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At least 253 records · Page 14

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2A AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2A AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2A AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. Furthermore, these developments will enable structure determination from smaller and/or weakly diffracting microcrystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Solar Time-based Analog Ensemble Method for Regional Solar Power Forecasting

This paper presents a new analog ensemble method for day-ahead regional photovoltaic (PV) power forecasting with hourly resolution. By utilizing open weather forecast and power measurement data, this prediction method is processed within a set of historical data with similar meteorological data (temperature and irradiance), and astronomical date (solar time and earth declination angle). Further, clustering and blending strategies are applied to improve its accuracy in regional PV forecasting. The robustness of the proposed method is demonstrated with three different numerical weather prediction models, the North American Mesoscale Forecast System, the Global Forecast System, and the Short-Range Ensemble Forecast, for both region level and single site level PV forecasts. Using real measured data, the new forecasting approach is applied to the load zone in Southeastern Massachusetts as a case study. In conclusion, the normalized root mean square error (NRMSE) has been reduced by 13.80%-61.21% when compared with three tested baselines.

14 SOLAR ENERGY↗

Shaler: in situ analysis of a fluvial sedimentary deposit on Mars

This article characterizes the detailed sedimentology of a fluvial sandbody on Mars for the first time and interprets its depositional processes and palaeoenvironmental setting. Despite numerous orbital observations of fluvial landforms on the surface of Mars, ground-based characterization of the sedimentology of such fluvial deposits has not previously been possible. Results from the NASA Mars Science Laboratory Curiosity rover provide an opportunity to reconstruct at fine scale the sedimentary architecture and palaeomorphology of a fluvial environment on Mars. This work describes the grain size, texture and sedimentary facies of the Shaler outcrop, reconstructs the bedding architecture, and analyses cross-stratification to determine palaeocurrents. On the basis of bedset geometry and inclination, grain-size distribution and bedform migration direction, this study concludes that the Shaler outcrop probably records the accretion of a fluvial barform. The majority of the outcrop consists of large-scale trough cross-bedding of coarse sand and granules. Palaeocurrent analyses and bedform reconstruction indicate that the beds were deposited by bedforms that migrated towards the north-east, across the surface of a bar that migrated south-east. Stacked cosets of dune cross-bedding suggest aggradation of multiple bedforms, which provides evidence for short periods of sustained flow during Shaler deposition. However, local evidence for aeolian reworking and the presence of potential desiccation cracks within the outcrop suggest that fluvial deposition may have been intermittent. The uppermost strata at Shaler are distinct in terms of texture and chemistry and are inferred to record deposition from a different sediment dispersal system with a contrasting provenance. The outcrop as a whole is a testament to the availability of liquid water on the surface of Mars in its early history.

58 GEOSCIENCES↗

New multicell model for describing the atomic structure of La{sub 3}Ga{sub 5}SiO{sub 14} piezoelectric crystal: Unit cells of different compositions in the same single crystal

Accurate X-ray diffraction study of langasite (La{sub 3}Ga{sub 5}SiO{sub 14}) single crystal has been performed using the data obtained on a diffractometer equipped with a CCD area detector at 295 and 90.5 K. Within the known La{sub 3}Ga{sub 5}SiO{sub 14} model, Ga and Si cations jointly occupy the 2d site. A new model of a “multicell” consisting of two different unit cells is proposed. Gallium atoms occupy the 2d site in one of these cells, and silicon atoms occupy this site in the other cell; all other atoms correspondingly coordinate these cations. This structure implements various physical properties exhibited by langasite family crystals. The conclusions are based on processing four data sets obtained with a high resolution (sin θ/λ ≤ 1.35 Å{sup –1}), the results reproduced in repeated experiments, and the high relative precision of the study (sp. gr. P321, Z = 1; at 295 K, a = 8.1652(6) Å, c = 5.0958(5) Å, R/wR = 0.68/0.68%, 3927 independent reflections; at 90.5 K, a = 8.1559(4) Å, c = 5.0913(6) Å, R/wR = 0.92/0.93%, 3928 reflections).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Exploring the Use of Novel Spatial Accelerators in Scientific Applications

