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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

Abstract Craniosynostosis, defined by premature fusion of one or multiple cranial sutures, is a common congenital defect affecting more than 1/2000 infants and results in restricted brain expansion. Single gene mutations account for 15%–20% of cases, largely as part of a syndrome, but the majority are nonsyndromic with complex underlying genetics. We hypothesized that the two noncoding genomic regions identified by a GWAS for craniosynostosis contain distal regulatory elements for the risk genes BMPER and BMP2. To identify such regulatory elements, we surveyed conserved noncoding sequences from both risk loci for enhancer activity in transgenic Danio rerio. We identified enhancers from both regions that direct expression to skeletal tissues, consistent with the endogenous expression of bmper and bmp2. For each locus, we also found a skeletal enhancer that also contains a sequence variant associated with craniosynostosis risk. We examined the activity of each enhancer during craniofacial development and found that the BMPER-associated enhancer is active in the restricted region of cartilage closely associated with frontal bone initiation. The same enhancer is active in mouse skeletal tissues, demonstrating evolutionarily conserved activity. Using enhanced yeast one-hybrid assays, we identified transcription factors that bind each enhancer and observed differential binding between alleles, implicating multiple signaling pathways. Our findings help unveil the genetic mechanism of the two craniosynostosis risk loci. More broadly, our combined in vivo approach is applicable to many complex genetic diseases to build a link between association studies and specific genetic mechanisms.

He(何璇), Xuan Anita (ORCID:0000000313221972)↗
DOE OSTI2025

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Abstract Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Effect of recoils on soft-drop-groomed observables in 𝛾-tagged jets in a multistage approach

We investigate medium-induced modifications to jet substructure observables that characterize hard components in central Pb-Pb collisions at $\sqrt{𝑠_{𝑁⁢𝑁}}$ = 5.02 TeV. Using a multistage Monte Carlo simulation of in-medium jet shower evolution, we explore flavor-dependent medium effects through simulations of inclusive and 𝛾-tagged jets. The results show that quark jets undergo a nonmonotonic modification compared with gluon jets in observables such as the Pb-Pb to 𝑝−𝑝 ratio of the soft drop prong angle 𝑟 𝑔 , the relative prong transverse momentum 𝑘 𝑇,𝑔 , and the groomed mass 𝑚 𝑔 distributions. Due to this nonmonotonic modification, 𝛾-tagged jets, enriched in quark jets, provide surprisingly clear signals of medium-induced structural modifications, distinct from effects dominated by selection bias. Further systematic studies demonstrate that these effects are dominated by recoil medium response. This work highlights the potential of hard substructures in 𝛾-tagged jets as powerful tools for probing the jet-medium interactions in high-energy heavy-ion collisions, in particular by enabling detailed investigations of jet-medium parton scatterings via their associated medium response. All simulations for 𝛾-tagged jet analyses carried out in this paper used triggered events containing at least one hard photon, which highlights the utility of these observables for future Bayesian analysis.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
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

Bayesian calibration of a hybrid nuclear collision model using $\textit{p}$₋Pb and Pb-Pb data at energies available at the CERN Large Hadron Collider

Here, we posit a unified hydrodynamic and microscopic description of the quark-gluon plasma (QGP) produced in ultrarelativistic p₋Pb and Pb-Pb collisions at $\sqrt{s}_\text{NN}$ = 5.02 TeV and evaluate our assertion using Bayesian inference. Specifically, we model the dynamics of both collision systems using initial conditions with parametric nucleon substructure, a preequilibrium free streaming stage, event-by-event viscous hydrodynamics, and a microscopic hadronic afterburner. Free parameters of the model, which describe the initial state and QGP medium are then simultaneously calibrated to fit charged-particle yields, mean $p_T$, and flow cumulants. We argue that the global agreement of the calibrated model with the experimental data strongly supports the existence of hydrodynamic flow in small collision systems at ultrarelativistic energies, and that the flow produced develops at length scales smaller than a single proton. Posterior estimates for the model's input parameters are obtained, and new insights into the temperature dependence of the QGP transport coefficients and event-by-event structure of the proton are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Traces of nonequilibrium effects, initial condition, bulk dynamics, and elementary collisions in the charm observables

