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At least 793 records · Page 44

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗

Constraints and variation in food web link-species space

Predicting food web structure in future climates is a pressing goal of ecology. These predictions may be impossible without a solid understanding of the factors that structure current food webs. Here, the most fundamental aspect of food web structure—the relationship between the number of links and species—is still poorly understood. Some species interactions may be physically or physiologically ‘forbidden'—like consumption by non-consumer species—with possible consequences for food web structure. We show that accounting for these ‘forbidden interactions' constrains the feasible link-species space, in tight agreement with empirical data. Rather than following one particular scaling relationship, food webs are distributed throughout this space according to shared biotic and abiotic features. Our study provides new insights into the long-standing question of which factors determine this fundamental aspect of food web structure.

59 BASIC BIOLOGICAL SCIENCES↗

Rapidity-dependent spin decomposition of the nucleon

We revisit the two-dimensional Fourier transform of generalized parton distributions (GPDs) at nonzero skewness. At 𝜂 = 0 it reduces to the standard impact-parameter density, while at 𝜂 ≠ 0 it is an off-forward amplitude that we interpret as a genuine parton–nucleon correlation. Its overall strength (the transverse-plane integral of the density) is fixed by the GPD at the kinematic point 𝑡 =−𝑐 𝜂 =−4⁢𝜂 2 ⁢𝑚$^{2}_{𝑁}$/(1 − 𝜂 2 ) and decreases monotonically with the rapidity gap Δ⁢𝑦 = ln⁡[(1+𝜂)/(1−𝜂)] = 2 artanh⁡(𝜂). This rapidity dependence implies rapidity-modified Ji identities that connect helicity, orbital, and total angular momenta of the correlation in closed form. To quantify these effects, we construct leading-twist quark and gluon GPDs in a string-based conformal framework: conformal moments are parametrized by linear open- and closed-string Regge trajectories with slopes constrained by parton distribution functions (PDFs), hadron/glueball spectroscopy, and form-factor data, and GPDs are reconstructed over the full (𝑥,𝜂,𝑡) domain by Mellin-Barnes inversion with next-to-leading order evolution. We find qualitative agreement (and fair quantitative agreement within quoted uncertainties) for several moments and selected nonsinglet 𝑥-space channels at 𝜇 = 2 GeV when compared with lattice QCD, while we also identify channels with visible tension and discuss likely sources (PDF priors and 𝑡-slope systematics).

Gauge-gravity dualities↗

Pressure-induced 𝐵⁢1 to 𝐵⁢2 phase transition in CeN studied by 𝑎⁢𝑏 𝑖⁢𝑛⁢𝑖⁢𝑡⁢𝑖⁢𝑜 correlation matrix renormalization theory calculations

We apply correlation matrix renormalization theory (CMRT) to cerium nitride (CeN) under pressure. For 𝐵⁢1 (NaCl-type) phase, CMRT gives an equation of state consistent with ambient pressure experiments. It produces electronic density-of-state (DOS) characterized by a sharp 4⁢𝑓 quasiparticle resonance peak pinned at the Fermi level and two subbands formed by strong hybridization between the localized Ce-4⁢𝑓 electrons and the itinerant Ce-5⁢𝑑 and N-2⁢𝑝 electrons below the Fermi level, consistent with x-ray photoemission spectroscopy experiments. Upon compression, CMRT predicts a first-order 𝐵⁢1 → 𝐵⁢2 (CsCl-type) transition with ∼11% volume collapse in agreement with experiments. Across the transition, the 4⁢𝑓 spectrum broadens, the 4⁢𝑓 orbital occupancy increases, and the hybridization with conduction states enhances, signaling a crossover from partially localized to more itinerant 4⁢𝑓 behavior. Furthermore, these features are in excellent agreement with experimental observations, demonstrating that CMRT provides a parameter-free description and prediction of correlation-driven structural and electronic transitions in rare-earth compounds.

