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At least 253 records · Page 14

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DOE OSTI2025

Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions

Synechococcus elongatus PCC 7942 is a model organism for studying circadian regulation and bioproduction, where precise temporal control of metabolism significantly impacts photosynthetic efficiency and CO 2 -to-bioproduct conversion. Despite extensive research on core clock components, our understanding of the broader regulatory network orchestrating genome-wide metabolic transitions remains incomplete. We address this gap by applying machine learning tools and network analysis to investigate the transcriptional architecture governing circadian-controlled gene expression. While our approach showed moderate accuracy in predicting individual transcription factor-gene interactions - a common challenge with real expression data - network-level topological analysis successfully revealed the organizational principles of circadian regulation. Our analysis identified distinct regulatory modules coordinating day-night metabolic transitions, with photosynthesis and carbon/nitrogen metabolism controlled by day-phase regulators, while nighttime modules orchestrate glycogen mobilization and redox metabolism. Through network centrality analysis, we identified potentially significant but previously understudied transcriptional regulators: HimA as a putative DNA architecture regulator, and TetR and SrrB as potential coordinators of nighttime metabolism, working alongside established global regulators RpaA and RpaB. This work demonstrates how network-level analysis can extract biologically meaningful insights despite limitations in predicting direct regulatory interactions. The regulatory principles uncovered here advance our understanding of how cyanobacteria coordinate complex metabolic transitions and may inform metabolic engineering strategies for enhanced photosynthetic bioproduction from CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Controlling rotational air lasing lineshape by carrier-envelope offset phase

The carrier-envelope offset phase (CEP) of a few-cycle optical pulse is commonly used to control electron dynamics on the attosecond timescale, whereas lasing spectra from transitions between rotational states are generally emitted over much longer durations, typically nanoseconds. Here, we demonstrate CEP control of the rotational lasing spectra corresponding to the transition from B 2 Σ$^+_u$ to X 2 Σ$^+_g$ (1) in N$^+_2$ cations, transforming its lineshape from a symmetric Lorentzian profile to an asymmetric Fano type–and vice versa. This lineshape modulation arises from the interference between the B-X coherence initiated by the main pulse and the supercontinuum (self seed) by self-phase modulation, resembling an “f-to-3f" interferometry. Additionally, for lasing lines with lower rotational quantum numbers, we observe a stronger coupling between adjacent lasing peaks, which originates from the amplification of both even- and odd-order rotational coherent emission lines. Our study presents a general framework for controlling lasing lineshapes and provides new insights into sub-optical-cycle dynamics in air lasing.

atomic and molecular interactions with photons↗

DOE OSTI2020

Modulation of crystal growth and structure within cerium-based metal–organic frameworks

The intriguing catalytic properties of cerium-based materials have motivated the development of Ce-based metal–organic frameworks (MOFs). However, the controlled crystallization of Ce MOFs remains nascent due to complications with the high reduction potential of Ce 4+ species. Modulators offer a route in other well-studied coordination networks to slow down crystallization processes to allow for corrective, uniform crystal growth. Herein, we report an investigation of modulator identity and concentration on the synthesis of a Ce-UiO-type MOF with 2,6-naphthalenedicarboxylic acid (NDC) as a linker. At low concentrations using both benzoic acid and trifluoroacetic acid, we observed a mononuclear Ce 3+ MOF (NU-350) through single-crystal X-ray diffraction studies. Higher modulator concentrations yielded pure-phase Ce-UiO-NDC, with uniform particle sizes observed with utilizing benzoic acid as a modulator. Moreover, we demonstrated the transferability of this synthesis through the pure-phase synthesis of Ce-UiO-66 with benzoic acid as a modulator. High-resolution transmission electron microscopy showed a single crystalline domain within Ce-UiO-NDC.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Proton Bunch Self-Modulation in Plasma with Density Gradient

