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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

HIV drug resistance during antiretroviral therapy scale-up in Uganda, 2012–19: a population-based, longitudinal study

Background With scale-up of antiretroviral therapy (ART) in sub-Saharan Africa, increasing pretreatment HIV drug resistance has been reported; however, the broader effect of ART expansion on population-level resistance patterns remains insufficiently quantified. We aimed to estimate the longitudinal prevalence of drug resistance and resistance-conferring mutations. Methods This study used data collected as part of the Rakai Community Cohort Study (RCCS), an open population-based census and cohort study conducted in southern Uganda. At each survey round, residents aged 15–49 years are invited to participate and receive a structured questionnaire that obtains sociodemographic, behavioural, and health information, including self-reported past and current ART use. Voluntary HIV testing is conducted using a rapid test algorithm and a venous blood sample. People with HIV provide samples for viral load quantification and deep sequencing. We analysed RCCS survey, HIV viral load, and deep sequencing (which was used to predict resistance) data from five survey rounds. The key outcomes were the population prevalence of viraemic people with HIV with non-nucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), protease inhibitor, or multiclass resistance among all participants (regardless of HIV serostatus) in the 2015 and 2017 surveys. Prevalence of class-specific resistance and resistance-conferring substitutions were estimated using robust log-Poisson regression. Findings Between Aug 10, 2011, and Nov 4, 2020, there were 43 361 participants in the RCCS and 7923 (18·27%) people with HIV. Over five survey rounds, 93 622 participant visits occurred, among which 17 460 (18·65%) were from people with HIV. Over the analysis period, the median age of study participants remained similar (28 years [22–35] in 2012 and 29 years [21–38] in 2019). Sufficient data were available to reliably genotype 4072 (90·03%) of 4523 participant visits from 3407 people with HIV for at least one drug. Overall population prevalence of resistance contributed by viraemic pretreatment people with HIV decreased between 2012 and 2017 from 0·56% (95% CI 0·42–0·75) to 0·25% (0·18–0·33) for NNRTI and from 0·24% (0·15–0·37) to 0·05% (0·02–0·10) for NRTI (prevalence ratio 0·44 [0·29–0·68] for NNRTI and 0·21 [0·09–0·47] for NRTI). Between 2012 and 2017, NNRTI resistance among viraemic pretreatment people with HIV increased from 4·86% (3·69–6·42) to 9·61% (7·27–12·7; prevalence ratio 1·98 [1·34–2·91]). The prevalence of NNRTI and NRTI resistance was substantially higher among viraemic treatment-experienced people with HIV (51·49% [46·24–57·34] for NNRTI and 36·46% [30·06–44·22] for NRTI in 2017) than among pretreatment people with HIV. NNRTI and NRTI resistance was predominantly attributable to rtK103N and rtM184V. inT97A was observed at a similar prevalence among viraemic treatment-experienced (9·96% [6·41–15·48]) and viraemic pretreatment (10·56% [8·01–13·93]) people with HIV; no major dolutegravir resistance mutations were observed. Interpretation Despite rising NNRTI resistance among pretreatment people with HIV, overall population prevalence of pretreatment HIV drug-resistant viraemia decreased due to increasing ART uptake and viral suppression. This finding underscores the crucial role of achieving and maintaining high ART coverage in reducing transmission of drug-resistant HIV. The high prevalence of mutations conferring resistance to components of first-line ART regimens among viraemic people with HIV is potentially concerning. Funding National Institutes of Health, Johns Hopkins University Center for AIDS Research, Bill & Melinda Gates Foundation, and the US Centers for Disease Control and Prevention.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tunable Second Harmonic Generation in Twisted Bilayer Graphene

