Network for Computational Nanotechnology - Engineered nanoBIO Node

计算纳米技术网络 - 工程化 nanoBIO 节点

• 批准号: 1720625
• 负责人: James Glazier
• 金额: $ 400万
• 依托单位: Indiana University
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1720625&HistoricalAwards=false
• 关键词: Network; Computational; Nanotechnology; Engineered; nanoBIO

In its original formulation due to Feynman almost six decades back, nanotechnology began around a simple but powerful vision of a device engineered to write the entire Encyclopedia Britannica on the head of a pin. Nanotechnology now is a multidisciplinary field where devices are designed for applications in a diverse array of fields such as electronics, medicine, and energy using principles from engineering, physics, materials science, chemistry, computing, and biology. The safe and successful application of nanotechnology in the biological realm demands an advance in the original vision of Feynman due to the inherent multiscale nature of biology. Engineering of these nanoBIO devices must be based on the knowledge of how nanotechnology-based devices interact with biological systems at the protein, cell, tissue, and organ levels. The Engineered nanoBIO node at Indiana University (IU) will develop a powerful set of integrated computational nanotechnology tools that address this complex, multiscale problem and facilitate the discovery of customized, efficient, and safe nanoscale devices for biological applications. These computational tools will be tested and validated experimentally, and they will be integrated with IU's key cyberinfrastructure strengths in high-performance computing and scalable data-analysis platforms. They will meet critical national health needs as they find applications in nanomedicine by significantly enhancing the targeting and imaging capabilities of engineered nanoparticles, thus increasing our ability to generate new life-saving medicines for cancer treatment.  The node will engage several groups at IU, including: the Department of Intelligent Systems Engineering (ISE), the Biocomplexity Institute, the Department of Chemistry, the Pervasive Technology Institute (PTI), and the Digital Science Center. It will integrate advanced parallel computing middleware with the Network for Computational Nanotechnology Cyber Platform (nanoHUB). The node will be headquartered at the ISE, a department that is uniquely positioned to make nanoHUB the place for collaborative interactions of the interdisciplinary nanoBIO community and training of students in nanoengineering and bioengineering focused subjects. The node will interact with Science Gateways Community Institute in a broad outreach program targeting under-represented communities through workshops and workforce development forums. Nanomaterials-based devices offer unprecedented opportunities for the targeting, imaging, and manipulation of biological systems and have the potential to revolutionize the diagnosis and treatment of many diseases including cancer. However, this excitement about the potential of nanotechnology in the biomedical field is tempered by concerns about the outcomes of the interactions between engineered nanomaterials and biological systems, because we lack a sufficient fundamental understanding to link intrinsic nanoparticle features and incubation conditions to nanoparticle assembly and transport, single-cell and multicellular behavior, and ultimately therapeutic response. The Engineered nanoBIO node at Indiana University will address this complex problem by developing new nanoscience modeling and computational tools that span a wide range of biologically relevant length and time scales. The node aims to create computational tools designed for cutting-edge research to develop biocompatible, safe, and efficient nanoscale devices. The node plans to contribute tools that: 1) design functional nanoparticles and self-assembled nanostructures with user-selected physicochemical, mechanical, and biocompatible properties, 2) evaluate and control nanodevice-cell interactions and establish nanodevice-cell phenotype links, and 3) enable the engineering of multicellular systems using the nanoscale design elements and the nanodevice-cell phenotype links. The tools will be open-sourced, helping to attract a global community of users employing the node's tools and a global community of developers enhancing them. By introducing enhancements to cyberinfrastructure capabilities in the Network for Computational Nanotechnology, the Engineered nanoBIO node will provide an overarching framework of integrated nanoBIO tools that will empower researchers to investigate macroscale biotransport and cell phenotype response to tweaks in the design of nanodevices. This will enable the development of metrics for nanodevice safety, intracellular stability, and nanodevice-based detection, imaging, and drug-delivery capabilities.