Heavy quarks produced in relativistic heavy-ion collisions are known to be sensitive probes of the hot and dense QCD matter they traverse. In this paper we study how their dynamics is affected by the nature of the bulk evolution of the QCD matter, the initial condition of the system, and the treatment of elementary interactions between heavy quarks and the surrounding medium. For the same initial condition and the same quark-gluon plasma (QGP) expansion scenario we discuss the consequences of the assumption of a local equilibrium by comparing the consequences for the nuclear modification factor $R_{AA}$ and the elliptic flows of charm quarks, scrutinizing the different components of the final distribution of charm quarks. For this purpose we employ the parton-hadron-string dynamics (PHSD) model, which is an off-shell microscopic transport approach, as well as the linearized-Boltzmann (LB) scheme obtained by coarse graining the PHSD bulk and assuming local equilibrium for the interactions of the charm quarks with the bulk. The $R_{AA}$ of charm quarks stemming from the later LB approach is also compared to a genuine fluid dynamics evolution initiated by the coarse grained PHSD, which allows us to further assess the consequences of reducing the full $\textit{n}$-body dynamics. We then proceed to a systematic comparison of PHSD (in its LB approximation) with MC@HQ, another transport model for heavy flavors which also relies on the LB approach. In particular, we investigate the consequences for the nuclear modification factor of charm quarks if we vary separately the initial heavy quark distribution function in matter, the expansion dynamics of the QGP, and the elementary interactions of heavy quarks of these models. We find that the results for both models vary significantly depending on the details of the calculation. However, both models achieve very similar predictions for key heavy quark observables for certain combinations of initial condition, bulk evolution, and interactions. In this work, we conclude that this ambiguity limits our ability to determine the different properties of the system based on the current set of observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Nonfuel antineutrino contributions in the ORNL High Flux Isotope Reactor (HFIR)

Reactor neutrino experiments have seen major improvements in precision in recent years. With the experimental uncertainties becoming lower than those from theory, carefully considering all sources of $\bar{ν}$ e is important when making theoretical predictions. One source of νe that is often neglected arises from the irradiation of the nonfuel materials in reactors. The $\bar{ν}$ e rates and energies from these sources vary widely based on the reactor type, configuration, and sampling stage during the reactor cycle and have to be carefully considered for each experiment independently. In this article, we present a formalism for selecting the possible $\bar{ν}$ e sources arising from the neutron captures on reactor and target materials. We apply this formalism to the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory, the $\bar{ν}$ e source for the the Precision Reactor Oscillation and Spectrum Measurement (PROSPECT) experiment. Overall, we observe that the nonfuel $\bar{ν}$ e contributions from HFIR to PROSPECT amount to 1% above the inverse beta decay threshold with a maximum contribution of 9% in the 1.8–2.0 MeV range. Nonfuel contributions can be particularly high for research reactors like HFIR because of the choice of structural and reflector material in addition to the intentional irradiation of target material for isotope production. We show that typical commercial pressurized water reactors fueled with low-enriched uranium will have significantly smaller nonfuel $\bar{ν}$ e contribution.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

Effective viscosities in a hydrodynamically expanding boost-invariant QCD plasma

Background: The near-equilibrium properties of a QCD plasma can be encoded into transport coefficients such as bulk and shear viscosity. In QCD, the ratio of these transport coefficients to entropy density, ζ/$\textit{s}$ and η/$\textit{s}$, depends nontrivially on the plasma's temperature. This is unlike in conformal systems where they take constant values such as η/$\textit{s}$ = 1/(4π). Purpose: In this work, we show that in a (0 + 1)D boost-invariant fluid with no transverse expansion, a temperature-dependent ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ can be described by an equivalent effective viscosity $\langleζ/s\rangle_{\text{eff}}$ or $\langleη/s\rangle_{\text{eff}}$. This effective viscosity combines the actual temperature-dependent ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ with the temperature profile of the fluid. Further, we extend the concept of effective viscosity in systems with transverse expansion and discuss how effective viscosities can be used to identify families of ζ/$\textit{s(T)}$ and η /$\textit{s(T)}$ that lead to similar hydrodynamic evolution. Methods: The Navier-Stokes relativistic hydrodynamic equations are used to provide a first definition of effective viscosity, in (0 + 1)D and (1 + 1)D. In the (0 + 1)D case, the analysis is extended to Israel-Stewart-type second-order hydrodynamics to clarify the effect of higher-order hydrodynamics corrections on the effective viscosity. Results: In a boost-invariant fluid with no transverse expansion [(0 + 1)D], the effective viscosity is expressed as a simple integral of ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ over temperature, with a weight determined by the speed of sound of the fluid. The result is general for any equation of state with a moderate temperature dependence of the speed of sound, including the QCD equation of state. This definition of effective viscosity can be used to identify infinite families of ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ that produce essentially indistinguishable temperature profiles. In a boost-invariant cylindrical system [(1 + 1)D], a similar definition of effective viscosity is obtained in terms of characteristic trajectories in time and transverse direction. This leads to an infinite number of constraints on an infinite functional space for ζ/$\textit{s(T)}$ and η/$\textit{s(T)}$. Realistic examples are presented by using a finite number of constraints on a finite functional space. Conclusions: The definition of effective viscosity in a (0 + 1)D system clarifies how infinite families of ζ/$\textit{s(T)}$ and η/$\textit{s(T)}$ can result in nearly identical hydrodynamic temperature profiles. By extending the study to a boost-invariant cylindrical [(1 + 1)D] fluid, we identify an approximate but more general definition of effective viscosity that highlights the potential and limits of the concept of effective viscosity in fluids with limited symmetries.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

