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At least 487 records · Page 27

The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants

Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bayesian inference of nuclear incompressibility from collective flow in mid-central Au+Au collisions at 400–1500 MeV/nucleon

The incompressibility K of symmetric nuclear matter (SNM) is determined through a Bayesian analysis of collective flow data from Au + Au collisions at beam energies $E = 400 -1500$ MeV/nucleon. This analysis utilizes a Gaussian process (GP) emulator applied to the isospin-dependent quantum molecular dynamics (IQMD) model for heavy-ion collisions, both with and without incorporating the momentum dependence of the single-nucleon potentials. Specifically, at the 68% confidence level, using rapidity and transverse velocity dependence of proton elliptic flow data with and without consideration of the momentum dependence, the inferred incompressibility values are $K=188.9^{+2.9}_{-4.5}$ MeV and $256.1^{+8.2}_{-8.7}$ MeV at $E = 400$ MeV/nucleon, respectively. When the transverse momentum dependence of proton-like directed flow data is included, the inferred incompressibility values become $K=222.3^{+9.0}_{-9.9}$ MeV and $K=285.5^{+6.7}_{-7.3}$ MeV, respectively. Furthermore, we found that the value of K derived from observables of proton elliptic flow increases with beam energy. Finally, this indicates that the equation of state (EoS) of nuclear matter hardens at higher densities and temperatures in reactions with higher beam energies.

Bayesian inference↗

Dose-Rate Effects of Protons and Light Ions for DNA Damage Induction, Survival and Transformation in Apparently Normal Primary Human Fibroblasts

In this work, we report on effects of low-dose exposures of accelerated protons delivered at high-dose rate (HDR) or a simulated solar-particle event (SPE) like low-dose rate (LDR) on immediate DNA damage induction and processing, survival and in vitro transformation of low passage NFF28 apparently normal primary human fibroblasts. Cultures were exposed to 50, 100 and 1,000 MeV monoenergetic protons in the Bragg entrance/plateau region and cesium-137 γ rays at 20 Gy/h (HDR) or 1 Gy/h (LDR). DNA double-strand breaks (DSB) and clustered DNA damages (containing oxypurines and abasic sites) were measured using transverse alternating gel electrophoresis (TAFE) and immunocytochemical detection/scoring of colocalized γ-H2AX pS139/53BP1 foci, with their induction being linear energy transfer (LET) dependent and dose-rate sparing observed for the different damage classes. Relative biological effectiveness (RBE) values for cell survival after proton irradiation at both dose-rates ranged from 0.61–0.73. Transformation RBE values were dose-rate dependent, ranging from ~1.8–3.1 and ~0.6–1.0 at low doses (≤30 cGy) for HDR and LDR irradiations, respectively. However peak transformation frequencies were significantly higher (1.3–7.3-fold) for higher doses of 0.5–1 Gy delivered at SPE-like LDR. Cell survival and transformation frequencies measured after low-dose 500 MeV/n He-4, 290 MeV/n C-12 and 600 MeV/n Si-28 ion irradiations also showed an inverse dose-rate effect for transformation at SPE-like LDR. This work demonstrates the existence of inverse dose-rate effects for proton and light-ion-induced postirradiation cell survival and in vitro transformation for space mission-relevant doses and dose rates.

59 BASIC BIOLOGICAL SCIENCES↗

EIC Yellow Report

he Electron-Ion Collider (EIC) is a new, innovative, large-scale particle accelerator conceived by U.S. nuclear physicists over two decades and planned for construction at Brookhaven National Laboratory on Long Island, New York by the U.S. Department of Energy in the 2020s. The EIC will study protons, neutrons and atomic nuclei with the most powerful electron microscope ever built, in terms of its unique versatility of resolving power and intensity. The resolution and intensity is achieved by colliding high-energy electrons with high-energy protons or (a range of different) ion beams. The EIC provides the capability of colliding beams of polarized electrons with polarized beams of light ions, and this all at high intensity. The EIC was established as the highest priority for new construction in the 2015 US Nuclear Physics Long Range Plan, was favorably endorsed by a committee established by the National Academy of Sciences in 2018 to assess the science case. In December 2019, the EIC was granted Critical Design Zero by the US Department of Energy, which launched the EIC as an official project of the US government

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Calibration of the DUNE Far Detector Using Cosmic-ray Muon Events