Ab initio calculations↗

182 W (𝑛,2⁢𝑛)⁢ 181 W cross-section data from threshold to 15 MeV

Measurements of the 182 W(n, 2n) 181 W cross section have been performed in the neutron energy range between 8 and 15 MeV using the activation technique. Such data are needed to help interpret results of laser shots at the National Ignition Facility using a new DT capsule design, featuring a high-Z inner shell, with tungsten as the favored material, and an outer shell made of a low-Z material. Our data are in very good agreement with the previous data of Frehaut et al., which are based on a different technique, and in fair agreement with the ENDF/B-VIII.0 and the JEFF-3.3 evaluations.

150 ≤ A ≤ 189↗

Missing baryons recovered: A measurement of the gas fraction in galaxies and groups with the kinematic Sunyaev-Zel’dovich effect and CMB lensing

We present new constraints on the halo masses and matter density profiles of DESI galaxy groups by cross-correlating samples of luminous red galaxies (LRGs) and bright galaxy survey (BGS) galaxies with the publicly available CMB lensing convergence map from ACT DR6. This provides an independent, lensing-based calibration of halo masses, complementary to methods relying on clustering or dynamics. We derive constraints on the mean halo mass for three DESI-selected samples, finding log⁡(𝑀 halo /(𝑀 ⊙ /ℎ)) ≈ 13.18, 13.03 and 13.02 for the main LRG, extended LRG, and BGS samples, respectively. Using a halo model approach, we also compare the projected galaxy-matter density profiles with previously reported gas profiles inferred from measurements of the kinematic Sunyaev-Zel’dovich (kSZ) effect. This work addresses one of the key uncertainties in interpreting kSZ signals—the unknown host halo mass distribution—by providing an independent and consistent mass calibration. The agreement between the gas and total mass profiles at large aperture suggests that sufficiently far from the group center (2–3 virial radii), we recover all the baryons, offering a resolution to the missing baryon problem. We further study the cumulative gas fractions for all galaxies as well as for the most massive galaxy groups in the sample [log⁡(𝑀 halo /(𝑀 ⊙ /ℎ)) ≈ 13.5], finding values that are physically sensible and in agreement with previous findings using kSZ and x-ray data: compared to the TNG300 simulation, the observed gas fractions are systematically lower at fixed radius by ≳ 4⁢𝜎, providing compelling, independent evidence for stronger baryonic feedback in the real Universe. These findings highlight the power of combining CMB lensing with galaxy surveys to probe the interplay between baryons and dark matter in group-sized halos.

Hadzhiyska, Boryana [Lawrence Berkeley National La↗

Multichannel photoelectron phase lag across atomic barium autoionizing resonances

Phase lag associated with coherent control where an excited system decays into more than one product channel has been subjected to numerous investigations. Although previous theoretical studies have treated the phase lag across resonances in model calculations, quantitative agreement has never been achieved between the theoretical model and an experimental measurement of the phase lag from the ω-2ω ionization of atomic barium. Yamazaki and Elliot, Phys. Rev. Lett. 98, 053001 (2007); Phys. Rev. A 76, 053401 (2007), suggesting that a toy model with phenomenological parameters is inadequate to describe the observed phase lag behavior. Here the phase lag is treated quantitatively in a multichannel coupling formulation, and our calculation based on a multichannel quantum defect and R-matrix treatment achieves good agreement with the experimental observations. Our treatment also develops formulas to describe the effects of hyperfine depolarization on multiphoton ionization processes. Moreover, we identify resonances between Ba + 5d 3/2 and 5d 5/2 thresholds that have apparently never been experimentally observed and classified.

74 ATOMIC AND MOLECULAR PHYSICS↗

All-electron, density-functional-based method for angle-resolved tunneling ionization in the adiabatic regime

Here we develop and test a method that integrates many-electron weak-field asymptotic theory (ME-WFAT) [O. I. Tolstikhin, L. B. Madsen, and T. Morishita, Phys. Rev. A 89, 013421 (2014)] in the integral representation (IR) into the density-functional-theory (DFT) framework. In particular, we present modifications of the integral formula in the IR ME-WFAT to incorporate the potential terms unique to DFT. By solving an adiabatic rate equation for the angle-resolved ionization yield in our DFT-based ME-WFAT method, we show that the results are in excellent agreement with those of real-time time-dependent density-functional-theory (TDDFT) simulations for NO, OCS, C⁢H 3 ⁢Br, and C⁢H 3 ⁢Cl interacting with one- and two-color laser fields with a fundamental wavelength of 800 nm. This agreement is significant because the WFAT calculations take only a small fraction of the time of full TDDFT calculations. These results suggest that in the wavelength region commonly used in strong-field experiments (800 nm and longer), our DFT-based WFAT treatment can be used to rapidly screen for the ionization properties of a large number of molecules as a function of alignment or orientation between the molecule and the strong field.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nature of polariton transport in a Fabry-Perot cavity

