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DOE OSTI2020

The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases

Abstract OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC−Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Subexponential Decay of Local Correlations from Diffusion-Limited Dephasing

Chaotic quantum systems at finite entropy density are expected to act as their own heat baths, rapidly dephasing local quantum superpositions. Here, we argue that in fact this dephasing is generically subexponential in one-dimensional systems with conservation laws: all local correlation functions decay as exp⁡[−𝒪⁡(𝑡 𝛼 )] with 0 ≤ 𝛼 ≤ 2/3, even when the operators are orthogonal to all hydrodynamic modes. The mechanism is diffusion-limited dephasing, in which rare low-entropy regions (“voids”) protect quantum coherences. This intrinsically quantum effect lies beyond standard hydrodynamics and disappears under extrinsic dephasing. In random charge-conserving circuits we find 𝛼 = 1/2, while in generic translation-invariant Floquet systems we bound 𝛼 ≤ 2/3. Our arguments are general, subject principally to the assumption that thermal fluctuations can create regions of zero entropy density. In systems with energy conservation, this assumption is automatically satisfied because of the third law of thermodynamics.

information scrambling↗

DOE OSTI2025

First Look at Quartic-in-Spin Binary Dynamics at Third Post-Minkowskian Order

We compute the conservative and radiation-reaction contributions to classical observables in the gravitational scattering between a spinning and a spinless black hole to the fourth order in spin and third order in the gravitational constant. The conservative results are obtained from two-loop amplitudes for the scattering process of a massive scalar with a massive spin-𝑠 field (𝑠=0, 1, 2) minimally coupled to gravity, employing the recently introduced spin interpolation method to resolve all spin-Casimir terms. The two-loop amplitude exhibits a spin-shift symmetry in both probe limits, which we conjecture to be a sign of yet unknown integrability of Kerr orbits through the quartic order in spin and to all orders in the gravitational constant. We obtain the radial action from the finite part of the amplitude and use it to compute classical observables, including the impulse and spin kick. This is done using the recently introduced covariant Dirac brackets, which allow for the computation of classical scattering observables for general (nonaligned) spin configurations. Finally, employing the radiation-reaction amplitude proposed by Alessio and Di Vecchia, together with the Dirac brackets, we obtain radiation-reaction contributions to observables at all orders in spin and beyond the aligned-spin limit. We find agreement with known results up to the quadratic order in spin for both conservative and radiation-reaction contributions. Our results advance the state of the art in the understanding of spinning binary dynamics in general relativity and demonstrate the power and simplicity of the Dirac bracket formalism for relating scattering amplitudes to classical observables.

general relativity↗

DOE OSTI2026

Transport-based initial conditions for heavy-ion collisions at finite densities

Here, we employ the SMASH transport model to provide event-by-event initial conditions for the energy-momentum tensor and conserved charge currents in hydrodynamic simulations of relativistic heavy-ion collisions. We study the fluctuations and dynamical evolution of three conserved charge currents (net baryon, net electric charges, and net strangeness) with a four-dimensional lattice-QCD-based equation of state, NEOS-4D, in the hydrodynamic phase. Out-of-equilibrium corrections at the particlization are generalized to finite densities to ensure the conservation of energy, momentum, and the three types of charges. These theoretical developments are integrated within the X-SCAPE code as a unified framework for studying the nuclear matter properties in the Beam Energy Scan program.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Localization from Hilbert space shattering: From theory to physical realizations

We show how a finite number of conservation laws can globally “shatter” Hilbert space into exponentially many dynamically disconnected subsectors, leading to an unexpected dynamics with features reminiscent of both many-body localization and quantum scars. A crisp example of this phenomenon is provided by a “fractonic” model of quantum dynamics constrained to conserve both charge and dipole moment. We show how the Hilbert space of the fractonic model dynamically fractures into disconnected emergent subsectors within a particular charge and dipole symmetry sector. This shattering can occur in arbitrary spatial dimensions. A large number of the emergent subsectors, exponentially many in system volume, have dimension one and exhibit strictly localized quantum dynamics—even in the absence of spatial disorder and in the presence of temporal noise. Other emergent subsectors display nontrivial dynamics and may be constructed by embedding finite-sized nontrivial blocks into the localized subspace. While “fractonic” models provide a particularly clean realization, the shattering phenomenon is more general, as we discuss. We also discuss how the key phenomena may be readily observed in near term ultracold atom experiments. In experimental realizations, the conservation laws are approximate rather than exact, so the localization only survives up to a prethermal timescale that we estimate. We comment on the implications of these results for recent predictions of Bloch/Stark many-body localization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Diffusive hydrodynamics from integrability breaking