We study experimentally the effect of linear plasma density gradients on the self-modulation of a 400 GeV proton bunch. Results show that a positive or negative gradient increases or decreases the number of microbunches and the relative charge per microbunch observed after 10 m of plasma. The measured modulation frequency also increases or decreases. With the largest positive gradient we observe two frequencies in the modulation power spectrum. Results are consistent with changes in wakefields’ phase velocity due to plasma density gradients adding to the slow wakefields’ phase velocity during self-modulation growth predicted by linear theory.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Simulations of ENSO Phase-locking in CMIP5 and CMIP6

The characteristics of El-Niño-Southern Oscillation (ENSO) phase-locking in observations and CMIP5 and CMIP6 models are examined in this study. Two metrics based on the peaking month histogram for all El Niño and La Niña events are adopted to delineate the basic features of ENSO phase-locking in terms of the preferred calendar month and strength of this preference. It turns out that most models are poor at simulating the ENSO phase-locking, either showing little peak strengths or peaking at the wrong seasons. By deriving ENSO’s linear dynamics based on the conceptual recharge oscillator (RO) framework through the seasonal linear inverse model (sLIM) approach, various simulated phase-locking behaviors of CMIP models are systematically investigated in comparison with observations. In observations, phase-locking is mainly attributed to the seasonal modulation of ENSO’s SST growth rate. In contrast, in a significant portion of CMIP models, phase-locking is co-determined by the seasonal modulations of both SST growth and phase-transition rates. Further study of the joint effects of SST growth and phase-transition rates suggests that for simulating realistic winter peak ENSO phase-locking with the right dynamics, climate models need to have four key factors in the right combination: (1) correct phase of SST growth rate modulation peaking at the fall; (2) large enough amplitude for the annual cycle in growth rate; (3) amplitude of semi-annual cycle in growth rate needs to be small; and (4) amplitude of seasonal modulation in SST phase-transition rate needs to be small.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Hardware design and testing of the generic rear transition module for the global trigger subsystem of ATLAS Phase-II Upgrade

Abstract In the framework of the ATLAS experiment’s Phase-II Upgrade at the High-Luminosity Large Hadron Collider (HL-LHC), new and improved trigger hardware and algorithms will be implemented onto a single-level, 10 μs-latency architecture. The Global Trigger is a new subsystem which will bring event-filter capabilities by performing offline-like algorithms on full-granularity calorimeter data. The implementation of the functionality is firmware-focused and composed of several processing nodes, which are hosted on identical hardware, made up of an Advanced Telecommunications Computing Architecture (ATCA) front board, called Global Common Module (GCM), and a rear transition module (RTM), called Generic RTM (GRM). The GRM, which was developed to mitigate the risks deriving from the complex design and power management of the GCM, features an advanced Xilinx Versal Prime system-on-chip and can handle communication with the GCM and Front-End Link eXchange (FELIX) subsystem and trigger processors through 124 25.8 Gb/s transceiver links, for readout and control. Additionally, the GRM mounts a Low-Power GigaBit Transceiver (lpGBT) chip which enables emulation of the detector front-ends for integration tests. This paper presents the GRM hardware design and its testing.

Instruments & Instrumentation↗

DOE OSTI2022

ENSO modulation of summertime tropospheric ozone over China

Ozone (O 3 ) is one of the most critical pollutants affecting air quality in China in recent years. In this study, different impacts of the El Niño–Southern Oscillation (ENSO) warm/cold phases on summertime tropospheric O 3 over China are examined based on model simulations, ground measurements, and reanalysis data. Summertime surface O 3 concentrations in China show a positive correlation with ENSO index during years 1990–2019, with the largest increases by 20% over southern China in El Niño (warm phase) relative to La Niña (cold phase) years. The ENSO modulation extends to the middle and even upper troposphere. Our analysis indicates that O 3 flux convergence associated with weakened southerlies is the primary reason for the increase in tropospheric O 3 over southern China. In addition, the O 3 increase during El Niño years is mainly from domestic emissions in China. This study highlights the potential significance of ENSO in modulating tropospheric O 3 concentrations in China, with great implications for O 3 pollution mitigation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

High-fidelity holographic beam shaping with optimal transport and phase diversity