JETSCAPE framework: p+p results

The JETSCAPE framework is a modular and versatile Monte Carlo software package for the simulation of high energy nuclear collisions. In this work we present a new tune of JETSCAPE, called PP19, and validate it by comparison to jet-based measurements in p + p collisions, including inclusive single jet cross sections, jet shape observables, fragmentation functions, charged hadron cross sections, and dijet mass cross sections. These observables in p+p collisions provide the baseline for their counterparts in nuclear collisions. Quantifying the level of agreement of JETSCAPE results with p+p data is thus necessary for meaningful applications of JETSCAPE to A+A collisions. The calculations use the JETSCAPE PP19 tune, defined in this paper, based on version 1.0 of the JETSCAPE framework. For the observables discussed in this work calculations using JETSCAPE PP19 agree with data over a wide range of collision energies at a level comparable to standard Monte Carlo codes. These results demonstrate the physics capabilities of the JETSCAPE framework and provide benchmarks for JETSCAPE users.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Determining the jet transport coefficient $\hat{q}$ from inclusive hadron suppression measurements using Bayesian parameter estimation

We report a new determination of $\hat{q}$, the jet transport coefficient of the quark-gluon plasma. We use the JETSCAPE framework, which incorporates a novel multistage theoretical approach to in-medium jet evolution and Bayesian inference for parameter extraction. The calculations, based on the Matter and Lbt jet quenching models, are compared to experimental measurements of inclusive hadron suppression in Au + Au collisions at the BNL Relativistic Heavy Ion Collider (RHIC) and Pb + Pb collisions at the CERN Large Hadron Collider (LHC). The correlation of experimental systematic uncertainties is accounted for in the parameter extraction. The functional dependence of $\hat{q}$ on jet energy or virtuality and medium temperature is based on a perturbative picture of in-medium scattering, with components reflecting the different regimes of applicability of Matter and Lbt. In the multistage approach, the switch between Matter and Lbt is governed by a virtuality scale Q 0 . Comparison of the posterior model predictions to the RHIC and LHC hadron suppression data shows reasonable agreement, with moderate tension in limited regions of phase space. The distribution of $\hat{q}/T^3$ extracted from the posterior distributions exhibits weak dependence on jet momentum and medium temperature T, with 90% credible region (CR) depending on the specific choice of model configuration. The choice of Matter + Lbt, with switching at virtuality Q 0 , has 90% CR of $2<\hat{q}/T^3<4$ for p T jet > 40 GeV=c. The value of Q 0 , determined here for the first time, is in the range 2.0-2.7 GeV.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Nonequilibrium effects and transverse spherocity in ultrarelativistic proton-nucleus collisions

