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DOE OSTI2022

Trivalent ion overcharging on electrified graphene

We report the structure of the electrical double layer (EDL) formed near graphene in aqueous environments strongly impacts its performance for a plethora of applications, including capacitive deionization. In particular, adsorption and organization of multivalent counterions near the graphene interface can promote nonclassical behaviors of EDL including overcharging followed by co-ion adsorption. In this paper, we characterize the EDL formed near an electrified graphene interface in dilute aqueous YCl 3 solution using in situ high resolution x-ray reflectivity (also known as crystal truncation rod) and resonant anomalous x-ray reflectivity (RAXR). These interface-specific techniques reveal the electron density profiles with molecular-scale resolution. We find that yttrium ions (Y 3+ ) readily adsorb to the negatively charged graphene surface to form an extended ion profile. This ion distribution resembles a classical diffuse layer but with a significantly high ion coverage, i.e., 1 Y 3+ per 11.4 ± 1.6 Å 2 , compared to the value calculated from the capacitance measured by cyclic voltammetry (1 Y 3+ per ~240 Å 2 ). Such overcharging can be explained by co-adsorption of chloride that effectively screens the excess positive charge. The adsorbed Y 3+ profile also shows a molecular-scale gap (≥ 5 Å) from the top graphene surfaces, which is attributed to the presence of intervening water molecules between the adsorbents and adsorbates as well as the lack of inner-sphere surface complexation on chemically inert graphene. We also demonstrate controlled adsorption by varying the applied potential and reveal consistent Y 3+ ion position with respect to the surface and increasing cation coverage with increasing the magnitude of the negative potential. This is the first experimental description of a model graphene-aqueous system with controlled potential and provides important insights into the application of graphene-based systems for enhanced and selective ion separations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

A conserved epitope III on hepatitis C virus E2 protein has alternate conformations facilitating cell binding or virus neutralization

Epitope III, a highly conserved amino acid motif of 524 APTYSW 529 on the hepatitis C virus (HCV) E2 glycoprotein, resides in the critical loop that binds to the host receptor CD81, thus making it one of the most important antibody targets for blocking HCV infections. Here, we have determined the X-ray crystal structure of epitope III at a 2.0-Å resolution when it was captured by a site-specific neutralizing antibody, monoclonal antibody 1H8 (mAb1H8). The snapshot of this complex revealed that epitope III has a relatively rigid structure when confined in the binding grooves of mAb1H8, which confers the residue specificity at both ends of the epitope. Such a high shape complementarity is reminiscent of the “lock and key” mode of action, which is reinforced by the incompatibility of an antibody binding with an epitope bearing specific mutations. By subtly positioning the side chains on the three residues of Tyr 527 , Ser 528 , and Trp 529 while preserving the spatial rigidity of the rest, epitope III in this cocrystal complex adopts a unique conformation that is different from previously described E2 structures. With further analyses of molecular docking and phage display–based peptide interactions, we recognized that it is the arrangements of two separate sets of residues within epitope III that create these discrete conformations for the epitope to interact selectively with either mAb1H8 or CD81. These observations thus raise the possibility that local epitope III conformational dynamics, in conjunction with sequence variations, may act as a regulatory mechanism to coordinate “mAb1H8-like” antibody-mediated immune defenses with CD81-initiated HCV infections.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗

DOE OSTI2024

Experimental Investigation of Low-Frequency Distributed Acoustic Sensor Responses to Two Parallel Propagating Fractures

Low-frequency distributed acoustic sensing (LF-DAS) is a diagnostic tool for hydraulic fracture propagation with far-field monitoring using fiber optic sensors. LF-DAS senses strain rate variation caused by stress field change due to fracture propagation. Fiber optic sensors are installed in the monitoring wells in the vicinity of a fractured well. From the strain responses, fracture propagation can be evaluated. To understand subsurface conditions with multiple propagating fractures, a laboratory-scale hydraulic fracture experiment was performed simulating the LF-DAS response to fracture propagation with embedded distributed optical fiber strain sensors under these conditions. The experiment was performed using a transparent cube of epoxy with two parallel radial initial flaws centered in the cube. Fluid was injected into the sample to generate fractures along the initial flaws. The experiment used distributed high-definition fiber optic strain sensors with tight spatial resolutions. The sensors were embedded at two different locations on opposite sides of the initial flaws, serving as observation/monitoring locations. We also employed finite element modeling to numerically solve the linear elastic equations of equilibrium continuity and stress–strain relationships. The measured strains from the experiment were compared to simulation results from the finite element model. The experimentally derived strain and strain-rate waterfall plots from this study show the responses to both fractures propagating, while the fracture at the lower position took most of the fluid during the experiment. Interestingly, a fracture first began propagating from the upper flaw of the two flaws, but once the lower fracture was initiated, it grew much faster than the upper fracture. Both fibers were intercepted by the lower fracture, further verifying the strain signature as a fracture is approaching and intersecting an offset fiber.

