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At least 487 records · Page 27

Modeling study on the cleavage step of the self-splicing reaction in group I introns

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.

NASA Discipline Exobiology↗

Robustness of quantum correlation in quantum energy teleportation

In this article, we explore a feedback-control protocol in different quantum field theories (QFTs) to study the quantum correlation in nonunitary evolution of quantum systems. Traditional studies on QFTs focus on quantum entanglement of pure states under the unitary evolution, however, we examine quantum correlation in mixed states using quantum energy teleportation (QET), which is an energy transfer protocol by utilizing ground state entanglement, and introduce quantum discord as a measure. QET involves a midcircuit measurement, which disrupts pure state entanglement. Despite this, our analysis demonstrates that quantum discord maintains the correlation throughout the QET process. We conducted numerical analyses with benchmark models including the Nambu-Jona-Lasinio (NJL) model, revealing that quantum discord consistently acts as an order parameter for phase transitions. The model is extended in a way that it has both the chiral chemical potential and the chemical potential, which are useful to study the phase structures mimicking the chiral imbalance between left- and right- quarks coupled to the chirality density operator. In all cases we studied, the quantum discord behaved as an order parameter of the phase transition. Published by the American Physical Society 2024

Ikeda, Kazuki (ORCID:0000000338212669)↗

Topological Mott transition in a two band model of spinless fermions with on-site Coulomb repulsion

Highlights: • The effect of the on-site Coulomb repulsion and the spin–orbit Rashba coupling lead to the 2D topological semimetal. • The ground state phase diagram is calculated. • The topological semimetal phase is characterized by the zero energy Majorana states. In the framework of mean field approach, we study topological Mott transition in a two band model of spinless fermions on a square lattice at half filling. We consider the combined effect of the on-site Coulomb repulsion and the spin–orbit Rashba coupling. The ground state phase diagram is calculated as a function of the strength of the spin–orbit Rashba coupling and the Coulomb repulsion. The spin–orbit Rashba coupling leads to a distinct phase of matter, the topological semimetal. We study a new type of phase transition between the non-topological insulator and topological semimetal states. Topological phase state is characterized by the zero energy Majorana states, which there are in defined region of the wave vectors and are localized at the boundaries of the sample. The region of existence of the zero energy Majorana states tends to zero at the point of the Mott phase transition. The zero energy Majorana states are dispersionless (they can be considered as flat bands), the Chern number and Hall conductance are equal to zero (note in two dimensional model).

36 MATERIALS SCIENCE↗

A simple and effective five-equation two-phase numerical model for liquid-vapor phase transition in cavitating flows

Numerical difficulties, notably the non-monotonic behavior of the Wood speed of sound and the volume fraction positivity, associated with the reduced five-equation two-phase flow model of Kapila et al. (2001) [A.K. Kapila, R. Menikoff, J.B. Bdzil, S.F. Son, D.S. Stewart, 2001. Two-phase modeling of deflagration-to-detonation transition in granular materials: reduced equations, Physics of Fluids 13(10), 3002–3024] have been resolved in the past through the introduction of a frozen speed of sound and an algebraic approach for mechanical relaxation afforded by a pressure non-equilibrium six-equation model proposed by [R. Saurel, F. Petitpas, R.A. Berry, 2009. Simple and efficient relaxation methods for interfaces separating compressible fluids, cavitating flows and shocks in multiphase mixture, J. Comput. Phys. 228, 1678–1712]. By contrast, it is explored and demonstrated in this work that these difficulties can in fact still be resolved within the numerical scheme for solving the reduced five-equation model by numerically replacing the Wood speed of sound for the estimates of wave speeds in the approximate Riemann solver HLLC with the monotonic mixture speed of sound for a transport five-equation model. For shock interface (artificial mixture separating pure or nearly pure fluids) interaction problems, with the apparent advantage of monotonic behavior of the speed of sound in the interface, the effect of the numerical replacement is also confined to the interface. Differences other than the behavior of the speed of sound within the interface in the solutions due to the replacement diminish with increasing resolution when reasonable solution can be obtained with Wood speed of sound. For cavitating/expansion problems in physical fluid mixture, it is pointed out and explained why acoustics in the numerical solutions still propagate at the Wood speed of sound (therefore consistent with the reduced five-equation model) even though in some cases a much higher speed of sound like the numerical replacement above for solving the reduced five-equation model or the frozen speed of sound for solving a six-equation model is used for the estimates of wave speeds in the HLLC scheme. A variant of the five-equation two-phase flow model by Saurel et al. (2008) [R. Saurel, F. Petitpas, R. Abgrall, 2008. Modelling phase transition in metastable liquids: application to cavitating and flashing flows, J. Fluid Mech. 607, 313–350] is then constructed for liquid-vapor phase transition in cavitating flows. The relaxation toward thermo-chemical equilibrium during phase transition is achieved by solving a simple system of algebraic equations for the equilibrium state variables for better efficiency, following Pelanti and Shyue (2014) [M. Pelanti, K.-M. Shyue, 2014. A mixture-energy-consistent six-equation two-phase numerical model for fluid with interfaces, cavitation and evaporation waves. J. Comput. Phys. 259, 331–357]. Therefore, the current model retains both the simplicity afforded by the five-equation model and the efficiency of the algebraic relaxation solver. An alternative algebraic approach for handling the non-conservative term (the so-called K∇ · u term) in the reduced five-equation model for mechanical equilibrium of a liquid-vapor mixture is also explored by enforcing the thermal equilibrium at the same time. Finally, numerical results of sample tests in both one and two dimensions in the literature as well as that in three dimensions demonstrate the effectiveness and ability of the proposed model to simulate cavitating flows. An interesting mechanism of shock generation by acoustics in water due to phase transition is then found by the numerical simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cosmic Ray Mediated Thermal Fronts in the Warm-Hot Circumgalactic Medium