Driven by the need to find alternative accelerators which can viably replace GPUs in next-generation Supercomputing systems, this paper proposes a methodology to enable agile application/hardware co-design. The application-first methodology provides the ability to come up with design of accelerators while working with real-world workloads, available accelerators, and system software. The iterative design process targets a set of kernels in a workload for performance estimates that can prune the design space for later phases of detailed architectural evaluations. To this effect, in this paper, a novel data-parallel device model is introduced that simulates the latency of performance-sensitive operations in an accelerator including data transfers and kernel computation using multi-core CPUs. The use of off-the-shelf simulators, such as pre-RTL simulator Aladdin or multiple tools available for exploring the design of deep neural network accelerators (e.g., Timeloop) is demonstrated for evaluation of various accelerator designs using applications with realistic inputs. Examples of multiple device configurations that are instantiable in a system are explored to evaluate the performance benefit of deploying novel accelerators. The proposed device is integrated with a programming model and system software to potentially explore the impacts of high-level programming languages/compilers and low-level effects such as task scheduling on multiple accelerators. We analyze our methodology for a set of applications that represent high-performance computing (HPC) and graph analytics. The applications include a computational chemistry kernel realized using tensor contractions, triangle counting, GraphSAGE and Breadth-first Search. These applications include kernels such as dense matrix-dense matrix multiplication, sparse matrix-spare matrix multiplication, and sparse matrix-dense vector multiplication. Our results indicate potential performance benefits and insights for system design by including accelerators that realize these kernels along-side general purpose accelerators.

AI, codesign, Accelerated Computing, Modeling and ↗

LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure (LoTToR) v1.0

The low-tilt tomographic reconstruction (LoTToR) method is a post-processing method to correct the missing-wedge artifact, which contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination. Moreover, the software can be used for hospital computer tomography (CT) to reduce the radiation damage to patients without reducing the CT image quality.

Ren, Gang↗

SSG (Scalable Service Groups)

SSG is a group membership microservice based on the Mercury RPC system. It provides mechanisms for bootstrapping sets of Mercury processes into logical groups and for managing the membership of these process groups over time. At a high-level, each group collectively maintains a group view, which is just a mapping from group member identifiers to Mercury address information. The initial group membership view is specified completely when the group is bootstrapped (created).

Carns, Phil↗

CrossSim

CrossSim is a simulator for modeling neural-inspired machine learning algorithms on analog hardware, such as resistive memory crossbars. It includes noise models for reading and updating the resistances, which can be based on idealized equations or experimental data. It can also introduce noise and finite precision effects when converting values from digital to analog and vice versa. All of these effects can be turned on or off as an algorithm processes a data set and attempts to learn its salient attributes so that it can be categorized in the machine learning training/classification context. CrossSim thus allows the robustness, accuracy, and energy usage of a machine learning algorithm to be tested on simulated hardware.

Plimpton, StevenJ.↗

Accessible Content Optimization for Research Needs (ACORN)

ACORN employs a set of automated processes for informing and/or enforcing defined content schemas to create standardized and highly structured data. Because of its standardized data source, ACORN easily applies computer automation to generate communication assets such as PDFs, Powerpoint presentations, and web pages. Built using the memory-safe Rust programming language, ACORN is portable and accessible for use on any Windows, Mac, or Linux machine.

Wohlgemuth, JasonHoward [Oak Ridge National Labora↗

The Effect of Flocculent, Dispersants, and Binder on Wet-laid Process for Recycled Glass Fiber/PA6 Composite

The papermaking industry has been using the wet-laid process to suspend paper pulp-derived fibers in water and drain the solution through a forming mesh. This process has recently been adopted to produce non-woven, wet-laid fiber-reinforced polymer matrix composite mats. The mats can be postmolded into different complex shapes using compression molding or related processes. The objective of this study was to produce composite panels from wet-laid mats and observe the effect of chemicals used during the process on the mechanical and thermal characteristics of the resulting composite. Two sets of mats were processed using recycled glass fiber with Polyamide 6 (PA6). Flocculent, dispersant and binder (poly(vinyl alcohol) (PVOH)) were added to one of the mats, and the second mat was processed without these chemicals. The addition of these chemicals enhanced the fiber distribution and reduced processing defects in the mats. This was reflected in the mechanical properties of the final product. It was noticed that the flocculent, dispersant and binder volatilized during the compression molding step. Furthermore, the additives were found not to affect the thermal properties of the consolidated part.

