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DOE OSTI2023

Intrinsic 1${T}^{{\prime} }$ phase induced in atomically thin 2 H -MoTe 2 by a single terahertz pulse

The polymorphic transition from 2H to 1${T}^{{\prime} }$-MoTe 2 , which was thought to be induced by high-energy photon irradiation among many other means, has been intensely studied for its technological relevance in nanoscale transistors due to the remarkable improvement in electrical performance. However, it remains controversial whether a crystalline 1${T}^{{\prime} }$ phase is produced because optical signatures of this putative transition are found to be associated with the formation of tellurium clusters instead. Here we demonstrate the creation of an intrinsic 1${T}^{{\prime} }$ lattice after irradiating a mono- or few-layer 2H-MoTe 2 with a single field-enhanced terahertz pulse. Unlike optical pulses, the low terahertz photon energy limits possible structural damages. We further develop a single-shot terahertz-pump-second-harmonic-probe technique and reveal a transition out of the 2H-phase within 10 ns after photoexcitation. Our results not only provide important insights to resolve the long-standing debate over the light-induced polymorphic transition in MoTe 2 but also highlight the unique capability of strong-field terahertz pulses in manipulating quantum materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Prime factorization using quantum variational imaginary time evolution

The road to computing on quantum devices has been accelerated by the promises that come from using Shor’s algorithm to reduce the complexity of prime factorization. However, this promise hast not yet been realized due to noisy qubits and lack of robust error correction schemes. Here we explore a promising, alternative method for prime factorization that uses well-established techniques from variational imaginary time evolution. We create a Hamiltonian whose ground state encodes the solution to the problem and use variational techniques to evolve a state iteratively towards these prime factors. We show that the number of circuits evaluated in each iteration scales as $O(n^{5}d)$ , where n is the bit-length of the number to be factorized and d is the depth of the circuit. We use a single layer of entangling gates to factorize 36 numbers represented using 7, 8, and 9-qubit Hamiltonians. We also verify the method’s performance by implementing it on the IBMQ Lima hardware to factorize 55, 65, 77 and 91 which are greater than the largest number (21) to have been factorized on IBMQ hardware.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Floquet engineering of tilted and gapped Dirac bandstructure in 1T$$^\prime$$-MoS$$_2$$

Abstract We have developed a rigorous theoretical formalism for Floquet engineering, investigating, and subsequently tailoring most crucial electronic properties of 1T $$^\prime$$ ′ -MoS $$_2$$ 2 by applying an external high-frequency dressing field within the off-resonance regime. It was recently demonstrated that monolayer semiconducting 1T $$^\prime$$ ′ -MoS $$_2$$ 2 exhibits tunable and gapped spin- and valley-polarized tilted Dirac bands. The electron-photon dressed states depend strongly on the polarization of the applied irradiation and reflect a full complexity of the low-energy Hamiltonian for non-irradiated material. We have calculated and analyzed the properties of the electron dressed states corresponding to linear and circular polarization of a dressing field by focusing on their symmetry, anisotropy, tilting, direct and indirect band gaps. Circularly polarized dressing field is known for transition into a new electronic state with broken time-reversal symmetry and a non-zero Chern number, and therefore, the combination of these topologically non-trivial phases and transitions between them could reveal some truly unique and previously unknown phenomena and applications. We have also computed and discussed the density of states for various types of 1T $$^\prime$$ ′ -MoS $$_2$$ 2 materials and its modification in the presence of a dressing field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

PRIME: a real-time cyber-physical systems testbed: from wide-area monitoring, protection, and control prototyping to operator training and beyond

As the power grid continues to evolve with advanced wide-area monitoring, protection, and control (WAMPAC) algorithms, there is an increasing need for realistic testbed environments with industry-grade software and hardware-in-the-loop (HIL) to perform verification and validation studies. Such testbed environments serve as ideal platforms to perform WAMPAC prototyping, operator training, and also to study the impacts of different types of cyberattack scenarios on the operation of the grid. In this paper, we introduce PRIME (PNNL cybeR physIcal systeMs tEstbed): the testbed that integrates real-time transmission system simulator with commercial industry grade energy management system (EMS) software and remote hardware-in-the-loop (RHIL). PRIME is an end-to-end, modular testbed that allows high-fidelity RHIL experimentation of a power system. We present two detailed case studies (fault location and clearing in transmission system, and operator training) to showcase the capabilities of our PRIME testbed. Finally, we briefly discuss some of the potential limitations of our testbed in terms of scalability and flexibility to setup larger test systems and identify directions for future work to address those limitations.

