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At least 577 records · Page 32

Fixed-target serial crystallography at the Structural Biology Center

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

59 BASIC BIOLOGICAL SCIENCES↗

Preparing research samples for safe arrival at centers and facilities: recipes for successful experiments

Preparation of biomacromolecules for structural biology studies is a complex and time-consuming process. The goal is to produce a highly concentrated, highly pure product that is often shipped to large facilities with tools to prepare the samples for crystallization trials or for measurements at synchrotrons and cryoEM centers. The aim of this article is to provide guidance and to discuss general considerations for shipping biomacromolecular samples. Details are also provided about shipping samples for specific experiment types, including solution- and cryogenic-based techniques. These guidelines are provided with the hope that the time and energy invested in sample preparation is not lost due to shipping logistics.

36 MATERIALS SCIENCE↗

Enhancing Discoverability and Management of Atmospheric Data at Scale: Solutions from the ARM Data Center

The Atmospheric Radiation Measurement (ARM) is a multi-laboratory and multi-institutional U.S. Department of Energy (DOE) Office of Science National User Facility. The ARM Data Center (ADC), located at Oak Ridge National Laboratory, collects, archives, and shares vast atmospheric data crucial for climate research. The ADC manages over 7 PB of data from 460 instruments worldwide, processing it into more than 11,000 diverse data products using the Network Common Data Form (NetCDF) for machine-independent accessibility. The primary challenge addressed in this paper is the efficient management and distribution of vast and diverse datasets essential for the climate research community, enhancing accessibility through advanced tools like Data Discovery. The ADC has developed advanced infrastructure and software architecture to handle the continuous influx of heterogeneous data to enhance data discoverability, resulting in increased scientific collaboration. In 2023, users from over 34 countries downloaded and utilized ARM data, resulting in 1,455 publications. The ADC’s efforts have significantly improved the discoverability and usability of atmospheric data, fostering extensive scientific research and collaboration. This paper details the solutions implemented by the ADC team for efficient data discovery and distribution, and it demonstrates ARM’s capability of staging processed data for scientific analysis.

Shah, Chirag [ORNL] (ORCID:0000000203145737)↗

Optimal Sizing and Operation of a Hybrid Clean Energy Center

In this paper, we consider the deployment of battery energy storage systems (BESSs) paired with photovoltaics (PV) to form a hybrid clean energy center (HCEC), where the BESS is equipped for two main purposes: i) reducing the volatility of PV output and ii) shifting energy to meet an export limit. We develop a linear dynamical model to characterize the output of an HCEC and express the volatility and export power as functions of the battery's dispatch operations. We also propose an optimal sizing method via second-order cone programming (SOCP) to maximize the net benefits of the HCEC. Numerical studies are performed to illustrate and validate the proposed method.

Battery energy storage systems, photovoltaics, sec↗

An Assessment of the Usability of Machine Learning Based Tools for the Security Operations Center

Gartner, a large research and advisory company, anticipates that by 2024 80% of security operation centers (SOCs) will use machine learning (ML) based solutions to enhance their operations. 1 1 https://www.ciodive.com/news/how-data-science-tools-can-lighten-the-load-for-cybersecurity-teams/572209/ In light of such widespread adoption, it is vital for the research community to identify and address usability concerns. This work presents the results of the first in situ usability assessment of ML-based tools. With the support of the US Navy, we leveraged the national cyber range-a large, air-gapped cyber testbed equipped with state-of-the-art network and user emulation capabilities-to study six US Naval SOC analysts' usage of two tools. Our analysis identified several serious usability issues, including multiple violations of established usability heuristics for user interface design. We also discovered that analysts lacked a clear mental model of how these tools generate scores, resulting in mistrust a and/or misuse of the tools themselves. Surprisingly, we found no correlation between analysts' level of education or years of experience and their performance with either tool, suggesting that other factors such as prior background knowledge or personality play a significant role in ML-based tool usage. Our findings demonstrate that ML-based security tool vendors must put a renewed focus on working with analysts, both experienced and inexperienced, to ensure that their systems are usable and useful in real-world security operations settings.

