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At least 595 records · Page 33

An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa

Hemostasis relies on a reaction network of serine proteases and their cofactors to form a blood clot. Coagulation factor IXa (protease) plays an essential role in hemostasis as evident from the bleeding disease associated with its absence. RNA aptamers specifically targeting individual coagulation factors have potential as anticoagulants and as probes of the relationship between structure and function. Here, we report X-ray structures of human factor IXa without a ligand bound to the active site either in the apo-form or in complex with an inhibitory aptamer specific for factor IXa. The aptamer binds to an exosite in the catalytic domain and allosterically distorts the active site. Our studies reveal a conformational ensemble of IXa states, wherein large movements of Trp 215 near the active site drive functional transitions between the closed (aptamer-bound), latent (apo), and open (substrate-bound) states. The latent state of the apo-enzyme may bear on the uniquely poor catalytic activity of IXa compared to other coagulation proteases. The exosite, to which the aptamer binds, has been implicated in binding VIIIa and heparin, both of which regulate IXa function. Our findings reveal the importance of exosite-driven allosteric modulation of IXa function and new strategies to rebalance hemostasis for therapeutic gain.

Science & Technology - Other Topics↗

Form-factor dependence of neutrino-nucleus cross sections using microscopic methods

To achieve its design goals, the next generation of neutrino-oscillation accelerator experiments requires percent-level predictions of neutrino-nucleus cross sections supplemented by robust estimates of the theoretical uncertainties involved. The latter arise from both approximations in solving the nuclear many-body problem and in the determination of the single- and few-nucleon quantities taken as input by many-body methods. To gauge the sensitivity of realistic nuclear many body methods to these few-nucleon quantities, we compute flux-averaged double-differential cross sections using the Green’s function Monte Carlo and spectral function methods as well as different parameterizations of the nucleon axial form factors based on either deuterium bubble-chamber data or lattice quantum chromodynamics calculations. The cross-section results are compared with available experimental data from the MiniBooNE and T2K collaborations. We also discuss the uncertainties associated with N → Δ transition form factors that enter the two-body current operator. We quantify the relations between neutrino-nucleus cross section and nucleon form factor uncertainties. These relations enable us to determine the form factor precision targets required to achieve a given cross-section precision.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Instantaneous mesh load factor ( K γ ) measurements in a wind turbine gearbox using fiber-optic strain sensors

The mesh load factor, K γ , describes how loads are shared between planet gears and has become one of the key design challenges in modern wind turbine gearboxes. Planet load sharing directly impacts tooth root stresses, a critical driver of torque density and gearbox reliability. Experimental evaluation of K γ is typically performed from sun gear tooth root strain gauge measurements, which are complex. Furthermore, such measurements can only provide an average value of load sharing. The present study describes an alternative method to evaluate the mesh load factor in wind turbine gearboxes based on fiber-optic strain sensors installed on the outer surface of the fixed ring gear. We present the results of an extensive measurement campaign to evaluate this novel sensing solution installed on the input planetary stage of a 2-MW wind turbine gearbox at the National Renewable Energy Laboratory's Flatirons Campus (Colorado, USA). The number of strain sensors on the ring gear was selected as an integer multiple of the number of planets, which has enabled an instantaneous evaluation of the mesh load factor. The effect of operating conditions on the planet load-sharing behavior of the gearbox has been investigated. The mesh load factor measured for operating conditions close to rated was below 1.05, well below IEC 61400-4 standard requirements.

17 WIND ENERGY↗

Impacts of abiotic and biotic factors on tundra productivity near Utqiaġvik, Alaska

Abstract Earlier snowmelt, warmer temperatures and herbivory are among the factors that influence high-latitude tundra productivity near the town of Utqiaġvik in northern Alaska. However, our understanding of the potential interactions between these factors is limited. MODIS observations provide cover fractions of vegetation, snow, standing water, and soil, and fractional absorption of photosynthetically active radiation by canopy chlorophyll (fAPAR chl ) per pixel. Here, we evaluated a recent time-period (2001–2014) that the tundra experienced large interannual variability in vegetation productivity metrics (i.e. fAPAR chl and APAR chl ), which was explainable by both abiotic and biotic factors. We found earlier snowmelt to increase soil and vegetation cover, and productivity in June, while warmer temperatures significantly increased monthly productivity. However, abiotic factors failed to explain stark decreases in productivity during August of 2008, which coincided with a severe lemming outbreak. MODIS observations found this tundra ecosystem to completely recover two years later, resulting in elevated productivity. This study highlights the potential roles of both climate and herbivory in modulating the interannual variability of remotely retrieved plant productivity metrics in Arctic coastal tundra ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Integrating the evidence from evidence factors in observational studies

