Coarse-graining complex interaction landscapes

M.加州大学圣巴巴拉分校的Scott Shell获得了化学系化学理论、模型和计算方法项目的奖项，以开发系统粗粒度的广泛算法。 计算机模拟的分子世界是一个既定的和宝贵的工具，了解如何音乐会的原子运动和相互作用引起观察到的性质，在生物学，材料，流体混合物等模拟也可能建议新的实验方向设计新的合成分子。 即使在最短的时间（百万分之一秒）内对分子中的每个原子进行建模，计算成本也非常高。 这一费用严重限制了可以进行的模拟的复杂性。 Shell博士和他的同事开发了一种方法，通过这种方法可以自动识别模拟中不必要的原子细节。 这些不必要的细节被需要更少计算的“粗粒度”模型所取代。反过来，这些粗糙的模型允许在更大的尺度上进行模拟。 这种能力开启了新的问题和研究体系。 该项目通过创建强大的方法来开发这种基本方法，以在高度粗糙的模型中保持高精度，并应用新技术来理解基于肽的材料。 该项目为各级学生提供教育机会，包括代表性不足群体的学生的参与。壳牌教授指导本科研究人员，并参加了几个校园范围内的多样性举措，有助于在UCSB的加州纳米系统研究所的专业发展和研究培训计划。该小组制定了战略，以改善理论和计算研究中女学生的招聘情况。Shell将杰出的女性研究人员带到校园，作为本科生，研究生和博士后的榜样。 虽然近年来一直在大力推行粗粒度方法，但主要的实践和概念障碍仍然存在，这些障碍会影响粗粒度（CG）模型的准确性，可移植性和自动化，从而限制了这些非常重要的建模方法的一般可靠性。 该项目利用Shell小组开发的相对熵框架来创建解决这些限制的通用新策略。 这些新方法植根于严格的统计力学理论和最先进的分子模拟技术。 具体而言，该项目创建了强大的策略，用于有效和准确地建模复杂的多体CG相互作用，包括状态条件，化学和系统，以及在自下而上的CG策略中无缝地包括外部约束（如实验信息）。 作为该技术的应用，这项工作开发了下一代，通用但序列敏感的CG肽模型，适用于理解和预测新兴的混合聚合物-肽材料中的超分子自组装。该奖项反映了NSF的法定使命，并已被认为是值得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的支持。

M. Scott Shell of the University of California Santa Barbara is supported by an award from the Chemical Theory, Models, and Computational Methods program in the Chemistry Division to develop broad-based algorithms for systematic coarse-graining. Computer simulations of the molecular world are an established and invaluable tool for understanding how the concert of atomic motions and interactions gives rise to observed properties in biology, materials, fluid mixtures, etc. Simulations may also suggest novel experimental directions for the design of new synthetic molecules. It is very computationally expensive to model every single atom in a molecule over even the shortest times (millionths of a second). This expense puts severe limits on the complexity of simulations that can be pursued. Dr. Shell and coworkers have developed an approach by which unnecessary atomic detail in simulations can be automatically identified. These unnecessary details are replaced by 'coarse-grained' models that require far fewer calculations. In turn, these coarse models permit simulations on dramatically larger scales. This capability opens new problems and systems of study. This project develops this basic approach by creating powerful ways to maintain high accuracy in highly coarse models and applies the new technique to understand peptide-based materials. This project provides educational opportunities for students at multiple levels, including involvement of those from underrepresented groups. Professor Shell mentors undergraduate researchers and participates in several campus-wide diversity initiatives that contribute to the professional development and research training programs at UCSB'sCalifornia Nanosystems Institute. The team develops strategies to improve the recruitment of women students in theoretical and computational research. A yearly seminar coordinated by Dr. Shell brings distinguished female researchers to campus to serve as role models for undergraduates, graduate students, and postdocs. While coarse-graining methods have been vigorously pursued in recent years, major practical and conceptual barriers remain that compromise coarse-grained (CG) model accuracy, transferability, and automation, and thus limit the general reliability of these all-important modeling approaches. This project leverages the relative entropy framework developed by the Shell group to create general new strategies for addressing these limitations. These new methods are rooted in rigorous statistical mechanical theory and state-of-the-art molecular simulation techniques. Specifically, the project creates robust strategies for efficiently and accurately modeling complex, multibody CG interactions across state conditions, chemistries, and systems, and for seamlessly including external constraints (like experimental information) in the bottom-up CG strategy. As an application of the techniques, this work develops a next-generation, general but sequence-sensitive CG peptide model suitable for understanding and predicting supramolecular self-assembly in emerging hybrid polymer-peptide materials.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.