Twisted stacking of van der Waals (vdW) materials introduces a new way in bandstructure engineering and has given rise to numerous extraordinary physical phenomena. Despite the absence of second harmonic generation (SHG) in non-gated monolayer graphene, artificially twisted bilayer graphene (tBLG) possesses more possible point-group symmetries including those with broken inversion-symmetry. Here, we report twist-angle-dependent SHG from tBLG, which is the first demonstration of an elemental material with intrinsically tunable nonlinearity. We show that depending on the twist angle, the susceptibility of the dominant chiral tensor component of tBLGs can vary from 0 to 28×10 4 pm 2 /V, which is at the same order of magnitude as on-resonance susceptibility of monolayer MoS 2 . These results shed light on the underlying symmetry of tBLG systems and electronic band-structure near van Hove singularities (vHs). More importantly, they introduce a new degree of freedom, the twisting, in creating efficient second-order nonlinear material form centrosymmetric constituents

36 MATERIALS SCIENCE↗
DOE OSTI2023

Wafer-scale growth of two-dimensional, phase-pure InSe

Two-dimensional (2D) indium monoselenide (InSe) has attracted significant attention as an ultrathin III–VI semiconductor with a combination of favorable attributes that are comparable to those of III–V semiconductors and van der Waals 2D transition-metal dichalcogenides. Nevertheless, there has been no demonstration of large-area synthesis of 2D InSe due to the complexity of the binary In-Se system and the difficulties in promoting lateral growth. Here, we report the polymorph-selective synthesis of epitaxial 2D InSe by metal-organic chemical vapor deposition (MOCVD) over 2-in wafers. We achieve polymorph-selective epitaxial growth of InSe on c-plane sapphire via flow modulation to control the Se/In ratio. The layer-by-layer growth allows thickness control with tunable optical properties comparable to those of bulk crystals. We also demonstrate gate-tunable electrical transport with a field-effect mobility comparable to that of single-crystalline flakes. Importantly, these results indicate that InSe grown by MOCVD could be an effective channel material for back-end-of-line integration in logic transistors.

2D materials↗
DOE OSTI2023

A review of crosstalk polymorphic circuits and their scalability

Using a control variable, the functionality of Polymorphic circuits can be modified, making them adaptable and useful for reconfiguring circuit behavior — all the way from gate level to system level. State-of-the art polymorphic circuits are based on custom non-linear circuit design or emerging devices such as ambipolar FET, configurable magnetic devices etc. While some of these approaches are inefficient in performance, others involve exotic devices. The Crosstalk computing based polymorphic circuits offer a fresh perspective. In Crosstalk, the interconnect interference between nanoscale metal lines is intentionally engineered to exhibit the programmable Boolean logic behavior. This approach relies on the coupling between metal lines and not on the transistors for computing, resulting in better scalability, security by obscurity, and fault tolerance by reconfiguration. Our novel approach is backed by the mathematical formulation that conveys the rationale to generalize and achieve a wide variety of polymorphic circuits. Our experiments, including design, simulation, and Power Performance Area (PPA) characterization results indicate that crosstalk circuits provide significant improvement in transistor count (about 3x), switching energy (2x), and speed (1.5x) for polymorphic logic circuits. In the best-case scenario, the transistor count reduction is 5x. This paper presents Crosstalk computing’s fundamentals, polymorphism and the scalability aspects to compete/co-exist with CMOS for digital logic implementations below 10 nm. Our scalability study uses Open Source 7 nm PDK, considers all process variation aspects and accommodates worst-case scenarios. The study results for various benchmark circuits show that the Crosstalk technology is a viable alternative to CMOS for digital logic implementations below 10 nm, having 48% density, 57% power, and 10% performance gains over equivalent CMOS counterparts. Finally, we compare Crosstalk Polymorphic Circuit design technique with similar approaches described in related works and discuss its features and constraints.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Electrochemically decorated gold nanoparticles on CVD graphene ChemFET sensor for the highly sensitive detection of As(III)

