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NASA NTRS1994

Method for imaging informational biological molecules on a semiconductor substrate

Imaging biological molecules such as DNA at rates several times faster than conventional imaging techniques is carried out using a patterned silicon wafer having nano-machined grooves which hold individual molecular strands and periodically spaced unique bar codes permitting repeatably locating all images. The strands are coaxed into the grooves preferably using gravity and pulsed electric fields which induce electric charge attraction to the molecular strands in the bottom surfaces of the grooves. Differential imaging removes substrate artifacts.

Coles, L. Stephen↗

DOE OSTI2024

Smart Pixels: In-pixel AI for on-sensor data filtering

We present a smart pixel prototype readout integrated circuit (ROIC) designed in CMOS 28 nm bulk process, with in-pixel implementation of an artificial intelligence (AI) / machine learning (ML) based data filtering algorithm designed as proof-of-principle for a Phase III upgrade at the Large Hadron Collider (LHC) pixel detector. The first version of the ROIC consists of two matrices of 256 smart pixels, each 25$\times$25 $\mu$m$^2$ in size. Each pixel consists of a charge-sensitive preamplifier with leakage current compensation and three auto-zero comparators for a 2-bit flash-type ADC. The frontend is capable of synchronously digitizing the sensor charge within 25 ns. Measurement results show an equivalent noise charge (ENC) of $\sim$30e$^-$ and a total dispersion of $\sim$100e$^-$ The second version of the ROIC uses a fully connected two-layer neural network (NN) to process information from a cluster of 256 pixels to determine if the pattern corresponds to highly desirable high-momentum particle tracks for selection and readout. The digital NN is embedded in-between analog signal processing regions of the 256 pixels without increasing the pixel size and is implemented as fully combinatorial digital logic to minimize power consumption and eliminate clock distribution, and is active only in the presence of an input signal. The total power consumption of the neural network is $\sim$ 300 $\mu$W. The NN performs momentum classification based on the generated cluster patterns and even with a modest momentum threshold, it is capable of 54.4% - 75.4% total data rejection, opening the possibility of using the pixel information at 40MHz for the trigger. The total power consumption of analog and digital functions per pixel is $\sim$ 6 $\mu$W per pixel, which corresponds to $\sim$ 1 W/cm$^2$ staying within the experimental constraints.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

Top-Down Analysis of Proteins in Low Charge States

The impact of charging methods on the dissociation behavior of intact proteins in low charge states is investigated using HCD and 193 nm UVPD. Low charge states are produced for seven different proteins using the following four different methods: (1) proton transfer reactions of ions in high charge states generated from conventional denaturing solutions; (2) ESI of proteins in solutions of high ionic strength to enhance retention of folded native-like conformations; (3) ESI of proteins in high pH solutions to limit protonation; and (4) ESI of carbamylated proteins. Comparison of sequence coverages, degree of preferential cleavages, and types and distribution of fragment ions reveals a number of differences in the fragmentation patterns depending on the method used to generate the ions. More notable differences in these metrics are observed upon HCD than upon UVPD. The fragmentation caused by HCD is influenced more significantly by the presence/absence of mobile protons, a factor that modulates the degree of preferential cleavages and net sequence coverages. Carbamylation of the lysines and the N-terminus of the proteins alters the proton mobility by reducing the number of proton-sequestering, highly basic sites as evidenced by decreased preferential fragmentation C-terminal to Asp or N-terminal to Pro upon HCD. UVPD is less dependent on the method used to generate the low charge states and favors non-specific fragmentation, an outcome which is important for obtaining high sequence coverage of intact proteins. .

