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At least 1,603 records · Page 89

Benchmarking Quantum Chemistry Computations with Variational, Imaginary Time Evolution, and Krylov Space Solver Algorithms

Quantum chemistry is a key application area for noisy-intermediate scale quantum (NISQ) devices, and therefore serves as an important benchmark for current and future quantum computer performance. Previous benchmarks in this field have focused on variational methods for computing ground and excited states of various molecules, including a benchmarking suite focused on the performance of computing ground states for alkali-hydrides under an array of error mitigation methods. State-of-the-art methods to reach chemical accuracy in hybrid quantum-classical electronic structure calculations of alkali hydride molecules on NISQ devices from IBM are outlined here. Here it is demonstrated how to extend the reach of variational eigensolvers with symmetry preserving Ansätze. Next, it is outlined how to use quantum imaginary time evolution and Lanczos as a complementary method to variational techniques, highlighting the advantages of each approach. Finally, a new error mitigation method is demonstrated which uses systematic error cancellation via hidden inverse gate constructions, improving the performance of typical variational algorithms. These results show that electronic structure calculations have advanced rapidly, to routine chemical accuracy for simple molecules, from their inception on quantum computers a few short years ago, and they point to further rapid progress to larger molecules as the power of NISQ devices grows.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On the penetration of a hot diapir through a strongly temperature-dependent viscosity medium

The ascent of a hot spherical body through a fluid with a strongly temperature-dependent viscosity has been studied using an axisymmetric finite element method. Numerical solutions range over Peclet numbers of 0.1 - 1000 from constant viscosity up to viscosity variations of 100,000. Both rigid and stress-free boundary conditions were applied at the surface of the sphere. The dependence of drag on viscosity variation was shown to have no dependence on the stress boundary condition except for a Stokes flow scaling factor. A Nusselt number parameterization based on the stress-free constant viscosity functional dependence on the Peclet number scaled by a parameter depending on the viscosity structure fits both stress-free and rigid boundary condition data above viscosity variations of 100. The temperature scale height was determined as a function of sphere radius. For the simple physical model studied in this paper pre-heating is required to reduce the ambient viscosity of the country rock to less than 10 to the 22nd sq cm/s in order for a 10 km diapir to penetrate a distance of several radii.

Daly, S. F.↗

High-Speed X-Ray Stereo Digital Image Correlation in a Shock Tube

X-ray stereo digital image correlation (DIC) measurements were performed at 10 kHz on the internal surface of a jointed structure in a shock tube at a shock Mach number of 1.42 and compared with optical stereo DIC measurements on the outer, visible surface of the structure. The shock tube environment introduces temperature and density gradients in the gas through which the structure was imaged, resulting in spatial and temporal index of refraction variations. These variations cause bias errors in optical DIC measurements due to beam-steering but have minimal influence on x-ray DIC measurements. These results demonstrate the utility of time-resolved x-ray DIC measurements in complicated environments where optical measurements suffer severe errors and/or are precluded by lack of optical access.

42 ENGINEERING↗

Recurrent modulation of galactic cosmic rays and the anomalous helium

The observations of 27 day variations in the intensity of low energy cosmic ray protons (29-67 MeV) and anomalous helium (11-20 MeV/nucleon) are reported. These observations were made with instruments on IMP-8 in the earth orbit on Pioneer 11 at heliographic latitudes up to 16 deg and on Pioneer 10 at heliocentric distances of from 4 to 14 AU. 27 day variations are observed at all locations, most strongly in the anomalous helium, and reflect the very large scale structure of the interplanetary medium. Intensity minima are most often associated with high speed solar wind streams, but the physical mechanism producing the variations is not clear.

Bastian, T. S.↗

Investigation of Tropical Dynamics and Transport with UARS Data

Our research focused on Kelvin waves in the tropical lower stratosphere, and resulted in three papers published or submitted to the Journal of Geophysical Research. The first of these, published in 2002, used temperature data from the Microwave Limb Sounder to examine the amplitude, frequency, phase, and spatial structure of leading modes of Kelvin waves. The second and third, submitted late in 2002 and currently in revision, described the response to Kelvin waves of various trace constituents measured by MLS and CLAES (methane, nitrous oxide, CFC-12, and ozone in the second paper; water vapor in the third paper). Water vapor is a special case because the vertical structure induced by Kelvin waves is convolved with water vapor's seasonally varying vertical profile induced by seasonal variations in temperature at the tropical tropopause. Forward modeling indicated that the vertical resolution of MLS was indeed adequate to capture this complicated structure, yet it was not visible in the MLS data, though the Kelvin wave signature was clear on certain UARS levels. The effects of Kelvin waves on the tropical tropopause and on stratosphere- troposphere exchange cannot be quantified from UARS data because of poor vertical resolution and sensitivity in that region. It is recommended that this analysis be repeated using data from the new MLS and HIRDLS instruments aboard Aura, and that priority be given to fine-scale retrievals of temperature, water vapor, and ozone in the tropical tropopause region.