We describe here the crossover from generalized to conventional hydrodynamics in nearly integrable systems. Integrable systems have infinitely many conserved quantities, which spread ballistically, in general. When integrability is broken, only a few of these conserved quantities survive. The remaining conserved quantities are generically transported diffusively; we further derive a compact and general diffusion equation for these. The diffusion constant depends on the matrix elements of the integrability-breaking perturbation; for a certain class of integrability-breaking perturbations, including long-range interactions, the diffusion constant can be expressed entirely in terms of generalized hydrodynamic data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Beam energy dependence of net- Λ fluctuations measured by the STAR experiment at the BNL Relativistic Heavy Ion Collider

The measurements of particle multiplicity distributions have generated considerable interest in understanding the fluctuations of conserved quantum numbers in the quantum chromodynamics (QCD) hadronization regime, in particular near a possible critical point and near the chemical freeze-out. Net-protons and net-kaons have been used as proxies for the net-baryon number and net-strangeness, respectively. We report the measurement of efficiency- and centrality-bin width-corrected cumulant ratios (C 2 /C 1 , C 3 /C 2 ) of net- Λ distributions, in the context of both strangeness and baryon number conservation, as a function of collision energy, centrality, and rapidity. The results are for Au + Au collisions at five beam energies ( √s NN = 19.6 , 27, 39, 62.4, and 200 GeV) recorded with the Solenoidal Tracker at RHIC (STAR). We compare our results to the Poisson and negative binomial (NBD) expectations, as well as to ultrarelativistic quantum molecular dynamics (UrQMD) and hadron resonance gas (HRG) model predictions. Both NBD and Poisson baselines agree with data within the statistical and systematic uncertainties. UrQMD describes the measured net- Λ C 1 and C 3 at 200 GeV reasonably well but deviates from C 2 , and the deviation increases as a function of collision energy. The ratios of the measured cumulants show no features of critical fluctuations. The chemical freeze-out temperatures extracted from a recent HRG calculation, which was successfully used to describe the net-proton, net-kaon, and net-charge data, indicate Λ freeze-out conditions similar to those of kaons. However, large deviations are found when comparing with temperatures obtained from net-proton fluctuations. The net- Λ cumulants show a weak but finite dependence on the rapidity coverage in the acceptance of the detector, which can be attributed to quantum number conservation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Multiparticle integral and differential correlation functions

This paper formalizes the use of integral and differential cumulants for measurements of multiparticle event-by-event transverse momentum fluctuations, rapidity fluctuations, as well as net-charge fluctuations. This enables the introduction of multiparticle balance functions, defined based on differential correlation functions (factorial cumulants), that suppress two- and three-prong resonance decays effects and enable measurements of underlying long-range correlations obeying quantum number conservation constraints. These multiparticle balance functions satisfy simple sum rules determined by quantum number conservation. It is additionally shown that these multiparticle balance functions arise as an intrinsic component of high-order net-charge cumulants. This implies that the magnitude of these cumulants, measured in a specific experimental acceptance, is strictly constrained by charge conservation and primarily determined by the rapidity and momentum width of these balance functions. The paper also presents techniques to reduce the computation time of differential correlation functions up to order n = 10 based on the methods of moments. Published by the American Physical Society 2024

Physics↗

DOE OSTI2024

Quantum field theory, worldline theory, and spin magnitude change in orbital evolution

