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征求的提案颁发的。数学与物理科学局、工程局、计算机与信息科学与工程局的网络基础设施办公室、材料研究部和多学科活动办公室为该奖项提供了资金。这个PetaApps项目的重点是混合量子力学-原子-中尺度模拟生物聚合物（如DNA和RNA）通过纳米级二氧化硅和氮化硅膜上的孔和通道的离子传输和易位。pi的目标是开发一个预测的分层千万亿级模拟框架：(1)高度精确的量子力学模拟来描述生物聚合物易位中的化学过程；(2)数十亿原子分子动力学模拟生物聚合物在固体膜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原子间相互作用；(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纳米孔/纳米通道表面附近，晶格玻尔兹曼嵌入流体的其余部分；(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、自调优的多核并行仿真算法；(6)自动模型转换，根据需要将高保真度的仿真嵌入到较粗的仿真中，并控制误差传播以量化不确定性。验证后，该分层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；(2)用于核苷酸序列鉴定的易位dna的电子特性；(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由压力驱动的液体流动产生的流动电流与通道高度、压力梯度和盐浓度的关系；(5)压力驱动的DNA在受限二氧化硅通道中的运输，用于新型诊断应用，如人工凝胶和熵阱阵列；(6)二氧化硅纳米管、纳米流体晶体管的表面功能化、极性开关和瞬态响应。该项目支持培训新一代的研究生开发解决复杂系统级问题所需的工具。他们将学习结合理论、建模和高性能计算机模拟。学生将参加一个双学位项目，他们将完成自己学科的博士学位要求和硕士学位要求。计算机科学学士学位，高性能计算和模拟专业。该奖项还支持为代表性不足的群体举办的计算科学研讨会。来自传统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沉浸式交互式可视化的特殊实践体验。南加州大学将招收非裔美国人、西班牙裔美国人和印第安人学生。s工程多样性中心和女性通过南加州大学？科学与工程专业的女性。非技术摘要：该奖项是根据提交给PetaApps征集的提案颁发的。网络基础设施办公室、数学和物理科学理事会、工程理事会以及计算机和信息科学与工程理事会为该奖项提供资金。该合同支持最先进的千兆级计算机软件的开发。高性能超级计算机将使模拟能够捕捉跨越长度和时间尺度的现象。pi将专注于一个特别重要的问题，即生物分子如何在二氧化硅和氮化硅等无机材料中的纳米级孔隙中移动。模拟可以捕获问题的详细物理原理，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在纳米尺度的通道中移动。“芯片实验室”有潜在的应用前景。将实验室分析功能缩小到电子设备芯片大小的技术。开发的软件将被分发，并可被广泛的研究人员社区用于各种学科和多学科研究，包括材料研究、化学、工程、物理和纳米技术。该项目支持培训新一代的研究生开发解决复杂系统级问题所需的工具。他们将学习结合理论、建模和高性能计算机模拟来解决复杂问题。学生将参加一个双学位项目，他们将完成自己学科的博士学位要求和硕士学位要求。计算机科学学士学位，高性能计算和模拟专业。该奖项还支持为代表性不足的群体举办的计算科学研讨会。来自传统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.