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DOE OSTI2019

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies

Human liver glycerol 3-phosphate dehydrogenase (hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme–substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. Here, these results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Molecular Dynamics Simulations of Anion Exclusion in Clay Interlayer Nanopores

© 2016, Clays and Clay Minerals. All rights reserved. The aqueous chemistry of water films confined between clay mineral surfaces remains an important unknown in predictions of radioelement migration from radioactive waste repositories. This issue is particularly important in the case of long-lived anionic radioisotopes ( 129 I - , 99 TcO - 4 , 36 Cl - ) which interact with clay minerals primarily by anion exclusion. For example, models of ion migration in clayey media do not agree as to whether anions are completely or partially excluded from clay interlayer nanopores. In the present study, this key issue was addressed for Cl - using MD simulations for a range of nanopore widths (6 to 15 Å) overlapping the range of average pore widths that exists in engineered clay barriers. The MD simulation results were compared with the predictions of a thermodynamic model (Donnan Equilibrium model) and two pore-scale models based on the Poisson-Boltzmann equation under the assumption that interlayer water behaves as bulk liquid water. The simulations confirmed that anion exclusion from clay interlayers is greater than predicted by the pore-scale models, particularly at the smallest pore size examined. This greater anion exclusion stems from Cl - being more weakly solvated in nano-confined water than it is in bulk liquid water. Anion exclusion predictions based on the Poisson-Boltzmann equation were consistent with the MD simulation results, however, if the predictions included an ion closest approach distance to the clay mineral surface on the order of 2.0 ± 0.8 Å. These findings suggest that clay interlayers approach a state of complete anion exclusion (hence, ideal semi-permeable membrane properties) at a pore width of 4.2 ± 1.5 Å.

Tournassat, Christophe↗

DOE OSTI2024

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Functional relaxant effect of 6,7-dipropoxy-2H-chromen-2-one is mainly by calcium channel blockade in ex vivo assay of tracheal rings

Asthma is a prevalent disease characterized by airway chronic inflammation, airway hyperresponsiveness, edema and excess of mucus production. Molecules with coumarin scaffold have shown multiple biological effects, including anti-asthmatic. This study describes relaxant effect and mechanism of action of novel semisynthetic 6,7-dipropoxy-2H-chromen-2-one (6,7-DPC) on smooth muscle airways and in silico approaches. 6,7-DPC induced significant relaxant effect on tracheal rings pre-contracted with carbachol (E{sub max} = 100%; EC{sub 50} = 89 µM). Concentration-response curve of 6,7-DPC showed a significant shift to the left with respect to theophylline (positive control). Moreover, pre-treatment with 6,7-DPC inhibited the carbachol-induced contraction in a concentration-dependent manner with suppression of the maximum response. Also, KCl [80 mM]-induced contraction was partially abolished by 6,7-DPC compared with nifedipine; however, CaCl{sub 2} contraction curve only reached 30% of maximal response in the tissues pre-incubated with the test sample. 6,7-DPC was docked on an outer cavity located on the intracellular side of the human L-type calcium channel model and interacts in the following chains and residues: IIIS5.M26, IIIP.T45, IIIP.F49, IIIP.G51, IIIP.P53, IVP.C46, IVP.G49, IVP.E50, IVP.A51, IVP.W52, IVP.Q53, IVP.D54, IVS6.I4, IVS6.F7, IVS6.I8, IVS6.F10, and IVS6.F11. Also, nifedipine made unique interactions with IIIP.E50, IIIP.W52, IIIP.L55. Meanwhile, 6,7-DPC interacted with IIIS5.A22, IIIS2.Q27, and IVS6.C14, exclusively. In conclusion, 6,7-DPC showed a relaxant effect due to combined mechanism of action on rat tracheal rings, through non-competitive muscarinic receptor functional antagonism and preventing the calcium influx. This provides pharmacological basis for the use of 6,7-DPC in airways disorders, such as asthma or chronic obstructive pulmonary disease (COPD).