We investigate the 1D plane-parallel front connecting the warm ($10^4$ K) and hot ($10^6$ K) phases of the circumgalactic medium (CGM), focusing on the influence of cosmic rays (CRs) in shaping these transition layers. We find that cosmic rays dictate the thermal balance while other fluxes (thermal conduction, radiative cooling, and gas flow) adjust to compensate. We compute column density ratios for selected transition temperature ions and compare them with observational data. While most of our models fail to reproduce the observations, a few are successful, although we make no claims for their uniqueness. Some of the discrepancies may indicate challenges in capturing the profiles in cooler, photoionized regions, as has been suggested for by previous efforts to model thermal transition layers.

79 ASTRONOMY AND ASTROPHYSICS↗

Skin Friction and Transition Location Measurement on Supersonic Transport Models

Flow visualization techniques were used to obtain both qualitative and quantitative skin friction and transition location data in wind tunnel tests performed on two supersonic transport models at Mach 2.40. Oil-film interferometry was useful for verifying boundary layer transition, but careful monitoring of model surface temperatures and systematic examination of the effects of tunnel start-up and shutdown transients will be required to achieve high levels of accuracy for skin friction measurements. A more common technique, use of a subliming solid to reveal transition location, was employed to correct drag measurements to a standard condition of all-turbulent flow on the wing. These corrected data were then analyzed to determine the additional correction required to account for the effect of the boundary layer trip devices.

Kennelly, Robert A., Jr.↗

Kepler Data Validation I: Architecture, Diagnostic Tests, and Data Products for Vetting Transiting Planet Candidates

The Kepler Mission was designed to identify and characterize transiting planets in the Kepler Field of View and to determine their occurrence rates. Emphasis was placed on identification of Earth-size planets orbiting in the Habitable Zone of their host stars. Science data were acquired for a period of four years. Long-cadence data with 29.4 min sampling were obtained for approx. 200,000 individual stellar targets in at least one observing quarter in the primary Kepler Mission. Light curves for target stars are extracted in the Kepler Science Data Processing Pipeline, and are searched for transiting planet signatures. A Threshold Crossing Event is generated in the transit search for targets where the transit detection threshold is exceeded and transit consistency checks are satisfied. These targets are subjected to further scrutiny in the Data Validation (DV) component of the Pipeline. Transiting planet candidates are characterized in DV, and light curves are searched for additional planets after transit signatures are modeled and removed. A suite of diagnostic tests is performed on all candidates to aid in discrimination between genuine transiting planets and instrumental or astrophysical false positives. Data products are generated per target and planet candidate to document and display transiting planet model fit and diagnostic test results. These products are exported to the Exoplanet Archive at the NASA Exoplanet Science Institute, and are available to the community. We describe the DV architecture and diagnostic tests, and provide a brief overview of the data products. Transiting planet modeling and the search for multiple planets on individual targets are described in a companion paper. The final revision of the Kepler Pipeline code base is available to the general public through GitHub. The Kepler Pipeline has also been modified to support the Transiting Exoplanet Survey Satellite (TESS) Mission which is expected to commence in 2018.