Oesch, T↗

Improved VOC in RbF-Treated Cu(In,Ga)Se2 Solar Cells via Passivation of Recombination Centers

Cu(In,Ga)Se 2 (CIGS) solar cells have benefited in recent years from the addition of heavy alkali elements, such as Rb, which increase the solar cell open-circuit voltage ( V OC ). To investigate the source of this improvement, here, we compare samples with and without Rb to perform a quantitative comparison of electronic defects and minority carrier lifetime. Deep-level transient and optical spectroscopy measurements were performed on two sets of rubidium fluoride (RbF)-treated and untreated CIGS, and three distinct traps were identified regardless of RbF treatment. The RbF treatment was found to reduce the concentration of the H2 trap, which was previously found to act as a recombination center and is located preferentially at CIGS grain boundaries. Time-resolved photoluminescence measurements showed an increase in effective lifetime after RbF and nearly all lifetime improvement resulted from reductions in bulk recombination. The observed V OC improvement is well correlated with increased minority carrier lifetime and acceptor concentration, which led to increases and decreases in electron and hole quasi-Fermi levels, respectively.

Cu(In Ga)Se2 (CIGS)↗

Energy Storage Control Capability Expansion: Achieving Better Technoeconomic Benefits at Portland General Electric's Salem Smart Power Center

This article reports a transformative project aimed at enhancing the control capabilities of a Portland General Electric (PGE) owned 5 MW/1.25 MWh ESS located at Salem Smart Power Center (SSPC), Salem, Oregon, USA toward achieving better techno-economic benefit. Steps for developing a value-driven control capability is illustrated starting from evaluation of economic opportunities that drive the coordination of multiple services to be delivered by an ESS to implementation and testing. Lessons learned during critical processes are identified for the benefit of the ESS industry.

Alam, Md Jan E.↗

A Comprehensive Calibration Framework for the Northwest River Forecast Center

We present a comprehensive framework developed by the Northwest River Forecast Center for calibrating hydrologically diverse basins. The framework includes models for snow, soil moisture, routing, channel loss, and consumptive use. Data inputs include a wide range of open-access datasets for meteorology, land use, topography, and land cover. The framework uses conceptual hydrologic models to handle basins with various hydrologic regimes including rain-driven and snowmelt-dominated basins. We also develop a flexible automatic calibration system that can handle numerous unobservable model parameters in a computationally efficient manner. A single-basin automatic calibration run can typically be completed on a modern laptop in under 10 min. We found that model performance metrics for this new approach match the quality of the NWRFC's previous labor-intensive manual calibrations. The model performance also rivals that of a state-of-the-art deep learning model at a fraction of the computational cost. This framework presents a new standard for the quality of calibrations possible with lumped conceptual hydrologic models, combining careful data curation, an objective calibration framework, and expert local knowledge. In addition, we have made software packages available for the entire suite of National Weather Service River Forecast System models, including SAC-SMA, SNOW-17, and Lag-K. These modern interfaces are intended to increase accessibility and facilitate future research.

Forecasting↗

The safety of pranlukast and montelukast during the first trimester of pregnancy: A prospective, two‐centered cohort study in Japan

Abstract For leukotriene receptor antagonists (LTRAs), especially pranlukast, safety data during pregnancy is limited. Therefore, we conducted a prospective, two‐centered cohort study using data from teratogen information services in Japan to clarify the effects of LTRA exposure during pregnancy on maternal and fetal outcomes. Pregnant women who being counseled on drug use during pregnancy at two facilities were enrolled. The primary outcome of this study was major congenital anomalies. The incidence of major congenital anomalies in women exposed to montelukast or pranlukast during the first trimester of pregnancy was compared with that of controls. Logistic regression analysis was performed to analyze the effects of maternal LTRA use during the first trimester of pregnancy on major congenital anomalies. The outcomes of 231 pregnant women exposed to LTRAs (montelukast n = 122; pranlukast n = 106; both n = 3) and 212 live births were compared with those of controls. The rate of major congenital anomalies in the LTRA group was 1.9%. Multivariable logistic regression analysis revealed that LTRA exposure was not a risk factor for major congenital anomalies (adjusted odds ratio, 0.78; 95% confidence interval, 0.23–2.05; p = 0.653). In addition, no significant difference was detected in stillbirth, spontaneous abortion, preterm birth, and low birth weight between the two groups. The present study revealed that montelukast and pranlukast were not associated with the risk of major congenital anomalies. Our findings suggest that LTRAs could be safely employed for asthma therapy during pregnancy.