42 ENGINEERING↗

DOE OSTI2024

CRISPR-prime editing, a versatile genetic tool to create specific mutations with a single nucleotide resolution in Leptospira

ABSTRACT Leptospirosis, caused by pathogenic bacteria from the genusLeptospira, is a global zoonosis responsible for more than one million human cases and 60,000 deaths annually. The disease also affects many domestic animal species. Historically, genetic manipulation ofLeptospirahas been difficult to perform, resulting in limited knowledge on pathogenic mechanisms of disease and the identification of virulence factors. The application of CRISPR/Cas9 and its variations have helped fill these gaps but the generation of knockout mutants remains challenging because double-strand breaks (DSBs) inflicted by Cas9 nuclease are lethal toLeptospiracells. The novel CRISPR prime editing (PE) strategy is the first precise genome-editing technology that allows deletions, insertions, and base substitutions without introducing DSBs. This revolutionary technique utilizes a nickase Cas9 that cleaves a single strand of DNA, coupled with an engineered reverse transcriptase and a modified single-guide RNA (termed prime editing guide RNA) containing an extended 3′ end with the desired edits. We demonstrate the application of CRISPR-PE in both saprophytic and pathogenicLeptospirafrom multiple species and serovars by introducing deletions or insertions into target DNA with a remarkable precision of just one nucleotide. Additionally, we demonstrate the ability to genetically manipulateLeptospira borgpetersenii, a prevalent pathogenic species of humans, domestic cattle, and wildlife animals. Rapid plasmid loss by mutated strains in liquid culture allows for the generation of knockout strains without selective markers, which can be readily used to elucidate virulence factors and develop optimized bacterin and/or live vaccines against leptospirosis. IMPORTANCE Leptospirosis is a geographically widespread bacterial zoonosis. Genetic manipulation of pathogenicLeptospiraspp. has been laborious and difficult to perform, limiting our ability to understand how leptospires cause disease. The application of the CRISPR/Cas9 system toLeptospiraenhanced our ability to generate knockdown and knockout mutants; however, the latter remains challenging. Here, we demonstrate the application of the CRISPR prime editing technique inLeptospira, allowing the generation of knockout mutants in several pathogenic species, with mutations comprising just a single nucleotide resolution. Notably, we generated a mutant in theLeptospira borgpeterseniibackground, a prevalent pathogenic species of humans and cattle. Our application of this method opens new avenues for studying pathogenic mechanisms ofLeptospiraand the identification of virulence factors across multiple species. These methods can also be used to facilitate the generation of marker-less knockout strains for updated and improved bacterin and/or live vaccines.

Microbiology↗

DOE OSTI2021

The diphoton $$q_T$$ spectrum at N$$^3$$LL$$^\prime $$ + NNLO

Abstract We present a $$q_T$$ q T -resummed calculation of diphoton production at order N $$^3$$ 3 LL $$^\prime $$ ′ + NNLO. To reach the primed level of accuracy we have implemented the recently published three-loop $${\mathcal {O}}(\alpha _s^3)$$ O ( α s 3 ) virtual corrections in the $$q\bar{q}$$ q q ¯ channel and the three-loop transverse momentum dependent beam functions and combined them with the existing infrastructure of , a code performing resummation at order N $${}^3$$ 3 LL. While the primed predictions are parametrically not more accurate, one typically observes from lower orders and other processes that they are the dominant effect of the next order. We include in both the $$q\bar{q}$$ q q ¯ and loop-induced gg channel the hard contributions consistently together at order $$\alpha _s^3$$ α s 3 and find that the resummed $$q\bar{q}$$ q q ¯ channel without matching stabilizes indeed. Due to large matching corrections and large contributions and uncertainties from the gg channel, the overall improvements are small though. We furthermore study the effect of hybrid-cone photon isolation and hard-scale choice on our fully matched results to describe the ATLAS $$\text {8}$$ 8 TeV data and find that the hybrid-cone isolation worsens agreement at small $$q_T$$ q T compared to smooth-cone isolation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space