A phase-only spatial light modulator (SLM) provides a powerful way to shape laser beams into arbitrary intensity patterns but at the cost of a hard computational problem of determining an appropriate SLM phase. Here, we show that optimal transport methods can generate approximate solutions to this problem that serve as excellent initializations for iterative phase retrieval algorithms, yielding vortex-free solutions with superior accuracy and efficiency. Additionally, we show that analogous algorithms can be used to measure the intensity and phase of the input beam incident upon the SLM via phase diversity imaging. These techniques furnish flexible and convenient solutions to the computational challenges of beam shaping with an SLM.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Fundamental Behavior of ENSO Phase Locking

El Niño–Southern Oscillation (ENSO) events tend to peak at the end of the calendar year, a phenomenon called ENSO phase locking. This phase locking is a fundamental ENSO property that is determined by its basic dynamics. The conceptual ENSO recharge oscillator (RO) model is adopted to examine the ENSO phase-locking behavior in terms of its peak time, strength of phase locking, and asymmetry between El Niño and La Niña events. The RO model reproduces the main phase-locking characteristics found in observations, and the results show that the phase locking of ENSO is mainly dominated by the seasonal modulation of ENSO growth/decay rate. In addition, the linear/nonlinear mechanism of ENSO phase preference/phase locking is investigated using RO model. The difference between the nonlinear phase-locking mechanism and linear phase-preference mechanism is largely smoothed out in the presence of noise forcing. Further, the impact on ENSO phase locking from annual cycle modulation of the growth/decay rate, stochastic forcing, nonlinearity, and linear frequency are examined in the RO model. The preferred month of ENSO peak time depends critically on the phase and strength of the seasonal modulation of the ENSO growth/decay rate. Furthermore, the strength of phase locking is mainly controlled by the linear growth/decay rate, the amplitude of seasonal modulation of growth/decay rate, the amplitude of noise, the SST-dependent factor of multiplicative noise, and the linear frequency. The asymmetry of the sharpness of ENSO phase locking is induced by the asymmetric effect of state-dependent noise forcing in El Niño and La Niña events.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Picometer sensitivity metrology for EUV absorber phase

With growing interest in EUV attenuated phase-shift masks due to their superior image quality for applications such as dense contact and pillar arrays, it is becoming critical to model, measure, and monitor the intensity and relative phase of multilayer and absorber reflections. We present a solution based on physical modeling of reflectometry data, which can achieve single picometer phase precision and sensitivity to changes in average film thickness below one atomic monolayer. We measure absorber and multilayer reflectivity to determine thin-film parameters with a multidimensional optimization and then acquire a new measurement of either multilayer or absorber to determine perturbations in surface contamination thickness. While it is difficult to assess the accuracy of the first step, the simplicity of the second step allows us to characterize our sensitivity to changes in contamination thickness. Thus, we apply this analysis using an initial set of measurements and repeated measurements after a period of storage. For the multilayer, the total contamination growth was 1068 pm, which occurred almost exclusively during storage (1085 pm) and decreased very slightly during repeated measurements (-17 pm). For the absorber, the behavior was quite different, with a total growth of 126 pm, which occurred much less during storage (28 pm) and primarily during repeated measurements (98 pm). Ultimately, the change in relative phase (absorber minus multilayer) was -0.86 deg for the multilayer and -1.12 deg for the absorber. We estimate the precision of the surface contamination measurement to be 3σ < 6 pm for measuring thickness and 3σ < 0.2 deg for measuring phase.

36 MATERIALS SCIENCE↗

DOE OSTI2022

A Wrapper to Use a Machine-Learning-Based Algorithm for Earthquake Monitoring

Seismology is one of the main sciences used to monitor volcanic activity worldwide. Fast, efficient, and accurate seismicity detectors are crucial to assess the activity level of a volcano in near–real time and to issue timely warnings. Traditional real–time seismic processing software uses phase onset pickers followed by a phase association algorithm to declare an event and estimate its location. The pickers typically do not identify whether the detected phase is a P or S arrival, which can have a negative impact on hypocentral location quality and complicates phase association. We implemented the deep–neural–network–based method PhaseNet to identify in real time P and S seismic waves on data from one– and three–component seismometers. We tuned the Earthworm binder_ew associator module to use the phase identification from PhaseNet to detect and locate the events, which we archive in a SeisComP3 database. We assessed the performance of the algorithm by comparing the results with existing catalogs built to monitor seismic and volcanic activity in Mayotte and the Lesser Antilles region. Our algorithm, which we refer to as PhaseWorm, showed promising results in both contexts and clearly outperformed the previous automatic method implemented in Mayotte. As a result, this innovative real–time processing system is now operational for seismicity monitoring in Mayotte and Martinique.