A previous paper [Z. Bern et al., Binary dynamics through the fifth power of spin at 𝑂⁡(𝐺 2 ), Phys. Rev. Lett. 130, 201402 (2023)] identified a puzzle stemming from the amplitudes-based approach to spinning bodies in general relativity: additional Wilson coefficients appear compared to current worldline approaches to conservative dynamics of generic astrophysical objects, including neutron stars. In this paper we clarify the nature of analogous Wilson coefficients in the simpler theory of electrodynamics. We analyze the original field-theory construction, identifying definite-spin states some of which have negative norms, and relating the additional Wilson coefficients in the classical theory to transitions between different quantum spin states. We produce a new version of the theory which also has additional Wilson coefficients, but no negative-norm states. We match, through 𝒪⁡(𝛼 2 ) and 𝒪⁡(𝑆 2 ), the Compton amplitudes of these field theories with those of a modified worldline theory with extra degrees of freedom introduced by releasing the spin supplementary condition. We build an effective two-body Hamiltonian that matches the impulse and spin kick of the modified field theory and of the worldline theory, displaying additional Wilson coefficients compared to standard worldline approaches. The results are then compactly expressed in terms of an eikonal formula. Our key conclusion is that, contrary to standard approaches, while the magnitude of the spin tensor is still conserved, the magnitude of the spin vector can change under conserved Hamiltonian dynamics and this change is governed by the additional Wilson coefficients. For specific values of Wilson coefficients the results are equivalent to those from a definite spin obeying the spin supplementary condition, but for generic values they are physically inequivalent. These results warrant detailed studies of the corresponding issues in general relativity.

classical black holes↗

DOE OSTI2025

Realizability-preserving discontinuous Galerkin method for spectral two-moment radiation transport in special relativity

Here we present a realizability-preserving numerical method for solving a spectral two-moment model to simulate the transport of massless, neutral particles interacting with a steady background material moving with relativistic velocities. The model is obtained as the special relativistic limit of a four-momentum-conservative general relativistic two-moment model. Using a maximum-entropy closure, we solve for the Eulerian-frame energy and momentum. The proposed numerical method is designed to preserve moment realizability, which corresponds to moments defined by a nonnegative phase-space density. The realizability-preserving method is achieved with the following key components: (i) a discontinuous Galerkin phase-space discretization with specially constructed numerical fluxes in the spatial and energy dimensions; (ii) a strong stability-preserving implicit-explicit time-integration method; (iii) a realizability-preserving conserved to primitive moment solver; (iv) a realizability-preserving implicit collision solver; and (v) a realizability-enforcing limiter. Component (iii) is necessitated by the closure procedure, which closes higher order moments nonlinearly in terms of primitive moments. The nonlinear conserved to primitive and the implicit collision solves are formulated as fixed-point problems, which are solved with custom iterative solvers designed to preserve the realizability of each iterate. With a series of numerical tests, we demonstrate the accuracy and robustness of this discontinuous-Galerkin-implicit-explicit method.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Fracton Hydrodynamics without Time-Reversal Symmetry

Here, we present an effective field theory for the nonlinear fluctuating hydrodynamics of a single conserved charge with or without time-reversal symmetry, based on the Martin-Siggia-Rose formalism. Applying this formalism to fluids with only charge and multipole conservation, and with broken time-reversal symmetry, we predict infinitely many new dynamical universality classes, including some with arbitrarily large upper critical dimensions. Using large scale simulations of classical Markov chains, we find numerical evidence for a breakdown of hydrodynamics in quadrupole-conserving models with broken time-reversal symmetry in one spatial dimension. Our framework can be applied to the hydrodynamics around stationary states of open systems, broadening the applicability of previously developed ideas and methods to a wide range of systems in driven and active matter.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Effect of interparticle fields and radiation reaction on beam dynamics

The dynamics of relativistic particles in an intense electromagnetic field can be described by the Landau-Lifshitz (LL) equation, where the radiation reaction (RR) is accounted for via a self-force, and interparticle fields are often neglected as an approximation. However, the inclusion of interparticle fields is necessary to ensure energy-momentum conservation, particularly during coherent emission. Here we present (i) an analytical proof showing that the energy-momentum conservation law of the Hamilton-Rohrlich-Dirac action, which is divergence free and describes a generic system of interacting charges, respects causality and provides physically sensible results; (ii) a simple generalization of the LL equation for many particles evaluated as a function of the total field, i.e., the sum of the external and interparticle fields. By performing first-principles numerical simulations of a neutral, relativistic bunch of electrons and positrons (e − /e + ) colliding with a laser pulse, this theory is shown to satisfy energy-momentum conservation when interparticle fields and RR are simultaneously taken into account; and (iii) the combined effect of interparticle fields and RR primarily affects the tail of the particle energy distribution. Additionally, our first-principles simulations show that the effect of interparticle fields on beam energy loss becomes smaller when most of the radiated energy is incoherent.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Acceptance dependence of factorial cumulants, long-range correlations, and the antiproton puzzle