纳米技术以Feynman的原始配方在其原始公式中，围绕着一个简单但有力的愿景，该设备设计为在PIN的头上编写整个Britannica的整个百科全书。 Nanotechnology现在是一个多学科领域，使用工程，物理，材料科学，化学，计算和生物学的原理，为在潜水领域（例如电子，医学和能源）的应用设计设备。由于生物学的继承性质，纳米技术在生物领域中的安全应用应用在生物领域中需要进步。这些纳米比设备的工程必须基于对基于纳米技术的设备如何与蛋白质，细胞，组织和器官水平上的生物系统相互作用的知识。印第安纳大学（IU）的工程纳米比节点将开发一套强大的集成计算纳米技术工具，以解决这一复杂，多尺度问题，并促进发现用于生物应用的定制，高效和安全的纳米级设备。这些计算工具将通过实验进行测试和验证，并将与IU的关键网络基础结构强度集成到高性能计算和可扩展的数据分析平台中。他们将通过显着增强工程纳米颗粒的靶向和成像能力，从而提高我们为癌症治疗生成新的挽救生命的药物的能力，从而满足关键的国家健康需求。该节点将在IU的几个小组中与：智能系统工程部（ISE），生物复杂研究所，化学系，普遍技术研究所（PTI）和数字科学中心。它将将高级并行计算中间件与计算纳米技术网络平台（NanoHub）的网络集成。该节点将位于ISE的总部，该部门的部门唯一位置，可以使纳米布成为跨学科的纳米比社区合作互动的地方，并在纳米工程和生物工程专注的主题中对学生进行培训。该节点将通过研讨会和劳动力发展论坛针对代表不足的社区的广泛推广计划与科学网关社区研究所进行互动。基于纳米材料的设备为生物系统的靶向，成像和操纵提供了前所未有的机会，并有可能改变包括癌症在内的许多疾病的诊断和治疗。但是，这种对生物医学领域中纳米技术潜力的兴奋受到对工程纳米材料和生物学系统之间相互作用的结果的关注，因为我们缺乏足够的基本理解，无法将固有的纳米粒子特征和孵化条件与纳米粒子组件组装和运输和多个抗反应，以及最终的单一构成行为，以及最终的影响，以及最终的影响。印第安纳大学的工程纳米比节点将通过开发新的纳米科学建模和计算工具来解决这个复杂的问题，这些工具跨越了广泛的生物学相关长度和时间尺度。该节点旨在创建旨在开发生物相容性，安全和高效纳米级设备的尖端研究的计算工具。 The node plans to contribute tools that: 1) design functional nanoparticles and self-assembled nanostructures with user-selected physical, mechanical, and biocompatible properties, 2) evaluation and control nanodevice-cell interactions and establish nanodevice-cell phenotype links, and 3) enable the engineering of multicellular systems using the nanoscale design elements and the nanodevice-cell phenotype links.工具将是开源的，有助于吸引使用节点工具的全球用户社区，以及一个全球开发人员社区来增强其。通过在计算纳米技术网络网络中引入网络基础设施能力的增强，工程的纳米比节点将提供综合纳米比奥工具的总体框架，该框架将使研究人员能够调查宏观生物传输和细胞表型对Nanodevices设计中的调整的响应。这将使指标能够开发用于纳米电视安全性，细胞内稳定性以及基于纳米维克的检测，成像和药物传递能力的指标。

项目成果

Machine Learning for Performance Enhancement of Molecular Dynamics Simulations

• DOI: 10.1007/978-3-030-22741-8_9
• 发表时间: 2019-06
• 作者: J. Kadupitiya;G. Fox;V. Jadhao

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

• DOI: 10.1093/bib/bbac212
• 发表时间: 2022-07-18
• 期刊: Briefings in bioinformatics
• 影响因子: 9.5

Reply to Bair: Crossover to Arrhenius behavior at high viscosities in squalane

回复 Bair：角鲨烷高粘度下与阿伦尼乌斯行为的交叉

• DOI: 10.1073/pnas.1715298114
• 发表时间: 2017
• 期刊: Proceedings of the National Academy of Sciences
• 作者: Jadhao, Vikram;Robbins, Mark O.
• 通讯作者: Robbins, Mark O.

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics

• DOI: 10.1093/bioinformatics/btaa096
• 发表时间: 2020-05-15
• 期刊: BIOINFORMATICS
• 影响因子: 5.8
• 作者: Hasnain, Zaki;Fraser, Andrew K.;Newton, Paul K.
• 通讯作者: Newton, Paul K.

Exact solution for the Anisotropic Ornstein–Uhlenbeck process

各向异性 Ornstein–Uhlenbeck 过程的精确解

• DOI: 10.1016/j.physa.2021.126526
• 发表时间: 2022
• 期刊: Physica A: Statistical Mechanics and its Applications
• 作者: de Almeida, Rita M.C.;Giardini, Guilherme S.Y.;Vainstein, Mendeli;Glazier, James A.;Thomas, Gilberto L.
• 通讯作者: Thomas, Gilberto L.