58 GEOSCIENCES↗

DOE OSTI2020

Volume III. DUNE far detector technical coordination

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay -- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. Volume III of this TDR describes how the activities required to design, construct, fabricate, install, and commission the DUNE far detector modules are organized and managed. This volume details the organizational structures that will carry out and/or oversee the planned far detector activities safely, successfully, on time, and on budget. It presents overviews of the facilities, supporting infrastructure, and detectors for context, and it outlines the project-related functions and methodologies used by the DUNE technical coordination organization, focusing on the areas of integration engineering, technical reviews, quality assurance and control, and safety oversight. Because of its more advanced stage of development, functional examples presented in this volume focus primarily on the single-phase (SP) detector module.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Frustrated mixed-spin ladders: Evidence for a bond-order wave phase between rung-singlet and Haldane phases

In frustrated spin ladders, the interplay of frustration and correlations leads to the familiar Haldane (H) and rung-singlet (RS) phases. The nature of the transition between these two phases is still under debate. In this paper we tackle this issue using tools of quantum information theory. We consider frustrated mixed-spin-(1, 1/2) ladders with antiferromagnetic leg, rung and diagonal couplings, and calculate various quantities, such as the entanglement entropy (EE), the Schmidt gap, and the level degeneracy of the entanglement spectrum (ES). We use two numerical techniques, the infinite time-evolving block decimation (iTEBD) and the density matrix renormalization group (DMRG). We demonstrate that there exists an intermediate phase in which the ES levels do not exhibit the characteristic degeneracies of the H and RS phases. To understand the underlying physics in this phase, here we investigate short-range spin correlations along legs, rungs and diagonals and show that in this intermediate phase long-wavelength modulations occur, akin to bond-order waves.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Multi‐Scale Temporal Variability of Turbulent Mixing During a Monsoon Intra‐Seasonal Oscillation in the Bay of Bengal: An LES Study

A process study using large‐eddy simulations is carried out to explore the dominant 1‐D processes that affect mixed layer (ML) properties during an event of summer Monsoon Intra‐seasonal Oscillations (MISO) in the Bay of Bengal (BOB). These simulations use realistic air‐sea fluxes and initial conditions that were collected during the summer 2018 MISO‐BOB field experiment to explore the roles of thermal inversion layer (TIL) and Langmuir turbulence (LT) in modulating ML properties. The simulations span an active period with heavy rain and strong winds and a break period with strong solar heat flux and little rain. The mixed layer depth (MLD), sea surface temperature (SST) and sea surface salinity (SSS) are most affected by the presence of near‐inertial oscillations, solar heating and precipitation, all of which occur at different timescales. The subsurface warming induced by the TIL reduces the SST variability at the MISO timescale when compared with the simulation without TIL. Comparison of simulations with and without LT indicates that LT enhances subsurface warming during the active phase and reduces diurnal SST modulation during the break phase. Finally, simulations with 1‐D mixing models show a wide disparity in the evolution of MLD, SST, and SSS.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Field-resolved observation of exciton coherence in a van der Waals magnet

The emergence of coherence among electronic quasiparticles underlies collective quantum phenomena from superconductivity to superradiance. In semiconductors, exciton coherence is generally thought to decay rapidly due to scattering and dephasing, limiting its persistence on ultrafast timescales. Here, in this work, we demonstrate a light-field-driven mechanism that creates and stabilizes exciton coherence in the layered antiferromagnet CrSBr. We directly record the coherent optical field emitted by excitons and track in real time how a deterministic phase, imprinted by the excitation laser, drives incoherent excitons to synchronize into a collective state. This ensemble remains phase coherent for more than 2 ps, whereas its resonance energy undergoes an ultrafast modulation mediated by spin and lattice interactions. The time-resolved field evolution indicates that the multiple peaks seen in conventional spectra originate from a single excitonic resonance subject to dynamic energy modulation. Our findings establish optical phase imprinting as a mechanism to control and sustain collective order in semiconducting magnets, bridging light-driven dynamics with excitonic and magnetic correlations in layered quantum materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

