Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's evolution is key to selecting the best candidates for new drugs, materials for manufacturing, and countless other practical applications. With today's technology, these simulations can encompass millions of unit transitions between discrete molecular structures, spanning up to several milliseconds of real time. Attempting to perform a brute-force analysis with data-sets of this size is not only computationally impractical, but would not shed light on the physically-relevant features of the data. Moreover, there is a need to analyze simulation ensembles in order to compare similar processes in differing environments. These problems call for an approach that is analytically transparent, computationally efficient, and flexible enough to handle the variety found in materials based research. In order to address these problems, we introduce MolSieve, a progressive visual analytics system that enables the comparison of multiple long-duration simulations. Using MolSieve, analysts are able to quickly identify and compare regions of interest within immense simulations through its combination of control charts, data-reduction techniques, and highly informative visual components. A simple programming interface is provided which allows experts to fit MolSieve to their needs. To demonstrate the efficacy of our approach, we present two case studies of MolSieve and report on findings from domain collaborators.

翻译：分子动力学（MD）模拟在尖端物理化学研究中应用广泛。它通过原子间相互作用模型，揭示物理系统随时间演化的关键机制。理解系统演化过程对于筛选新药候选分子、制造材料及众多实际应用具有重要意义。当前技术可模拟离散分子结构间数百万次单元跃迁，覆盖长达数毫秒的真实时间跨度。对此规模的数据集进行穷举分析不仅计算成本高昂，更无法揭示数据的物理相关特征。此外，研究人员还需分析模拟集成数据以比较不同环境中的相似过程。这些问题要求一种兼具分析透明性、计算高效性且能灵活处理材料研究中多样化数据的方法。为此，我们提出MolSieve——一种支持多时长模拟比较的渐进式可视分析系统。通过控制图、数据降维技术及高信息量可视化组件的结合，分析师能快速识别并比较海量模拟中的关键区域。系统提供简洁的编程接口，便于领域专家定制化使用。为验证方法有效性，我们展示了两个MolSieve的案例研究，并报告了领域合作者的分析成果。