1,693 research outputs found

    Unsupervised landmark analysis for jump detection in molecular dynamics simulations

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    Molecular dynamics is a versatile and powerful method to study diffusion in solid-state ionic conductors, requiring minimal prior knowledge of equilibrium or transition states of the system's free energy surface. However, the analysis of trajectories for relevant but rare events, such as a jump of the diffusing mobile ion, is still rather cumbersome, requiring prior knowledge of the diffusive process in order to get meaningful results. In this work, we present a novel approach to detect the relevant events in a diffusive system without assuming prior information regarding the underlying process. We start from a projection of the atomic coordinates into a landmark basis to identify the dominant features in a mobile ion's environment. Subsequent clustering in landmark space enables a discretization of any trajectory into a sequence of distinct states. As a final step, the use of the smooth overlap of atomic positions descriptor allows distinguishing between different environments in a straightforward way. We apply this algorithm to ten Li-ionic systems and conduct in-depth analyses of cubic Li7_{7}La3_{3}Zr2_{2}O12_{12}, tetragonal Li10_{10}GeP2_{2}S12_{12}, and the β\beta-eucryptite LiAlSiO4_{4}. We compare our results to existing methods, underscoring strong points, weaknesses, and insights into the diffusive behavior of the ionic conduction in the materials investigated

    Efficient deep data assimilation with sparse observations and time-varying sensors

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    Variational Data Assimilation (DA) has been broadly used in engineering problems for field reconstruction and prediction by performing a weighted combination of multiple sources of noisy data. In recent years, the integration of deep learning (DL) techniques in DA has shown promise in improving the efficiency and accuracy in high-dimensional dynamical systems. Nevertheless, existing deep DA approaches face difficulties in dealing with unstructured observation data, especially when the placement and number of sensors are dynamic over time. We introduce a novel variational DA scheme, named Voronoi-tessellation Inverse operator for VariatIonal Data assimilation (VIVID), that incorporates a DL inverse operator into the assimilation objective function. By leveraging the capabilities of the Voronoi-tessellation and convolutional neural networks, VIVID is adept at handling sparse, unstructured, and time-varying sensor data. Furthermore, the incorporation of the DL inverse operator establishes a direct link between observation and state space, leading to a reduction in the number of minimization steps required for DA. Additionally, VIVID can be seamlessly integrated with Proper Orthogonal Decomposition (POD) to develop an end-to-end reduced-order DA scheme, which can further expedite field reconstruction. Numerical experiments in a fluid dynamics system demonstrate that VIVID can significantly outperform existing DA and DL algorithms. The robustness of VIVID is also accessed through the application of various levels of prior error, the utilization of varying numbers of sensors, and the misspecification of error covariance in DA

    Structure of plastically compacting granular packings

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    The developing structure in systems of compacting ductile grains were studied experimentally in two and three dimensions. In both dimensions, the peaks of the radial distribution function were reduced, broadened, and shifted compared with those observed in hard disk- and sphere systems. The geometrical three--grain configurations contributing to the second peak in the radial distribution function showed few but interesting differences between the initial and final stages of the two dimensional compaction. The evolution of the average coordination number as function of packing fraction is compared with other experimental and numerical results from the literature. We conclude that compaction history is important for the evolution of the structure of compacting granular systems.Comment: 12 pages, 12 figure

    Developing Algorithms for Quantifying the Super Resolution Microscopic Data: Applications to the Quantification of Protein-Reorganization in Bacteria Responding to Treatment by Silver Ions

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    Histone-like nucleoid structuring proteins (HNS) play significant roles in shaping the chromosomal DNA, regulation of transcriptional networks in microbes, as well as bacterial responses to environmental changes such as temperature fluctuations. In this work, the intracellular organization of HNS proteins in E. coli bacteria was investigated utilizing super-resolution fluorescence microscopy, which surpasses conventional microscopy by 10–20 fold in spatial resolution. More importantly, the changes of the spatial distribution of HNS proteins in E. coli, by addition of silver ions into the growth medium were explored. To quantify the spatial distribution of HNS in bacteria and its changes, an automatic method based on Voronoi diagram was implemented. The HNS proteins localized in super-resolution fluorescence microscopy were segmented and clustered based on several quantitative parameters, such as molecular areas, molecular densities, and mean inter-molecular distances of the k-th rank, all of which were computed from the Voronoi diagrams. These parameters, as well as the associated clustering analysis, allowed us to quantify how the spatial organization of HNS proteins responds to silver, and provided insight into understanding how microbes adapt to new environments

    Geospatial Tessellation in the Agent-In-Cell Model: A Framework for Agent-Based Modeling of Pandemic

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    Agent-based simulation is a versatile and potent computational modeling technique employed to analyze intricate systems and phenomena spanning diverse fields. However, due to their computational intensity, agent-based models become more resource-demanding when geographic considerations are introduced. This study delves into diverse strategies for crafting a series of Agent-Based Models, named "agent-in-the-cell," which emulate a city. These models, incorporating geographical attributes of the city and employing real-world open-source mobility data from Safegraph's publicly available dataset, simulate the dynamics of COVID spread under varying scenarios. The "agent-in-the-cell" concept designates that our representative agents, called meta-agents, are linked to specific home cells in the city's tessellation. We scrutinize tessellations of the mobility map with varying complexities and experiment with the agent density, ranging from matching the actual population to reducing the number of (meta-) agents for computational efficiency. Our findings demonstrate that tessellations constructed according to the Voronoi Diagram of specific location types on the street network better preserve dynamics compared to Census Block Group tessellations and better than Euclidean-based tessellations. Furthermore, the Voronoi Diagram tessellation and also a hybrid -- Voronoi Diagram - and Census Block Group - based -- tessellation require fewer meta-agents to adequately approximate full-scale dynamics. Our analysis spans a range of city sizes in the United States, encompassing small (Santa Fe, NM), medium (Seattle, WA), and large (Chicago, IL) urban areas. This examination also provides valuable insights into the effects of agent count reduction, varying sensitivity metrics, and the influence of city-specific factors

    Fluid dynamics and mass transfer in porous media: Modelling fluid flow and filtration inside open-cell foams

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