36 MATERIALS SCIENCE↗

Post-fire time series photos from five sites across the Oak Creek watershed, Washington

This dataset supports a broader study examining wildfire impacts on hydrologic connectivity across 5 sites within the Oak Creek watershed and the resulting biogeochemical impacts. Sites were selected using the Advanced Terrestrial Simulator (ATS) hydrologic model to identify locations with varying groundwater contributions and hydrologic responses across different burn severity scenarios. The Retreat Fire burned from July 23 to August 2, 2024, affecting all five sites. This dataset provides time series game camera photos, while the broader study includes continuous water quality monitoring, biogeochemical sampling of water and soils, precipitation data, and organic matter analysis. The other data types and additional metadata (include site environmental information) can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3018020. Because this study is ongoing, this data package will be updated regularly to include newly collected photos. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and (6) folders of game camera photos. The game camera photos are organized by site with subfolders by month of collection. The field metadata contains a subset of the information collected that is most relevant to photo-processing. The full set of field metadata can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3018020. All files are .csv, .pdf, or .jpg.

Burn severity↗

Physical Chemistry of Reaction Dynamics in Ionic Liquids

The Margulis group BES funded research at the University of Iowa is part of a broader collaborative effort that includes the groups of Blank (U. Minnesota), Castner (Rutgers U.), Maroncelli (Penn. State U.) and Wishart (BNL). The goal of this group of PIs is to better understand from an experimental and a theoretical perspective different aspects of photo-initiated electron transfer processes in a set of different room-temperature ionic-liquid systems. The Margulis contribution is theoretical and computational. Details are presented in the attached documentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photo-electrochemical Investigation of Radiation-Enhanced Galvanic Coupling and Hydrogen Permeation in TPBAR-related Materials

Research conducted in FY17 used photo-electrochemical methods to investigate the potential for radiationenhanced galvanic coupling in tritium-producing burnable absorber rod (TPBAR) materials. Specifically, a laboratory electrochemical cell was coupled with UV light in order to perform electrochemical opencircuit voltage and galvanic current measurements, techniques that have been used successfully in previous studies to replicate galvanic processes in reactor settings. UV irradiation can mimic reactor-like behavior because, similar to both directly and indirectly ionizing radiation, UV photons with energy greater than the band gap of the material will generate free charge carriers (electrons and holes) and can substantially alter the passivating effect of metal oxides.

36 MATERIALS SCIENCE↗

Deep Exclusive Pseudoscalar Meson Production at Jefferson Lab Hall C

Measurements of exclusive meson production are a useful tool in the study of hadronic structure. In particular, one can discern the relevant degrees of freedom at different distance scales through these studies. In the transition region between low momentum transfer (where a description of hadronic degrees of freedom in terms of effective hadronic Lagrangians is valid) and high momentum transfer (where the degrees of freedom are quarks and gluons), the predictive power of Quantum Chromodynamics (QCD), the theory of the strong interaction, is limited due to the absence of a complete solution. Thus, one has to rely upon experimental data from the non-perturbative intermediate-energy regime to thoroughly understand the onset of perturbative QCD (pQCD) as the momentum transfer is increased. This work involves two deep exclusive meson electroproduction experiments at Jefferson Lab (JLab). The p(e,e'pi+)n reaction is studied at fixed Q^2 and W of 2.5 GeV2 and 2.0 GeV, respectively, while varying the four momentum transfer to the nucleon -t from 0.2 to 2.1 GeV2 . As -t is increased, the hadronic interaction scale is reduced independently of the observation scale of the virtual photon, providing valuable information about the hard- scattering process in general. The data was taken at JLab Hall C in 2003, as a part of the experiment E01-004, Fpi-2, using the High Momentum Spectrometer (HMS) and Short Orbit Spectrometer (SOS), and in this work, the results of the differential cross section analysis are presented and compared to prior data, as well as two theoretical models. Using these results over a wide -t range, the transition from hard to soft QCD is also studied. In addition, the p(e,e'K+)Lambda(Sigma0) reactions are also studied. Despite their importance in elucidating the reaction mechanism underlying strangeness production, we still do not have complete understanding of these reactions above the resonance region. The experiment, E12- 09-011, intends to perform, for the first time, a full Rosenbluth (L/T/LT/TT) separation of p(e,e'K+)Lambda(Sigma0) cross sections above the resonance region using the newly upgraded standard equipment, Super High Momentum Spectrometer (SHMS) at JLab Hall C. The separated data will allow us to better understand the Kaon production reaction mechanism and the hard-soft QCD transition in exclusive processes. The kinematic settings being studied in the experiment ranges from Q^2 of 0.4 to 5.5 GeV2, W of 2.3 to 3.1 GeV, and -t of 0.06 to 0.53 GeV2. Here, the results from some pre-experimental studies with regards to estimations of singles rates as well as real and accidental coincidence rates are presented, using two different models. The implications of these projections on the runplan for the experiment are also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