Here, in this paper, we report a novel reusable receptor-free chemically sensitive field-effect transistor (ChemFET) sensor for the sensitive detection of As(III) using electrochemical doping of Au nanoparticles (AuNPs)-chemical vapour deposition (CVD) graphene (Gr) sensing film (AuNPs-Gr). The sensor consists of a single-gap gold electrode and a single layer of CVD graphene as a conducting/sensing channel decorated with a thin layer of electrochemically deposited AuNPs to catalyze the electroreduction of As(III) ions onto the sensing channel. A new detection strategy was proposed by measuring the resistance change rate of the AuNPs-Gr sensing channel modified between the source electrode and drain electrode, wherein the resistance change was caused by the electrochemical doping of As(0). The results indicated that the electrochemical doping of As(0) onto the sensing channel led to an increase in resistance through the doping interaction among As(0), AuNPs and graphene, enabling the proposed sensor to have an extraordinary detection performance with a high sensitivity. Moreover, the proposed sensor can be recycled by removing the As(0) deposited on the sensing film with the aid of a simple electrochemical oxidization process. Additionally, the mechanism of the sensing strategy based on the electrochemical n-doping of As(0) into the AuNPs-Gr sensing film was investigated using a top liquid gate electrode. The As(III) concentration detected by the AuNPs-Gr ChemFET sensor was as low as 0.001 μg/L, demonstrating that such sensors with a compatible sensing strategy can be used to detect As(III) with high sensitivity, easy fabrication, fast response and can be recycled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A comparison of machine learning surrogate models of street-scale flooding in Norfolk, Virginia

Low-lying coastal cities, exemplified by Norfolk, Virginia, face the challenge of street flooding caused by rainfall and tides, which strain transportation and sewer systems and can lead to personal and property damage. While high-fidelity, physics-based simulations provide accurate predictions of urban pluvial flooding, their computational complexity renders them unsuitable for real-time applications. Using data from Norfolk rainfall events between 2016 and 2018, this study compares the performance of a previous surrogate model based on a random forest algorithm with two deep learning models: Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU). The comparison of deep learning to the random forest algorithm is motivated by the desire to utilize a machine learning architecture that allows for the future inclusion of common uncertainty quantification techniques and the effective integration of relevant, multi-modal features.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Layered topological semimetal GaGeTe: New polytype with non-centrosymmetric structure

GaGeTe is a layered van der Waals material composed of germanene and GaTe sublayers that has been recently predicted to be a basic Z 2 topological semimetal. To date, only one polytype of GaGeTe is known with trigonal centrosymmetric structure (α phase, space group R-3m, No. 166). Here we show that as-grown samples of GaGeTe show traces of at least another polytype with hexagonal non-centrosymmetric structure (β phase, space group P6 3 mc, No. 186). Moreover, we suggest that another bulk hexagonal polytype (γ phase, space group P-3m1, No. 164) could also be found near room conditions. Both α and β polytypes have been identified and characterized by means of X-ray diffraction and Raman scattering measurements with the support of ab initio calculations. We provide the vibrational properties of both polytypes and show that the Raman spectrum reported for GaGeTe almost forty years ago and attributed to the α phase, was, in fact, that of the secondary β phase. Additionally, we show that a Fermi resonance occurs in α-GaGeTe under non-resonant excitation conditions, but not under resonant excitation conditions. Theoretical calculations show that bulk β-GaGeTe is a non-centrosymmetric weak topological semimetal with even smaller lattice thermal conductivity than centrosymmetric bulk α-GaGeTe. In perspective, our work paves the way for the control and engineering of GaGeTe polytypes to design and implement complex van der Waals heterostructures formed by a combination of centrosymmetric and non-centrosymmetric layers of up to three different polytypes in a single material, suitable for a number of fundamental studies and technological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae

CRISPR interference (CRISPRi) technologies have revolutionized bioengineering by providing precise tools for gene expression modulation, enabling targeted gene perturbation and metabolic pathway optimization. Despite these advances, achieving dynamic control over gene expression by CRISPR-based regulation remains a challenge due to its inherently static nature. Utilizing toehold-mediated strand displacement and ligand-responsive ribozymes (aptazymes), this study introduces switchable guide RNAs (gRNAs) that facilitate tunable gene expression mediated by mRNA or small molecule signals. We demonstrate complete silencing of gRNA via strategically designed 5’ or 3’ extensions that impede the gRNA spacer or the dCas9 handle, with subsequent restoration of function through sequestration or cleavage of the obstructive sequence. The resulting toehold-embedded or aptazyme-embedded gRNAs can be deactivated by specific signals, including two full-length translatable mRNAs and two small molecule triggers, thereby lifting CRISPRi repression on targeted genes. This modular approach allows for gRNA-based biocomputing through multi-layer or multi-input genetic logic gates in Saccharomyces cerevisiae . Offering a versatile strategy for post-CRISPR regulation in response to environmental signals or cellular states, this methodology expands the toolkit in eukaryotic systems for reversible control of gene expression.

Aptazyme↗
DOE OSTI2021

A PIPS + SrI 2 (Eu) detector for atmospheric radioxenon monitoring

The PIPS–SrI 2 (Eu) is a prototype atmospheric radioxenon detection system designed at Oregon State University in support of international efforts towards monitoring clandestine nuclear weapon testing activities. This detector aims to address some shortcomings found in currently deployed beta–gamma atmospheric radioxenon detection systems, such as lackluster energy resolution and memory effect, by employing modern detection materials and readout. The system uses a PIPSBox, a silicon-based gas cell, for electron detection, and a pair of ultrabright, D-shaped SrI 2 (Eu) scintillators coupled to silicon photomultipliers for photon detection. A custom eight-channel digital pulse processor equipped with a field programmable gate-array (FPGA) identifies electron–photon coincidences between the volumes in near real-time. Gas samples of the four radioxenon isotopes of interest were independently measured with the PIPS–SrI 2 (Eu) detection system to determine energy resolution and efficiency. Application of FPGA-based coincidence discrimination in near real-time reduced the ambient background count rate by 95.85 ± 0.04%. Using parameters from the Xenon International gas processing unit and assuming a blank sample and zero memory effect the minimum detectable concentrations (MDCs) for the isotopes were calculated to be 0.12 ± 0.03, 0.27 ± 0.05, 0.15 ± 0.02, and 1.00 ± 0.08 mBq/m 3 air for 131m Xe, 133 Xe, 133m Xe, and 135 Xe, respectively. These MDC estimates compare well with other radioxenon detection systems employed in the International Monitoring System (IMS) and indicate that the PIPS–SrI 2 (Eu) is in compliance with the Comprehensive Nuclear Test-Ban-Treaty Organization (CTBTO) sensitivity requirement of ≤ 1 mBq/m 3 for 133 Xe.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

The effects of low- Z shielding on uranium isotope discrimination using the time-emission profiles of long-lived delayed neutrons

Characteristic radiation signals can often be obscured or distorted by relatively small amounts of shielding, as is the case for highly-enriched uranium (HEU). Methods that can detect and identify special nuclear material (SNM) even in the presence of shielding are therefore of high value in many nuclear security and nonproliferation applications. It has been previously shown that the buildup and decay time profiles of long-lived delayed neutron emission from induced fission are unique and can be used to successfully discriminate between uranium isotopes and infer enrichment without the need for a calibration standard. Because the long-lived delayed neutron precursors exhibit decay times on the order of tens of seconds, their time profiles are not sensitive to the delays associated with scattering or diffusion in shielding materials, which occur on much shorter time scales. The use of capture-based neutron detectors can also mitigate the effects of shielding, because unlike recoil-based detectors, they do not have a low-energy detection threshold, so that neutrons that lose their energy in the shielding are still detectable. In this work, the effects of low-Z shielding on the discrimination of uranium isotopes using delayed neutron time profile measurements are investigated for the first time. Furthermore, the delayed neutron buildup and decay time profiles of polyethylene-shielded HEU and depleted uranium objects are measured using two different capture-gated detector designs. The recorded profiles show good agreement with the shapes predicted from six-group delayed neutron models even with the shielding in place, and the enrichment of the HEU and DU objects was estimated accurately to within 5%. While this method shows potential for discriminating and characterizing extreme cases of enrichment when a moderate amount of shielding is present, simulation results suggest that significant limitations exist for intermediate enrichment levels due to distortions to the delayed neutron time profile caused by neutron reflection in the shielding.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Improvement of the AC orbit bump method of local kick factor measurement using reference bunches

