57 Search Results

Infrared spectroscopy is a cost-effective, non-destructive, and environmentally benign technology that is increasingly recognized as an important solution for meeting the global demand for soil data. While both near-infrared (NIR) and mid-infrared (MIR) diffuse reflectance spectroscopy enable rapid estimation of soil properties, they present a significant trade-off: NIR offers superior scalability and lower operational costs, whereas MIR provides higher analytical fidelity by capturing fundamental molecular vibrations. In this study, we propose a self-supervised, multi-fidelity learning framework designed to bridge this gap. Our approach leverages large-scale MIR spectral libraries to learn a compact, transferable latent representation, into which NIR spectra aremore » subsequently aligned for downstream prediction. The workflow consists of pretraining a latent model on a large MIR library, adapting the representation using a smaller paired NIR–MIR dataset, and evaluating generalization on an independent external test set. Across a range of chemical and physical soil properties, we found that MIR-derived embeddings improved prediction accuracy relative to baseline models that used raw MIR inputs. Predictions derived from the spectrum conversion (NIR to MIR) task did not match the performance of the original MIR spectra but were similar or superior to predictive performance of NIR-only models, suggesting the unified spectral latent space can effectively leverage the larger and more diverse MIR dataset for prediction of soil properties not well represented in current NIR libraries.« less

Understanding the complex chemistry of organic materials under dynamic compression is important for many applications, but it is challenging due to the large number of reactions occurring at various time scales. Here, in this study, we develop a machine learning potential based on Chebyshev polynomials to study the insensitive energetic material 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under detonation. We discuss a strategy for constructing diverse training data needed to capture the complex chemistry of TATB. Our potential demonstrates strong transferability across a wide range of thermodynamic conditions and other explosives, enabling accurate and reliable chemical modeling of organic materials under extreme conditions. Themore » efficiency of our approach allows for simulations over several nanoseconds and for large system sizes, providing detailed insights into the chemistry of shocked TATB. The model accurately reproduces experimental Hugoniot equation of state data, and our simulations reveal the rapid formation of nitrogen-rich carbon clusters following shock. The methods and datasets developed here offer a robust framework for accurate chemical modeling of other shocked organic energetic materials.« less

KRAS4a and KRAS4b are important regulators of signaling, and their interactions with the plasma membrane are dynamic and influenced by lipid composition. KRAS 4a and 4b have nearly identical globular domains but differ in their membrane-associated hyper variable region (HVR). The functional distinctions between these isoforms remain unclear, particularly with regards to their dependence on specific lipids and the membrane environment. Previous work showed that the membrane orientation of KRAS4b affects its ability to bind to RAF kinase RBDCRD and that the KRAS–RBDCRD complex adopts different poses on the membrane as well as influences the size and composition of themore » lipid environment. To model differences between KRAS 4a and 4b protein–lipid interactions, we extended the Multiscale Machine-Learned Modeling Infrastructure (MuMMI) to incorporate continuum simulations in the grand canonical ensemble, enabling sampling across macroscopic, coarse-grained, and all-atom resolutions. Using this framework, we systematically altered PIP2 concentrations, KRAS 4a versus 4b, and RAF RBDCRD complexation to assess impacts on membrane–protein interactions and dynamics. Our results reveal that reducing PIP2 shifts and broadens the membrane orientational preference of both KRAS 4b and 4a, with stronger effects on 4b HVR localization versus 4a. We demonstrate that with depletion of the strong negatively charged PIP2 lipid, the less charged phosphatidylserine replaces PIP2. Our findings highlight similarities and distinctions in the dynamics and lipid dependency of KRAS isoforms and suggest that ordering of the local lipid composition by HVRs is a shared property and key modulator of RAS-mediated signaling at the plasma membrane.« less

Additive manufacturing (AM) is revolutionizing the production of custom components with complex internal geometries, essential for high-performance applications in diverse fields such as medicine and defense. These AM parts optimize strength while minimizing weight by utilizing internal lattice structures consisting of large quantities of small interconnected struts. However, the complexity of these structures, combined with the challenges of using X-ray Computed Tomography (XCT) data, makes validation of part reliability difficult. This ultimately inhibits the development of novel parts for our collaborating material scientists. Here, we introduce LatticeAnalytics, a novel framework specifically designed for visual inspection of defects in these latticemore » structures. Our framework offers an end-to-end solution that includes the data management of XCT scans, enables remote access for geographically dispersed teams through a web-based dashboard, and incorporates novel visualizations. Our analysis is facilitated by a coarse alignment between the lattice’s nominal model, a spatial graph, and the XCT data. We employ a simple VR-based approach for fast and rough alignment, followed by an offline registration and identification of the struts. With the nodes and struts aligned and identified in the volume, our framework allows querying of subvolumes containing a single strut at multiple resolutions. This avoids computation over the entire lattice and also allow for easy parallelization of down-stream computations, such as strut-specific metrics. To depict a fast overview of the strut quality, we introduce two innovative visual encodings, crucial for our collaborators’ research in creating novel AM parts: the Contour View and the Roughness Map, which depict critical geometrical and surface features of individual struts in standardized two 2D views. We evaluated the integrated system through expert interviews. The feedback confirms the framework’s practicality and its effectiveness in enhancing current inspection workflows. It solves major bottlenecks for our collaborators, ultimately helping them create novel parts with advanced properties.« less

