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At least 1,405 records · Page 78

RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Abstract Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.

60 APPLIED LIFE SCIENCES↗

A parametric SPICE model for the simulation of spark gap switches

The use of SPICE-based software for the simulation of pulsed power systems—even large complex systems—has become commonplace in the pulsed power community. This is in contrast to earlier work in the field that relied on specially developed simulation codes such as Sandia’s Screamer or the Navy Research Lab’s Bertha, which natively incorporated models for common pulsed power components such as spark gap switches. Unlike these programs, SPICE programs provide a simple and familiar user interface and wide availability. However, SPICE programs do not include realistic models for key pulsed power circuit devices—including the spark gap switch. While simple switch models do exist in SPICE programs, these can only crudely approximate the behavior of a spark gap. This effort focuses on developing an SPICE circuit model for a gas-filled spark gap switch that is physically realistic while being simple enough to permit simulations to run in reasonable times on typical personal computers. Detailed information is provided for implementation in two common versions of SPICE: LTspice and Orcad PSPICE. Adaptation to other SPICE programs is possible with minimal modification. The model is intended as a design tool that uses physical parameters as inputs to connect it directly to the development of useable pulsed power systems. Data collected from the operation of a high-pressure pulsed-charged switch and a complete 12-stage Marx generator have been used to demonstrate the implementation and accuracy of the model over a wide range of parameters.

Pouncey, J. Cameron (ORCID:0000000153500816)↗

Review of the second charged-particle transport coefficient code comparison workshop

We report the results of the second charged-particle transport coefficient code comparison workshop, which was held in Livermore, California on 24–27 July 2023. This workshop gathered theoretical, computational, and experimental scientists to assess the state of computational and experimental techniques for understanding charged-particle transport coefficients relevant to high-energy-density plasma science. Data for electronic and ionic transport coefficients, namely, the direct current electrical conductivity, electron thermal conductivity, ion shear viscosity, and ion thermal conductivity were computed and compared for multiple plasma conditions. Additional comparisons were carried out for electron–ion properties such as the electron–ion equilibration time and alpha particle stopping power. Overall, 39 participants submitted calculated results from 18 independent approaches, spanning methods from parameterized semi-empirical models to time-dependent density functional theory. In the cases studied here, we find significant differences—several orders of magnitude—between approaches, particularly at lower temperatures, and smaller differences—roughly a factor of five—among first-principles models. We investigate the origins of these differences through comparisons of underlying predictions of ionic and electronic structure. The results of this workshop help to identify plasma conditions where computationally inexpensive approaches are accurate, where computationally expensive models are required, and where experimental measurements will have high impact.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Using ground state and excited state density functional theory to decipher 3d dopant defects in GaN

Abstract Using ground state density functional theory (DFT) and implementing an occupation-constrained DFT (occ-DFT) for self-consistent excited state calculations, we decipher the electronic structure of the Mn dopant and other 3 d defects in GaN across the band gap. Our analysis, validated with broad agreement with defect levels (ground-state calculations) and photoluminescence data (excited-state calculations), mandates reinterpretation and reassignment of 3 d defect data in GaN. The Mn Ga defect is determined to span stable charge states from (1−) in n -type GaN through (2+) in p -type GaN. The Mn(2+) is predicted to be a d 2 ground state spin triplet defect with a singlet excited state, isoelectronic with the defect associated with the 1.19 eV photoluminescence in n -type GaN. The combined analysis of defect levels and excited states invites reassessment of all d 2 -capable dopants in GaN. We demonstrate that the 1.19 eV defect, a candidate defect for optically controlled quantum applications, cannot be the Cr(1+) assumed in literature and instead must be the V(0). The combined ground-state/excited-state DFT analysis is shown to be able to chemically fingerprint defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Observation of a pseudoscalar excess at the top quark pair production threshold

A search for resonances in top quark pair ($t\overline{t}$) production in final states with two charged leptons and multiple jets is presented, based on proton–proton collision data collected by the CMS experiment at the CERN LHC at $\sqrt{s}$ = 13 TeV , corresponding to 138 fb −1 . The analysis explores the invariant mass of the $t\overline{t}$ system and two angular observables that provide direct access to the correlation of top quark and antiquark spins. A significant excess of events is observed near the kinematic $t\overline{t}$ threshold compared to the non-resonant production predicted by fixed-order perturbative quantum chromodynamics (pQCD). The observed enhancement is consistent with the production of a color-singlet pseudoscalar ($^1S^{[1]}_{0}$) quasi-bound toponium state, as predicted by non-relativistic quantum chromodynamics. Using a simplified model for $^1S^{[1]}_{0}$ toponium, the cross section of the excess above the pQCD prediction is measured to be $8.8^{+1.2}_{-1.4}$ pb.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