data analysis↗

Study of the atmospheric general circulation as an initial value problem with the NCAR Community Climate Model

The essential elements of the transition of a model atmosphere to the equilibrium state from two extreme rest states, a cold (240 K) state and a warm (310 K) state, were examined using the NCAR Community Climate Model. It is shown that the same equilibrium state was reached in the two spinup conditions, which was also the same that was reported for this model by Williamson and Williamson (1984), who started from still a different initial condition. The spinup from the cold initial condition was faster than that from the warm condition, although the final stages of the approach to equilibrium were very simular in both cases. It was also found that the spinup of the barotropic flow lagged behind that of the baroclinic flow and the thermal field, and the model tropics spinup was faster than that of the mid-latitudes.

Chen, Tsing-Chang↗

Molecular orbital projectors in non-empirical jmDFT recover exact conditions in transition-metal chemistry

Low-cost, non-empirical corrections to semi-local density functional theory are essential for accurately modeling transition-metal chemistry. Here, we demonstrate the judiciously modified density functional theory (jmDFT) approach with non-empirical U and J parameters obtained directly from frontier orbital energetics on a series of transition-metal complexes. We curate a set of nine representative Ti(III) and V(IV) d 1 transition-metal complexes and evaluate their flat-plane errors along the fractional spin and charge lines. We demonstrate that while jmDFT improves upon both DFT+U and semi-local DFT with the standard atomic orbital projectors (AOPs), it does so inefficiently. We rationalize these inefficiencies by quantifying hybridization in the relevant frontier orbitals. To overcome these limitations, we introduce a procedure for computing a molecular orbital projector (MOP) basis for use with jmDFT. We demonstrate this single set of d 1 MOPs to be suitable for nearly eliminating all energetic delocalization and static correlation errors. In all cases, MOP jmDFT outperforms AOP jmDFT, and it eliminates most flat-plane errors at non-empirical values. Unlike DFT+U or hybrid functionals, jmDFT nearly eliminates energetic delocalization and static correlation errors within a non-empirical framework.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular-Based Optical Measurement Techniques for Transition and Turbulence in High-Speed Flow

High-speed laminar-to-turbulent transition and turbulence affect the control of flight vehicles, the heat transfer rate to a flight vehicle's surface, the material selected to protect such vehicles from high heating loads, the ultimate weight of a flight vehicle due to the presence of thermal protection systems, the efficiency of fuel-air mixing processes in high-speed combustion applications, etc. Gaining a fundamental understanding of the physical mechanisms involved in the transition process will lead to the development of predictive capabilities that can identify transition location and its impact on parameters like surface heating. Currently, there is no general theory that can completely describe the transition-to-turbulence process. However, transition research has led to the identification of the predominant pathways by which this process occurs. For a truly physics-based model of transition to be developed, the individual stages in the paths leading to the onset of fully turbulent flow must be well understood. This requires that each pathway be computationally modeled and experimentally characterized and validated. This may also lead to the discovery of new physical pathways. This document is intended to describe molecular based measurement techniques that have been developed, addressing the needs of the high-speed transition-to-turbulence and high-speed turbulence research fields. In particular, we focus on techniques that have either been used to study high speed transition and turbulence or techniques that show promise for studying these flows. This review is not exhaustive. In addition to the probe-based techniques described in the previous paragraph, several other classes of measurement techniques that are, or could be, used to study high speed transition and turbulence are excluded from this manuscript. For example, surface measurement techniques such as pressure and temperature paint, phosphor thermography, skin friction measurements and photogrammetry (for model attitude and deformation measurement) are excluded to limit the scope of this report. Other physical probes such as heat flux gauges, total temperature probes are also excluded. We further exclude measurement techniques that require particle seeding though particle based methods may still be useful in many high speed flow applications. This manuscript details some of the more widely used molecular-based measurement techniques for studying transition and turbulence: laser-induced fluorescence (LIF), Rayleigh and Raman Scattering and coherent anti-Stokes Raman scattering (CARS). These techniques are emphasized, in part, because of the prior experience of the authors. Additional molecular based techniques are described, albeit in less detail. Where possible, an effort is made to compare the relative advantages and disadvantages of the various measurement techniques, although these comparisons can be subjective views of the authors. Finally, the manuscript concludes by evaluating the different measurement techniques in view of the precision requirements described in this chapter. Additional requirements and considerations are discussed to assist with choosing an optical measurement technique for a given application.

