Collaborative Research: Frameworks: Cyberloop for Accelerated Bionanomaterials Design

合作研究：框架：加速生物纳米材料设计的 Cyber​​loop

• 批准号: 1931343
• 负责人: Wonpil Im
• 金额: $ 59万
• 依托单位: Lehigh University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-10-01 至 2024-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1931343&HistoricalAwards=false
• 关键词: Collaborative; Research; Frameworks; Cyberloop; Accelerated

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.

生物和材料系统的进化必须在许多尺度上理解，以实现突破性的进展。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。分子模拟使用复杂的模型和配置发挥越来越大的作用，在这样的努力。它们解决了在非常小的时间和长度尺度上研究事件的实验的局限性。由于所研究系统的复杂性，这种模拟需要大量的专业知识。以及所使用的工具。这对于含有无机和生物材料的系统尤其如此。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，并评估结果的不确定性。他们将帮助开发Cyberloop计算基础设施。Cyberloop将大大减少执行最先进模拟所需的时间。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-GUI）整合到一个统一的框架中。这些系统将共同工作，使用户能够设置复杂的生物纳米材料配置，选择可靠的验证力场，为流行的模拟平台生成输入脚本，并评估结果的不确定性。这些工具的整合需要大量的技术和科学创新，包括：自动化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，将原子间模型开放知识库（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，在CHARMM-GUI中开发新的Nanomaterial Builder和Bionano Builder模块。Cyberloop满足了用户社区的关键需求，即发现和设计新的多组分生物纳米材料，以创造下一代治疗方法，能量转换材料和超强复合材料。该项目将促进在参与机构培训研究生、本科生和博士后学者，包括代表性不足的学生和少数民族学生，以培养一支在网络技术方面具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纳米材料研究的参与。该奖项由美国国家科学基金会高级网络基础设施办公室（NSF Office of Advanced Cyberinfrastructure）、美国国家科学基金会数学和物理科学理事会（NSF Directorate of Mathematical and Physical Sciences）下属的材料研究部（Division of Materials Research）和化学部（Division of Chemistry）共同支持。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane.

• DOI: 10.1021/acs.jctc.0c01144
• 发表时间: 2021-04-13
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Choi YK;Cao Y;Frank M;Woo H;Park SJ;Yeom MS;Croll TI;Seok C;Im W
• 通讯作者: Im W

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.

• DOI: 10.1021/acs.jctc.1c00996
• 发表时间: 2022-01-11
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Choi YK;Kern NR;Kim S;Kanhaiya K;Afshar Y;Jeon SH;Jo S;Brooks BR;Lee J;Tadmor EB;Heinz H;Im W
• 通讯作者: Im W

CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers.

• DOI: 10.1021/acs.jctc.1c00169
• 发表时间: 2021-04-13
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Choi YK;Park SJ;Park S;Kim S;Kern NR;Lee J;Im W
• 通讯作者: Im W

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications.

• DOI: 10.1021/acs.jctc.2c01246
• 发表时间: 2023-04-25
• 期刊: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
• 影响因子: 5.5
• 作者: Feng, Shasha;Park, Soohyung;Choi, Yeol Kyo;Im, Wonpil
• 通讯作者: Im, Wonpil