The Deep Underground Neutrino Experiment (DUNE) aims to set new limits on parameters associated with neutrino oscillations, neutrino astrophysics, and beyond the Standard Model (SM) searches such as nucleon decay. DUNE will quantify the magnitude of CP violation in the lepton sector, and determine the neutrino mass ordering. These benefit highly from the large target mass and excellent imaging, tracking, and particle identification capabilities of Liquid Argon Time Projection Chambers (LArTPCs). Detector calibration is essential to make precise physics measurements. For instance, accurate energy reconstruction is necessary for measuring many of the aforementioned quantities with the precision required for discovering new physics and fully exploiting the capabilities of the detector. Cosmic muons are a freely available natural source of calorimetric data and can be used for calibrating various detector parameters. This thesis provides an analysis of simulated cosmic-ray muon events generated with the Muon Simulation Underground (MUSUN) generator in the DUNE horizontal drift (HD) far detector (FD). The study focuses on analysing the energy and angular distribution of various classes of muon events, as well as characterising the different particles produced by cosmic muon interactions. The analysis of π0 → 2γ events within the cosmic-ray muon sample is presented in this thesis with a detailed study of reconstructing electromagnetic showers. The π0 mass is reconstructed within the DUNE FD, yielding a value of (136 ± 7) MeV/c2. Additionally, the thesis introduces methods for dE/dx calibration using simulated and reconstructed muon tracks. A calibration constant Ccal = (5.469 ± 0.003) × 10−3 ADC × tick/e is obtained through a model-dependent calibration process, where 1 tick corresponds to 500 ns of sampling time of an ADC. Furthermore, a calibration technique is presented, demonstrating precise translation from dQ/dx to dE/dx. This calibration method is applied to stopping muons, charged pions, and protons in the DUNE FD, addressing the measurement of energy loss in the detector volume. These are important calibrations of the DUNE FD and will contribute to achieving the exciting physics goals of the experiment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Iridium metallene oxide for acidic oxygen evolution catalysis

Exploring new materials is essential in the field of material science. Especially, searching for optimal materials with utmost atomic utilization, ideal activities and desirable stability for catalytic applications requires smart design of materials’ structures. Herein, we report iridium metallene oxide: 1 T phase-iridium dioxide (IrO 2 ) by a synthetic strategy combining mechanochemistry and thermal treatment in a strong alkaline medium. This material demonstrates high activity for oxygen evolution reaction with a low overpotential of 197 millivolt in acidic electrolyte at 10 milliamperes per geometric square centimeter (mA cm geo –2 ). Together, it achieves high turnover frequencies of 4.2 s UPD –1 (3.0 s BET –1 ) at 1.50 V vs. reversible hydrogen electrode. Furthermore, 1T-IrO 2 also shows little degradation after 126 hours chronopotentiometry measurement under the high current density of 250 mA cm geo –2 in proton exchange membrane device. Theoretical calculations reveal that the active site of Ir in 1T-IrO 2 provides an optimal free energy uphill in *OH formation, leading to the enhanced performance. The discovery of this 1T-metallene oxide material will provide new opportunities for catalysis and other applications.

36 MATERIALS SCIENCE↗

Particle Accelerators: Their Triumphant History and Uncertain Future

The history of particle physics can be considered nothing less than a huge triumph for science. Over the course of a little more than a century of effort, our understanding of the world of atomic and subatomic physics went from a vague understanding of atoms, to one that is much more detailed. Early in this hundred-year-long period, we learned about electrons (1897), then how they circle a dense nucleus (1911), followed by the discovery of the protons (1917) and neutrons (1932) that form the nucleus. From the 1930s onward, researchers used both cosmic rays and particle accelerators to discover antimatter (1932), and particles that don’t exist in atoms (e.g., the muon [1936] and neutrino [1956], as well as a huge number of others).

43 PARTICLE ACCELERATORS↗

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex

Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo–electron microscopy (cryo-EM) structure of yeast V o proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V o that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V o that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of Electro-Sprayed Porous Electrodes on the Performance and Stability of Water Electrolysis