Here we have improved the AC orbit bump technique of local kick factor measurement. This technique, developed at NSLS-II a few years ago, is based on local sine-wave excitation of the electron beam by four fast correctors adjacent to the impedance location. By implementing reference bunches and the time gate function of beam position monitors, we are now able to measure the AC orbits of bunches with different intensities simultaneously. This improvement allows us to obtain the impedance-driven orbit distortion in a single measurement, significantly improving the measurement accuracy and reducing the measurement time.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The scintillation light detection system of ICARUS-T600: Hardware implementation and early results

The ICARUS-T600 Liquid Argon (LAr) Time Projection Chamber (TPC) is taking data with the Fermilab Booster Neutrino Beam-line (BNB) in the Short Baseline Neutrino (SBN) program to search for a possible LSND-like sterile neutrino signal. A light detection system, based on 360 Hamamatsu R5912-MOD Photo-Multiplier Tubes (PMTs) deployed behind the TPC wire chambers, has been realized to detect vacuum ultraviolet (VUV) photons produced by ionizing particles in LAr. This system is fundamental for the detector operation, providing an efficient trigger and contributing to the 3D reconstruction of events. Moreover, since the TPC is exposed to a huge flux of cosmic rays due to its shallow depths operations, the light detection system allows for the time reconstruction of events, contributing to the identification and to the selection of neutrino interactions within the beam spill gates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Generalized method for the optimization of pulse shape discrimination parameters

Organic scintillators exhibit fast timing, high detection efficiency for fast neutrons and pulse shape discrimination (PSD) capability. PSD is essential in mixed radiation fields, where different types of radiation need to be detected and discriminated. In neutron measurements for nuclear security and non proliferation effective PSD is crucial, because a weak neutron signature needs to be detected in the presence of a strong gamma-ray background. Here, the most commonly used deterministic PSD technique is charge integration (CI). This method requires the optimization of specific parameters to obtain the best gamma-neutron separation. These parameters depend on the scintillating material and light readout device and typically require a lengthy optimization process and a calibration reference measurement with a mixed source. In this paper, we propose a new method based on the scintillation fluorescence physics that enables to find the optimum PSD integration gates using only a gamma-ray emitter. We demonstrate our method using three organic scintillation detectors: deuterated trans-stilbene, small-molecule organic glass, and EJ-309. In all the investigated cases, our method allowed finding the optimum PSD CI parameters without the need of iterative optimization.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

The data acquisition system of the LZ dark matter detector: FADR

The Data Acquisition System (DAQ) for the LUX-ZEPLIN (LZ) dark matter detector is described. The signals from 745 PMTs, distributed across three subsystems, are sampled with 100-MHz 32-channel digitizers (DDC-32s). A basic waveform analysis is carried out on the on-board Field Programmable Gate Arrays (FPGAs) to extract information about the observed scintillation and electroluminescence signals. This information is used to determine if the digitized waveforms should be preserved for offline analysis. The system is designed around the Kintex-7 FPGA. In addition to digitizing the PMT signals and providing basic event selection in real time, the flexibility provided by the use of FPGAs allows us to monitor the performance of the detector and the DAQ in parallel to normal data acquisition. Furthermore, the hardware and software/firmware of this FPGA-based Architecture for Data acquisition and Realtime monitoring (FADR) are discussed and performance measurements are described.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Proton discrimination in CLYC for fast neutron spectroscopy