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

From hard spheres to hard-core spins

A system of hard spheres exhibits physics that is controlled only by their density. This comes about because the interaction energy is either infinite or zero, so all allowed configurations have exactly the same energy. The low-density phase is liquid, while the high-density phase is crystalline, an example of “order by disorder” as it is driven purely by entropic considerations. Here we study a family of hard spin models, which we call hard-core spin models, where we replace the translational degrees of freedom of hard spheres with the orientational degrees of freedom of lattice spins. Their hard-core interaction serves analogously to divide configurations of the many spin system into allowed and disallowed sectors. We present detailed results on the square lattice in d = 2 for a set of models with $\mathbb{Z}_n$ symmetry, which generalize Potts models, and their U(1) limits, for ferromagnetic and antiferromagnetic senses of the interaction, which we refer to as exclusion and inclusion models. As the exclusion and inclusion angles are varied, we find a Kosterlitz-Thouless phase transition between a disordered phase and an ordered phase with quasi-long-ranged order, which is the form order by disorder takes in these systems. These results follow from a set of height representations, an ergodic cluster algorithm, and transfer matrix calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

Glucan Binding Protein C of Streptococcus mutans Mediates both Sucrose-Independent and Sucrose-Dependent Adherence

The high-resolution structure of glucan binding protein C (GbpC) at 1.14 Å, a sucrose-dependent virulence factor of the dental caries pathogen Streptococcus mutans , has been determined. GbpC shares not only structural similarities with the V regions of AgI/II and SspB but also functional adherence to salivary agglutinin (SAG) and its scavenger receptor cysteine-rich domains (SRCRs). This is not only a newly identified function for GbpC but also an additional fail-safe binding mechanism for S. mutans . Despite the structural similarities with S. mutans antigen I/II (AgI/II) and SspB of Streptococcus gordonii , GbpC remains unique among these surface proteins in its propensity to adhere to dextran/glucans. The complex crystal structure of GbpC with dextrose (β- d -glucose; Protein Data Bank ligand BGC) highlights exclusive structural features that facilitate this interaction with dextran. Targeted deletion mutant studies on GbpC's divergent loop region in the vicinity of a highly conserved calcium binding site confirm its role in biofilm formation. Finally, we present a model for adherence to dextran. The structure of GbpC highlights how artfully microbes have engineered the lectin-like folds to broaden their functional adherence repertoire.

Mieher, Joshua L.↗

DOE OSTI2026

Seeing through the nucleus: A review of color transparency phenomena

In this work, we review the current status of the phenomenon of color transparency (CT), a fundamental consequence of the description of hadrons from quantum chromodynamics. CT refers to the vanishing of final (and/or initial) state interactions with the nuclear medium for exclusive process at sufficiently high enough momentum transfers. We discuss the current experimental observations relating to CT and their theoretical implications for other high energy processes. Future CT experiments and facilities are also described.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Sensitivity to Cabibbo-Suppressed $\Lambda$ Production in MicroBooNE

We present a procedure to measure a flux averaged, restricted phase space cross section for direct (Cabibbo suppressed) Λ production using the MicroBooNE detector. This is a rare process, exclusively occurring in anti-neutrino interactions and to maximise the sensitivity of this analysis we combine predictions using the NuMI flux from two data taking periods, one in which this beam was run in neutrino mode and one in anti-neutrino mode. The event selection for this analysis was previously described in MicroBooNE public note 1097. The calculation of systematic uncertainties is shown and a method to propagate them through to the final cross section calculation is described, with final sensitivities shown in the form of Bayesian posterior distributions on the extracted cross section.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

Rotary seal with improved film distribution

The present invention is a generally circular rotary seal that establishes sealing between relatively rotatable machine components for lubricant retention and environmental exclusion, and incorporates seal geometry that interacts with the lubricant during relative rotation to distribute a lubricant film within the dynamic sealing interface. The features of a variable inlet size, a variable dynamic lip flank slope, and a reduction in the magnitude and circumferentially oriented portion of the lubricant side interfacial contact pressure zone at the narrowest part of the lip, individually or in combination thereof, serve to maximize interfacial lubrication in severe operating conditions, and also serve to minimize lubricant shear area, seal torque, seal volume, and wear, while ensuring retrofitability into the seal grooves of existing equipment.