High-Order, Stable, and Conservative Boundary Schemes for Central and Compact Finite Differences

Stable and conservative numerical boundary schemes are constructed such that they do not diminish the overall accuracy of the method for interior schemes of orders 4, 6, and 8 using both explicit (central) and compact finite differences. Previous attempts to develop stable numerical boundary schemes for non-linear problems have resulted in schemes which significantly reduced the global accuracy and/or required some form of artificial dissipation. Thus, the schemes developed are the first to not require this tradeoff, while also ensuring discrete conservation and allowing for direct boundary condition enforcement. After outlining a general procedure for the construction of conservative boundary schemes of any order, a simple, yet novel, optimization strategy which focuses directly on the compressible Euler equations is applied. The result of this non-linear optimization process is a set of high-order, stable, and conservative numerical boundary schemes which demonstrate excellent stability and convergence properties on an array of linear and non-linear hyperbolic problems.

97 MATHEMATICS AND COMPUTING↗

Open Radiation Monitoring: Histogram Builder Module Design

The Open Radiation Monitoring Project seeks to develop and demonstrate a modular radiation detection architecture designed specifically for use in arms control treaty verification (ACTV) applications that will facilitate rapid development of trusted systems to meet the needs of potential future treaties. A modular architecture can be used to reduce more complex systems to a series of single purpose building blocks, thereby facilitating equipment inspection and in turn building trust in the equipment by all treaty parties. Furthermore, a modular architecture can be used to control data flow within the measurement system, reducing the risk of "hidden switches" and constraining the amount of sensitive information that could potentially be inadvertently leaked. This report details the first revision of a prototype circuit that will convert analog pulses directly into a histogrammed data set for further processing. The circuit was designed with both spectroscopy and multiplicity analysis in mind but can, in principle, be used to reduce any raw data stream into a histogram. The number of output channels is limited, and the histogram bin ranges are user configurable to allow for non-uniform and discontinuous bins, which makes it possible to restrict the information being passed down stream if desired. Pulse processing relies entirely on analog circuitry and non- programmable logic, which enables operation without the need for a central processor or other programmable control unit. The circuit remains untested under the Open Radiation Monitoring project due to the closure of the sponsoring program. However, further development and testing is scheduled to take place in support of a purpose-built trusted verification system development effort known as COGNIZANT, which demonstrates the potential benefit of developing a suite of modular trusted system components.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

FY2021 Rotating Bed Reactor for Iodine Removal from ETF Feed to Support DFLAW Start-Up

In FY20, Washington River Protection Solutions, LLC (WRPS) began a program of work to evaluate potential technologies for removal of iodine from the ETF feed. Work at the Pacific Northwest National Laboratory (PNNL) focused on ion exchange media and conventional column based deployment while Atkins and VSL focused on ion exchange media in a Rotating Bed Reactor (RBR) system. In the RBR system, the ion exchange media is loaded into a packed bed, which is rotated in the liquid to be treated. The work described in this report builds on the results from FY20 work, in particular, with regard to improving iodate removal, extending the data set to support process modeling, further comparison of RBR versus column performance, and RBR scale-up testing.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Can Error Mitigation Improve Trainability of Noisy Variational Quantum Algorithms?

Variational Quantum Algorithms (VQAs) are often viewed as the best hope for near-term quantum advantage. However, recent studies have shown that noise can severely limit the trainability of VQAs, e.g., by exponentially flattening the cost landscape and suppressing the magnitudes of cost gradients. Error Mitigation (EM) shows promise in reducing the impact of noise on near-term devices. Thus, it is natural to ask whether EM can improve the trainability of VQAs. In this work, we first show that, for a broad class of EM strategies, exponential cost concentration cannot be resolved without committing exponential resources elsewhere. This class of strategies includes as special cases Zero Noise Extrapolation, Virtual Distillation, Probabilistic Error Cancellation, and Clifford Data Regression. Second, we perform analytical and numerical analysis of these EM protocols, and we find that some of them (e.g., Virtual Distillation) can make it harder to resolve cost function values compared to running no EM at all. As a positive result, we do find numerical evidence that Clifford Data Regression (CDR) can aid the training process in certain settings where cost concentration is not too severe. Our results show that care should be taken in applying EM protocols as they can either worsen or not improve trainability. On the other hand, our positive results for CDR highlight the possibility of engineering error mitigation methods to improve trainability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