Hatakeyama, Shiro↗

A Continuum Dislocation Dynamics Crystal Plasticity Approach to Irradiated Body-Centered Cubic α-Iron

Radiation-induced embrittlement of reactor pressure vessel (RPV) steels can potentially limit the operating life of nuclear power plants. Over extended exposure to radiation doses, these body-centered cubic (BCC) irons demonstrate irradiation damage. Here, we present a continuum dislocation density (CDD) crystal plasticity model to capture the interaction among dislocations and self-interstitial atom (SIA) loops in α-iron. We demonstrate the importance of modeling cross slip using a combined stochastic Monte Carlo approach and the role of slip system strength anisotropy in capturing stochastic cross slip interactions. Through these captured interactions, the CDD crystal plasticity model can capture both the stress response and the physical evolution of dislocations on different slip system planes. Single-crystal verification experiments are used to calibrate the CDD crystal plasticity model, and a set of simplified polycrystalline simulations demonstrates the model’s ability to capture the stress response from tensile experiments on α-iron.

36 MATERIALS SCIENCE↗

Hidden vibronic and excitonic structure and vibronic coherence transfer in the bacterial reaction center

We report two-dimensional electronic spectroscopy (2DES) experiments on the bacterial reaction center (BRC) from purple bacteria, revealing hidden vibronic and excitonic structure. Through analysis of the coherent dynamics of the BRC, we identify multiple quasi-resonances between pigment vibrations and excitonic energy gaps, and vibronic coherence transfer processes that are typically neglected in standard models of photosynthetic energy transfer and charge separation. We support our assignment with control experiments on bacteriochlorophyll and simulations of the coherent dynamics using a reduced excitonic model of the BRC. We find that specific vibronic coherence processes can readily reveal weak exciton transitions. While the functional relevance of such processes is unclear, they provide a spectroscopic tool that uses vibrations as a window for observing excited state structure and dynamics elsewhere in the BRC via vibronic coupling. Vibronic coherence transfer reveals the upper exciton of the “special pair” that was weakly visible in previous 2DES experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Charge separation in the photosystem II reaction center resolved by multispectral two-dimensional electronic spectroscopy

The photosystem II reaction center (PSII RC) performs the primary energy conversion steps of oxygenic photosynthesis. While the PSII RC has been studied extensively, the similar time scales of energy transfer and charge separation and the severely overlapping pigment transitions in the Qy region have led to multiple models of its charge separation mechanism and excitonic structure. Here, we combine two-dimensional electronic spectroscopy (2DES) with a continuum probe and two-dimensional electronic vibrational spectroscopy (2DEV) to study the cyt b559-D1D2 PSII RC at 77 K. This multispectral combination correlates the overlapping Qy excitons with distinct anion and pigment-specific Q x and mid-infrared transitions to resolve the charge separation mechanism and excitonic structure. Through extensive simultaneous analysis of the multispectral 2D data, we find that charge separation proceeds on multiple time scales from a delocalized excited state via a single pathway in which Pheo D1 is the primary electron acceptor, while Chl D1 and P D1 act in concert as the primary electron donor.

30 DIRECT ENERGY CONVERSION↗

Decoding the interstitial/vacancy nature of dislocation loops with their morphological fingerprints in face-centered cubic structure

Dislocation loops are critical defects inducing detrimental effects like embrittlement and swelling in materials under irradiation. Distinguishing their nature (interstitial- or vacancy-type) is a long-standing challenge with great implications for understanding radiation damage. Here, we demonstrate that the morphology of radiation-induced Frank loops can unveil their nature in face-centered cubic (fcc) structure: Circular loops are interstitial-type in all fcc materials, while segmented loops are vacancy-type in high stacking fault energy (SFE) alloys but varied-type in low SFE and high-entropy alloys. The polygonal shape is attributed to the dissociation of an a 0 /3<111> dislocation into an a 0 /6<112> Shockley partial and an a 0 /6<110> stair-rod dislocation. The dissociation of vacancy loops is energetically favorable, whereas interstitial loops require external stimuli to promote dislocation propagation. This “morphology-nature” correlation not only highlights the asymmetry of vacancy/interstitial loops but also offers an efficient way to distinguish loop nature for a wide range of materials.

