Frontiers of Coarse-graining

粗粒度的前沿

• 批准号: 2102677
• 负责人: Gregory Voth
• 金额: $ 48万
• 依托单位: University of Chicago
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2102677&HistoricalAwards=false
• 关键词: Frontiers; Coarse; graining

Gregory Voth of the University of Chicago is supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry to develop and apply systematic theory and computer simulation methods that can bridge the various length and time scales inherent in complex systems, in order to model their overall behavior. The objective of these new multi-scale theory and simulation methods is to connect molecular behaviors at small length and time scale scales with the phenomena they cause at significantly larger length and time scales, in systems such as in biological cells, new materials, and liquids. The broader impacts of the project include STEM (Science, Technology, Engineering and Mathematics) development of members of underrepresented groups through active mentorship. In the longer term, this research also has the potential to improve the well-being of society (i) by helping to lay the fundamental groundwork for computer simulation-aided advances in the health sciences (e.g. modeling the molecular basis of viral infection) and in materials science (e.g. new biologically-inspired materials),(ii) by building increased partnerships between academia and industry (e.g. to model therapeutic antibody formulations via simulation models), and (iii) by providing enhanced infrastructure to the community in providing the basis for open source software devoted to multi-scale computer modeling. This research project from the Voth group at the University of Chicago is focused upon the development of theoretical and computational methodology to study complex condensed phase systems, including biomolecules, soft materials, and liquids, in new ways. The conceptual basis for the research relates to expanding the frontiers of systematic coarse-graining methods at various levels of resolution, as well as expanding their application to key macromolecular problems. The mathematical basis for the project lies in the implementation of equilibrium and non-equilibrium statistical mechanics and dynamics for multi-scale modeling. The project will also develop transformative computer simulation approaches from these theoretical advances to help reveal and understand the molecular-level features that define the functional behavior of, e.g., biomolecular systems at large length and time scales. Various connected resolutions of the theoretical framework will be considered, including the highly (ultra) coarse-grained as well as the more finely resolved coarse-grained. New techniques from machine learning will be introduced to develop models and quantify errors, as well as new computer algorithms implemented to define and solve coarse-grained molecular models.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.

芝加哥大学的 Gregory Voth 获得化学系化学理论、模型和计算方法项目的奖项支持，致力于开发和应用系统理论和计算机模拟方法，这些方法可以弥合复杂系统固有的各种长度和时间尺度，以模拟他们的整体行为。这些新的多尺度理论和模拟方法的目标是将小长度和时间尺度上的分子行为与它们在生物细胞、新材料和液体等系统中在更大长度和时间尺度上引起的现象联系起来。该项目更广泛的影响包括通过积极指导，促进代表性不足群体成员的 STEM（科学、技术、工程和数学）发展。 从长远来看，这项研究还有潜力改善社会福祉（i）通过帮助为计算机模拟辅助的健康科学进步奠定基础（例如对病毒感染的分子基础进行建模）和在材料科学（例如新的生物启发材料）中，（ii）通过在学术界和工业界之间建立更多的伙伴关系（例如通过模拟模型对治疗性抗体制剂进行建模），以及（iii）通过向社区提供增强的基础设施来提供致力于多尺度计算机建模的开源软件的基础。芝加哥大学 Voth 小组的这个研究项目专注于理论和计算方法的发展，以新的方式研究复杂的凝聚相系统，包括生物分子、软材料和液体。该研究的概念基础涉及在不同分辨率水平上扩展系统粗粒度方法的前沿，以及将其应用扩展到关键的大分子问题。该项目的数学基础在于实现多尺度建模的平衡和非平衡统计力学和动力学。该项目还将利用这些理论进展开发变革性的计算机模拟方法，以帮助揭示和理解分子水平的特征，这些特征定义了例如大长度和时间尺度的生物分子系统的功能行为。 将考虑理论框架的各种相关分辨率，包括高度（超）粗粒度以及更精细分辨率的粗粒度。将引入机器学习新技术来开发模型和量化误差，以及实施新的计算机算法来定义和解决粗粒度分子模型。该奖项反映了 NSF 的法定使命，并通过使用基金会的评估进行评估，认为值得支持。智力价值和更广泛的影响审查标准。

项目成果

Understanding dynamics in coarse-grained models. II. Coarse-grained diffusion modeled using hard sphere theory

了解粗粒度模型中的动力学。

• DOI: 10.1063/5.0116300
• 发表时间: 2023-01
• 期刊: The Journal of Chemical Physics
• 作者: Jin, Jaehyeok;Schweizer, Kenneth S.;Voth, Gregory A.
• 通讯作者: Voth, Gregory A.

Coarse-Graining of Imaginary Time Feynman Path Integrals: Inclusion of Intramolecular Interactions and Bottom-up Force-Matching

虚数时间费曼路径积分的粗粒度：包含分子内相互作用和自下而上的力匹配

• DOI: 10.1021/acs.jpca.2c04349
• 发表时间: 2022-09-08
• 期刊: The Journal of Physical Chemistry. a
• 作者: Ryu, Won Hee;Voth, Gregory A.
• 通讯作者: Voth, Gregory A.

Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship

了解粗粒度模型中的动力学。

• DOI: 10.1063/5.0116299
• 发表时间: 2023-01
• 期刊: The Journal of Chemical Physics
• 作者: Jin, Jaehyeok;Schweizer, Kenneth S.;Voth, Gregory A.
• 通讯作者: Voth, Gregory A.

Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles

利用机器学习通过虚拟粒子极大扩展自下而上粗粒度模型的范围和精度

• DOI: 10.1021/acs.jctc.2c01183
• 发表时间: 2022-12-08
• 期刊: Journal of Chemical Theory and Computation
• 影响因子: 5.5
• 作者: Patrick G. Sahrmann;Timothy D Loose;Aleks;er E. P. Durumeric;er;G. Voth
• 通讯作者: G. Voth

Bottom-up Coarse-Graining: Principles and Perspectives

自下而上的粗粒度：原则和观点

• DOI: 10.1021/acs.jctc.2c00643
• 发表时间: 2022-10-11
• 期刊: Journal of Chemical Theory and Computation
• 影响因子: 5.5
• 作者: Jin, Jaehyeok;Pak, Alexander J.;Durumeric, Aleksander E. P.;Loose, Timothy D.;Voth, Gregory A.
• 通讯作者: Voth, Gregory A.