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2018

Electron-neutrino selection and reconstruction in the MicroBooNE LArTPC using the Pandora multi-algorithm pattern recognition

MicroBooNE (the Micro Booster Neutrino Experiment) is a liquid argon time-projection chamber experiment designed for short-baseline neutrino physics, currently running at Fermilab. It aims to address the anomalous excess of low-energy events observed by the MiniBooNE experiment. In this note we present a fully automated event selection algorithm to identify charged-current electron neutrino event candidates with no pions and at least one proton in the final state (ν e CC0π-Np). The efficiency of the current selection algorithm is (46.5±0.3) %. We also show some cuts on kinematic and geometric variables which reject background events. These cuts have been validated by analyzing two event samples orthogonal to our signal. Future improvements have been identified which will improve the reconstruction efficiency, especially at low energy.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2011

Measurement of absolute charge-exchange cross sections for He{sup 2+} collisions with He and H{sub 2}

Reported are total, absolute charge-exchange cross sections for collisions of {sup 3}He{sup 2+} ions with He and H{sub 2}. Measurements are reported at fixed energies between 0.33 and 4.67 keV/amu. Both the present results and earlier results of others are analyzed in terms of available experimental small-angle differential cross sections as a function of collision energy, and hence the geometry of the exit aperture of the gas-collision cells used by the various experimental groups. In addition, the effective length of gas-collision cells is studied using fluid dynamic and molecular flow simulations to address the density patterns near the cell entrance and exit apertures. When small acceptance-angle corrections were applied, the results of present and previous measurements for the single electron capture in these systems were brought into good accord in the relevant energy ranges. Taken in their entirety, the present data for {sup 3}He{sup 2+} with He and H{sub 2} lend themselves to new theoretical calculations of the multichannel charge-exchange cross sections.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2016

Self-Repair and Patterning of 2D Membrane-Like Peptoid Materials

Two-dimensional materials are of increasing interest for use in filtration, sensing, nanoelectronics, and biomedical devices. Peptoids are a class of biomimetic sequence-defined polymers for which certain amphiphillic sequences self-assemble into 2D crystalline materials with properties that mimic those of cell membranes. Using in situ AFM to both dissect these membrane-like materials and image their subsequent behavior, we explore their ability to self-repair on a range of solid substrates. We show that, in a suitable range of pH, self-repair occurs on both negatively and positively charged substrates and can even occur in the absence of an underlying surface. Following dissection of pre-assembled peptoid membranes and upon introduction of a peptoid monomer solution, peptoids repair the damage by assembling at the newly created edges. The speed of the advancing edge depends on the edge orientation, reflecting the two-fold symmetry of the underlying peptoid lattice. Moreover, because the membranes are stabilized by hydrophobic interactions, if the solution contains peptoids possessing an identical sequence in the hydrophobic block but a distinct hydrophilic block, filling of the defects creates membranes that are patterned at the nanoscale. Consequently, we can utilize this ability to create nm-sized patterns of distinct functional groups within a single coherent membrane.

Jiao, Fang↗

DOE OSTI2015

Two-dimensional simulation of spatiotemporal generation of dielectric barrier columnar discharges in atmospheric helium

A two-dimensional (2D) fluid model is presented to investigate the spatiotemporal generation and dynamic mechanics of dielectric barrier columnar discharges in atmospheric helium. The model was examined with discharge currents measured in experiments and images taken by an intensified charge couple device camera. Based on the model, a columnar discharge was simulated for several cycles after being ignited. The discharge could be regarded as an initial unstable stage for the first three and a half cycles, then a steady state for the following cycles. In the initial stage, the discharge evolves from a uniform pattern into a columnar one. The calculated equipotential lines, 2D radial electric field, and electron density distributions at the edge of uniform discharges show the radial electric field accounts for the shrinking discharge area and the formation of discharge columns in the end. The columnar glow discharges and the Townsend discharges beyond the columns could coexist in the initial stage, and a Townsend discharge might develop into a new glow column in the next half-cycle. The radial electric field surrounding a glow discharge column has an inhibiting effect on the ionization in the peripheral area.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2019

Neutrinos below 100 TeV from the southern sky employing refined veto techniques to IceCube data

