Elements: Enabling multi-resolution simulations at the interface of biology and nanotechnology with ARBD

要素：利用 ARBD 在生物学和纳米技术的界面上实现多分辨率模拟

• 批准号: 2311550
• 负责人: Aleksei Aksimentiev
• 金额: $ 59.69万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2026-07-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2311550&HistoricalAwards=false
• 关键词: Elements; Enabling; multi; resolution; simulations

At the interface of biology and nanotechnology, the unfamiliar combinations of materials, physical laws and design principles promise the most radical advancements in science and technology. Transforming this promise into practical applications requires precise characterization of the unfamiliar interactions, which presents major challenges to existing experimental probes. This project aims to overcome these challenges by providing the research community with a robust and versatile computational framework capable of accurate description of mesoscale bionano systems. Rather than modeling such systems as a collection of atoms, the framework trades resolution for computational efficiency, allowing the computational effort to be applied where it is needed. The project’s outcome will permit computational characterization of a wide range of previously intractable systems, including large self-assembled DNA nanostructures, systems for single molecule reading of biological information, viruses, organelles, and even small bacterial cells.This CSSI Elements program aims to provide a general framework for modeling systems at the interface of biology and nanotechnology by transforming the Atomic Resolution Brownian Dynamics (ARBD) code into a general-purpose mesoscale simulation engine supporting multiple hardware platforms, multi-node and multi-GPU parallelism. The implementation of advanced simulation methods in ARBD is expected to greatly simplify modeling and simulation tasks common to the research communities specializing in nanoscale transport, plasmonics, DNA self-assembly, and biomolecular physics. Using a test-driven software development approach, the project transforms ARBD by implementing new parallel data structures that target multiple hardware types and provide multiple levels of parallel communication. The project introduces additional flexibility into modelling of complex processes through its support for collective variables and multi-copy simulations. The project aims to make the ARBD framework widely accessibility through its integration with a python-based force-field library, creation of detailed documentation and tutorials, and hands-on workshops.This award by the NSF Office of Advanced Cyberinfrastructure is jointly supported by the Division of Materials Research.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在生物学和纳米技术的交汇处，材料、物理定律和设计原理的不熟悉组合有望实现科学技术方面最根本的进步，将这一承诺转化为实际应用需要对不熟悉的相互作用进行精确表征，这对现有实验提出了重大挑战。该项目旨在通过为研究界提供一个强大且多功能的计算框架来克服这些挑战，该框架能够准确描述介观生物纳米系统，而不是将此类系统建模为原子集合，而是以分辨率换取计算效率。要应用的计算工作量该项目的成果将允许对以前难以处理的各种系统进行计算表征，包括大型自组装 DNA 纳米结构、生物信息、病毒、细胞器甚至小细菌细胞的单分子读取系统。 Elements计划旨在通过将原子分辨率布朗动力学（ARBD）代码转换为支持多个硬件平台的通用介观模拟引擎，为生物学和纳米技术接口的建模系统提供通用框架， ARBD 中先进模拟方法的实施预计将大大简化专门从事纳米级传输、等离激元、DNA 自组装和生物分子物理研究领域的建模和模拟任务。驱动的软件开发方法，该项目通过实现针对多种硬件类型的新并行数据结构进行改造，并提供多级并行通信。该项目通过支持集体变量和多副本，为复杂过程的建模引入了额外的灵活性。该项目旨在通过与基于 Python 的力场库的集成、创建详细文档和教程以及实践研讨会，使 ARBD 框架得到广泛使用。该奖项由 NSF 高级网络基础设施办公室共同支持。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。