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At least 1,333 records · Page 74

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics↗

The many-body electronic interactions of Fe(II)–porphyrin

Fe(II)–porphyrin complexes exhibit a diverse range of electronic interactions between the metal and macrocycle. Herein, the incremental full configuration interaction method is applied to the entire space of valence orbitals of a Fe(II)–porphyrin model using a modest basis set. A novel visualization framework is proposed to analyze individual many-body contributions to the correlation energy, providing detailed maps of this complex’s highly correlated electronic structure. Furthermore, this technique is used to parse the numerous interactions of two low-lying triplet states ( 3 A 2 g and 3 E g ) and to show that strong metal d–d and macrocycle π–π orbital interactions preferentially stabilize the 3 A 2 g state. d–π interactions, on the other hand, preferentially stabilize the 3 E g state and primarily appear when correlating six electrons at a time. Ultimately, the Fe(II)–porphyrin model’s full set of 88 valence electrons are correlated in 275 orbitals, showing the interactions up to the 4-body level, which covers the great majority of correlations in this system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aura Atmospheric Data Products and Their Availability from NASA Goddard Earth Sciences DAAC

NASA's EOS-Aura spacecraft was launched successfully on July 15, 2004. The four instruments onboard the spacecraft are the Microwave Limb Sounder (MLS), the Ozone Monitoring Instrument (OMI), the Tropospheric Emission Spectrometer (TES), and the High Resolution Dynamics Limb Sounder (HBDLS). The Aura instruments are designed to gather earth sciences measurements across the ultraviolet, visible, infra-red, thermal and microwave regions of the electromagnetic spectrum. Aura will provide over 70 distinct standard atmospheric data products for use in ozone layer and surface UV-B monitoring, air quality forecast, and atmospheric chemistry and climate change studies (http://eosaura.gsfc.nasa.gov/). These products include earth-atmosphere radiances and solar spectral irradiances; total column, tropospheric, and profiles of ozone and other trace gases, surface W-B flux; clouds and aerosol characteristics; and temperature, geopotential height, and water vapor profiles. The MLS, OMI, and HIRDLS data products will be archived at the NASA Goddard Earth Sciences (GES) Distributed Active Archive Center (DAAC), while data from TES will be archived at NASA Langley Research Center DAAC. Some of the standard products which have gone through quick preliminary checks are already archived at the GES DAAC (http://daac.nsfc.nasa.gov/) and are available to the Aura science team and data validation team members for data validation; and to the application and visualization software developers, for testing their application modules. Once data are corrected for obvious calibration problems and partially validated using in-situ observations, they would be made available to the broader user community. This presentation will provide details of the whole suite of Aura atmospheric data products, and the time line of the availability of the rest of the preliminary products and of the partially validated provisional products. Software and took available for data access, visualization, and data mining will also be discussed.

Ahmad, S.↗

The Marine and Hydrokinetic ToolKit (MHKiT) for Data Quality Control and Analysis [Slides]

The ability to collect, ingest, condition, reduce, quality control, process, visualize, and store data in a standardized way is critical at all stages of Marine Energy (ME) research and technology/project development. MHKiT is an open-source, standardized suite of ME data processing functions that provides the ability to ingest, condition, reduce, quality control, process, visualize and store ME data. MHKiT is developed in both Python and Matlab.

16 TIDAL AND WAVE POWER↗

Marangoni Effects on Near-Bubble Microscale Transport During Boiling of Binary Fluid Mixtures