Many Galactic sources of gamma rays, such as supernova remnants, are expected to produce neutrinos with a typical energy cutoff well below 100 TeV. For the IceCube Neutrino Observatory located at the South Pole, the southern sky, containing the inner part of the Galactic plane and the Galactic Center, is a particularly challenging region at these energies, because of the large background of atmospheric muons. In this paper, we present recent advancements in data selection strategies for track-like muon neutrino events with energies below 100 TeV from the southern sky. The strategies utilize the outer detector regions as veto and features of the signal pattern to reduce the background of atmospheric muons to a level which, for the first time, allows IceCube searching for point-like sources of neutrinos in the southern sky at energies between 100 GeV and several TeV in the muon neutrino charged current channel. We report no significant clustering of neutrinos above background expectation was observed in four years of data recorded with the completed IceCube detector. Upper limits on the neutrino flux for a number of spectral hypotheses are reported for a list of astrophysical objects in the southern hemisphere.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

A facile one-step synthesis of Mn{sub 3}O{sub 4} nanoparticles-decorated TiO{sub 2} nanotube arrays as high performance electrode for supercapacitors

Via a facile one-step chemical bath deposition route, homogeneously dispersed Mn{sub 3}O{sub 4} nanoparticles have been successfully deposited onto the inner surface of TiO{sub 2} nanotube arrays (TNAs). The content and size of Mn{sub 3}O{sub 4} can be controlled by changing the deposition time. Field emission scanning electron microscopy and transmission electron microscopy analysis reveal the morphologies structures of Mn{sub 3}O{sub 4}/TNAs composites. The crystal-line structures are characterized by the X-ray diffraction patterns and Raman spectra. X-ray photoelectron spectroscopy further confirms the valence states of the sample elements. The electrochemical properties of Mn{sub 3}O{sub 4}/TNAs electrodes are systematically investigated by the combine use of cyclic voltammetry, galvanostatic charge-discharge and electrochemical impedance spectroscopy. The resulting Mn{sub 3}O{sub 4}/TNAs electrode prepared by deposition time of 3 h shows the highest specific capacitance of 570 F g{sup −1} at a current density of 1 A g{sup −1}. And it also shows an excellent long-term cycling stability at a current density of 5 A g{sup −1}, which remaining 91.8% of the initial capacitance after 2000 cycles. Thus this kind of Mn{sub 3}O{sub 4} nanoparticles decorated TNAs may be considered as an alternative promising candidate for high performance supercapacitor electrodes. - Graphical abstract: Mn{sub 3}O{sub 4} nanoparticles have been uniformly deposited onto the inner surfaces of TiO{sub 2} nanotube arrays through a facile one-step chemical bath deposition method. As electrodes for supercapacitors, they exhibit a relatively high specific capacity and excellent cycling stability. - Highlights: • Mn{sub 3}O{sub 4} nanoparticles have been deposited onto TiO{sub 2} nanotube arrays by chemical bath deposition. • The Mn{sub 3}O{sub 4}/TNAs exhibits a highest specific capacitance of 570 F g{sup –1} at a current density of 1 A g{sup –1}. • The Mn{sub 3}O{sub 4}/TNAs electrode shows an excellent cycling stability of 91.8% after 2000 cycles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Solvent-dependent transition from concerted electron–proton to proton transfer in photoinduced reactions between phenols and polypyridine Ru complexes with proton-accepting sites