ALS mutations disrupt self-association between the ubiquilin STI1 hydrophobic groove and internal placeholder sequences

Ubiquilins are molecular chaperones that play multifaceted roles in proteostasis, with point mutations in UBQLN2 leading to altered phase-separation properties and amyotrophic lateral sclerosis (ALS). Our mechanistic understanding of this essential process has been hindered by a lack of structural information on the STI1 domain, which is essential for ubiquilin chaperone activity and phase separation. Here, we present the first crystal structure of a ubiquilin-family STI1 domain bound to a transmembrane domain (TMD), and show that ALS mutations disrupt the STI1-TMD interaction. We further demonstrate that ubiquilins contain multiple conserved internal sequences that bind to the STI1 domain, including the PXX-repeat region that is a hotspot for ALS mutations. We propose that these placeholder sequences prevent solvent exposure of the STI1 hydrophobic groove and contribute to the multivalency that drives ubiquilin phase-separation. Together, this work provides a new paradigm for understanding how STI1 domains modulate ubiquilin chaperone activity and phase separation, and offers insights into the molecular basis of ALS pathogenesis.

Onwunma, Joan [Univ. of Toledo, OH (United States)↗

DOE OSTI2022

Titanium doped kagome superconductor CsV 3–x Ti x Sb 5 and two distinct phases

The vanadium-based kagome superconductor CsV 3 Sb 5 has attracted tremendous attention due to its unexcepted anomalous Hall effect (AHE), charge density waves (CDWs), nematicity, and a pseudogap pair density wave (PDW) coexisting with unconventional strong-coupling superconductivity. The origins of CDWs, unconventional superconductivity, and their correlation with different electronic states in this kagome system are of great significance, but so far, are still under debate. Chemical doping in the kagome layer provides one of the most direct ways to reveal the intrinsic physics, but remains unexplored. Here, we report, for the first time, the synthesis of Ti-substituted CsV 3 Sb 5 single crystals and its rich phase diagram mapping the evolution of intertwining electronic states. The Ti atoms directly substitute for V in the kagome layers. CsV 3–x Ti x Sb 5 shows two distinct superconductivity phases upon substitution. The Ti slightly-substituted phase displays an unconventional V-shaped superconductivity gap, coexisting with weakening CDW, PDW, AHE, and nematicity. The Ti highly-substituted phase has a U-shaped superconductivity gap concomitant with a short-range rotation symmetry breaking CDW, while long-range CDW, twofold symmetry of in-plane resistivity, AHE, and PDW are absent. Furthermore, we also demonstrate the chemical substitution of V atoms with other elements such as Cr and Nb, showing a different modulation on the superconductivity phases and CDWs. These findings open up a way to synthesise a new family of doped CsV 3 Sb 5 materials, and further represent a new platform for tuning the different correlated electronic states and superconducting pairing in kagome superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Relaxation time estimation in surface NMR

Technologies including NMR relaxation time estimation methods and corresponding apparatus are disclosed. Example techniques may include performing at least one single-pulse acquisition sequence, the single-pulse acquisition sequence comprising transmitting a single modulated pulse with a surface coil, wherein the phase, frequency, or amplitude of the single modulated pulse is varied during the single modulated pulse, and wherein the single modulated pulse excites a transverse magnetization component within a subsurface fluid. The resulting NMR signal may be recorded on at least one receiving device, including recording the NMR signal associated with the transverse magnetization component excited by the single modulated pulse. Processing techniques may be applied in which recorded NMR response data are used to estimate NMR properties and the relaxation times T1 and T2* as a function of position as well as one-dimensional and two-dimension distributions of T1 versus T2* as a function of subsurface position.

58 GEOSCIENCES↗