In earlier investigations, Marangoni effects were observed to be the dominant mechanism of boiling transport in 2-propanol/water mixtures under reduced gravity conditions. In this investigation we have examined the mechanisms of binary mixture boiling by exploring the transport near a single bubble generated in a binary mixture between a heated surface and cold surface. The temperature field created in the liquid around the bubble produces vaporization over the portion of its interface near the heated surface and condensation over portions of its interface near the cold surface. Experiments were conducted using different mixtures of water and 2-propanol under 1g conditions and under reduced gravity conditions aboard the KC135 aircraft. Since 2-propanol is more volatile than water, there is a lower concentration of 2-propanol near the hot surface and a higher concentration of 2-propanol near the cold plate relative to the bulk quantity. This difference in interface concentration gives rise to strong Marangoni effects that move liquid toward the hot plate in the near bubble region for 2-propanol and water mixtures. In the experiments in this study, the pressure of the test system was maintained at about 5 kPa to achieve the full spectrum of boiling behavior (nucleate boiling, critical heat flux and film boiling) at low temperature and heat flux levels. Heat transfer data and visual documentation of the bubble shape were extracted from the experimental results. In the 1-g experiments at moderate to high heat flux levels, the bubble was observed to grow into a mushroom shape with a larger top portion near the cold plate due to the buoyancy effect. The shape of the bubble was somewhat affected by the cold plate subcooling and the superheat of the heated surface. At low superheat levels for the heated surface, several active nucleation sites were observed, and the vapor stems from them merged to form a larger bubble. The generation rate of vapor is moderate in this regime and the bubble shape is cylindrical in appearance. In some instances, the bubble interface appeared to oscillate. At higher applied heat flux levels, the top of the bubble became larger, apparently to provide more condensing interface area adjacent to the cold plate. Increasing the applied heat flux ultimately led to dry-out of the heated surface, with conditions just prior to dryout corresponding to the maximum heat flux (CHF). A more stable bubble was observed when the system attained the minimum heat flux (for film boiling). In this regime, most of the surface under the bottom of the bubble was dry with nucleate boiling sometimes occuring around the contact perimeter of the bubble at heated surface. Different variations (e.g. gap between two plates, molar concentration of the liquid mixture) of the experiments were examined to determine parametric effects on the boiling process and to determine the best conditions for the KC135 reduced gravity tests. Variation of the gap was found to have a minor impact on the CHF. However, reducing the gap between the hot and cold surface was observed to significantly reduce the minimum heat flux for fixed molar concentration of 2-propanol. In the reduced gravity experiments aboard the KC135 aircraft, the bubble formed in the 6.4 mm gap was generally cylindrical or barrel shaped and it increased its extent laterally as the surface superheat increased. In reduced gravity experiments, dryout of the heated surface under the bubble was observed to occur at a lower superheated temperature than for 1g conditions. Observed features of the boiling process and heat transfer data under reduced gravity will be discussed in detail. The results of the reduced gravity experiments will also be compared to those obtained in comparable 1g experiments. In tandem with the experiments we are also developing a computational model of the transport in the liquid surrounding the bubble during the boiling process. The computational model uses a level set method to model motion of the interface. It will incorporate a macroscale treatment of the transport in the liquid gap between the surfaces and a microscale treatment of transport in the regions between the bubble interface and the solid surfaces. The features of the model will be described in detail. Future research directions suggested by the results to date will also be discussed.

V. Carey↗

LANL Regular Employee Population and Demographics, FY15-21

This document summarizes an effort to compile and analyze the LANL regular employee population’s demographic attributes and trends between FY15-FY21 using MicroStrategy, a web-based data analytics and visualization tool. LANL’s HR Division collected and prepared data for the Weapons Program’s annual reporting activities for the 2017 through 2023 NNSA Stockpile Stewardship and Management Plan (SSMP). Los Alamos workforce data represent the fiscal year-end snapshot of the permanent employee population who are categorized by the Common Occupational Classification System (COCS). This work enables further analyses, including trends for all workforce attributes presented in the SSMPs as well as a definition of a crosswalk between COCS categorization and the internal laboratory job classification hierarchy. Data for other sites and the federal workforce, as shown in the SSMPs, are included and corresponding figures can be visualized within the MicroStrategy tool. A portable, Excel-based version of the tool was developed and shared with the multi-site workforce working group. This summary highlights selected aspects of the LANL regular workforce. The data analyses and visualizations communicate insights within three major themes regarding permanent LANL employees: 1) demographic transformation, 2) attrition, and 3) skills. Regarding demographic transformation, and consistent with the general trend across the enterprise, early career regular employees are the fastest growing group, with growth ranging between 12-34% year-to-year over the seven-year period analyzed. The data also reflect effects of internal and external factors on attrition; the large spike in separations in FY18 aligns with the contract transition from LANS to Triad and the dip in attrition between FY20-FY21 is likely a result of the global pandemic. The population of regular employees in general management, engineer, and operator COCS categories have the fastest growth rates amongst all the occupational categories. The MicroStrategy and Excel tools provide additional details and trends.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Automated compatibility checking of prefabricated components using 3D as-built models and BIM

There have been recent efforts to use reality capture technologies to perform remote quality control in construction. However, there is a lack of research efforts in detecting construction incompatibilities in modular construction using reality capture technologies. The construction incompatibilities in modular construction often cause reworks and delays in the project schedule. To address this issue, this paper presents a general compatibility analysis method that propose scanning the modules in manufacturing plant and construction site, and check module-to-module compatibility remotely, prior to the shipment and installation. This study provides three sample module-to-module compatibility scenarios to validate the proposed compatibility analysis. The case study results show that the compatibility analysis method was able to identify the compatibility issues with high accuracy. Lastly, the compatibility analysis method was validated in terms of accuracy and time performance in six scenarios that was defined on the modules.