The bimolecular rate coefficients ($k_q^{obs}$) for quenching the metal-to-ligand charge transfer excited states of two Ru polypyridine complexes containing H-bond accepting sites by six p-substituted phenols exhibit abrupt deviations from the expected linear correlations of log$k_q^{obs}$ with phenol’s Hammett σ p constant. This pattern is attributed to a transition of the quenching mechanism from a concerted electron-proton transfer (EPT) to a proton transfer (PT); the latter becomes predominant for the most acidic phenols in MeCN, but not in CH 2 Cl 2 . This assertion is supported by a detailed thermochemical analysis, which also excludes the quenching pathways involving electron transfer from phenols with or without deprotonation of phenols to the solvent, either concerted or sequential. The transition from EPT to PT upon the σ p increase is consistent/supported by the magnitudes of the measured and computed PhOH/OD kinetic isotope effects and by the observed reduction of the EPT product yields upon replacing the low σ p methoxyphenol by the high σ p nitrophenol. In addition to modulating the relative contribution of the EPT and PT quenching pathways, the solvent strongly affects the bimolecular rate coefficients for the EPT quenching proper. Unlike with H-atom transfer reactions, this kinetic solvent effect could not be quantitatively accounted for by the phenol-solvent H-bonding alone, which suggests a solvent effect on the H-bonding constants in the phenol-Ru complex precursor exciplexes and/or on the unimolecular EPT rate coefficients within these exciplexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Tunable silica shell and its modification on photoluminescent properties of Y{sub 2}O{sub 3}:Eu{sup 3+}-SiO{sub 2} nanocomposites

The core-shell rare earth (RE) doped nanophosphors are attracting current interests owing to their potential application in bio-images. Understanding the modification of core-shell structure on photoluminescent (PL) properties of RE ions is important in obtaining efficient nanophosphors. In this paper, Y{sub 2}O{sub 3}:Eu{sup 3+}-SiO{sub 2} composites with fixed cubic Y{sub 2}O{sub 3}:Eu{sup 3+} core ({approx}80 nm) and controllable thickness of silica shell ({approx}3-21 nm) were synthesized via a modified Stoeber method and characterized by x-ray diffraction patterns, transmission electronic microscope images, and Fourier-transform infrared absorption spectra. The dependences of PL properties of Y{sub 2}O{sub 3}:Eu{sup 3+} on the thickness of the silica shell and excitation power density were systemically studied under charge transfer excitation (254 nm) and {sup 7}F{sub J}-{sup 5}D{sub 2} inner-shell excitation (460-486 nm). It is interesting to observe that under {sup 7}F{sub J}-{sup 5}D{sub 2} excitation the intensity ratio of {sup 5}D{sub 0}-{sup 7}F{sub 2}/{sup 5}D{sub 0}-{sup 7}F{sub J} (J {ne} 2) for Eu{sup 3+} increases considerably with the increase of shell thickness and decreases with the increasing excitation power density, which confirms the variation of long-scale radiative energy transfer (RET) among Eu{sup 3+} ions and redistribution of {sup 5}D{sub 0}-{sup 7}F{sub J}(J = 0-4) transitions. And more, the radiative decay time of {sup 5}D{sub 0}-{sup 7}F{sub J} as a function of shell thickness demonstrates an optimum, which are assigned to the co-impacts of effective refractive index (n{sub eff}) and RET among Eu{sup 3+} ions.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Accelerated domain switching speed in single-crystal LiNbO{sub 3} thin films

By using ionic implantation and wafer bonding technologies, we peeled off a single-crystal LiNbO{sub 3} thin film in the atomic-layer smoothness from the surface of a bulk Z-cut LiNbO{sub 3} single crystal. X-ray diffraction patterns showed only (00l) orientation of the film. From positive-up-negative–down pulse characterization, we measured domain switching current transients under various short-pulse voltages, where we observed domain switching currents to occur separately at time after initial capacitor charging currents. This is similar to early observations in bulk ferroelectric single crystals, where apparent positive/negative coercive fields of domain switching determined from polarization-electric field hysteresis loops always equal maximum/minimum applied fields. However, after pulse stressing of the film for more than 1000 cycles, the domain switching speed is accelerated, where domain switching current overlaps with the initial capacitor charging current with a well-defined coercive field independent of the applied-field strength. Finally, we simulated the whole domain switching current transients with the assumption of the resistance degradation across interfacial passive layers between the film and electrodes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Charged particle tracking in real-time using a full-mesh data delivery architecture and associative memory techniques