Fabry-Perot microcavities can strongly enhance interactions between light and molecules, leading to the formation of hybrid light-matter states known as polaritons. Polaritons possess much smaller effective masses and much larger group velocities when the molecules are resonant with cavity modes that have finite (nonzero) in-plane wave vectors, giving rise to the possibilities of long-range and ultrafast ballistic transport. In this paper, we present the results of numerical simulations of the ultrafast ballistic transport phenomenon in real space and time during and after initialization with a short, spatially localized pulse. Here, we address this problem with two approaches: the standard transfer-matrix method (TMM) for planar structures and a second simulation based on the numerical solution of the Maxwell-Bloch equations that can be used for general configurations (complex metasurfaces, for instance) and excitation modes. The agreement between the TMM and the full numerical calculation with the Maxwell-Bloch equations when applied to multilayer planar configurations provides proof of the validity of both approaches for the present analyses. Overall, we find that the transport of the molecular excitons inside the cavity synchronize with the evolution of the enhanced electromagnetic field inside the cavity. Moreover, the synchronized transport rate is in good agreement with the group velocities predicted from a calculated dispersion relation across a wide range of frequencies. Finally, we relate the group velocity to the Hopfield coefficient obtained from quantum modeling and suggest that the dependence of light-matter coupling on the in-plane wave vector can be an important but overlooked factor for understanding the transport behavior of polaritons. These simulations provide an intuitive tool for understanding the collective motion of light and excitons and helps us to better understand how experimental observations of polaritons should be interpreted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Band gap renormalization, carrier mobilities, and the electron-phonon self-energy in crystalline naphthalene

Organic molecular crystals are expected to feature appreciable electron-phonon interactions that influence their electronic properties at zero and finite temperature. Here, we report first-principles calculations and an analysis of the electron-phonon self-energy in naphthalene crystals. We compute the zero-point renormalization and temperature dependence of the fundamental band gap, and the resulting scattering lifetimes of electronic states near the valence- and conduction-band edges employing density functional theory. Further, our calculated phonon renormalization of the GW-corrected quasiparticle band structure predicts a fundamental band gap of 5 eV for naphthalene at room temperature, in good agreement with experiments. From our calculated phonon-induced electron lifetimes, we obtain the temperature-dependent mobilities of electrons and holes in good agreement with experimental measurements at room temperature. Finally, we show that an approximate energy self-consistent computational scheme for the electron-phonon self-energy leads to the prediction of strong satellite bands in the electronic band structure. We find that a single calculation of the self-energy can reproduce the self-consistent results of the band gap renormalization and electrical mobilities for naphthalene, provided that the on-the-mass-shell approximation is used, i.e., if the self-energy is evaluated at the bare eigenvalues.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Direct observation of the momentum distribution and renormalization factor in lithium

We have measured the momentum distribution and renormalization factor $Z_{k_F}$ in liquid and solid lithium by high-resolution Compton scattering. High-resolution data over a wide momentum range exhibit a clear feature of the renormalization and a sharp drop of momentum densities at the Fermi momentum $k_F$. In this work, these results are compared with those computed by quantum Monte Carlo simulation performed both on a disordered crystal and a liquid exhibiting very good agreement. Asymptotic behavior of the experimental and theoretical momentum distributions are examined to estimate $Z_{k_F}$. The experimentally obtained $Z_{k_F} = 0.43^{+0.11}_{–0.01}$ for liquid Li and $0.54^{+0.11}_{–0.02}$ for solid Li are in good agreement with theoretical results of 0.54 ± 0.01 and 0.64 ± 0.01, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Experimental observation of magnetic dimers in diluted Yb:YAlO 3