Summary A sensitivity analysis for an observational study assesses how much bias, due to nonrandom assignment of treatment, would be necessary to change the conclusions of an analysis that assumes treatment assignment was effectively random. The evidence for a treatment effect can be strengthened if two different analyses, which could be affected by different types of biases, are both somewhat insensitive to bias. The finding from the observational study is then said to be replicated. Evidence factors allow for two independent analyses to be constructed from the same dataset. When combining the evidence factors, the Type I error rate must be controlled to obtain valid inference. A powerful method is developed for controlling the familywise error rate for sensitivity analyses with evidence factors. It is shown that the Bahadur efficiency of sensitivity analysis for the combined evidence is greater than for either evidence factor alone. The proposed methods are illustrated through a study of the effect of radiation exposure on the risk of cancer. An R package, evidenceFactors, is available from CRAN to implement the methods of the paper.

Karmakar, B.↗

Topological protection in a Landau flat band at v = 7/11, a candidate filling factor for unconventional correlations

Strong interactions in Landau flat bands are known to stabilize correlated states that do not form in other types of flat bands. We report hallmarks of topological protection at the Landau level filling factor v = 7/11 in a 2D electron system. The v = 7/11 filling factor is the particle-hole conjugate of v = 4/11⁠, a filling factor intensely studied for the possibility of realizing unconventional electronic correlations. Our data establish a new instance for an unusual fractional quantum Hall state and opens up possibilities for the study of unconventional correlations in an enlarged parameter space. We report and discuss transport signatures developing at other filling factors of interest v = 7/11, 5/8⁠, and 8/13⁠, which however in our sample do not exhibit topological protection.

composite fermions↗

Characterization of dot-specific and tunable effective g factors in a GaAs/AlGaAs double quantum dot single-hole device

Difference in g factors in multidot structures can form the basis of dot-selective spin manipulation under global microwave irradiation. Here employing electric dipole spin resonance facilitated by strong spin-orbit interaction (SOI), we observe differences in the extracted values of the single-hole effective g factors of the constituent quantum dots of a GaAs/AlGaAs double quantum dot device at the level of ~ 5 %–10%. We examine the continuous change in the hole g factor with electrical detuning over a wide range of interdot tunnel couplings and for different out-of-plane magnetic fields. The observed tendency of the quantum dot effective g factors to steadily increase on decreasing the interdot coupling or on increasing the magnetic field is attributed to the impact on the SOI of changing the dot confinement potential and heavy-hole light-hole mixing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ab initio simulations of the dynamic ion structure factor of warm dense lithium

Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible target inhomogeneities on x-ray scattering spectra.

36 MATERIALS SCIENCE↗

Factorization breaking of A d T for polarized deuteron targets in a relativistic framework

We discuss the possible factorization of the tensor asymmetry $A^T_d$ measured for polarized deuteron targets within a relativistic framework. We define a reduced asymmetry and find that factorization holds only in plane wave impulse approximation and if $p$-waves are neglected. Our numerical results show a strong factorization breaking once final state interactions are included. We also compare the $d$-wave content of the wave functions with the size of the factored, reduced asymmetry and find that there is no systematic relationship of this quantity to the d-wave probability of the various wave functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Transition form factors: γ * + p → Δ ( 1232 ) , Δ ( 1600 )