The Cs 2 LiYCl 6 :Ce (CLYC) elpasolite scintillator is known for its response to fast and thermal neutrons along with good γ-ray energy resolution. While the 35 Cl(n,p) reaction has been identified as a potential means for CLYC-based fast neutron spectroscopy in the absence of time-of-flight (TOF), previous efforts to functionalize CLYC as a fast neutron spectrometer have been thwarted by the inability to isolate proton interactions from 6 Li(n,α) and 35 Cl(n,α) signals. This work introduces a new approach to particle discrimination in CLYC for fission spectrum neutrons using a multi-gate charge integration algorithm that provides excellent separation between protons and heavier charged particles. Neutron TOF data were collected using a 252 Cf source, an array of EJ-309 organic liquid scintillators, and a 6 Li-enriched CLYC scintillator outfitted with fast electronics. Modal waveforms were constructed corresponding to the different reaction channels, revealing significant differences in the pulse characteristics of protons and heavier charged particles at ultrafast, fast, and intermediate time scales. These findings informed the design of a pulse shape discrimination algorithm, which was validated using the TOF data. This study also proposes an iterative subtraction method to mitigate contributions from confounding reaction channels in proton and heavier charged particle pulse height spectra, opening the door for CLYC-based fast neutron and γ-ray spectroscopy while preserving sensitivity to thermal neutron capture signals.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Optimization with the OpenACC-to-FPGA framework on the Arria 10 and Stratix 10 FPGAs

The reconfigurable computing paradigm with field programmable gate arrays (FPGAs) has received renewed interest in the high-performance computing field due to FPGAs’ unique combination of performance and energy efficiency. However, difficulties in programming and optimizing FPGAs have prevented them from being widely accepted as general-purpose computing devices. In accelerator-based heterogeneous computing, portability across diverse heterogeneous devices is also an important issue, but the unique architectural features in FPGAs make this difficult to achieve. To address these issues, a directive-based, high-level FPGA programming and optimization framework was previously developed. In this work, developed optimizations were combined holistically using the directive-based approach to show that each individual benchmark requires a unique set of optimizations to maximize performance. We perform this exploration on Intel Arria 10 and Stratix 10 FPGAs. We also explored the relationships between performance, resource usages, and compilation times, and investigated implications for performance portability. Finally, we present an initial evaluation of a real-world proxy application, LULESH.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Systematic many-fermion Hamiltonian input scheme and spectral calculations on quantum computers

We present a novel input scheme for general second-quantized Hamiltonians of relativistic or non-relativistic many-fermion systems. This input scheme incorporates the fermionic anticommutation relations, particle number variations, and respects the symmetries of the Hamiltonian. Based on our input scheme, we propose a hybrid quantum-classical framework for spectral calculations on future quantum hardwares. We provide explicit circuit designs and the associated gate cost. We demonstrate our hybrid framework by solving the low-lying spectra of 42 Ca and 46 Ca. Our input scheme provides new pathways to solving the spectra and dynamics of the relativistic and nonrelativistic many-fermion systems via first-principles approaches.

Hybrid spectral calculation framework↗
DOE OSTI2021

A review of ptychographic techniques for ultrashort pulse measurement

The measurement of optical ultrafast laser pulses is done indirectly because the required bandwidth to measure these pulses exceeds the bandwidth of current electronics. As a result, this measurement problem is often posed as a 1-D phase retrieval problem, which is fraught with ambiguities. The phase retrieval method known as ptychography solves this problem by making it possible to measure ultrafast pulses in either the time domain or the frequency domain. One well known algorithm is the principal components generalized projections algorithm (PCGPA) for extracting pulses from Frequency-Resolved Optical Gating (FROG) measurements. In this work, we discuss the development of the PCPGA and introduce new developments including an operator formalism that allows for the convenient addition of external constraints and the development of more robust algorithms. A close cousin, the ptychographic iterative engine will also be covered and compared to the PCGPA. Additional developments using other algorithmic strategies will also be discussed along with new developments combining optics and high-speed electronics to achieve megahertz measurement rates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