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.

必须在许多尺度上理解生物和材料系统的演变，以实现突破性的进步。受影响的领域包括健康科学，材料科学，能量转换，可持续性和整体生活质量。使用复杂模型和配置的分子模拟在此类努力中起着越来越多的作用。他们解决了在很小的时间和长度尺度上研究事件的实验的局限性。由于所研究的系统的复杂性，此类模拟需要大量的专业知识。以及所使用的工具。对于包含无机材料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，并评估结果中的不确定性。它们将有助于开发网络卢比计算基础架构。网络卢比将大大减少执行最新模拟所需的时间。他们还将帮助将下一代研究人员在这一重要领域进行教育。Cyber​​loop将将三个现有的软件和固态模拟平台（IFF，OpenKim和Charmm-GUI）整合到一个统一的框架中。这些系统将共同努力，使用户能够设置复杂的BionAnomatial配置，选择可靠的经过验证的力场，为流行的仿真平台生成输入脚本，并评估结果中的不确定性。 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 charmm-gui中的模块。 Cyber​​loop满足了用户社区的关键需求，以发现和设计新的多组分BionAnomatials，以创建下一代的治疗方法，用于能源转化的材料和Ultrastrong复合材料。该项目将促进研究生，本科生和博士后学者（包括代表性不足和少数族裔学生）在参与机构的培训，以准备一名跨学科的科学劳动力，并在网络支持技术方面具有丰富的经验。在线教育材料和教程将有助于增加参与学术界和政府的Bionanomeatial研究。该奖项由NSF高级网络基础设施办公室共同支持，NSF数学和物理科学局内的材料研究和化学划分。该奖项反映了NSF的法定任务，并被认为是通过基金会的知识分子和更广泛影响的评估来评估CRITEIA CRITERIA CRITERIA，通过评估的支持值得。

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 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

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 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