We report that electroproduction form factors describing the γ * p → Δ + ( 1232 ) , Δ + ( 1600 ) transitions are computed using a fully dynamical diquark-quark approximation to the Poincaré-covariant three-body bound-state problem in relativistic quantum field theory. In this approach, the Δ ( 1600 ) is an analogue of the Roper resonance in the nucleon sector, appearing as the simplest radial excitation of the Δ ( 1232 ) . Precise measurements of the γ * p → Δ + ( 1232 ) transition already exist on 0 ≤ Q 2 ≲ 8 GeV 2 , and the calculated results compare favorably with the data outside the meson-cloud domain. The predictions for the γ * p → Δ + ( 1600 ) magnetic dipole and electric quadrupole transition form factors are consistent with the empirical values at the real photon point, and extend to Q 2 ≈ 6 m p 2 , enabling a meaningful direct comparison with experiment once analysis of existing data is completed. In both cases, the electric quadrupole form factor is particularly sensitive to deformation of the Δ -baryons. Interestingly, while the γ * p → Δ + ( 1232 ) transition form factors are larger in magnitude than those for γ * p → Δ + ( 1600 ) in some neighborhood of the real photon point, this ordering is reversed on Q 2 ≳ 2 m p 2 , suggesting that the γ * p → Δ + ( 1600 ) transition is more localized in configuration space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Covariant calculation of a two-loop test of nonrelativistic QCD factorization

In this work we test the nonrelativistic QCD factorization conjecture for inclusive quarkonium production at two loops by carrying out a covariant calculation of the nonrelativistic quantum chromodynamics (NRQCD) long-distance matrix element (LDME) for a heavy-quark pair in an S-wave, color-octet state to fragment into a heavy-quark pair in a color-singlet state of arbitrary orbital angular momentum. The NRQCD factorization conjecture for the universality of the LDME requires that infrared divergences that it contains be independent of the direction of the Wilson line that appears in its definition. We find this to be the case in our calculation. The results of our calculation differ in some respects from those of a previous calculation that was carried out by Nayak, Qiu, and Sterman using light-cone methods. We have identified the sources of some of these differences. The results of both calculations are consistent with the NRQCD factorization conjecture. However, the general principle that underlies this confirmation of NRQCD factorization at two-loop order has yet to be revealed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Interplay between the factorization of the Jarlskog invariant and location of the solar and atmospheric resonances for neutrino oscillations in matter

The Jarlskog invariant which controls the size of intrinsic CP violation in neutrino oscillation appearance experiments is modified by Wolfenstein matter effects for neutrinos propagating in matter. In this paper we give the exact factorization of the Jarlskog invariant in matter into the vacuum Jarlskog invariant times two, two-flavor matter resonance factors that control the matter effects for the solar and atmospheric resonances independently. We compare the location of the minima of the factorizing resonance factors with the location of the solar and atmospheric resonances, precisely defined. They are not identical but the fractional differences are both found to be less than 0.1%. In addition, we explain why symmetry polynomials of the square of the mass of the neutrino eigenvalues in matter, such as inverse of the square of the Jarlskog invariant in matter, can be given as polynomials in the matter potential.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Anomaly detection in collider physics via factorized observables

To maximize the discovery potential of high-energy colliders, experimental searches should be sensitive to unforeseen new physics scenarios. This goal has motivated the use of machine learning for unsupervised anomaly detection. In this paper, we introduce a new anomaly detection strategy called : factorized observables for regressing conditional expectations. Our approach is based on the inductive bias of factorization, which is the idea that the physics governing different energy scales can be treated as approximately independent. Assuming factorization holds separately for signal and background processes, the appearance of nontrivial correlations between low- and high-energy observables is a robust indicator of new physics. Under the most restrictive form of factorization, a machine-learned model trained to identify such correlations will in fact converge to the optimal new physics classifier. We test on a benchmark anomaly detection task for the Large Hadron Collider involving collimated sprays of particles called jets. By teasing out correlations between the kinematics and substructure of jets, our method can reliably extract percent-level signal fractions. This strategy for uncovering new physics adds to the growing toolbox of anomaly detection methods for collider physics with a complementary set of assumptions. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Breakdown of collinear factorization in the exclusive photoproduction of a π 0 γ pair with large invariant mass

We study the exclusive photoproduction of a π 0 γ pair with large invariant mass M γ π 2 , which is sensitive to the exchange of either two quarks or two gluons in the t channel. In this paper, we show that the process involving two-gluon exchanges does factorize in the Bjorken limit at the leading twist. This can be explicitly demonstrated by the fact that there exist diagrams, which contribute at the leading twist, for which are , due to the pinching of the contour integration of the plus and minus component of the Glauber gluon momentum. For the same reason, π 0 -nucleon scattering to two photons also suffers from the same issue. On the other hand, we stress that there are no issues with respect to collinear factorization for the quark channels. By considering an analysis of all potential reduced diagrams of leading pinch-singular surfaces, we argue that the quark channel is safe from Glauber pinches, and therefore, a collinear factorization in that case follows through without any problems. This means that processes where gluon exchanges are forbidden, such as the exclusive photoproduction of π ± γ and ρ 0 , ± γ , are unaffected by the factorization breaking effects we point out in this paper. Published by the American Physical Society 2025