We present a flexible and scalable approach to address the challenges of charged particle track reconstruction in real-time event filters (Level-1 triggers) in collider physics experiments. The method described here is based on a full-mesh architecture for data distribution and relies on the Associative Memory approach to implement a pattern recognition algorithm that quickly identifies and organizes hits associated to trajectories of particles originating from particle collisions. We describe a successful implementation of a demonstration system composed of several innovative hardware and algorithmic elements. The implementation of a full-size system relies on the assumption that an Associative Memory device with the sufficient pattern density becomes available in the future, either through a dedicated ASIC or a modern FPGA. We demonstrate excellent performance in terms of track reconstruction efficiency, purity, momentum resolution, and processing time measured with data from a simulated LHC-like tracking detector.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Distribution System Planning for Growth in Residential Electric Vehicle Adoption

Anticipated growth in Electric Vehicles (EV) adoption could stress distribution system circuits beyond their original design limits. Uncertainties related to when households will begin buying EVs in large numbers challenges existing distribution system planning approaches and complicates efforts to assess grid impacts. Anticipated location, timing, and demand for EV charging is critical information for distribution system planners as it guides investment strategies for infrastructure upgrades to ensure continued reliability. This research makes two significant contributions: an EV adoption model that uses socioeconomic data to forecast location and year-specific adoption patterns through a bottoms-up approach, and an EV hosting capacity assessment methodology that offers improvements to current utility planning and asset management practices for infrastructure investments. Both contributions are applied to a Southern California Edison feeder in 7 adoption years from 2025 to 2050, with the results indicating that they are likely valuable additions to distribution systems planning capabilities.

Sridhar, Siddharth↗

DOE OSTI2025

Evaluation of data driven low-rank matrix factorization for accelerated solutions of the Vlasov equation

Low-rank methods have shown success in accelerating simulations of a collisionless plasma described by the Vlasov equation, but still rely on computationally costly linear algebra every time step. We propose a data-driven factorization method using artificial neural networks, specifically with convolutional layer architecture, that trains on existing simulation data. At inference time, the model outputs a low-rank decomposition of the distribution field of the charged particles, and we demonstrate that this step is faster than the standard linear algebra technique. Numerical experiments show that the method achieves comparable reconstruction accuracy for interpolation tasks, generalizing to unseen test data in a manner beyond just memorizing training data; patterns in factorization also inherently followed the same numerical trend as those within algebraic methods (e.g., truncated singular-value decomposition). However, when training on the first 70% of a time-series data and testing on the remaining 30%, the method fails to meaningfully extrapolate. Despite this limiting result, the technique may have benefits for simulations in a statistical steady-state or otherwise showing temporal stability. These results suggest that while the model offers a computationally efficient alternative for datasets with temporal stability, its current formulation is best suited for interpolation rather than for predicting future states in time-evolving systems. This study thus lays the groundwork for further refinement of neural network-based approaches to low-rank matrix factorization in high-dimensional plasma simulations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

AN ALL-SKY SEARCH FOR THREE FLAVORS OF NEUTRINOS FROM GAMMA-RAY BURSTS WITH THE ICECUBE NEUTRINO OBSERVATORY

We present the results and methodology of a search for neutrinos produced in the decay of charged pions created in interactions between protons and gamma-rays during the prompt emission of 807 gamma-ray bursts (GRBs) over the entire sky. This three-year search is the first in IceCube for shower-like Cherenkov light patterns from electron, muon, and tau neutrinos correlated with GRBs. We detect five low-significance events correlated with five GRBs. These events are consistent with the background expectation from atmospheric muons and neutrinos. The results of this search in combination with those of IceCube’s four years of searches for track-like Cherenkov light patterns from muon neutrinos correlated with Northern-Hemisphere GRBs produce limits that tightly constrain current models of neutrino and ultra high energy cosmic ray production in GRB fireballs.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1999