In this paper, we present a comprehensive experimental investigation of Yb magnetic dimers in Yb 0.04 Y 0.96 AlO 3 , an Yb-doped yttrium aluminum perovskite YAlO3, by means of specific heat, magnetization, and high-resolution inelastic neutron scattering (INS) measurements. In our sample, the Yb ions are randomly distributed over the lattice and ~7% of Yb ions form quantum dimers due to nearest-neighbor antiferromagnetic coupling along the c axis. At zero field, the dimer formation manifests itself in an appearance of an inelastic peak at Δ ≈ 0.2 meV in the INS spectrum and a Schottky-like anomaly in the specific heat. The structure factor of the INS peak exhibits a cosine modulation along the $L$ direction, in agreement with the $c$-axis nearest-neighbor intradimer coupling. A careful fitting of the low-temperature specific heat shows that the excited state is a degenerate triplet, which indicates a surprisingly small anisotropy of the effective Yb-Yb exchange interaction despite the low crystal symmetry and anisotropic magnetic dipole contribution, in agreement with previous reports for the Yb parent compound, YbAlO 3 , and in contrast to Yb 2 Pt 2 Pb. The obtained results are precisely reproduced by analytical calculations for the Yb dimers.

36 MATERIALS SCIENCE↗

Temperature-dependent phonon lifetimes and thermal conductivity of silicon by inelastic neutron scattering and ab initio calculations

In this paper, inelastic neutron scattering on a single crystal of silicon was performed at temperatures from 100 to 1500 K. These experimental data were reduced to obtain phonon spectral intensity at all wave vectors $\overset{→}{Q}$ and frequencies ω in the first Brillouin zone. Thermal broadenings of the phonon peaks were obtained by fitting and by calculating with an iterative ab initio method that uses thermal atom displacements on an ensemble of superlattices. Agreement between the calculated and experimental broadenings was good, with possible discrepancies at the highest temperatures. Distributions of phonon widths versus phonon energy had similar shapes for computation and experiment. These distributions grew with temperature but maintained similar shapes. Parameters from the ab initio calculations were used to obtain the thermal conductivity from the Boltzmann transport equation, which was in good agreement with experimental data. Despite the high group velocities of longitudinal acoustic phonons, their shorter lifetimes reduced their contribution to the thermal conductivity, which was dominated by transverse acoustic modes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Measurement of the sound velocity and Grüneisen parameter of polystyrene at inertial confinement fusion conditions

The principal Hugoniot, sound velocity, and Grüneisen parameter of polystyrene were measured at conditions relevant to shocks in inertial confinement fusion implosions, from 100 to 1000 GPa. The sound velocity is in good agreement with quantum molecular dynamics calculations and all tabular equation of state models at pressures below 200 GPa. Above 200 GPa, the experimental results agree with two of the examined tables, but do not agree with the most recent table developed for design of ICF experiments. The Grüneisen parameter increases with density below ~3.1 g/cm 3 and approaches the asymptotic value for an ideal gas after complete dissociation. This behavior is in good agreement with quantum molecular dynamics results and previous work but is not represented by any of the tabular models. Finally, the discrepancy between tabular models and experimental measurement of the sound velocity and Grüneisen parameter is sufficient to impact simulations of ICF experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Cohesion and excitations of diamond-structure silicon by quantum Monte Carlo: Benchmarks and control of systematic biases

We have carried out quantum Monte Carlo (QMC) calculations of silicon crystal focusing on the accuracy and systematic biases that affect the electronic structure characteristics. The results show that 64 and 216 atom supercells provide an excellent consistency for extrapolated energies per atom in the thermodynamic limit for ground, excited, and ionized states. We have calculated the ground state cohesion energy with both systematic and statistical errors below ≈ 0.05 eV. The ground state exhibits a fixed-node error of only 1.3(2)% of the correlation energy, suggesting an unusually high accuracy of the corresponding single-reference trial wave function. We obtain a very good agreement between optical and quasiparticle gaps that affirms the marginal impact of excitonic effects. Our most accurate results for band gaps differ from the experiments by about 0.2 eV. This difference is assigned to a combination of residual finite-size and fixed-node errors. In conclusion, we have estimated the crystal Fermi level referenced to vacuum that enabled us to calculate the edges of valence and conduction bands in agreement with experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High-pressure phase diagram of beryllium from ab initio free-energy calculations