Chemistry↗

DOE OSTI2020

Identification of Possible Stellar Companions via Speckle Interferometry in a Sample of Be Stars

We present speckle interferometric measurements of Be stars made with the 1.60 m Perkin-Elmer telescope at the Pico dos Dias Observatory of the Laboratório Nacional de Astrofísica in Brazil. Using three different filters (V, R, and I), we obtained astrometric measurements for 23 stars, during three observing runs allocated in 2017 March, 2018 April, and 2019 July. We identified pairs with angular separation ranging from 0.″10 to 6.″69, including six systems with separations smaller than 1.″0. We estimated a mean error in separation of 15 mas, 1.°2 in position angle, and 0.29 mag for the magnitude difference. We discovered three new possible double systems that are not identified in the literature: HD 174886, HD 159032, and HD 168135 with an average angular separation of 0.″20, 3.″23, and 5.″41, respectively. In addition, we identified four new pairs in multiple systems previously known in the Washington Double Star Catalog. However, for 16 stars of our sample, we did not find evidence of binarity, based on the diffraction-limited resolution, the field of view, and/or the sensitivity of our observations. From the cross-match with data from Gaia Data Release 2, we verified the possibility of some of these systems be gravitationally bound or not.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

The CLAS12 Forward Time-of-Flight system

The Forward Time-of-Flight system for the large-acceptance CLAS12 spectrometer in Hall B at the Thomas Jefferson National Accelerator Facility is described. The system is positioned at distances in the range from 6.2 m to 7.2 m from the beam–target interaction point and spans laboratory polar angles from 5 deg → 45 deg and nearly the full azimuth. The system consists of 540 individual scintillation counters with double-ended readout that range in length from 17 cm to 426 cm of discrete widths of 6 cm, 15 cm, and 22 cm, and of discrete thicknesses of 5 cm and 6 cm. We see the effective counter time resolution for passing charged particles varies from 50 ps for the shortest counters at small angles to 200 ps for the longest counters at large angles. The detectors are part of the forward-angle particle identification system for CLAS12 during offline event reconstruction and are a component of the online data acquisition trigger to select final state event topologies with forward-going charged particles.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Performance of a triple-GEM detector with capacitive-sharing 3-coordinate (X–Y–U)-strip anode readout

The concept of capacitive-sharing readout, described in detail in a previous study, offers the possibility for the development of high-performance three-coordinates (X--Y--U)-strip readout for Micro Pattern Gaseous Detectors (MPGDs) using simple standard PCB fabrication techniques. Capacitive-sharing (X--Y--U)-strip readout allows simultaneous measurement of the Cartesian coordinates x and y of the position of the particles together with a third coordinate u along the diagonal axis in a single readout PCB. This provides a powerful tool to address multiple-hit ambiguity and enable pattern recognition capabilities in moderate particle flux environment of collider or fixed target experiments in high energy physics HEP) and nuclear physics (NP). We present in this paper the performance of a 10 cm × 10 cm triple-GEM detector with capacitive-sharing (X--Y--U)-strip anode readout. Spatial resolutions of the order of $\sigma_{x}^{res}$ = 71.6 $\pm$ 0.8 $\mu$m for X-strips, $\sigma_{y}^{res}$ = 56.2 $\pm$ 0.9 $\mu$m for Y-strips and $\sigma_{u}^{res}$ = 75.2 $\pm$ 0.9 $\mu$m for U-strips have been obtained at a beam test at Thomas Jefferson National Accelerator Facility (Jefferson Lab). Modifications of the readout design of future prototypes to improve the spatial resolution and challenges in scaling to large-area MPGDs are discussed.