42 ENGINEERING↗

DOE OSTI2025

Expanding the physics reach of DUNE in the near and far detectors

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long-baseline neutrino oscillation experiment. Its primary goal is the determination of the neutrino mass hierarchy and the CP-violating phase. The DUNE physics programme also includes the detection of astrophysical neutrinos and the search for beyond the Standard Model (BSM) phenomena. DUNE will consist of a near detector (ND) complex placed at Fermilab, and a modular Liquid Argon Time Projection Chamber (LArTPC) far detector (FD) to be built in the Sanford Underground Research Facility (SURF), approximately 1300 km away from the neutrino production point. This thesis describes three different projects within DUNE. First, a novel strategy to improve the triggering capabilities of the DUNE FD is proposed. It uses matched filters to enhance the production of online hits across all charge collection planes. Next, the possibility of detecting neutrinos coming from dark matter (DM) annihilations in the Sun with the FD is explored. The complementarity of DUNE to this kind of DM searches is shown. Finally, the simulation and reconstruction framework of ND-GAr, the gas argon ND proposed for Phase II of DUNE, is presented. A number of additions to this are described, particularly focused on the development of the particle identification (PID) capabilities of the detector. These are then used to perform the first event selection studies with an end-to-end simulation in ND-GAr, in particular the selection of pion exclusive samples in $\nu_{\mu}$ CC interactions. All three of these projects share the common goal of enhancing the physics programme of DUNE.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2015

LHC forward physics

The goal of this report is to give a comprehensive overview of the rich field of forward physics, with a special attention to the topics that can be studied at the LHC. The report starts presenting a selection of the Monte Carlo simulation tools currently available, chapter 2, then enters the rich phenomenology of QCD at low, chapter 3, and high, chapter 4, momentum transfer, while the unique scattering conditions of central exclusive production are analyzed in chapter 5. The last two experimental topics, Cosmic Ray and Heavy Ion physics are presented in the chapter 6 and 7 respectively. Chapter 8 is dedicated to the BFKL dynamics, multiparton interactions, and saturation. The report ends with an overview of the forward detectors at LHC. Each chapter is correlated with a comprehensive bibliography, attempting to provide to the interested reader with a wide opportunity for further studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Evaluation of a coastal acoustic buoy for cetacean detections, bearing accuracy and exclusion zone monitoring

Abstract There is strong socio‐political support for offshore wind development in US territorial waters and construction is planned off several east coast states. Some of the planned development sites coincide with important habitat for critically endangered North Atlantic right whales. Both exclusion zones and passive acoustic monitoring are important tools for managing interactions between marine mammals and human activities. Understanding where animals are with respect to exclusion zones is important to avoid costly construction delays while minimizing the potential for negative impacts. Impact piling from construction of hundreds of offshore wind turbines likely require exclusion zones as large as 10 km. We have developed a three‐hydrophone passive acoustic monitoring system that provides bearing information along with marine mammal detections to allow for informed management decisions in real‐time. Multiple units form a monitoring system designed to determine whether marine mammal calls originate from inside or outside of an exclusion zone. In October 2021, we undertook a full system validation, with a focus on evaluating the detection range and bearing accuracy of the system with respect to right whale upcalls. Five units were deployed in Mid‐Atlantic waters and we played more than 3500 simulated right whale upcalls at known locations to characterize the detection function and bearing accuracy of each unit. The modelled results of the detection function error were then used to compare the effectiveness of a bearing‐based system to a single sensor that can only detect a signal but not ascertain directivity. Field trials indicated maximum detection ranges from 4–7.3 km depending on source and ambient noise levels. Simulations showed that incorporating bearing detections provide a substantial improvement in false alarm rates (6 to 12 times depending on number of units, placement and signal to noise conditions) for a small increase in the risk of missed detections inside of an exclusion zone (1%–3%). We show that the system can be used for monitoring exclusion zones and clearly highlight the value of including bearing estimation into exclusion zone monitoring plans while noting that placement and configuration of units should reflect anticipated ambient noise conditions.

17 WIND ENERGY↗

DOE OSTI2023

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Pauli energy contribution to nucleus-nucleus interaction

The investigation delves into understanding how the Pauli exclusion principle influences the bare potential between atomic nuclei through the application of advanced theoretical methodologies. Specifically, the application of the novel Frozen-Hartree-Fock (DCFHF) technique is employed. The resulting potentials demonstrate a noticeable repulsion at short distances, attributed to the effects of the Pauli exclusion principle. To account for dynamic phenomena, such as nucleon transfer processes, the density-constrained time-dependent Hartree-Fock (DC-TDHF) method is utilized. This approach integrates isovector contributions into the potential, shedding light on their influence on fusion reactions. Notably, the inclusion of isovector effects leads to a reduction or enhancement in the inner part of the potential, suggesting a nuanced role of transfer in the fusion process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Sensitivity to low-mass WIMPs with an improved liquid argon ionization response model within the DarkSide program