In this report we use first-principles molecular dynamics simulations coupled with the thermodynamic integration method to study the hexagonal close-packed (hcp) to body-centered cubic (bcc) transition and melting of beryllium up to a pressure of 1600 GPa. We derive the melting line by equating solid and liquid Gibbs free energies and represent it by a Simon-Glatzel fit T m = 1564 K [1 + P/(15.6032 GPa)] 0.383 , which is in good agreement with previous two-phase simulations <6000 K. We also derive the hcp-bcc solid-solid phase boundary and show that the quasiharmonic approximation underestimates the stability of the hcp structure, predicting lower transition pressures between hcp and bcc phases. Our results are consistent with the stability regime predicted by the phonon quasiparticle method. We also predict that the hcp-bcc-liquid triple point is located at 164.7 GPa and 4314 K. In addition, we compute the shock Hugoniot curve and show that it is in good agreement with experiments, intersecting our derived melting curve at ~235 GPa and 4900 K. Finally, we make predictions for future ramp compression experiments. Starting with an isentropic compression of the liquid, we predict the path to intersect the melting line at low pressure and temperature, then to continue along the melting line over a large temperature interval of 7000 K as the sample remains in the mixed solid-liquid state before it enters the solid phase.

36 MATERIALS SCIENCE↗

Real-space representation of the quasiparticle self-consistent GW self-energy and its application to defect calculations

The quasiparticle self-consistent (QS) GW (G for Green's function, W for screened Coulomb interaction) approach incorporates the corrections of the quasiparticle energies from their Kohn-Sham density functional theory (DFT) eigenvalues by means of an energy-independent and Hermitian self-energy matrix usually given in the basis set of the DFT eigenstates. By expanding these into an atom-centered basis set (specifically here the linearized muffin-tin orbitals) a real space representation of the self-energy corrections becomes possible. In this work, We show that this representation is relatively short-ranged. This offers opportunities to construct the self-energy of a complex system from parts of the system by a cut-and-paste method. Specifically for a point defect, represented in a large supercell, the self-energy can be constructed from those of the host and a smaller defect-containing cell. The self-energy of the periodic host can be constructed simply from a GW calculation for the primitive cell. We show for the case of the As Ga in GaAs that the defect part can already be well represented by a minimal eight-atom cell and allows us to construct the self-energy for a 64-atom cell in good agreement with direct QSGW calculations for the large cell. Using this approach to an even larger 216-atom cell shows the defect band approaches an isolated defect level. The calculations also allow us to identify a second defect band which appears as a resonance near the conduction band minimum. The results on the extracted defect levels agree well with Green's function calculations for an isolated defect and with experimental data.

36 MATERIALS SCIENCE↗

Assessing the accuracy of compound formation energies with quantum Monte Carlo

Accurately predicting the formation energy of a compound, which describes its thermodynamic stability, is a key challenge in materials physics. Here, we employ a many-body quantum Monte Carlo (QMC) with single-reference trial functions to compute the formation energy of two electronically disparate compounds, the intermetallic VPt2 and the semiconductor CuI, for which standard density functional theory (DFT) predictions using both the Perdew-Burke-Ernzerhof (PBE) and the strongly constrained and appropriately normed (SCAN) density functional approximations deviate markedly from available experimental values. For VPt2, we find an agreement between QMC, SCAN, and PBE0 estimates, which therefore remain in disagreement with the much less exothermic experimental value. For CuI, the QMC result agrees with neither SCAN nor PBE pointing towards DFT exchange-correlation biases, likely related to the localized Cu 3d electrons. Compared to the behavior of some density functional approximations within DFT, spin-averaged QMC exhibits a smaller but still appreciable deviation when compared to experiment. The QMC result is slightly improved by incorporating spin-orbit corrections for CuI and solid I 2 , so that experiment and theory are brought into imperfect but reasonable agreement within about 120 meV/atom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