We investigate the effects of nonequilibrium dynamics in small colliding systems by comparing a nonequilibrium transport approach, Parton-Hadron-String Dynamics (PHSD), with a (2+1)-dimensional viscous hydrodynamic model, VISHNew. Focusing on p + Pb collisions at energies available at the Large Hadron Collider, we extract the initial conditions for the hydrodynamic model from PHSD, in order to reduce the impact of the early out-of-equilibrium dynamics and focus on the traces of nonequilibrium in the ensuing medium evolution. We find that in the transport approach quantities like energy density and bulk viscous pressure are highly inhomogeneous on the transverse plane during the whole evolution, whereas the hydrodynamic simulations dissolve more efficiently the initial spatial irregularities, still keeping a high degree of inhomogeneity due to the smaller size and lifetime of the medium produced in p + Pb collisions with respect to heavy-ion reactions. As a first step that will help to identify the impact of these nonequilibrium effects on final observables in proton-nucleus collisions, we perform an analysis of the transverse spherocity, an event-shape observable able to distinguish between jetty and isotropic configurations of transverse momenta. We found that the spherocity distribution in PHSD is slightly shifted towards the isotropic limit with respect to the hydrodynamic result. Even though this dissimilarity is partially due to the difference in the final charged particle production, it mainly comes from the different description within the two frameworks of the medium produced in small colliding systems. This finding supports the idea that multidifferential measurements, such as those based on event categorization according to multiplicity and spherocity, are useful to study final-state observables in ultrarelativistic proton-nucleus collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Inclusive jet and hadron suppression in a multistage approach

We present a new study of jet interactions in the quark-gluon plasma created in high-energy heavy-ion collisions, using a multistage event generator within the jetscape framework. We focus on medium-induced modifications in the rate of inclusive jets and high transverse momentum (high-p T ) hadrons. Scattering-induced jet energy loss is calculated in two stages: a high virtuality stage based on the matter model, in which scattering of highly virtual partons modifies the vacuum radiation pattern, and a second stage at lower jet virtuality based on the LBT model, in which leading partons gain and lose virtuality by scattering and radiation. Coherence effects that reduce the medium-induced emission rate in the matter phase are also included. The TRENTO model is used for initial conditions, and the (2 + 1)dimensional VISHNU model is used for viscous hydrodynamic evolution. Jet interactions with the medium are modeled via 2-to-2 scattering with Debye screened potentials, in which the recoiling partons are tracked, hadronized, and included in the jet clustering. Holes left in the medium are also tracked and subtracted to conserve transverse momentum. Calculations of the nuclear modification factor (R AA ) for inclusive jets and high-p T hadrons are compared to experimental measurements at the BNL Relativistic Heavy Ion Collider (RHIC) and the CERN Large Hadron Collider (LHC). Within this framework, we find that with one extra parameter which codifies the transition between stages of jet modification—along with the typical parameters such as the coupling in the medium, the start and stop criteria, etc.—we can describe these data at all energies for central and semicentral collisions without a rescaling of the jet transport coefficient q.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Multiscale evolution of charmed particles in a nuclear medium

Parton energy-momentum exchange with the quark gluon plasma (QGP) is a multiscale problem. In this work, we calculate the interaction of charm quarks with the QGP within the higher twist formalism at high virtuality and high energy using the Modular All Twist Transverse-scattering Elastic-drag and Radiation (MATTER) model, while the low-virtuality and high-energy portion is treated via a linearized Boltzmann transport formalism. Coherence effect that reduces the medium-induced emission rate in the MATTER model is also taken into account through a virtuality-dependent qˆ, leaving the simultaneous dependence of qˆ on heavy quark mass and virtuality for future studies. The interplay between these two formalisms is studied phenomenologically and used to produce a first description of the D-meson and charged hadron nuclear modification factor R AA across multiple centralities. As a result, all calculations were carried out utilizing the Jet Energy-loss Tomography with a Statistically and Computationally Advanced Program Envelope framework.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Hadronization of heavy quarks

Heavy-flavor hadrons produced in ultrarelativistic heavy-ion collisions are a sensitive probe for studying hadronization mechanisms of the quark-gluon-plasma. In this paper, we survey how different transport models for the simulation of heavy-quark diffusion through a quark-gluon plasma in heavy-ion collisions implement hadronization and how this affects final state observables. Utilizing the same input charm-quark distribution in all models at the hadronization transition, we find that the transverse-momentum dependence of the nuclear modification factor of various charm hadron species has significant sensitivity to the hadronization scheme. In addition, the charm-hadron elliptic flow exhibits a nontrivial dependence on the elliptic flow of the hadronizing partonic medium.

Atomic, Nuclear and Particle Physics↗