42 ENGINEERING↗

AIMSim : An accessible cheminformatics platform for similarity operations on chemicals datasets

The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Further, most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a Graphical User Interface for code-free utilization with fully interactive plots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energy-water interdependencies across the three major United States electric grids: A multi-sectoral analysis

As water availability and timing of delivery fluctuates and the US electric grid sees rapid transformation and reconfiguration under decarbonization and resource adequacy strategies, there is a critical need for information and data that supports understanding the water-energy interdependency landscape. The United States currently lacks comprehensive data, informative visualizations, and analysis of energy-water interdependencies at scales necessary to support resource and operational decision-making. This article provides US electricity interconnection-level Sankey diagrams that show the relative reliance of water and energy across various economic sectors. A deeper analysis is additionally provided at the county level to illustrate trends and potential opportunities related to resiliency and efficiency in multi-sectoral water and energy flow distributions and intensities. We find that the electricity interconnections in the US vary dramatically in their water and energy interdependencies across applications and economic sectors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

nmrrr : A Reproducible Workflow for Binning and Visualizing NMR Spectra From Environmental Samples

Nuclear magnetic resonance (NMR) spectroscopy is a useful tool for detection and identification of molecular structural information, with increasing applications in environmental sciences. NMR instrument outputs are however heterogeneous and require extensive post-processing, creating barriers to their use and application by non-specialists. Here, we report on a new open-source R package, nmrrr, that processes and visualizes spectral data obtained from one-dimensional solution-state and solid-state NMR experiments; the package also performs relevant calculations commonly applied in natural organic matter communities, such as computing the relative abundance of various functional groups. We document the package's installation, dependencies, and functions; and provide a standard workflow for processing NMR data. This package is currently available on CRAN and GitHub, and community contributions are welcome.

54 ENVIRONMENTAL SCIENCES↗

HunStat2 – a simple and low-cost potentiostat with electrochemical impedance spectroscopy capability

We have developed a low-cost (30 USD), simple do-it-yourself (DIY) potentiostat with cyclic voltammetry (CV), open circuit potential (OCP) and electrochemical impedance spectroscopy (EIS) capability. The HunStat2 potentiostat is based on Analog Devices' AD5941 Analog Front End chip, which significantly simplifies the construction of potentiostats for both direct and alternating current (DC and AC, respectively) techniques. Interested readers are provided with circuit diagrams and a bill of materials to build the potentiostat on their own. In addition, control software is also provided free of charge. The software enables acquisition and visualization of data. In summary, HunStat2 introduces a simple and low-cost DIY potentiostat recommended for both analytical and educational purposes.

Vamos, Istvan [Lajos Petrik Vocational Chemistry S↗

A new chapter for RCSB Protein Data Bank Molecule of the Month in 2025

The online Molecule of the Month series authored by David S. Goodsell and published by the Research Collaboratory for Structural Biology Protein Data Bank at PDB101.RCSB.org has highlighted stories about the biomolecular structures driving fundamental biology, biomedicine, bioenergy, and biotechnology since January 2000. A new chapter begins in 2025: Janet Iwasa has taken over as the series creator of stories about critically important biological macromolecules in a rapidly changing world.