Ma, Kan [City Univ. of Hong Kong, Kowloon (Hong Ko↗

Search for dark matter from the center of the Earth with 10 years of IceCube data

The nature of dark matter remains unresolved in fundamental physics. Weakly Interacting Massive Particles (WIMPs), which could explain the nature of dark matter, can be captured by celestial bodies like the Sun or Earth, leading to enhanced self-annihilation into Standard Model particles including neutrinos detectable by neutrino telescopes such as the IceCube Neutrino Observatory. This article presents a search for muon neutrinos from the center of the Earth performed with 10 years of IceCube data using a track-like event selection. We considered a number of WIMP annihilation channels (χχ→τ+τ-$$\chi \chi \rightarrow \tau ^+\tau ^-$$/W+W-$$W^+W^-$$/bb¯$$b\bar{b}$$) and masses ranging from 10 GeV to 10 TeV. No significant excess over background due to a dark matter signal was found while the most significant result corresponds to the annihilation channel χχ→bb¯$$\chi \chi \rightarrow b\bar{b}$$ for the mass mχ=250$$m_{\chi }=250$$ GeV with a post-trial significance of 1.06σ$$1.06\sigma $$. Our results are competitive with previous such searches and direct detection experiments. Our upper limits on the spin-independent WIMP scattering are world-leading among neutrino telescopes for WIMP masses mχ>100$$m_{\chi }>100$$ GeV.

Abbasi, R↗

Nuclear recoil detection with color centers in bulk lithium fluoride

We present initial results on the detection of nuclear recoils in lithium fluoride (LiF) through the fluorescence of color centers created by particle interactions in the crystal lattice. Using light-sheet fluorescence microscopy, we image nuclear recoil tracks from both fast and thermal neutron interactions deep within a cubic-centimeter-scale sample. Automated three-dimensional feature extraction based on machine-learning tools enables the identification and classification of individual events. We observe that the fluorescence response of LiF to gamma irradiation is strongly suppressed, by a factor of 30–50 compared to neutron exposure, demonstrating intrinsic insensitivity to electromagnetic backgrounds. The observed and simulated event characteristics are consistent, including their number, size, and topology. These results establish the feasibility of LiF as a scalable detection medium for rare nuclear-recoil events and constitute a first step toward 10–1000 g scale detectors with single-event sensitivity for applications in reactor-neutrino detection, neutron spectroscopy, and dark matter searches.

Aroujo, G R [University of Zurich]↗

Functional Mock-up Interface - Machine Learning Center (FMI-MLC) v1

The Functional Mock-up Interface - Machine Learning Center is a tool to interface the Python-Tensorflow library with building simulation models, to develop and train machine learning-based controls. In particular, this framework allows the use of reinforcement learning through the standardized Functional Mock-up Interface, an open industry standard for co-simulation. First application was the development of a controller for dynamic façade and heating ventilation and air conditioning (HVAC) systems.

Gehbauer, Christoph↗

High Performance Computing Innovation Center Open Source Developer Tools

The High Performance Computing Innovation Center (HPCIC) aims to ease the transition for developers to use open source software provided by the lab. HPCIC Developer Tools is a collection of software, containers, cloud configurations, and associated documentation that make it easy to deploy tutorials or small apps to demonstrate lab-developed software. For example, building a tutorial container that includes lab software and interactive interfaces; a command line or web-based tool that accepts user preferences for the tutorial; supporting tools and software development kits (SDKs) for developer interactions or productivity in different languages embraced by the larger developer community such as Go, Rust, and Python; and automation in version control to support continued update of software and associated resources. These tools are best developed in an open source environment such as GitHub, not only to champion the lab's open source software, but for purposes of branding and demonstrating the lab's leadership in open source. Such an effort that brings in more developers to use and contribute to lab software can further improve the quality of the software, and developer experience at the lab.

Beckingsale, DavidA↗

Bioenergy Research Centers Data Sharing Portal

The bioenergy.org website is the end product of the Data Sharing Shared Research objective for the Bioenergy Centers. The objective is to Enhance BRC data legacy through the development and use of shared software tools to make previously published datasets more findable and accessible through the Inter-BRC Data Products Portal, and to explore the use of generative AI to assist in the exploration of published datasets. The software repository is released per the license information below.

Thrower, Nicholas↗