Background Protein language models (PLMs) have revolutionized protein fitness prediction, yet their application to rapidly evolving viral pathogens is often confounded by extreme sequence homology. This homology leads to “data leakage” in standard random validation splits, yielding inflated performance metrics that fail to translate into real-world biosurveillance utility. Results We present Protein Representation Inference for Mutation Evaluation (PRIME), a framework that integrates domain-specific fine-tuning with a rigorous position-stratified validation protocol to evaluate viral threats. Using a dataset of 347,432 SARS-CoV-2 receptor binding domain (RBD) sequences, we demonstrate that while random training data split yields deceptive R 2 values (> 0.90), they fail to generalize to novel mutational sites. By benchmarking models up to 650 M parameters, we show that domain-specific fine-tuning of the ESM-C 600 M model with correctly stratified data provides an initial demonstration of predictive signal for binding affinity and expression at unseen mutational sites of binding affinity and expression on unseen sites (R 2 ~0.23), a significant advancement over base foundation models which exhibit no predictive power (R 2 <0). PRIME’s embedding-based clustering identified 3.03% of bat coronavirus sequences as candidates for further experimental prioritization based on their functional similarity to human-infective strains in embedding space, offering a perspective complementary to traditional phylogenetic methods. Conclusion PRIME establishes a new benchmark for the application of PLMs in pathogen surveillance. Our findings demonstrate that state-of-the-art models and fine-tuning, when paired with stratified validation, provide biologically meaningful insights into pathogen evolution and zoonotic risk.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Tracing priming effects in palsa peat carbon dynamics using a stable isotope-assisted metabolomics approach

Introduction: Peatlands store up to a third of global soil carbon, and in high latitudes their litter inputs are increasing and changing in composition under climate change. Although litter significantly influences peatland carbon and nutrient dynamics by changing the overall lability of peatland organic matter, the physicochemical mechanisms of this impact—and thus its full scope—remain poorly understood. Methods: We applied multimodal metabolomics (UPLC-HRMS, 1 H NMR) paired with 13 C Stable Isotope-Assisted Metabolomics (SIAM) to track litter carbon and its potential priming effects on both existing soil organic matter and carbon gas emissions. Through this approach, we achieved molecule-specific tracking of carbon transformations at unprecedented detail. Results: Our analysis revealed several key findings about carbon dynamics in palsa peat. Microbes responded rapidly to litter addition, producing a short-term increase in CO 2 emissions, fueled nearly exclusively by transformations of litter carbon. Litter inputs significantly contributed to the organic nitrogen pool through amino acids and peptide derivatives, which served as readily accessible nutrient sources for microbial communities. We traced the fate of plant-derived polyphenols including flavonoids like rutin, finding evidence of their degradation through heterocyclic C-ring fission, while accumulation of some polyphenols suggested their role in limiting overall decomposition. The SIAM approach detected subtle molecular changes indicating minimal and transient priming activity that was undetectable through conventional gas measurements alone. This transient response was characterized by brief microbial stimulation followed by rapid return to baseline metabolism. Pre-existing peat organic matter remained relatively stable; significant priming of its consumption was not observed, nor was its structural alteration. Discussion: This suggests that while litter inputs temporarily increase CO 2 emissions, they don’t sustain long-term acceleration of stored carbon decomposition or substantially decrease peat’s carbon store capacity. Our findings demonstrate how technological advancements in analytical tools can provide a more detailed view of carbon cycling processes in complex soil systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research

Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as “prime editing,” has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Pyrolysis temperature and soil depth interactions determine PyC turnover and induced soil organic carbon priming

Pyrogenic organic carbon (PyC) is a complex, heterogeneous class of thermally altered organic substrates, but its dynamics and how its behavior changes with soil depth remain poorly understood. We conducted a laboratory incubation study to investigate the interactive effects of pyrolysis temperature and soil depth on the turnover of PyC compared to its precursor wood and native SOC (NSOC). We incubated dual-labeled (13C and 15N) jack pine pyrogenic organic matter produced at 300 °C (PyC300), 450 °C (PyC450), and their precursor pine wood in a fine-loamy, mixed-conifer forest soil for 745 days. A mixture of surface (0–10 cm) and subsurface (50–70 cm) forest soils, with and without labeled biomass were incubated in the dark at 55% soil water field capacity and 25 °C. Total 13C from PyC and wood mineralized as 13C-CO2 (as % of C added to soil) declined with an increase in pyrolysis temperature as follows: 54 ± 7.7% for wood, 3.1 ± 0.2% for PyC300, and 0.94 ± 0.08% for PyC450. Furthermore, after 2 years, soil depth interacted with pyrolysis temperature to affect C turnover, with total wood C losses significantly declining from 70.6% in surface soils to 37.5% in subsurface soil, while total losses of PyC300 and PyC450 were unaffected by differences between surface and subsurface soils. Wood induced negative priming (i.e., decreased mineralization rates) in surface soil at days 3 and 60, while PyC300 induced positive priming (i.e., increased mineralization rates) in subsurface soil at day 60. After 2 years, unlabeled NSOC losses increased from 9.2 ± 0.8% of NSOC in unamended treatments to 16.5 ± = 2.6% of NSOC with PyC450 additions. Our results suggest that PyC pyrolyzed at a given temperature can mineralize at similar rates between soil depths, and high amounts of PyC450 in subsurface soils can stimulate NSOC losses. These findings indicate that soil depth imposes critical controls on PyC dynamics belowground.