(X-Y-U) strip↗

DOE OSTI2021

Global field reconstruction from sparse sensors with Veronoi tessellation-assisted deep learning

Achieving accurate and robust global situational awareness of a complex time-evolving field from a limited number of sensors has been a longstanding challenge. This reconstruction problem is especially difficult when sensors are sparsely positioned in a seemingly random or unorganized manner, which is often encountered in a range of scientific and engineering problems. Moreover, these sensors can be in motion and can become online or offline over time. The key leverage in addressing this scientific issue is the wealth of data accumulated from the sensors. As a solution to this problem, we propose a data-driven spatial field recovery technique founded on a structured grid-based deep-learning approach for arbitrary positioned sensors of any numbers. It should be noted that the naïve use of machine learning becomes prohibitively expensive for global field reconstruction and is furthermore not adaptable to an arbitrary number of sensors. In the present work, we consider the use of Voronoi tessellation to obtain a structured-grid representation from sensor locations enabling the computationally tractable use of convolutional neural networks. One of the central features of the present method is its compatibility with deep-learning based super-resolution reconstruction techniques for structured sensor data that are established for image processing. The proposed reconstruction technique is demonstrated for unsteady wake flow, geophysical data, and three-dimensional turbulence. The current framework is able to handle an arbitrary number of moving sensors, and thereby overcomes a major limitation with existing reconstruction methods. The presented technique opens a new pathway towards the practical use of neural networks for real-time global field estimation.

Fukami, Kai↗

DOE OSTI2022

Cryotrapping peroxide in the active site of human mitochondrial manganese superoxide dismutase crystals for neutron diffraction

Structurally identifying the enzymatic intermediates of redox proteins has been elusive due to difficulty in resolving the H atoms involved in catalysis and the susceptibility of ligand complexes to photoreduction from X-rays. Cryotrapping ligands for neutron protein crystallography combines two powerful tools that offer the advantage of directly identifying hydrogen positions in redox-enzyme intermediates without radiolytic perturbation of metal-containing active sites. However, translating cryogenic techniques from X-ray to neutron crystallography is not straightforward due to the large crystal volumes and long data-collection times. Here, methods have been developed to visualize the evasive peroxo complex of manganese superoxide dismutase (MnSOD) so that all atoms, including H atoms, could be visualized. The subsequent cryocooling and ligand-trapping methods resulted in neutron data collection to 2.30 Å resolution. The P 6 1 22 crystal form of MnSOD is challenging because it has some of the largest unit-cell dimensions ( a = b = 77.8, c = 236.8 Å) ever studied using high-resolution cryo-neutron crystallography. The resulting neutron diffraction data permitted the visualization of a dioxygen species bound to the MnSOD active-site metal that was indicative of successful cryotrapping.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Spatially correlated incommensurate lattice modulations in an atomically thin high-temperature Bi 2.1 Sr 1.9 CaCu 2.0 O 8+y superconductor

Strong variations in superconducting critical temperatures in different families of the cuprate perovskites, even with similar hole doping in their copper-oxygen planes, suggest the importance of lattice modulation effects. The one-dimensional incommensurate lattice modulation (ILM) of Bi 2 Sr 2 CaCu 2 O 8+y , with the average atomic positions perturbed beyond the unit cell6, offer s an ideal test ground for studying the interplay between superconductivity and the long-range incommensurate lattice fluctuations. Here we report Scanning nano X-ray Diffraction (SnXRD) imaging of incommensurate lattice modulations in Bi 2 Sr 2 CaCu 2 O 8+y Van der Waals heterostructures of thicknesses down to two-unit cells. Using SnXRD, we probe that the long-range and short-range incommensurate lattice modulations in bulk sample surface with spatial resolution below 100 nm. We find that puddle-like domains of ILM of size uniformly evolving with dimensionality. In the 2-unit cell thin sample, it is observed that the wavevectors of the long- and short-range orders become anticorrelated with emerging spatial patterns having a directional gradient. The emerging patterns, originated by tiny tuning of lattice strain, induce static mesoscopic charge density waves. Finally, our findings thus demonstrate that the strain can be used to tune and control the electromagnetic properties of two-dimensional high-temperature superconductors.

