalization, polarity switching, and transient response of silica nanotube, nanofluidic transistors.This project supports training a new generation of graduate students to develop the tools needed to attack complex system level problems. They will learn to combine theory, modeling, and high performance computer simulation. Students will participate in a dual-degree program in which they will fulfill Ph.D. requirements within their own discipline and master?s degree requirements in computer science with specialization in high performance computing and simulations. This award also supports the computational science workshops for underrepresented groups. Undergraduate students and faculty mentors from Historically Black Colleges and Universities and Minority Serving Institutions participate in a special one-week intense hands-on experience in parallel computing and immersive and interactive visualization. African American, Hispanic and Native American students will be recruited through USC?s Center for Engineering Diversity and women through USC?s Women in Science and Engineering Program. NON-TECHNICAL SUMMARY:This award is made on a proposal submitted to the PetaApps Solicitation. The Office of Cyberinfrastructure, the Mathematical and Physical Sciences Directorate, the Engineering Directorate, and the Computer and Information Science and Engineering Directorate contribute funds to this award. This award supports the development of software for the most advanced, ?petascale,? high performance supercomputers that will enable simulations that can capture phenomena that span across a range of length and time scales. The PIs will focus on a problem of particular importance, how biomolecules move through nanometer-sized pores in inorganic materials like silica and silicon nitride. The simulation can capture detailed physics of the problem and may illuminate possible applications to sequencing DNA and RNA molecules. The PIs will also focus on how charged atoms and molecules move through channels with dimensions on nanometer length scales more generally. There are potential applications to evolving ?lab-on-a-chip? technologies that seek to miniaturize laboratory analysis functions to the size of electronic device chips. Developed software will be distributed and can be used by a broad community of researchers in a variety of disciplinary and multidiscplinary research involving materials research, chemistry, engineering, physics, and nanotechnology. This project supports training a new generation of graduate students to develop the tools needed to attack complex system level problems. They will learn to combine theory, modeling, and high performance computer simulation to solve complex problems. Students will participate in a dual-degree program in which they will fulfill Ph.D. requirements within their own discipline and master?s degree requirements in computer science with specialization in high performance computing and simulations. This award also supports the computational science workshops for underrepresented groups. Undergraduate students and faculty mentors from Historically Black Colleges and Universities and Minority Serving Institutions participate in a special one-week intense hands-on experience in parallel computing and immersive and interactive visualization.