Collaborative Research: Frameworks: Cyberloop for Accelerated Bionanomaterials Design

为了取得突破性进展，必须在多个尺度上了解生物和材料系统的进化。受影响的领域包括健康科学、材料科学、能源转换、可持续性和整体生活质量。使用复杂模型和构型的分子模拟在这种努力中发挥着越来越大的作用。它们解决了在非常小的时间和长度范围内研究事件的实验的局限性。由于正在研究的系统的复杂性，这样的模拟需要很高的专业知识。以及所使用的工具。对于同时包含无机和生物材料的系统来说，情况尤其如此。该项目将帮助研究人员快速建立复杂的模拟，以高精度进行模拟，并评估结果中的不确定性。他们将帮助开发Cyberloop计算基础设施。Cyberloop将极大地减少执行最先进的模拟所需的时间。Cyberloop将把现有的三个成功的软物质和固态模拟平台(IFF、OpenKIM和CHARMM-图形用户界面)整合到一个统一的框架中。这些系统将协同工作，使用户能够设置复杂的生物异常材料配置，选择可靠的经验证的力场，为流行的模拟平台生成输入脚本，并评估结果中的不确定性。这些工具的集成需要大量的技术和科学创新，包括：自动电荷分配协议和文件转换，将界面力场(IFF)扩展到新系统，生成新的表面模型，将开放原子间模型知识库(OpenKIM)扩展到键合力场，开发基于机器学习的力场选择和不确定性工具，以及在CHARMM-图形用户界面中开发新的纳米材料Builder和Bionano Builder模块。Cyberloop满足了用户群体的一项关键需求，即发现和设计新的多组分生物异常材料，以创建下一代疗法、能量转换材料和超强复合材料。该项目将促进参与机构对研究生、本科生和博士后学者的培训，包括任职人数不足的学生和少数族裔学生，以培养一支在网络技术方面拥有丰富经验的跨学科科学队伍。在线教育材料和教程将有助于增加学术界和政府对生物异常材料研究的参与。该奖项由NSF高级网络基础设施办公室、NSF数学和物理科学局内的材料研究部和化学部共同支持。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The evolution of biological and materials systems must be understood at many scales in order to achieve groundbreaking advances. Areas that are impacted include the health sciences, materials sciences, energy conversion, sustainability, and overall quality of life. Molecular simulations using complex models and configurations play an increasing role in such efforts. They address the limitations of experiments which study events over very small time and length scales. Such simulations require great expertise due to the complexity of the systems being studied. and the tools being used. This is particularly true for systems containing both inorganic and biological materials. This project will help researchers to quickly set up complex simulations, carry out the simulations with high accuracy, and assess uncertainties in the results. They will help develop the Cyberloop computational infrastructure. Cyberloop will dramatically reduce the time required to perform state-of-the-art simulations. They will also help to educate the next generation of researchers in this important field.Cyberloop will integrate three existing successful platforms for soft matter and solid state simulations (IFF, OpenKIM, and CHARMM-GUI) into a single unified framework. These systems will work together to enable users to set up complex bionanomaterial configurations, select reliable validated force fields, generate input scripts for popular simulation platforms, and assess the uncertainty in the results. The integration of these tools requires a host of technological and scientific innovations including: automated charge assignment protocols and file conversions, expansion of the Interface force field (IFF) to new systems, generation of new surface models, extension of the Open Knowledgebase of Interatomic Models (OpenKIM) to bonded force fields, development of machine learning based force field selection and uncertainty tools, and development of new Nanomaterial Builder and Bionano Builder modules in CHARMM-GUI. Cyberloop fulfils a critical need in the user community to discover and engineer new multi-component bionanomaterials to create the next generation of therapeutics, materials for energy conversion, and ultrastrong composites. The project will facilitate the training of graduate students, undergraduate students, and postdoctoral scholars, including underrepresented and minority students, at the participating institutions to prepare an interdisciplinary scientific workforce with significant experience in cyber-enabled technology. Online educational materials and tutorials will help increase participation in bionanomaterial research across academia and government. This award is jointly supported by the NSF Office of Advanced Cyberinfrastructure, and the Division of Materials Research and the Division of Chemistry within the NSF Directorate of Mathematical and Physical Sciences.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.