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CDS&E: MPATHS - Microscopic Pathway Analysis Toolkit for High-throughput Studies

CDS

基本信息

批准号：
2302470
负责人：
Sharon Glotzer
金额：
$ 66万
依托单位：
Regents of the University of Michigan - Ann Arbor
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2023
资助国家：
美国
起止时间：
2023-05-01 至 2027-04-30
项目状态：
未结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2302470&HistoricalAwards=false
关键词：
CDS&amp MPATHS Microscopic Pathway Analysis

项目摘要

Non-technical summaryFrom the freezing of water into ice, to the ordering of proteins into arrays for analysis and drug design, to the assembly of nanoparticles into crystals that direct light, changes that occur in the structural arrangements of atoms, molecules, macromolecules and particles is ubiquitous in nature and in the synthesis and manufacturing of many materials and products. Understanding how these structural arrangements occur during a change from one phase of matter to another is critical to understanding self-organization processes in nature and to designing and making new materials that build themselves – predictively, reliably, and inexpensively -- from the bottom-up. By controlling the assembly process, novel materials that combine unique properties in important, unprecedented ways become possible, impacting everything from protective coatings and light-sensitive paints to materials that store and convert energy to stealth technologies and sports equipment.This project aims to develop and broadly disseminate powerful scientific software to aid researchers in tracking, analyzing, studying, and eventually engineering phase transition “pathways” that a system of material building blocks follows as it self-assembles and changes from one phase to another. The envisioned toolkit -- Microscopic Pathway Analysis Toolkit for High-Throughput Study (MPATHS) -- will be accessible, be easy to use, and exploit the fastest available computer architectures. It will make possible systematic, high-throughput studies of different types of phase transition pathways in ways that will make cross-system comparisons easy and will interoperate seamless with other open-source packages used by researchers who study phase transitions via simulations or experiments.Because MPATHS will reveal microscopic, mechanistic details of how order emerges from disorder during assembly processes, MPATHS will be of immediate interest to the nanoparticle and soft matter communities who can use it to study thermodynamic self-assembly of colloidal crystals and other complex structures, as well as swarming processes in active matter systems. MPATHS will also be of immediate and even broader interest to the materials, engineering, and chemistry communities interested in atomic and molecular self-assembly processes. An emphasis on accessibility to researchers outside of scientific computing fields will facilitate the adoption of MPATHS by a broader community.Technical summaryPhase transitions in which the structure of a multi-particle system changes from one state to another are ubiquitous in nature and have been widely utilized for industrial purposes, such as the manufacturing of pharmaceuticals and the fabrication of materials, including metals, ceramics, plastics, nanocomposites and more. Therefore, understanding the mechanistic details of exactly how these structural transitions occur (i.e., the transition pathway) is crucial for a wide range of potential applications, including predicting and designing novel materials with desired properties as well as increasing yields or driving down costs for ones already in use. Hence, considerable research is devoted to the study of such phase transitions, especially from the point of view of thermodynamics and kinetics, including the study of such bulk quantities as free energy barriers to nucleation of ordered phases and nucleation rates. Such studies are informative but do not reveal the microscopic, particle-level details of how a particular sample changes from one state to another. For example, structural transitions such as crystallization, where a liquid solidifies into an ordered solid phase, are driven by a change in thermodynamic quantities such as temperature or pressure, which triggers changes in local structure involving a subset of particles (atoms, molecules, nanoparticles) that eventually spans the entire system. Microscopic details of how the local structure changes along the transition pathway controls the quality of the resulting crystal, as well as whether the resulting crystal is the thermodynamically preferred one or a metastable polymorph. However, despite the recent advances in computational power and experimental approaches, automated, system-agnostic tracking of structure evolution and detection of local and global changes in particle organization is largely nonexistent in materials and other fields of science and engineering, hindering the studies needed to predictively link processing parameters and particle attributes (such as shape and interaction patchiness in the case of nanoparticles) to final product. With such microscopic information in hand, researchers could precisely tailor not only processing parameters but also nanoparticle attributes to stabilize certain polymorphs over others, improve structural quality of the product, and optimize yield.This project will develop a generalized computational toolkit that will enable the systematic study and cross-system comparisons of structure evolution across a wide range of self-assembling materials. The system-agnostic nature of the toolkit will eliminate error- and bias-prone manual intervention, thereby accelerating the discovery, understanding, and engineering of pathways for multiple classes of materials. Using particle positions, orientations, and properties from either experimental or computational raw data as input, the Microscopic Pathway Analysis Toolkit for High-throughput Studies (MPATHS) will enable users to identify and label local structural motifs and track their development across the entire transition pathway. The project team will develop and package within MPATHS powerful and system-agnostic routines for finding neighbors, calculating per-particle order parameters and their cross-correlations, detecting local and global structural events using methods from information theory, and visualizing systems based on this information. MPATHS will enable expert workflows by non-experts and be system-agnostic so it can be used intuitively and with little-to-no computational expertise by researchers working on structural transitions across many disciplines. MPATHS will incorporate easy-to-use interfaces that abide by TRUE (transferable, reproducible, usable by others and extensible) principles, including a python scripting interface to facilitate the scripting of customized MPATHS analyses, a graphical user interface to foster accessibility, and a powerful command line interface. MPATHS will be made widely available and usable as either an offline or online tool to enable either post-analysis or on-the-fly control of simulations or experiments.MPATHS will permit the study of fundamental processes that only now are able to be studied due to advances in computing power that allow for detailed molecular simulations of complex structural transitions over long times with fine temporal detail, and exciting developments in in-situ electron microscopy that allow, for the first time, the visualization of dynamic nanoparticle rearrangements during the self-assembly of colloidal crystals of nanoparticles. MPATHS will be used to discover the microscopic processes driving two different structural transitions in simulated systems as exemplars: (i) assembly pathways of isostructural complex crystals from atoms and nanoparticles and emergence of ordered structures such as three-phase coexistence in active matter systems.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.