Quantitation of Radiation Induced Deletion and Recombination Events Associated with Repeated DNA Sequences

Manned exploration of space exposes the explorers to a complex and novel radiation environment. The galactic cosmic ray and trapped belt radiation (predominantly proton) components of this environment are relatively constant, and the variations with the solar cycle are well understood and predictable. The level of radiation encountered in low earth orbits is determined by several factors, including altitude, inclination of orbit with respect to the equator, and spacecraft shielding. At higher altitudes, and on a Mars mission, the level of radiation exposure will increase significantly. A significant fraction of the dose may be delivered by solar particle events which vary dramatically in dose rate and incident particle spectrum. High-LET radiation is of particular concern. High-LET radiation, a component of galactic cosmic rays (GCR), is comprised of a variety of charged particles of various energies (10 MeV/n to 10 GeV/n), including about 87% photons, 12% helium ions, and heavy ions (including iron). These high energy particles can cause significant damage to target cells. The different particle types and energies result in different patterns of energy deposition at the molecular and cellular level in a primary target cell. They can also cause significant damage to other, nearby cells as a result of secondary particles. Protons, for instance produce secondaries that include photons, neutrons, pions, heavy particles, as well as gamma rays. Heavy ions deposit energy in a "track" in which the magnitude of the damage varies as the particle loses energy. Heavy ions produce secondary delta rays, or electrons. The distribution of damage through tissue is described by a Bragg curve which will be characteristic for different energies. Needless to say there are differences in the RBE of protons and a particles. High-LET heavy ions are particularly damaging to cells as they do continual damage throughout their track. Differences in these energy deposition patterns can significantly influence the nature of DNA damage and the ability of cellular systems to repair such damage. It has been suspected that these differences also affect the spatial distribution of damage within the DNA of the interphase cell nucleus and produce corresponding differences in endpoints related to health effects. The interaction of a single high-LET particle with chromatin has been suggested to cause multiple double strand breaks within a relatively short distance. In part this is due to the organization of DNA into chromatin fibers in which distant regions of the DNA helix can be physically juxtaposed by the various levels of coiling of the DNA. This prediction was confirmed by the detection of the generation of double strand DNA fragments of 100-2000 bp following exposure to high-LET ions (including iron).

Sinden, Richard R.↗

DOE OSTI2023

Optimisation of the Search for CP-symmetry Violation at the Deep Underground Neutrino Experiment

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long baseline experiment, which will be situated in South Dakota. Its detectors will utilise liquid-argon time projection chamber technology, which is able to capture neutrino interactions with an incredible spatial and calorimetric resolution. With what will become the world’s most intense neutrino beam, a highly capable near detector, and four (10kt fducial mass) far detector modules, DUNE will be able to achieve an ambitious physics programme. Most notably, DUNE will determine whether charge-parity symmetry is broken in neutrino oscillations - a finding that would have significant implications for the understanding of the matter-antimatter asymmetry in our Universe.This thesis presents the optimisation of a CP-violation analysis at DUNE using thePandora pattern-recognition software. The analysis assumes a 3.5 year exposure (1.36 × 1023 protons on target) to a neutrino and an antineutrino beam (7 year total). Only the predicted data of the far detector modules is used; near detector samples are not included. The initial sensitivity to CP-violation is found to be 3.8σ+0.9σ−1.1σ in an estimate that includes oscillation parameter uncertainties, systematic uncertainties and statistical fluctuations, and assumes a normal-ordering of the neutrino mass hierarchy. The performance of the Pandora event reconstruction is linked to that of the analysis, which is found to be limited by the reconstruction of the initial track-like region of electrons and photons. The ShowerRefinement algorithm is developed in response to this and its implementation into the analysis workflow results in an improved sensitivity to CP-violation of 4.6σ+0.9σ−1.0σ. With a perfected neutrino interaction vertex placement, this is further increased to 5.1σ+1.0σ−1.1σ.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