We analyze joint factorial cumulants of protons and antiprotons in relativistic heavy-ion collisions and point out that they obey the scaling Ĉnmp,p¯∝〈Np〉n〈Np¯〉m as a function of acceptance when only long-range correlations are present in the system, such as global baryon conservation and volume fluctuations. This hypothesis can be directly tested experimentally without the need for corrections for volume fluctuations. We show that if correlations among protons and antiprotons are driven by global baryon conservation and volume fluctuations only, the equality Ĉ2p/〈Np〉2=Ĉ2p¯/〈Np¯〉2 holds for large systems created in central collisions. We point out that the experimental data of the STAR Collaboration from phase I of the Relativistic Heavy Ion Collider (RHIC) beam energy scan (BES) are approximately consistent with the scaling Ĉnmp,p¯∝〈Np〉n〈Np¯〉m, but the normalized antiproton correlations are stronger than those of protons, −Ĉ2p¯/〈Np¯〉2>−Ĉ2p/〈Np〉2. Existing theoretical baselines, based on global baryon conservation and volume fluctuations, cannot explain the data, which we refer to as the antiproton puzzle. We also discuss high-order factorial cumulants which can be measured with sufficient precision within phase II of RHIC-BES.

Bzdak, Adam↗

DOE OSTI2025

Indications for Freeze-Out of Charge Fluctuations in the Quark-Gluon Plasma at the LHC

The D-measure of net-charge fluctuations quantifies the variance of net charge in strongly interacting matter. It was introduced over 20 years ago as a potential signal of quark-gluon plasma (QGP) in heavy-ion collisions, where it is expected to be suppressed due to the fractional electric charges of quarks. Measurements have been performed at RHIC and LHC, but the conclusion has been elusive in the absence of quantitative calculations for both scenarios. We address this issue by employing a recently developed formalism of density correlations and incorporate resonance decays, local charge conservation, and experimental kinematic cuts. We find that the hadron gas scenario is in fair agreement with the ALICE data for $\sqrt{{𝑠}_{\textrm{NN}}}$ = 2.76 TeV Pb–Pb collisions only when a very short rapidity range of local charge conservation is enforced, while the QGP scenario is in excellent agreement with experimental data and largely insensitive to the range of local charge conservation. A Bayesian analysis of the data utilizing different priors yields moderate evidence for the freeze-out of charge fluctuations in the QGP phase relative to hadron gas. The upcoming high-fidelity measurements from LHC Run 2 will serve as a precision test of the two scenarios.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Identification of ancestral gnathostome Gli3 enhancers with activity in mammals

Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15–21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. In conclusion, these results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Local adaptation of switchgrass drives trait relations to yield and differential responses to climate and soil environments

Abstract Switchgrass, a potential biofuel crop, is a genetically diverse species with phenotypic plasticity enabling it to grow in a range of environments. Two primary divergent ecotypes, uplands and lowlands, exhibit trait combinations representative of acquisitive and conservative growth allocation strategies, respectively. Whether these ecotypes respond differently to various types of environmental drivers remains unclear but is crucial to understanding how switchgrass varieties will respond to climate change. We grew two upland, two lowland, and two intermediate/hybrid cultivars of switchgrass at three sites along a latitudinal gradient in the central United States. Over a 4‐year period, we measured plant functional traits and biomass yields and evaluated genotype‐by‐environment (G × E) interaction effects by analyzing switchgrass responses to soil and climate variables. We found substantial evidence of G × E interactions on biomass yield, primarily due to deviations in the response of the southern lowland cultivar Alamo, which produced more biomass in hotter and drier environments relative to other cultivars. While lowland cultivars had the highest potential for yield, their yields were more variable year‐to‐year compared to other cultivars, suggesting greater sensitivity to environmental perturbations. Models comparing soil and climate principal components as explanatory variables revealed soil properties, especially nutrients, to be most effective at predicting switchgrass biomass yield. Also, positive correlations between biomass yield and conservative plant traits, such as high stem mass and tiller height, became stronger at lower latitudes where the climate is hotter and drier, regardless of ecotype. Lowland cultivars, however, showed a greater predisposition to exhibit these conservative traits. These results suggest switchgrass trait allocation trade‐offs that prioritize aboveground biomass production are more tightly associated in hot, dry environments and that lowland cultivars may exhibit a more specialized strategy relative to other cultivars. Altogether, this research provides essential knowledge for improving the viability of switchgrass as a biofuel crop.

