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征集的提案而颁发的。网络基础设施办公室，材料研究部和数学和物理科学局多学科活动办公室，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。 这个PetaApps项目的重点是混合量子力学-原子-介观模拟离子传输和生物聚合物的易位，如DNA和RNA通过二氧化硅和氮化硅膜中的纳米级孔和通道。PI旨在开发一个预测性的分层千万亿次模拟框架，用于：（1）高度精确的量子力学模拟，以描述生物聚合物移位的化学过程;（2）数十亿原子的分子动力学模拟，用于固态膜中受限流体环境中生物聚合物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原子间的相互作用;（3）混合分子动力学和自适应晶格玻尔兹曼模拟，其中分子动力学嵌入到纳米孔/纳米通道的表面附近，并且晶格玻尔兹曼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）元可扩展的、自调整的多核并行模拟算法;以及（6）自动化模型转换，以根据需要将更高保真度的模拟嵌入到更粗糙的模拟中，并控制误差传播以量化不确定性。经过验证，这种分级千万亿次模拟框架将用于研究：（1）DNA通过二氧化硅和氮化硅纳米孔的易位动力学和动力学;（3）纳米孔/纳米通道中表面电荷的离子屏蔽;（4）在单独的二氧化硅纳米通道中由压力驱动的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）用于新型诊断应用如人工凝胶和熵阱阵列的受限二氧化硅通道中的压力驱动的DNA运输;以及（6）二氧化硅纳米管的表面功能化、极性转换和瞬态响应，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。他们将学习联合收割机理论，建模和高性能计算机仿真相结合。学生将参加双学位课程，他们将完成博士学位。要求在自己的学科和掌握？计算机科学专业的硕士学位要求，专门从事高性能计算和仿真。该奖项还支持代表性不足的群体的计算科学研讨会。来自历史上的黑人学院和大学以及少数民族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沉浸式交互式可视化的特殊实践体验。非裔美国人，西班牙裔和美洲原住民学生将通过南加州大学招募？的工程多样性中心和妇女通过南加州大学？妇女参与科学和工程方案。非技术摘要：本奖项是根据提交给PetaApps征集的提案而颁发的。网络基础设施办公室，数学和物理科学局，工程局，计算机和信息科学与工程局为该奖项提供资金。该奖项支持最先进的软件开发，？千万亿次？高性能的超级计算机，将使模拟，可以捕捉跨越一系列的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孔移动。模拟可以捕获问题的详细物理学，并可能阐明DNA和RNA分子测序的可能应用。PI还将关注带电原子和分子如何更普遍地通过纳米长度尺度的通道移动。进化有潜在的应用吗？芯片实验室寻求将实验室分析功能扩展到电子设备芯片大小的技术。开发的软件将被分发，并可用于各种学科和多学科研究，涉及材料研究，化学，工程，物理和纳米技术的研究人员的广泛社区。 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。他们将学习结合联合收割机理论，建模和高性能计算机仿真来解决复杂的问题。学生将参加双学位课程，他们将完成博士学位。要求在自己的学科和掌握？计算机科学专业的硕士学位要求，专门从事高性能计算和仿真。该奖项还支持代表性不足的群体的计算科学研讨会。来自历史上的黑人学院和大学以及少数民族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沉浸式交互式可视化的特殊实践体验。

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.