First operation of a multi-channel Q-Pix prototype: measuring transverse electron diffusion in a gas time projection chamber

We report measurements of the transverse diffusion of electrons in P-10 gas (90% Ar, 10% CH 4 ) in a laboratory-scale time projection chamber (TPC) utilizing a novel pixelated signal capture and digitization technique known as Q-Pix. The Q-Pix method incorporates a precision switched integrating transimpedance amplifier whose output is compared to a threshold voltage. Upon reaching the threshold, a comparator sends a 'reset' signal, initiating a discharge of the integrating capacitor. The time difference between successive resets is inversely proportional to the average current at the pixel in that time interval, and the number of resets is directly proportional to the total collected charge. We developed a 16-channel Q-Pix prototype fabricated from commercial off-the-shelf components and coupled them to 16 concentric annular anode electrodes to measure the spatial extent of the electron swarm that reaches the anode after drifting through the uniform field of the TPC. The swarm is produced at a gold photocathode using pulsed UV light. The measured transverse diffusion agrees with simulations in PyBoltz across a range of operating pressures (200–1500 Torr). These results demonstrate that a Q-Pix readout can successfully reconstruct the ionization topology in a TPC.

47 OTHER INSTRUMENTATION↗

Measurement of nuclear effects in neutrino-argon interactions using generalized kinematic imbalance variables with the MicroBooNE detector

We present a set of new generalized kinematic imbalance variables that can be measured in neutrino scattering. These variables extend previous measurements of kinematic imbalance on the transverse plane and are more sensitive to modeling of nuclear effects. We demonstrate the enhanced power of these variables using simulation and then use the MicroBooNE detector to measure them for the first time. We report flux-integrated single- and double-differential measurements of charged-current muon neutrino scattering on argon using a topology with one muon and one proton in the final state as a function of these novel kinematic imbalance variables. These measurements allow us to demonstrate that the treatment of charged current quasielastic interactions in genie version 2 is inadequate to describe data. As a result, they reveal tensions with more modern generator predictions particularly in regions of phase space where final state interactions are important.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for a scalar or pseudoscalar dilepton resonance produced in association with a massive vector boson or top quark-antiquark pair in multilepton events at s = 13 TeV

A search for beyond the standard model spin-0 bosons, ϕ , that decay into pairs of electrons, muons, or tau leptons is presented. The search targets the associated production of such bosons with a W or Z gauge boson, or a top quark-antiquark pair, and uses events with three or four charged leptons, including hadronically decaying tau leptons. The proton-proton collision data set used in the analysis was collected at the LHC from 2016 to 2018 at a center-of-mass energy of 13 TeV, and corresponds to an integrated luminosity of 138 fb - 1 . The observations are consistent with the predictions from standard model processes. Upper limits are placed on the product of cross sections and branching fractions of such new particles over the mass range of 15 to 350 GeV with scalar, pseudoscalar, or Higgs-boson-like couplings, as well as on the product of coupling parameters and branching fractions. Several model-dependent exclusion limits are also presented. For a Higgs-boson-like ϕ model, limits are set on the mixing angle of the Higgs boson with the ϕ boson. For the associated production of a ϕ boson with a top quark-antiquark pair, limits are set on the coupling to top quarks. Finally, limits are set for the first time on a fermiophilic dilaton-like model with scalar couplings and a fermiophilic axion-like model with pseudoscalar couplings.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Artificial Magnetic Tripod Ice

We study the collective behavior of interacting arrays of nanomagnetic tripods. These objects have six discrete moment states, in contrast to the usual two states of an Ising-like moment. Our experimental data demonstrate that triangular lattice arrays form a “tripod ice” that exhibits charge ordering among the effective vertex magnetic charges, in direct analogy to artificial kagome spin ice. The results indicate that the interacting tripods have effective moments that act as emergent local variables, with strong connections to the well-studied Potts and clock models. In addition, the tripod moments display a tendency toward a nearest neighbor alignment in our thermalized samples that separates this system from kagome spin ice. In conclusion, our results open a path toward the study of the collective behavior of nonbinary moments that is unavailable in other physical systems.