36 MATERIALS SCIENCE↗

DOE OSTI2024

From Data to Insights: A Covariate Analysis of the IARPA BRIAR Dataset for Multimodal Biometric Recognition Algorithms at Altitude and Range

This paper examines covariate effects on fused whole body biometrics performance in the IARPA BRIAR dataset, specifically focusing on UAV platforms, elevated positions, and distances up to 1000 meters. The dataset includes outdoor videos compared with indoor images and controlled gait recordings. Normalized raw fusion scores relate directly to predicted false accept rates (FAR), offering an intuitive means for interpreting model results. A linear model is developed to predict biometric algorithm scores, analyzing their performance to identify the most influential covariates on accuracy at altitude and range. Weather factors like temperature, wind speed, solar loading, and turbulence are also investigated in this analysis. The study found that resolution and camera distance best predicted accuracy and findings can guide future research and development efforts in long-range/elevated/UAV biometrics and support the creation of more reliable and robust systems for national security and other critical domains.

Bolme, David↗

DOE OSTI2023

Multisensor Agile Adaptive Sampling (MAAS): A Methodology to Collect Radar Observations of Convective Cell Life Cycle

Abstract Multisensor Agile Adaptive Sampling (MAAS), a smart sensing framework, was adapted to increase the likelihood of observing the vertical structure (with little to no gaps), spatial variability (at subkilometer scale), and temporal evolution (at ∼2-min resolution) of convective cells. This adaptation of MAAS guided two mechanically scanning C-band radars (CSAPR2 and CHIVO) by automatically analyzing the latest NEXRAD data to identify, characterize, track, and nowcast the location of all convective cells forming in the Houston domain. MAAS used either a list of predetermined rules or real-time user input to select a convective cell to be tracked and sampled by the C-band radars. The CSAPR2 tracking radar was first tasked to collect three sector plan position indicator (PPI) scans toward the selected cell. Edge computer processing of the PPI scans was used to identify additional targets within the selected cell. In less than 2 min, both the CSAPR2 and CHIVO radars were able to collect bundles of three to six range–height indicator (RHI) scans toward different targets of interest within the selected cell. Bundles were successively collected along the path of cell advection for as long as the cell met a predetermined set of criteria. Between 1 June and 30 September 2022 over 315 000 vertical cross-section observations were collected by the C-band radars through ∼1300 unique isolated convective cells, most of which were observed for over 15 min of their life cycle. To the best of our knowledge, this dataset, collected primarily through automatic means, constitutes the largest dataset of its kind.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (Φ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5's orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, Φ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Ultra-high Information-content Chemical Imaging with Broadband Coherent Anti-Stokes Raman and Two-photon Fluorescence Lifetime Microscopy

Raman fingerprint spectroscopy and fluorescence lifetime imaging are emerging tools for studying metabolic profiles of biological specimens. While Raman fingerprint spectroscopy detects intrinsic molecular vibrations that reflect the molecular composition and chemical environment of a sample, fluorescence lifetime imaging measures changes in the excited-state lifetime of fluorophores that are sensitive to their microenvironments. Here, we present a multimodal imaging platform combining broadband coherent anti-Stokes Raman scattering (BCARS) and two-photon fluorescence lifetime imaging (2p-FLIM) microscopy that can acquire biologically relevant Raman fingerprint spectra and fluorescence lifetime signals in vivo and simultaneously. The tremendous chemical information obtained from spatially co-registered BCARS and 2p-FLIM images allows us to characterize the subtle differences between sub-cellular compartments and verify the potential false-positive results generated by fluorescence imaging alone. This is demonstrated by directly comparing the BCARS, 2p-FLIM, and two-photon excitation fluorescence(TPEF) signals simultaneously obtained from the same dye-stained organelle in the live, intact C. elegans expressing a green fluorescent protein (GFP) marker. In this work, we introduce the BCARS/2p-FLIM/TPEF setup scheme, the image acquisition steps, data processing, and representative results showing that the cross-modality imaging method enables rigorous characterization and in vivo detection at sub-cellular resolution. Furthermore, this protocol provides a framework for simultaneous chemical and fluorescence lifetime imaging to improve the accuracy of biological interpretation in complex living systems.