Bathel, Brett F.↗

Quantum computation of phase transition in the massive Schwinger model

Abstract As pointed out by Coleman, physical quantities in the Schwinger model depend on a parameter θ that determines the background electric field. There is a phase transition for θ = π only. We develop a momentum space formalism on a lattice and use it to perform a quantum computation of the critical point of this phase transition on the NISQ device IMB Q Lima. After error mitigation, our results give strong indication of the existence of a critical point at m / e ≃ 0.32, where m is the bare fermion mass and e is the coupling strength, in good agreement with the classical numerical result m / e ≃ 0.3335.

Physics↗

NASA GSFC CCMC Recent Model Validation Activities

The Community Coordinated Modeling Center (CCMC) holds the largest assembly of state-of-the-art physics-based space weather models developed by the international space physics community. In addition to providing the community easy access to these modern space research models to support science research, its another primary goal is to test and validate models for transition from research to operations. In this presentation, we provide an overview of the space science models available at CCMC. Then we will focus on the community-wide model validation efforts led by CCMC in all domains of the Sun-Earth system and the internal validation efforts at CCMC to support space weather servicesjoperations provided its sibling organization - NASA GSFC Space Weather Center (http://swc.gsfc.nasa.gov). We will also discuss our efforts in operational model validation in collaboration with NOAA/SWPC.

Rastaetter, L.↗

Modeling Magnetic Disk Wind State Transitions in Black Hole X-Ray Binaries

We analyze three prototypical black hole X-ray binaries, 4U 1630–472, GRO J1655–40, and H1743–322, in an effort to systematically understand the intrinsic state transition of the observed accretion disk winds between wind-on and wind-off states by utilizing state-of-the-art Chandra/HETGS archival data from multi-epoch observations. We apply our magnetically driven wind models in the context of magnetohydrodynamic(MHD)calculations to constrain(1)their global density slope(p),(2)their density (n17) at the foot point of the inner most launching radius, and(3)the abundances of heavier elements(AFe,S,Si). Incorporating the MHD winds into xstar photoionization calculations in a self-consistent manner, we create a library of synthetic absorption spectra given the observed X-ray continua. Our analysis clearly indicates a characteristic bimodal transition of multi-ion X-ray winds; i.e., the wind density gradient is found to steepen(fro mp∼1.2–1.4 to∼1.4–1.5)while its density normalization declines as the source transitions from the wind-onto the wind-off state. The model implies that the ionized wind remains physically present even in the wind-off state, despite its apparent absence in the observed spectra. Super solar abundances for heavier elements are also favored. Our global multi-ion wind models, taking into account soft X-ray ions as well as Fe K absorbers, show that the internal wind condition plays an important role in wind transitions besides photoionization changes. Simulated XRISM/Resolve and Athena/X-IFU spectra are presented to demonstrate a high fidelity of the multi-ion wind model for a better understanding of these powerful ionized winds in the coming decades

Keigo Fukumura↗

Magnetic field induced phase transitions of the triangular spin model

In this work, motivated by a recent inelastic neutron scattering experiment on YbMgGaO 4 , I study the homogeneous spin model on the triangular lattice using the cluster mean-field theory and exact diagonalization. Phase diagrams with and without magnetic field are computed. The results show that the magnetic field can induce the phase transition from the spin liquid state (or the stripe state) to the 120 ° antiferromagnetic state. These phase transitions are suppressed by the next-nearest-neighbor exchange interaction J 2 / J 1 and vanish as J 2 / J 1 > 0.11 . I analyze a parameter space at J 2 / J 1 = 0.1 , where a field induced phase transition can occur, and find that the deviation of the theoretical spin excitation energy from the experimental data is only about 0.054. These results imply that an effective homogeneous spin model still applies to YbMgGaO 4 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Tropical and Subtropical Cloud Transitions in Weather and Climate Prediction Models: The GCSS/WGNE Pacific Cross-Section Intercomparison (GPCI)

