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

CDS

• 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& MPATHS; Microscopic; Pathway; Analysis; CDS& MPATHS; Microscopic; Pathway; Analysis

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.

从将水冻结成冰的非技术总结到将蛋白质冻结为分析和药物设计阵列的顺序，再到将纳米颗粒组装成直接照明的晶体，在原子，分子，分子，大分子和颗粒的结构排列中发生的变化，在自然界和许多材料和制造中都是无处不在的。了解这些结构排列如何在从一个阶段到另一阶段的变化中发生，对于理解自然界中的自组织过程以及设计和制造新材料的自下而上至关重要。 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自组成和从一个阶段变为另一个阶段。设想的工具包 - 高通量研究（MPATHS）的微观途径分析工具包将是可访问的，易于使用，并利用最快的可用计算机体系结构。它将以可能使跨系统比较的方式对不同类型的相过渡途径进行系统的系统，高通量研究，并将与研究人员使用模拟或实验进行阶段过渡研究的研究人员使用的其他开源包进行比较。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，以及活跃物质系统中的蜂群。对原子和分子自组装过程感兴趣的材料，工程和化学界也将立即甚至更广泛的兴趣。强调科学计算领域以外的研究人员的可访问性将有助于通过更广泛的社区采用M Path。技术摘要过渡，其中多粒子系统的结构从一个状态变为另一个状态是无处不在的，并且已广泛用于工业用途，例如构成了制造的材料，包括制造材料，构成了制造材料，构成了制造的材料。纳米复合材料等。因此，了解这些结构过渡如何发生的机械细节（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属性的新型材料以及增加产量或降低已经使用的材料。因此，大量的研究致力于研究此类相变的研究，尤其是从热力学和动力学的角度来看，包括研究有序相和成核速率核定的大量自由能壁垒的研究。此类研究是有益的，但并未揭示特定样本如何从一个状态变为另一个状态的微观粒子级详细信息。例如，液体凝固成有序的固相等结构过渡是由热力学数量或压力等热力学量的变化驱动的，这些变化会触发涉及粒子（原子，分子，纳米颗粒）的局部结构的变化，最终跨越了整个系统。局部结构如何沿着过渡途径变化的微观细节控制所得晶体的质量，以及所得的晶体是热力学优选的一个还是亚稳态的多晶型物。 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.借助手头上的微观信息，研究人员不仅可以准确地量身定制处理参数，还可以纳米颗粒属性属性，以稳定某些多晶型物而不是其他多晶型物，提高产品的结构质量并优化产量。该项目将开发一个广义的计算工具包，该工具包将使系统研究和交叉系统比较跨越大型材料的结构范围。该工具包的系统不足的性质将消除易于和偏见的手动干预，从而加速了多种材料的途径的发现，理解和工程。使用来自实验或计算原始数据的粒子位置，方向和特性作为输入，用于高通量研究（MPATHS）的微观途径分析工具包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其发展。项目团队将在MPATH中开发和包装功能强大且无知的例程，以查找邻居，计算每粒子订单参数及其互相关，并使用信息理论中的方法检测本地和全球结构事件，并基于此信息可视化系统。 MPATHS将通过非专家来实现专家工作流程，并具有系统不可屈服的功能，因此可以直观地使用它，而在许多学科的结构过渡方面，研究人员几乎没有计算专业知识。 MPATH将结合易于使用的界面，这些界面符合真实的（可转移，可再现，可转移，可由他人使用并可扩展）原则，包括将python脚本接口到MPATH的脚本，将广泛使用，并可以作为离线或在线工具作为一种启用后的分析或能够在线启动的工具。为了在计算能力方面的进步，允许对复杂的M人的详细分子模拟进行详细的分子模拟，以发现驱动模拟系统中的两个不同结构过渡的显微镜过程，作为示例：（i）来自原子和纳米粒子的等构建复杂晶体的组装途径，以及在诸如三个范围的统计范围内的有序结构，并在诸如三度统计中的统计范围内的统计信息。使用基金会的智力优点和更广泛的影响审查标准通过评估来支持。