Xu, Haoyu [Georgia Institute of Technology, Atlant↗

DOE OSTI2022

Resolving the Chemical Formula of Nesquehonite via NMR Crystallography, DFT Computation, and Complementary Neutron Diffraction

Nesquehonite is a magnesium carbonate mineral relevant to carbon sequestration envisioned for carbon capture and storage of CO 2 . Its chemical formula remains controversial today, assigned as either a hydrated magnesium carbonate [MgCO 3 · 3H 2 O], or a hydroxy- hydrated- magnesium bicarbonate [Mg(HCO 3 )OH · 2H 2 O]. Here, the resolution of this controversy is central to understanding this material‘s thermodynamic, phase, and chemical behavior. In an NMR crystallography study, using rotational-echo double-resonance 13 C{ 1 H} (REDOR), 13 C- 1 H distances are determined with precision, and the combination of 13 C static NMR lineshapes and density functional theory (DFT) calculations are used to model different H atomic coordinates. [MgCO 3 · 3H 2 O] is found to be accurate, and evidence from neutron powder diffraction bolsters these assignments. Refined H positions can help understand how H-bonding stabilizes this structure against dehydration to MgCO 3 . More broadly, these results illustrate the power of NMR crystallography as a technique for resolving questions where X-ray diffraction is inconclusive.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

FLOWERS AEP: An Analytical Model for Wind Farm Layout Optimization

Annual energy production (AEP) is commonly used in objective functions for wind farm layout optimization. AEP is proportional to wind farm power production integrated over an annual distribution of free-stream wind conditions. Physics-based estimates of wind farm power production typically rely on low-fidelity engineering wake models that approximate the steady-state wind farm flow field. AEP estimates are then obtained by performing independent simulations for discrete wind conditions and using rectangular quadrature to account for each condition's expected frequency of occurrence. Depending on the number of simulated discrete wind conditions, this numerical integral could be hampered by poor accuracy or high computational costs. The FLOWERS AEP model instead poses an analytical integral of the engineering wake model over the variable wind conditions, yielding a closed-form, analytical function for wind farm AEP. This paper derives the analytical functions for FLOWERS AEP and its derivatives with respect to turbine position, which are useful for gradient-based wind farm layout optimization, in nondimensional form. We then analyze the benefits of the FLOWERS AEP model over conventional reference models, focusing on its low cost, adequate wake loss predictions, and smooth design space. Although the FLOWERS approach is found to predict the exact value of AEP with some error relative to the reference model (within 14% on average), it dramatically reduces computation time by an order of magnitude, produces a qualitatively similar design space at relatively low resolution, and yields comparable optimal layouts. This significant speed improvement is critical in layout optimization applications, where determining an optimal layout in an efficient manner is more important than precise AEP prediction.

17 WIND ENERGY↗

DOE OSTI2020

Observation of the molecular response to light upon photoexcitation

Abstract When a molecule interacts with light, its electrons can absorb energy from the electromagnetic field by rapidly rearranging their positions. This constitutes the first step of photochemical and photophysical processes that include primary events in human vision and photosynthesis. Here, we report the direct measurement of the initial redistribution of electron density when the molecule 1,3-cyclohexadiene (CHD) is optically excited. Our experiments exploit the intense, ultrashort hard x-ray pulses of the Linac Coherent Light Source (LCLS) to map the change in electron density using ultrafast x-ray scattering. The nature of the excited electronic state is identified with excellent spatial resolution and in good agreement with theoretical predictions. The excited state electron density distributions are thus amenable to direct experimental observation.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL). The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the Mycobacterium tuberculosis β-lactamase to be followed using time-resolved crystallography in real time. It is shown how a diffusion coefficient in enzyme crystals can be derived directly from the X-ray data, enabling the determination of ligand and enzyme–ligand concentrations at any position in the crystal volume as a function of time. In addition, the structure of the irreversible inhibitor sulbactam bound to the enzyme at a 66 ms time delay after mixing is described. This demonstrates that the EuXFEL can be used as an important tool for biomedically relevant research.

36 MATERIALS SCIENCE↗