36 MATERIALS SCIENCE↗

First Measurement of R ( X τ / ℓ ) as an Inclusive Test of the b → c τ ν Anomaly

We measure the tau-to-light-lepton ratio of inclusive B -meson branching fractions R ( X τ / ℓ ) ≡ B ( B → X τ ν ) / B ( B → X ℓ ν ) , where ℓ indicates an electron or muon, and thereby test the universality of charged-current weak interactions. We select events that have one fully reconstructed B meson and a charged lepton candidate from 189 fb − 1 of electron-positron collision data collected with the Belle II detector. We find R ( X τ / ℓ ) = 0.228 ± 0.016 ( stat ) ± 0.036 ( syst ) , in agreement with standard-model expectations. This is the first direct measurement of R ( X τ / ℓ ) . Published by the American Physical Society 2024

Physics↗

First Measurement of $𝜈_𝑒$ and $\bar{𝜈}_𝑒$ Charged-Current Single Charged-Pion Production Differential Cross Sections on Argon Using the MicroBooNE Detector

Understanding electron neutrino interactions is crucial for measurements of neutrino oscillations and searches for new physics in neutrino experiments. We present the first measurement of the flux-averaged $𝜈_𝑒$ + $\bar{𝜈}_𝑒$ charged-current single charged-pion production cross section on argon using the MicroBooNE detector and data from the NuMI neutrino beam. The total cross section is measured to be [0.93 ± 0.13⁢(stat) ± 0.27⁢(syst)] × 10 −39 cm 2 /nucleon at a mean $𝜈_𝑒$ + $\bar{𝜈}_𝑒$ energy of 730 MeV. Differential cross sections are also reported in electron energy, electron and pion angles, and electron-pion opening angle.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Location Selection of Fast-Charging Station for Heavy-Duty EVs Using GIS and Grid Analysis

This work presents a systematic methodology for the location selection of fast-charging stations for heavy-duty electric vehicles (EVs) based on both geospatial and electric grid analysis. The geospatial analysis is based on real-world geographic information system (GIS) data of road networks and existing supportive infrastructures. The grid analysis is implemented based on node-level analysis of potential impacts on voltages and power losses in the distribution system. A case study using a realistic, three-phase, unbalanced distribution feeder from California and extracted real-world GIS data is used to demonstrate the intuitiveness and effectiveness of the proposed methodology for the location selection of fast-charging stations for heavy-duty EVs considering both electric and existing transportation infrastructures.

47 OTHER INSTRUMENTATION↗

Dispersive corrections in elastic electron-nucleus scattering: an investigation in the intermediate energy regime and their impact on the nuclear matter

Measurements of elastic electron scattering data within the past decade have highlighted two-photon exchange contributions as a necessary ingredient in theoretical calculations to precisely evaluate hydrogen elastic scattering cross sections. This correction can modify the cross section at the few percent level. In contrast, dispersive effects can cause significantly larger changes from the Born approximation. The purpose of this experiment is to extract the carbon-12 elastic cross section around the first diffraction minimum, where the Born term contributions to the cross section are small to maximize the sensitivity to dispersive effects. The analysis uses the LEDEX data from the high resolution Jefferson Lab Hall A spectrometers to extract the cross sections near the first diffraction minimum of 12 C at beam energies of 362 MeV and 685 MeV. The results are in very good agreement with previous world data, although with less precision. The average deviation from a static nuclear charge distribution expected from linear and quadratic fits indicate a 30.6% contribution of dispersive effects to the cross section at 1 GeV. The magnitude of the dispersive effects near the first diffraction minimum of 12 C has been confirmed to be large with a strong energy dependence and could account for a large fraction of the magnitude for the observed quenching of the longitudinal nuclear response. These effects could also be important for nuclei radii extracted from parity-violating asymmetries measured near a diffraction minimum.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The nucleardatapy toolkit for simple access to experimental nuclear data, astrophysical observations, and theoretical predictions