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Up, down, and strange nucleon axial form factors from lattice QCD

Here, we report a calculation of the nucleon axial form factors $G_A^q(Q^2)$ and $G_P^q(Q^2)$ for all three light quark flavors $q\in\{u,d,s\}$ in the range $0\leq Q^2\lesssim 1.2\text{ GeV}^2$ using lattice QCD. Our work was done using a single ensemble with pion mass 317 MeV and made use of the hierarchical probing technique to efficiently evaluate the required disconnected loops. We perform nonperturbative renormalization of the axial current, including a nonperturbative treatment of the mixing between light and strange currents due to the singlet-nonsinglet difference caused by the axial anomaly. The form factor shapes are fit using the model-independent $z$ expansion. From $G_A^q(Q^2)$, we determine the quark contributions to the nucleon spin and axial radii. By extrapolating the isovector $G_P^{u-d}(Q^2)$, we obtain the induced pseudoscalar coupling relevant for ordinary muon capture and the pion-nucleon coupling constant. We also found that the disconnected contributions to $G_P$ form factors are large, and give an interpretation based on the dominant influence of the pseudoscalar poles in these form factors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measurement of Conduction and Valence Bands g -Factors in a Transition Metal Dichalcogenide Monolayer

The electron valley and spin degree of freedom in monolayer transition-metal dichalcogenides can be manipulated in optical and transport measurements performed in magnetic fields. The key parameter for determining the Zeeman splitting, namely, the separate contribution of the electron and hole g factor, is inaccessible in most measurements. Here we present an original method that gives access to the respective contribution of the conduction and valence band to the measured Zeeman splitting. It exploits the optical selection rules of exciton complexes, in particular the ones involving intervalley phonons, avoiding strong renormalization effects that compromise single particle g -factor determination in transport experiments. These studies yield a direct determination of single band g factors. We measure g c1 = 0.86 ± 0.1, g c2 = 3.84 ± 0.1 for the bottom (top) conduction bands and g v = 6.1 ± 0.1 for the valence band of monolayer WSe 2 . These measurements are helpful for quantitative interpretation of optical and transport measurements performed in magnetic fields. In addition, the measured g factors are valuable input parameters for optimizing band structure calculations of these 2D materials.

36 MATERIALS SCIENCE↗

Nucleation of stoichiometric compounds from liquid: Role of the kinetic factor

The nucleation rate depends on the free-energy barrier and the kinetic factor. While the role of the free energy barrier is a text-book subject, the importance of the kinetic factor is frequently underestimated. Here in this study, we applied the mean first-passage time method, to obtain the free-energy landscape and kinetic factor directly from the molecular dynamics (MD) simulations of the nucleation of the face-centered cubic (fcc) phase in the pure Ni and the B2 phases in the Ni 50 Al 50 and Cu 50 Zr 50 alloys. The obtained data show that while the free-energy barrier for nucleation is higher in pure Ni the nucleation rate is considerably lower in the Ni 50 Al 50 alloy. This result can be explained by the slow attachment kinetics in the N i 50 A l 50 alloy, which was related to the ordered nature of the B2 phase. Even smaller fraction of the antisite defects in the C u 50 Z r 50 alloy leads to such a slow attachment kinetics that the nucleation is never observed for this alloy in the course of the MD simulation. Finally, this is consistent with the experimental facts that the Cu 50 Zr 50 alloy is a good glass forming alloy and the Ni 50 Al 50 alloy is not. Thus the present study demonstrates that the atom attachment rate can be the critical factor that controls the nucleation process under certain conditions.

36 MATERIALS SCIENCE↗

Beyond integration: modeling every pixel to obtain better structure factors from stills

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (10 4 -10 6 ) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb 3+ L -III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.

59 BASIC BIOLOGICAL SCIENCES↗