A model evaluation approach is proposed in which weather and climate prediction models are analyzed along a Pacific Ocean cross section, from the stratocumulus regions off the coast of California, across the shallow convection dominated trade winds, to the deep convection regions of the ITCZ the Global Energy and Water Cycle Experiment Cloud System Study/Working Group on Numerical Experimentation (GCSS/ WGNE) Pacific Cross-Section Intercomparison (GPCI). The main goal of GPCI is to evaluate and help understand and improve the representation of tropical and subtropical cloud processes in weather and climate prediction models. In this paper, a detailed analysis of cloud regime transitions along the cross section from the subtropics to the tropics for the season June July August of 1998 is presented. This GPCI study confirms many of the typical weather and climate prediction model problems in the representation of clouds: underestimation of clouds in the stratocumulus regime by most models with the corresponding consequences in terms of shortwave radiation biases; overestimation of clouds by the 40-yr ECMWF Re-Analysis (ERA-40) in the deep tropics (in particular) with the corresponding impact in the outgoing longwave radiation; large spread between the different models in terms of cloud cover, liquid water path and shortwave radiation; significant differences between the models in terms of vertical cross sections of cloud properties (in particular), vertical velocity, and relative humidity. An alternative analysis of cloud cover mean statistics is proposed where sharp gradients in cloud cover along the GPCI transect are taken into account. This analysis shows that the negative cloud bias of some models and ERA-40 in the stratocumulus regions [as compared to the first International Satellite Cloud Climatology Project (ISCCP)] is associated not only with lower values of cloud cover in these regimes, but also with a stratocumulus-to-cumulus transition that occurs too early along the trade wind Lagrangian trajectory. Histograms of cloud cover along the cross section differ significantly between models. Some models exhibit a quasi-bimodal structure with cloud cover being either very large (close to 100%) or very small, while other models show a more continuous transition. The ISCCP observations suggest that reality is in-between these two extreme examples. These different patterns reflect the diverse nature of the cloud, boundary layer, and convection parameterizations in the participating weather and climate prediction models.

Teixeira, J.↗

Information transfer with a twist

Holographic duals for CFTs compactified on a Riemann surface Σ with a twist are cast in the language of wedge holography. Σ starts as part of the field theory geometry in the UV and becomes part of the internal space in the IR. This allows to associate entanglement entropies with splits of the internal space in the IR geometry. Decomposing the internal space in the IR and geometrizing the corresponding subsystems separately leads to two interacting gravitational systems, similar to the intermediate holographic description in braneworld models. For Σ = T 2 the setups are used to model information transfer from a black hole to a gravitating bath. This leads to Page curves with a phase structure which precisely mirrors that in braneworld models. The transition from geometric to non-geometric entropies is also discussed for Σ = S 2 as a model for more general internal spaces in AdS/CFT.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A simulation framework for evaluating electronic order workflows in integrated health records

Electronic health record (EHR) systems are critical to modern healthcare delivery, yet the dynamic workflows that govern electronic order processing remain underexplored. Inefficiencies in these digital pathways can cause delays in care, repetitive workloads, and even patient harm. This study presents a discrete-event simulation framework used to reconstruct and evaluate EHR-based order workflows in a large integrated healthcare system. Using real-world data extracted from the Veterans Health Administration’s Corporate Data Warehouse, the authors mapped order events to standardized state transitions and modeled their progression across different facilities of varying complexity levels. After being calibrated with empirical distributions of transition times and validated against observed time-in-system metrics, the simulation demonstrates close alignment with historical performance. Scenario analyses reveal that resource capacity constraints significantly amplify the impact of electronic order surges, which are reflected in the disproportionate growth in backlogs and processing delays. Adjustments in transition probabilities further increased recirculation and extended workflow paths. Network-based analysis identified Reserved, InProgress, and Completed as structurally critical states that function as hubs within the process network but the transitions in-between also act as major bottlenecks. These results showcased the effectiveness of simulation-based approaches in monitoring EHR order processing performance and evaluating consequences of workflow changes on healthcare network resources planning. The proposed simulation framework provides a scalable data-driven tool to support operational decision-making and improve the efficiency of electronic order management in complex healthcare environments.

Engineering↗