13C-labeling↗

DOE OSTI2023

Tree-level Unitarity in $$ \textrm{SU}{(2)}_L\times \textrm{U}{(1)}_Y\times \textrm{U}{(1)}_{Y^{\prime }} $$ Models

Abstract In models with a U(1) gauge extension beyond the Standard Model, one can derive sum rules for the couplings of the theory that are a consequence of tree-level unitarity. In this paper, we provide a comprehensive list of coupling sum rules for a general$$ \textrm{SU}{(2)}_L\times \textrm{U}{(1)}_Y\times \textrm{U}{(1)}_{Y^{\prime }} $$ SU 2 L × U 1 Y × U 1 Y ′ gauge theory coupled to an arbitrary set of fermion and scalar multiplets. These results are of particular interest for models of dark matter that employ an extended gauge sector mediated by a new (dark)Z ′ gauge boson. For the case of a minimal extension of the Standard Model with a$$ \textrm{U}{(1)}_{Y^{\prime }} $$ U 1 Y ′ gauge boson, we clarify the definitions of the weak mixing angle and the electroweakρparameter. We demonstrate the utility of a generalizedρparameter (denoted byρ ′ ) whose definition naturally follows from the unitarity sum rules developed in this paper.

Physics↗

DOE OSTI2025

Particle‐In‐Cell Simulations of Starfish Prime

The Starfish Prime high altitude nuclear test created a transient diamagnetic cavity in the Earth's magnetic field above Johnston Island and launched an electromagnetic pulse (EMP) that was detected around the globe. For this work, we use the ion‐kinetic particle‐in‐cell code Topanga to simulate diamagnetic cavity evolution and the E3 EMP signal for Starfish Prime out to over a minute of physical time. The simulation domain has a longitudinal and latitudinal extent of 60° X 60° and a vertical extent of 2,000 km from the surface of the Earth. We compare our simulated results to magnetometer measurements taken in space and on the ground, finding good agreement in both cases. The diamagnetic cavity in the simulation forms in about a second, while the associated debris flux tube takes approximately 30 s to decay. The debris flux tube undergoes significant motion during this timeframe, rising upward. The measured E3 EMP signal on the ground consists of several components, all of which are present in our simulations. We discuss the physical origin of these components in relation to E3a (blast) and E3b (heave).

Belyaev, Mikhail A. [Lawrence Livermore National L↗

DOE OSTI2024

Priming antibody responses to the fusion peptide in rhesus macaques

Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to prime and elicit antibody responses against the conserved fusion peptide (FP). GC responses and antibody specificities were tracked longitudinally using lymph node fine-needle aspirates and electron microscopy polyclonal epitope mapping (EMPEM), respectively, to show antibody responses to the FP/N611 glycan hole region were primed, although exhibited limited neutralization breadth. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Trivalent mosaic or consensus HIV immunogens prime humoral and broader cellular immune responses in adults

Mosaic and consensus HIV-1 immunogens provide two distinct approaches to elicit greater breadth of coverage against globally circulating HIV-1 and have shown improved immunologic breadth in nonhuman primate models. This double-blind randomized trial enrolled 105 healthy HIV-uninfected adults who received 3 doses of either a trivalent global mosaic, a group M consensus (CON-S), or a natural clade B (Nat-B) gp160 env DNA vaccine followed by 2 doses of a heterologous modified vaccinia Ankara–vectored HIV-1 vaccine or placebo. We performed prespecified blinded immunogenicity analyses at day 70 and day 238 after the first immunization. T cell responses to vaccine antigens and 5 heterologous Env variants were fully mapped. Env-specific CD4 + T cell responses were induced in 71% of the mosaic vaccine recipients versus 48% of the CON-S recipients and 48% of the natural Env recipients. The mean number of T cell epitopes recognized was 2.5 (95% CI, 1.2–4.2) for mosaic recipients, 1.6 (95% CI, 0.82–2.6) for CON-S recipients, and 1.1 (95% CI, 0.62–1.71) for Nat-B recipients. Mean breadth was significantly greater in the mosaic group than in the Nat-B group using overall (P = 0.014), prime-matched (P = 0.002), heterologous (P = 0.046), and boost-matched (P = 0.009) measures. Overall T cell breadth was largely due to Env-specific CD4 + T cell responses. Priming with a mosaic antigen significantly increased the number of epitopes recognized by Env-specific T cells and enabled more, albeit still limited, cross-recognition of heterologous variants. Mosaic and consensus immunogens are promising approaches to address global diversity of HIV-1.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Prime Impact Fund (Final Technical Report)