09 BIOMASS FUELS↗

DOE OSTI2026

Impacts of Pasture Conversion to Sugarcane on Water Fluxes and Water Use Efficiency in the Southeastern US

The expansion of sugarcane (cane), a high-yielding perennial crop, will likely reshape the bioenergy landscape in the Southeastern US. However, its ecohydrological implications, particularly following conversion from grazed pastures, a dominant land use in the region, remain highly uncertain. We investigated the impact of cane expansion on evapotranspiration (ET) and its partitioning, and the mechanisms influencing both ET components and water use efficiency (WUE) across multiple scales and growth cycles in subtropical Florida. We combined eddy covariance, biometric measurements, and process-based stomatal conductance (g s ) models. ET was 1.7% lower in cane than in improved pasture (IMP) but exceeded that in semi-native pasture (SN) by 21%. Transpiration (T) followed a similar pattern, consistent with lower g s in cane relative to IMP. Cane had more conservative water use and greater sensitivity of g s to vapor pressure deficit (VPD) compared to IMP pasture, suggesting cane may be more tolerant of increasing atmospheric water demand. In contrast, SN showed lower g s and weaker stomatal sensitivity to VPD compared to cane, resulting in lower T. In cane, stomatal regulation and T varied across growth cycles, with stomata becoming less water conservative as stands matured, highlighting the importance of incorporating stand age-dependent stomatal regulation into hydrological models. Evaporation (E) was higher in cane than pastures (19%–26%), partially offsetting WUE gains. Cane exhibited higher intrinsic WUE (GPP/g s ; Gross Primary Productivity), ecosystem WUE (GPP/ET), and harvest WUE (harvest/ET) than both pasture types. Large-scale pasture-to-cane conversion could produce widely contrasting hydrological outcomes. The net regional impact will depend on the proportion of each pasture type converted and on cane's high g s sensitivity to VPD, which triggers tight stomatal regulation and conservative water use, both of which will become increasingly consequential under intensifying atmospheric water demand.

bioenergy↗

DOE OSTI2023

Benefits and Cautions in Data Assimilation Strategies: An Example of Modeling Groundwater Recharge

Assimilating recent observations improves model outcomes for real-time assessments of groundwater processes. This is demonstrated in estimating time-varying recharge to a shallow fractured-rock aquifer in response to precipitation. Results from estimating the time-varying water-table altitude (h) and recharge, and their error covariances, are compared for forecasting, filtering, and fixed-lag smoothing (FLS), which are implemented using the Kalman Filter as applied to a data-driven, mechanistic model of recharge. Forecasting uses past observations to predict future states and is the current paradigm in most groundwater modeling investigations; filtering assimilates observations up to the current time to estimate current states; and FLS estimates states following a time lag over which additional observations are collected. Results for forecasting yield a large error covariance relative to the magnitude of the expected recharge. With assimilating recent observations of h, filtering and FLS produce estimates of recharge that better represent time-varying observations of h and reduce uncertainty in comparison to forecasting. Although model outcomes from applying data assimilation through filtering or FLS reduce model uncertainty, they are not necessarily mass conservative, whereas forecasting outcomes are mass conservative. Mass conservative outcomes from forecasting are not necessarily more accurate, because process errors are inherent in any model. Improvements in estimating real-time groundwater conditions that better represent observations need to be weighed for the model application against outcomes with inherent process deficiencies. In conclusion, results from data assimilation strategies discussed in this investigation are anticipated to be relevant to other groundwater processes models where system states are sensitive to system inputs.

aquifer recharge↗