从将水冻结成冰，到将蛋白质排列成用于分析和药物设计的阵列，再到将纳米粒子组装成引导光线的晶体，原子、分子、大分子和粒子的结构排列发生的变化在自然界中以及在许多材料和产品的合成和制造中无处不在。了解这些结构安排在物质从一个阶段到另一个阶段的变化过程中是如何发生的，对于理解自然界中的自组织过程，以及设计和制造自底向上、可预测、可靠、廉价地自我构建的新材料至关重要。通过控制装配过程，以重要的、前所未有的方式结合独特性能的新型材料成为可能，影响从保护涂层和光敏涂料到存储和转换能量的材料，再到隐身技术和运动设备。该项目旨在开发并广泛传播强大的科学软件，以帮助研究人员跟踪、分析、研究并最终设计相变“路径”，即材料构建块系统在自组装和从一个阶段到另一个阶段的变化过程中遵循的“路径”。设想的工具包-用于高通量研究的微观途径分析工具包(MPATHS) -将易于访问，易于使用，并利用最快的可用计算机架构。它将使对不同类型的相变路径进行系统的、高通量的研究成为可能，这种研究方式将使跨系统比较变得容易，并将与通过模拟或实验研究相变的研究人员使用的其他开源软件包无缝互操作。由于MPATHS将揭示组装过程中有序如何从无序中产生的微观机械细节，因此纳米粒子和软物质群落将对MPATHS产生直接兴趣，他们可以使用它来研究胶体晶体和其他复杂结构的热力学自组装，以及活性物质系统中的蜂群过程。对于对原子和分子自组装过程感兴趣的材料、工程和化学社区来说，MPATHS也将引起直接的甚至更广泛的兴趣。强调科学计算领域以外的研究人员的可访问性将促进更广泛的社区采用MPATHS。技术概述多粒子系统结构从一种状态转变为另一种状态的相变在自然界中无处不在，并已广泛应用于工业用途，如制药和材料制造，包括金属、陶瓷、塑料、纳米复合材料等。因此，了解这些结构转变发生的机制细节（即过渡途径）对于广泛的潜在应用至关重要，包括预测和设计具有所需性能的新材料，以及提高产量或降低已经在使用的材料的成本。因此，人们对这类相变进行了大量的研究，特别是从热力学和动力学的角度，包括对有序相成核的自由能垒和成核速率等大量问题的研究。这类研究提供了信息，但没有揭示特定样品如何从一种状态变化到另一种状态的微观、粒子级细节。例如，结构转变，如结晶，液体凝固成有序的固相，是由热力学量的变化（如温度或压力）驱动的，这引发了涉及粒子子集（原子、分子、纳米粒子）的局部结构的变化，最终跨越整个系统。局部结构如何沿着转变途径变化的微观细节控制了所得晶体的质量，以及所得晶体是热力学首选晶体还是亚稳多晶。然而，尽管最近在计算能力和实验方法方面取得了进展，但在材料和其他科学与工程领域，基本上不存在自动的、与系统无关的结构演变跟踪以及粒子组织局部和全局变化检测，这阻碍了将加工参数和粒子属性（如纳米粒子的形状和相互作用斑块）与最终产品预测联系起来所需的研究。有了这些微观信息，研究人员不仅可以精确地定制加工参数，还可以精确地定制纳米颗粒属性，以稳定某些多晶型，提高产品的结构质量，并优化产量。该项目将开发一个通用的计算工具包，使系统研究和跨系统比较各种自组装材料的结构演变成为可能。该工具包的系统不可知特性将消除容易产生错误和偏差的人工干预，从而加速发现、理解和设计多种材料的途径。使用来自实验或计算原始数据的粒子位置、方向和属性作为输入，用于高通量研究的微观途径分析工具包（MPATHS）将使用户能够识别和标记局部结构基序，并在整个过渡途径中跟踪它们的发展。项目团队将在MPATHS中开发和封装强大的系统无关例程，用于查找邻居、计算每粒子顺序参数及其相互关联、使用信息论方法检测局部和全局结构事件，以及基于这些信息的可视化系统。MPATHS将使非专家的专家工作流程成为可能，并且与系统无关，因此研究人员可以直观地使用它，几乎不需要计算专业知识，就可以跨多个学科进行结构转换。MPATHS将结合易于使用的接口，遵守TRUE（可转移、可复制、可被他人使用和可扩展）原则，包括一个python脚本界面，以促进定制MPATHS分析的脚本编写，一个图形用户界面，以促进可访问性，以及一个强大的命令行界面。MPATHS将作为离线或在线工具广泛提供和使用，以实现模拟或实验的后期分析或实时控制。由于计算能力的进步，可以对长时间复杂结构转变进行详细的分子模拟，并且具有精细的时间细节，MPATHS将允许对基本过程进行研究，并且原位电子显微镜的令人兴奋的发展首次允许在纳米颗粒胶体晶体自组装过程中动态纳米颗粒重排的可视化。MPATHS将被用来发现驱动模拟系统中两种不同结构转变的微观过程，作为例子：(i)原子和纳米颗粒的等结构复杂晶体的组装途径，以及活性物质系统中三相共存等有序结构的出现。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。