PRIME Coalition Inc. constructed a first-of-its-kind impact investment fund comprised exclusively of charitable capital from grant and program-related investment-makers (private foundations, community foundations, corporate foundations, donor-advised funds, an d other corporate, family office, and individual donors). Prime Impact Fund was purpose-built to address the "innovation valley of death" in the energy sector, stepping into the capital gap with a new investment model.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

The REDTOP experiment: Rare $\eta/\eta^{\prime}$ Decays To Probe New Physics

The $\eta$ and $\eta^{\prime}$ mesons are nearly unique in the particle universe since they are almost Goldstone bosons and the dynamics of their decays are strongly constrained. The integrated $\eta$-meson samples collected in earlier experiments amount to $\sim10^{9}$ events. A new experiment, REDTOP (Rare Eta Decays To Probe New Physics), is being proposed, with the intent of collecting a data sample of order 10$^{14}$ $\eta$ (10$^{12}$ $\eta^{\prime}$) for studying very rare decays. Such statistics are sufficient for investigating several symmetry violations, and for searching for particles and fields beyond the Standard Model. In this work we present several studies evaluating REDTOP sensitivity to processes that couple the Standard Model to New Physics through all four of the so-called \emph{portals}: the Vector, the Scalar, the Axion and the Heavy Lepton portal. The sensitivity of the experiment is also adequate for probing several conservation laws, in particular $CP$, $T$ and Lepton Universality, and for the determination of the $\eta$ form factors, which is crucial for the interpretation of the recent measurement of muon $g-2$.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Blood treatment device priming devices, methods, and systems

Simple-to-use systems, methods, and devices for priming replacement blood treatment devices, for swapping the blood treatment devices out, for replacing swapped-out blood treatment devices, and other related operations are described. In embodiments, a blood treatment device can be primed while a therapy is still running. When the replacement blood treatment device is needed, the therapy can be stopped momentarily (less than a minute) for the rapid and safe swap of the blood treatment device. Blood loss can be minimized. The down time from therapy can be minimized.

Brugger, James M.↗

DOE OSTI2020

Pyrolysis of Radioactive Spent Resins in the PRIME Installation - 20190

Montair and Belgoprocess developed the pilot PRIME (Pyrolysis Resins In Mobile Electric) Installation for treatment of spent resins in one single reactor without pre-treatment and without intermixing of other waste, allowing for easy traceability and isotopic characterization of the end product. Both low level waste (LLW, < 2 mSv/h) and medium level waste (MLW, > 2 mSv/h) can be treated in the installation. The PRIME pilot installation is designed to treat 2 batches of 100 liter of saturated ion exchange resins over a period of 24 hours. A dosing unit with screw feeder is used for the dosing of the saturated ion exchange resins to the pyrolysis reactor. This completely new developed innovative pyrolysis reactor contains a special design mechanical stirrer and can operate at a temperature of up to 600 deg. C under inert conditions. As a result, the organic molecules will decompose at an accelerated rate until only the mineralized material remains. The lower temperature and the absence of oxygen also prevent the breakdown of ion exchange resins into (powdery) ash, which is a considerable advantage during further handling. Gases that are released during drying and pyrolysis are treated in an also newly developed thermal oxidizer, which uses an innovative, electrically heated design instead of a traditional natural gas- or fuel oil secondary combustion chamber design. After passing through the thermal oxidizer, the gases are cooled down to saturation temperature and treated in the wet scrubbing system. An extraction fan keeps the system under negative pressure to prevent the possibility of any off-gas leakage out of the system. A series of tests were performed successfully with wet cationic resins, anionic resins and a mixture of both. The results of these tests are described in the presentation. For intellectual property protection, the system and process of pyrolysis of organic waste and the system of thermal oxidation of pyrolysis gases described in this paper are patent pending. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