Systematic comparisons across theoretical predictions for the properties of dense matter, nuclear physics data, and astrophysical observations (also called meta-analyses) are performed. Existing predictions for symmetric nuclear and neutron matter properties are considered, and they are shown in this paper as an illustration of the present knowledge. Asymmetric matter is constructed assuming the isospin asymmetry quadratic approximation. It is employed to predict the pressure at twice saturation energy-density based only on nuclear-physics constraints, and we find it compatible with the one from the gravitational-wave community. To make our meta-analysis transparent, updated in the future, and to publicly share our results, the Python toolkit nucleardatapy is described and released here. Hence, this paper accompanies nucleardatapy, which simplifies access to nuclear-physics data, including theoretical calculations, experimental measurements, and astrophysical observations. This Python toolkit is designed to easily provide data for: (i) predictions for uniform matter (from microscopic or phenomenological approaches); (ii) correlation among nuclear properties induced by experimental and theoretical constraints; (iii) measurements for finite nuclei (nuclear chart, charge radii, neutron skins or nuclear incompressibilities, etc.) and hypernuclei (single particle energies); and (iv) astrophysical observations. This toolkit provides data in a unified format for easy comparison and provides new meta-analysis tools. It will be continuously developed, and we expect contributions from the community in our endeavor.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

C3PU:Real-Time Predictive Charge Control Software for Battery Management Systems (Code for Charge Control and Predictive Unit) [SWR-21-48]

C3PU sets up a model predictive control formulation for the optimal charging control of battery packs and can be deployed for real-time operation on an embedded microprocessor. C3PU uses electrochemical and thermal models of battery packs to predict the charging trajectories of the battery pack over a time horizon under different operating conditions. It then selects the optimal charging trajectory such that a pre-defined objective is minimized, which in the present state of the code is to minimize the charging duration of the battery pack. The optimal charging trajectory is obtained by solving an underlying mathematical problem. However, C3PU is flexible to incorporate other charging objectives. The underlying battery models can be swapped as well, as long as they follow certain mathematical properties. Mathematically, optimal control problems (in this case, optimally controlling the charging current of the battery pack) are computationally expensive. C3PU implements advanced numerical techniques, namely pseudo-spectral optimization, to reduce the computational burden of the underlying problem to solve. This allows for the problem to be solved in real-time in an embedded system. Once the optimal charging trajectory is computed over a time horizon, C3PU can package such data and send it out via appropriate communication protocols.

Mishra, Partha↗

Bike and Scoot to Transit

In this project, we developed a micromobility first-mile service for customers to access public transit. We launched this service as a pilot in the Seattle area that incentivized transit customers to bike or scoot to transit. The objective was to learn how to integrate different micromobility services and provide a unified reward program. Our pilot was called “Bike and Scoot to Transit” and ran from November 2022 to September 2023. More than a dozen locations were selected near transit hubs and light rail/train stations as preferred parking locations. Trips ending at those locations were partially funded. The pilot supported 19,226 qualified trips and distributed $73,000 in total benefits for the participants of the pilot. This dataset was collected from our pilot, which includes the following: - Monthly data: Monthly trip and funding summaries. - Data summary: Data broken down based on the micromobility service provider and equipment. - Trip data: List of all trips recorded during the pilot. - Pricing models: Fees charged by micromobility service providers. ![bike to transit](bike-transit.png)

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

High-Accuracy Simulations to Model Pyrometallurgical Processes in a Secondary Lead Reverberatory Furnace

The US manufacturing industry produces about 1.3 million tons of refined lead each year using secondary sources consisting mainly of lead batteries. ORNL is partnering with Gopher resource, the second largest lead recycling company in the United States, and GTI, to develop a high-fidelity CFD model of a directly fired, reverberatory-style, secondary lead furnace. These High Performance Computing (HPC) simulations are aimed to use first principles modeling for combustion and melting processes of the secondary lead feed while accounting for complex interphase interactions between the gas, solid charge (lead) material, slag, and metal phases. Through validation against operating plant data, this effort will enable significant improvements in design, operational parameters, and energy efficiency, thus improving productivity and refractory lifetime of secondary lead melting furnaces. Estimated savings/reduction of, at least, 1 trillion BTU, 1 million ton/year of greenhouse gas emissions, and $\$50$ million/year to the US lead industry can be expected. ORNL resources and expertise in high-performance computing and multicomponent, multiphase flows were utilized to realize this goal while advancing the understanding of the smelting and melting processes occurring within the furnace.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