Advanced manufacturing creates increasingly complex objects with material compositions that are often difficult to characterize by a single modality. Our collaborating domain scientists are going beyond traditional methods by employing both X-ray and neutron computed tomography to obtain complementary representations expected to better resolve material boundaries. However, the use of two modalities creates its own challenges for visualization, requiring either complex adjustments of bimodal transfer functions or the need for multiple views. Together with experts in nondestructive evaluation, we designed a novel interactive bimodal visualization approach to create a combined view of the co-registered X-ray and neutron acquisitions of industrialmore » objects. Using an automatic topological segmentation of the bivariate histogram of X-ray and neutron values as a starting point, the system provides a simple yet effective interface to easily create, explore, and adjust a bimodal visualization. Here, we propose a widget with simple brushing interactions that enables the user to quickly correct the segmented histogram results. Our semiautomated system enables domain experts to intuitively explore large bimodal datasets without the need for either advanced segmentation algorithms or knowledge of visualization techniques. We demonstrate our approach using synthetic examples, industrial phantom objects created to stress bimodal scanning techniques, and real-world objects, and we discuss expert feedback.« less

Computational techniques such as all-atom (AA) molecular dynamics (MD) simulations and coarse-grained (CG) models have been essential to study various biological problems over a wide range of scales. While AA simulations provide detailed insights, they are computationally expensive for capturing dynamics over longer length and time scales. CG approaches, particularly ultra-coarse-grained (UCG) models as considered in this study, have addressed this limitation by simplifying molecular representations, enabling the study of larger systems and longer time scales. This work focuses on the development of UCG models of proteins and their integration into the Multiscale Machine-Learned Modeling Infrastructure (MuMMI) to efficiently samplemore » protein conformations, exemplified by the RAS-RBDCRD protein complex. By employing a combination of essential dynamics coarse graining (EDCG) and heterogeneous elastic network modeling (hENM) with anharmonic modifications, we developed UCG models based on the fluctuations observed in the higher resolution Martini CG simulations. These models allow the accurate sampling of protein configurations and long-range conformational changes. The incorporation of an implicit membrane model further enhanced the exploration of protein− membrane dynamics. Additionally, a novel machine-learning-based backmapping approach was developed to convert UCG structures to Martini CG representations, resulting in improved prediction accuracy. Finally, the integration of UCG models into MuMMI significantly enhances the exploration of protein configurations, offering critical insights into the role of protein dynamics in biological processes.« less

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructuremore » uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.« less

The integration of machine-learning techniques into inertial confinement fusion (ICF) simulations has emerged as a powerful approach for enhancing computational efficiency. By replacing the costly nonlocal thermodynamic equilibrium (NLTE) model with machine-learning models, significant reductions in calculation time have been achieved. However, determining how to optimize machine-learning-based NLTE models in order to match ICF simulation dynamics remains challenging, underscoring the need for physically relevant error metrics and strategies to enhance model accuracy with respect to these metrics. Thus, we propose novel physics-informed transformations designed to emphasize energy transport, use these transformations to establish new error metrics, and demonstrate that theymore » yield smaller errors within reduced principal-component spaces compared to conventional transformations.« less

Digital twins (DTs) are an emerging capability in additive manufacturing (AM), set to revolutionize design optimization, inspection, in situ monitoring, and root cause analysis. AM DTs typically incorporate multimodal data streams, ranging from machine toolpaths and in-process imaging to X-ray CT scans and performance metrics. Despite the evolution of DT platforms, challenges remain in effectively inspecting them for actionable insights, either individually or in a multidisciplinary, geographically distributed team setting. Quality assurance, manufacturing departments, pilot labs, and plant operations must collaborate closely to reliably produce parts at scale. This is particularly crucial in AM where complex structures require a collaborativemore » and multidisciplinary approach. Additionally, the large-scale data originating from different modalities and their inherent 3D nature pose significant hurdles for traditional 2D desktop-based inspection methods. To address these challenges and increase the value proposition of DTs, we introduce a novel virtual reality (VR) framework to facilitate collaborative and real-time inspection of DTs in AM. This framework includes advanced features for intuitive alignment and visualization of multimodal data, visual occlusion management, streaming large-scale volumetric data, and collaborative tools, substantially improving the inspection of AM components and processes to fully exploit the potential of DTs in AM.« less

Deep learning approaches have provided state-of-the-art performance in many applications by relying on large and overparameterized neural networks. However, such networks are very brittle and are difficult to deploy on resource-limited platforms. Model pruning, i.e., reducing the size of the network, is a widely adopted strategy that can lead to a more robust and compact model. Many heuristics exist for model pruning, but our understanding of the pruning process remains limited due to the black-box nature of a neural network model. Empirical studies show that some heuristics improve performance whereas others can make models more brittle. Here, this work aimsmore » to shed light on how different pruning methods alter the network’s internal feature representation and the corresponding impact on model performance. To facilitate a comprehensive comparison and characterization of the high-dimensional model feature space, we introduce a visual geometric analysis of feature representations. We evaluated a set of critical geometric concepts decomposed from the commonly adopted classification loss and used them to design a visualization system to compare and highlight the impact of pruning on model performance and feature representation. The proposed tool provides an environment for an in-depth comparison of pruning methods and a comprehensive understanding of how the model responds to common data corruption. By leveraging the proposed visualization, machine learning researchers can reveal the similarities between pruning methods and redundancy in robustness evaluation benchmarks, obtain geometric insights about the differences between pruned models that achieve superior robustness performance, and identify samples that are robust or fragile to model pruning and common data corruption.« less