Bioenergy↗

Hydrodynamic conditions in laser irradiated buried layer experiments

The calculation of open shell ionization level and radiative properties of materials in Non-Local Thermal Equilibrium (NLTE) is currently still a major challenge for any atomic model. The predictions of various NLTE atomic codes at these conditions still differ significantly. In recent years, a new buried layer platform was developed at the Lawrence Livermore National Laboratory and the Laboratory for Laser Energetics. This platform is used to measure ionization distribution and emission of open L-shell, mid-Z ions and open M-shell, high-Z ions at NLTE conditions that are relevant in many laser plasma applications. These experiments offer a unique chance for benchmarking the atomic models. In order to perform these experiments, a uniform well characterized plasma source is required. In this work, we present one-dimensional (1D) and two-dimensional simulations of the experimental platform. These simulations were used for both the design and the analysis of the experiments. The simulations demonstrate the different phases of hydrodynamic evolution of the target and identify the time windows in which uniform conditions can be achieved. A 1D expansion of the target was found to be adequate to describe the target's evolution for most of the experiment duration. The fast 1D simulations were compared with recent experimental results from the Omega laser facility. The sensitivity of the results to several modeling parameters such as the electron flux limiter and laser resonant absorption is reported.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Clustering-Based Scenario Generation Framework for Power Market Simulation with Wind Integration

A critical step in stochastic optimization models of power system analysis is to select a set of appropriate scenarios and significant numbers of scenario generation methods exist in the literature. This paper develops a clustering based scenario generation method, which aims to improve the performance of existing scenario generation techniques by grouping a set of correlated wind sites into clusters according to their cross-correlations. Copula based models are utilized to model spatiotemporal correlations and the Gibbs sampling is then used to generate scenarios for day-ahead markets. Our results show that the generated scenarios based on clustered wind sites outperform existing approaches in terms of reliability and sharpness and can reduce the total computational time for scenario generation and reduction significantly. The clustering-based framework can therefore provide a better support for real-world market simulations with high wind penetration.

data visualization↗

A novel, magnetically driven convergent Richtmyer–Meshkov platform

Here, we introduce a novel experimental platform for the study of the Richtmyer–Meshkov instability in a cylindrically converging geometry using a magnetically driven cylindrical piston. Magnetically driven solid liner implosions are used to launch a shock into a liquid deuterium working fluid and, ultimately, into an on-axis rod with a pre-imposed perturbation. The shock front trajectory is tracked through the working fluid and up to the point of impacting the rod through the use of on axis photonic Doppler velocimetry. This configuration allows for precise characterization of the shock state as it impacts the perturbed rod interface. Monochromatic x-ray radiography is used to measure the post-shock interface evolution and rod density profile. The ALEGRA MHD model is used to simulate the dynamics of the experiment in one dimension. We show that late in time the perturbation growth becomes non-linear as evidenced by the observation of high-order harmonics, up to n = 5. Two dimensional simulations performed using a combination of the GORGON MHD code and the xRAGE radiation hydrodynamics code suggest that the late time non-linear growth is modified by convergence effects as the bubbles and spikes experience differences in the pressure of the background flow.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Creation of large temperature anisotropies in a laboratory plasma

Ion temperature anisotropy in an expanding magnetized plasma is investigated using laser induced fluorescence. Parallel and perpendicular ion velocity distribution functions (IVDFs) were measured simultaneously with high spatial resolution in the expanding plasma. Large ion temperature anisotropies (T ⊥i /T ∥i ~ 10) are observed in a conical region at the periphery of the expanding plasma plume. A simple 2D Boris stepper model that incorporates the measured electric field structure is able to reproduce the gross features of the measured perpendicular IVDFs. Here, a Nyquist stability analysis of the measured IVDFs suggests that multiple instabilities with k ⊥ρi ~ 1 and k ||ρi ~ 0.2 are likely to be excited in these plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High spatial resolution and contrast radiography of hydrodynamic instabilities at the National Ignition Facility

In this work, we are developing techniques for studying the Rayleigh–Taylor (RT) and Richtmyer–Meshkov (RM) instabilities in a planar geometry at high-energy-densities at the National Ignition Facility (NIF). In particular, through the improvement of experimental imaging quality, we are progressing toward the study of the turbulent regime of the mixing regions in capsule implosion experiments for inertial confinement fusion, which requires few micrometers resolution. Using 60 NIF beams, a solid shock tube is driven launching a shock wave that crosses the interface between a dense and a light material pre-machined in the target to obtain sinusoidal ripples, which results in RM and RT instabilities that are imaged using the NIF Crystal Backlighter Imager. High-quality images were obtained with a mean resolution of 7 μm and improved contrast. While the obtained resolution does not allow the observation of the smallest scale of the “turbulent” energy spectrum, the generated image encompasses 63% of the total flow energy, a 50% improvement over previous studies, which is observed for the first time a roll-up feature in a high energy density-type RT experiment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