The efficiency of proton exchange membrane water electrolysis (PEMWE) is a critical issue in realizing the production of green hydrogen. Here, the coexistence of three phases in the catalyst layer of PEMWE causes the mass transport limitation at the interfaces between them. In particular, the vigorous production of gaseous hydrogen and oxygen derived from liquid water is generated in the form of bubbles that seriously deactivate the membrane-electrode assembly (MEA). In this study, we investigated the effect of porous structure in the electrode on the efficiency of hydrogen production at high current density, which is highly related to the mass transport limitation. A widely used commercial catalyst (IrO 2 ) were directly coated on the membrane by the electro-spray method. The porous electrodes on the membrane were formed by the charged catalyst particles that repulsed each other due to the electrostatic forces of the particles. Our membrane electrode assembly (MEA) exhibited outstanding electrolysis performances such as 5.3 A cm -2 and 3.2 A cm -2 at 2.0 V and 1.8 V, respectively, which are the highest values compared with the results published in the current studies. In addition to the porosity, it was confirmed that optimum binder contents positively affect the hydrophobicity and contact resistance of MEA. Through a simple porosity-controlled technique, the performance of PEMWE, in which three phases coexist, can be improved by more than 60 %. Accordingly, we expect that our systematic study on the role of porosity in the electrodes opens a new era to efficiently produce green hydrogen.

catalysts↗

Quantifying spatial resolution in a fast neutron radiography system

Neutron imaging is a powerful nondestructive examination modality that has been employed in various applications. Fast neutrons provide advantages over lower energy neutrons, such as examining thicker samples and inducing negligible activation and transmutations. However, fast neutrons interact mostly via elastic scattering with both the neutron detector and the object, causing degradation in spatial resolution. This study explores the quantification of spatial resolution caused by the testing target itself and suggests proper candidate materials for characterizing spatial resolution in terms of modulation transfer function. Knife-edge radiographs of 3 mm, 6 mm, and 5 cm thick Tantalum (Ta) foils, and a 2.54 cm Tungsten (W) cube were acquired using a CCD-based imaging system and a Polyvinyl Toluene (PVT) scintillator at the Ohio State Research Reactor (OSURR)’s fast neutron beam facility. The spatial resolutions calculated were 195 ± 20 μm, 224 ± 22 μm, 248 ± 25 μm, and 435 ± 44 μm for 3 mm, 6 mm, and 5 cm Ta foils, and 2.54 cm W cube, respectively. The results showed a worsening spatial resolution with increasing target thickness. Simulations and calculations estimate that elastic scattering kinematics between neutrons and protons in the PVT medium also limits spatial resolution, and it sets a lower limit of ~44 μm on the spatial resolution for 2 MeV neutrons.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?

The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with H 2 O 2 have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe IV -OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe III –O •– ) character. Such states offer insight into the nature of ferryl heme.

Williams, Lewis J. [University of Essex, Colcheste↗

Action at a distance: The remarkable coupling of CO 2 uptake to electron transfer in specialized cyanobacterial NDH-1 complexes

Cyanobacteria achieve highly efficient photosynthesis using a CO 2 -concentrating mechanism relying on specialized Type I (NDH-1) complexes. Among these, NDH-1 3 and NDH-1 4 catalyze redox-coupled hydration of CO 2 to bicarbonate, supporting carbon fixation in carboxysomes. The mechanism of coupling electron transfer to CO 2 -hydration by these variant NDH-1 complexes remains unknown. We engineered a Synechococcus PCC7942 strain that expresses exclusively the high flux/low affinity NDH-14 complex, enabling the observation of the coupling of CO 2 hydration to cyclic electron flow in isolation from the other NDH-1 isoforms normally present in cells. We found that inhibition of the CupB protein by the carbonic anhydrase inhibitor ethoxzolamide (EZ) suppressed CO 2 uptake, slowed photosystem I rereduction, and abolished proton pumping as probed by acridine orange fluorescence. These effects were absent in strains lacking Cup proteins, confirming specificity. The results demonstrate that CO 2 hydration and electron transfer through NDH-14 are tightly coupled via proton translocation across the thylakoid membrane. These findings provide direct evidence for the bidirectional interaction in bioenergetic coupling between the plastoquinone reduction and the CO 2 uptake at the distal Zn-site over a span of ~150 Å and support a proton-removal hypothesis involving the proton transfer pathways from the Zn-site of CO2 hydration to an energetically coupled proton loading site evolutionarily repurposed from the ancestral proton pumping mechanism to enable energetic CO 2 uptake.