Dark matter detection experiments using liquid argon rely on a precise characterization of the ionization response to nuclear recoils, especially in the keV energy range relevant for light dark matter interactions. In this work, we present a comprehensive analysis that combines new measurements from the ReD setup, part of the DarkSide experimental program, with calibration data from DarkSide-50, as well as results from the ARIS and SCENE experiments. These combined datasets enable improved constraints on atomic screening effects in the modeling of the ionization response of liquid argon to nuclear recoils. The analysis is performed within the Thomas-Imel recombination framework adopted in previous DarkSide studies, and is here further constrained by the inclusion of ReD data, which allow the screening function to be determined from calibration measurements. By including the updated ionization model into the DarkSide-50 analysis framework, we obtain stronger exclusion limits on low-mass weakly interacting massive particle (WIMP) interactions, setting new world-leading constraints in the 1 – 3 GeV / c 2 WIMP mass range. Finally, we recast the sensitivity projections for the upcoming DarkSide-20k detector, demonstrating a significantly enhanced discovery potential for low-mass dark matter candidates.

Acerbi, F. [Fond. Bruno Kessler, Trento]↗

DOE OSTI2024

Constraints on Covariant Dark-Matter–Nucleon Effective Field Theory Interactions from the First Science Run of the LUX-ZEPLIN Experiment

The LUX-ZEPLIN (LZ) experiment is a dual-phase xenon time project chamber operating in the Sanford Underground Research Facility in South Dakota, USA. We report on the results of a relativistic extension to the nonrelativistic effective field theory (NREFT) from a 5.5 t fiducial mass and 60 live days of exposure. We present constraints on couplings from covariant interactions arising from the coupling of vector, axial currents, and electric dipole moments of the nucleon to the magnetic and electric dipole moments of the weakly interacting massive particle which cannot be described by recasting previous results described by an NREFT. Using a profile-likelihood ratio analysis, in an energy region between 0 keV nr to 270 keV nr , we report 90% confidence level exclusion limits on the coupling strength of five interactions in both the isoscalar and isovector bases. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

U-net architected deep material network training with microstructure local field information

The Deep Material Network (DMN) has recently emerged as a powerful reduced-order modeling framework for simulating the mechanical response of heterogeneous materials such as composites. Unlike most data-driven approaches that directly learn a material’s response under prescribed loading, the DMN acts as a homogenization operator, learning the kinematic constraints and mechanical interactions of the underlying microstructure. However, traditional DMN training relies exclusively on homogenized effective properties derived from Direct Numerical Simulations (DNS), discarding the rich local field data that govern microstructural interactions. In this work, we extend the DMN framework to incorporate such local field information into the offline training process. Utilizing a U-Net architecture, we augment the DMN training objective to include the first and second statistical moments of the local stress fields obtained from linear DNS. This ensures that the learned network topology not only fits the effective stiffness but also accurately reflects the internal local stress and strain partitioning of the microstructure. The results confirm that supervising the localization process during training yields a superior surrogate model, reducing local prediction errors by an order of magnitude and significantly improving generalization to unseen nonlinear constitutive behaviors compared to traditional DMNs.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Search for Electron Neutrinos in Multiple Topologies with the MicroBooNE Experiment

This note presents the status of the measurement of electron neutrinos from the Fermilab Booster Neutrino Beamline (BNB) with the MicroBooNE experiment. The analysis is aimed at investigating the nature of the low energy excess of electromagnetic activity observed by the MiniBooNE experiment. The $ν_e$ event selection relies on topological and calorimetric information to characterise particles produced in these interactions, leveraging the Pandora multi-algorithm reconstruction framework as well as custom particle identification and pattern recognition tools. Results presented in this note use 5.88 × 10 20 protons on target of data collected between 2015 and 2018. These include the performance of particle identification tools for $\mu/p$ and $e/\gamma$ separation, along with electromagnetic shower calibration with the largest sample of $\pi^0$ events measured on argon. Progress towards the completion of this analysis is shown through the measurement of high-energy charged-current $ν_e$ interactions and their kinematic distributions using both inclusive (1eX) and exclusive (1$e$0$p$0$\pi$ and 1$e$N$p$0$\pi$) channels. Measurements of charged-current $ν_µ$ interactions aimed at constraining flux and cross-section systematic uncertainties are also shown. We present the analysis’ preliminary sensitivity of an electron-like signal hypothesis to the MiniBooNE excess which includes flux, cross-section, and detector systematic uncertainties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