59 BASIC BIOLOGICAL SCIENCES↗

First Flight of the Advanced Thin Ionization Calorimeter (ATIC) Balloon Experiment

The ATILT instrument is designed to measure the composition and energy spectra of Z = 1 to 28 cosmic rays over the energy range -10 GeV - 100 TeV. ATIC was launched as a long duration test balloon flight on 12/28/00 local time from McMurdo, Antarctica. The operations preceding and during launch went very smoothly. During the first -20 hr while the instrument remained within line of sight (LOS), a full system check out was conducted, the experiment was operated in several test configurations, and all major tuning was completed. Preliminary analysis of the science data indicates that the overall detector system is functioning as expected. With our fully functioning analysis software we were able to monitor the data in nearly real time. Each event was reconstructed event-by-event to confirm the detector performance. The shower profiles indicate that the shower maximum location is deeper in the calorimeter for higher energy events, as expected. The energy spectra of protons, Helium nuclei, and "all particles" appear to follow power laws. Both the Si matrix and top scintillator layer of the charge module show clear charge separation for p and He. As the statistics increase, heavy nuclei charge separation will be evaluated. We will present preliminary results of the LOS data, as well as other data that will be available from the flight-data hard disk,

Case, G.↗

Shields-1 Energetic Proton Dose Comparison from Solar Minimum and Active Periods

Shields-1 has been operating in polar low earth orbit since December 2018 as part of the CubeSat Launch Initiative (CSLI) Educational Launch of Nanosatellites (ELaNa)XIX Mission. Shields-1 has 8 Teledyne µdosimeters behind shielding. These shielded µdosimeters have high minimum proton energy thresholds. The Shields-1 electronics enclosure µdosimeter has a minimum proton threshold energy of 151 MeV. The annualized total ionizing dose (TID) in the electronics enclosure was 75.6 +/- 3.2 RAD from July-August 2019, which was a solar minimum period. In contrast, the annualized TID was 61.0 +/- 2.5 RAD in July 2023, a solar active month. The TID change can be attributed to both the reduction in radiation at the South Atlantic Anomaly (SAA) and the decrease in galactic cosmic radiation during increasing solar activity. The measured GCR dose over the poles was reduced during the July 2023 solar active period in comparison with the July 2019 solar minimum period, using the most sensitive µdosimeter channel for the measurement. Shields-1 has demonstrated the capability of measuring the changes in high energy protons in polar low earth orbit during changes in solar activity, which contributes to the understanding of Earth in the heliosphere.

Shields-1 Dosimetry Space Sciences↗

Is Deprotonation of the Oxygen-Evolving Complex of Photosystem II during the S 1 → S 2 Transition Suppressed by Proton Quantum Delocalization?

We address the protonation state of the water-derived ligands in the oxygen-evolving complex (OEC) of photosystem II (PSII), prepared in the S 2 state of the Kok cycle. We perform quantum mechanics/molecular mechanics calculations of isotropic proton hyperfine coupling constants, with direct comparisons to experimental data from two-dimensional hyperfine sublevel correlation (HYSCORE) spectroscopy and extended X-ray absorption fine structure (EXAFS). We find a low-barrier hydrogen bond with significant delocalization of the proton shared by the water-derived ligand, W1, and the aspartic acid residue D1–D61 of the D1 polypeptide. The lowering of the zero-point energy of a shared proton due to quantum delocalization precludes its release to the lumen during the S 1 → S 2 transition. Retention of the proton facilitates the shuttling of a proton during the isomerization of the tetranuclear manganese–calcium–oxo (Mn 4 Ca–oxo) cluster, from the “open” to “closed” conformation, a step suggested to be necessary for oxygen evolution from previous studies. Our findings suggest that quantum-delocalized protons, stabilized by low-barrier hydrogen bonds in model catalytic systems, can facilitate the accumulation of multiple oxidizing equivalents at low overpotentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fermilab Cryogenic Test Facilities

Fermi National Accelerator Laboratory (Fermilab) has multiple cryogenic test facilities, undertaking testing of superconducting magnets, Superconducting Radio Frequency (SRF) cavities, SRF cryomodules and other helium cryogenic components. The test areas within Fermilab include: Meson Cryogenic Test facility (Meson), Industrial Building 1 (IB-1), Heavy Assembly Building/Illinois Accelerator Research Center (HAB/IARC), New Muon Lab, (NML) and the Cryomodule Test Facility (CMTF). Meson and HAB/IARC utilize repurposed Tevatron era reciprocating engine based cryogenic refrigerator systems, whereas CMTF and IB-1 utilize gas bearing turbine based coldboxes. Each of these test areas support the various Fermilab projects and collaborations including the Linear Coherent Light Source II (LCLS-II), Proton Improvement Plan II (PIP-II), High Luminosity Large Hadron Collider (HL-LHC), and Mu2e. This paper outlines the diverse and extensive cryogenic test capabilities within Fermilab.

43 PARTICLE ACCELERATORS↗