Jackman, Charles↗

Multiwavelength anomalous X-ray diffraction for combined imaging of atomic displacement and strain

The X-ray Bragg coherent diffractive imaging (CDI) technique assumes that the structure factor holds constant over the measured crystal. This approximation breaks down for materials exhibiting variations in the unit-cell configuration, such as piezo- and ferroelectrics. In that case, the strain field cannot be reliably determined from the reconstruction because the lattice deformation and the structure factor contribute concomitantly. Proposed here is a solution to this problem achieved by combining Bragg CDI and the multiwavelength anomalous diffraction approach that measures a Friedel pair of reflections at two different photon energies near an absorption edge. Comparing the obtained reconstructions with a parametric model that includes calculating the scattering amplitude as a function of wavelength and the unit-cell configuration, the contributions of the lattice deformation and the structure factor are separated. Simulations of the ferroelectric material BaTiO 3 demonstrate the possibility of simultaneous probing of the strain and displacement of the Ti atoms. The proposed method opens up an opportunity to apply coherent X-ray diffraction for nanoscale-resolved 3D mapping of polarization domains in micro- and nanocrystals.

lattice deformation↗

Space Shuttle guidance for multiple main engine failures during first stage

This paper presents contingency abort guidance schemes recently developed for multiple Space Shuttle main engine failures during the first two minutes of flight (first stage). The ascent and entry guidance schemes greatly improve the possibility of the crew and/or the Orbiter surviving a first stage contingency abort. Both guidance schemes were required to meet certain structural and controllability constraints. In addition, the systems were designed with the flexibility to allow for seasonal variations in the atmosphere and wind. The ascent scheme guides the vehicle to a desirable, lofted state at solid rocket booster burnout while reducing the structural loads on the vehicle. After Orbiter separation from the solid rockets and the external tank, the entry scheme guides the Orbiter through one of two possible entries. If the proper altitude/range/velocity conditions have been met, a return-to-launch-site 'Split-S' maneuver may be attempted. Otherwise, a down-range abort to an equilibrium glide and subsequent crew bailout is performed.

Sponaugle, Steven J.↗

High-resolution seismic reflection survey at the Manson crater, Iowa

Approximately 17.4 km of high-resolution reflection data were acquired along an east-west radius of the Manson Impact Structure (MIS) to delineate the shallow (upper 300 m) subsurface structural configuration. The geometry of the shallow structure is poorly known due to a 30-90 m thick Pleistocene till cover. The resolution of the new seismic data is roughly 5-10 times that of existing Vibroseis data. Data quality varies rapidly along the line from exceptional to poor, due primarily to velocity variations associated with the geological complexity of the area. Preliminary results indicate subsurface structural blocks previously envisioned to be several hundreds of meters in size are actually an order of magnitude smaller and more complex. A seismogram-by-seismogram analysis is necessary to confidently identify intricate stratigraphic and structural relationships seen on preliminary CDP sections, as numerous faults, diffractions, and complicated reflection patterns create potential pitfalls.

Keiswetter, D. A.↗

Impact of storage and extraction methods on peat soil microbiomes

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modifiedPowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations.

Science & Technology - Other Topics↗

Quantum computation of silicon electronic band structure

Development of quantum architectures during the last decade has inspired hybrid classical–quantum algorithms in physics and quantum chemistry that promise simulations of fermionic systems beyond the capability of modern classical computers, even before the era of quantum computing fully arrives. Strong research efforts have been recently made to obtain minimal depth quantum circuits which could accurately represent chemical systems. Here, we show that unprecedented methods used in quantum chemistry, designed to simulate molecules on quantum processors, can be extended to calculate properties of periodic solids. In particular, we present minimal depth circuits implementing the variational quantum eigensolver algorithm and successfully use it to compute the band structure of silicon on a quantum machine for the first time. We are convinced that the presented quantum experiments performed on cloud-based platforms will stimulate more intense studies towards scalable electronic structure computation of advanced quantum materials.

36 MATERIALS SCIENCE↗

Wake Structure Induced by Seal Whisker: Effects of Angle of Incidence

Seal whiskers have been found to produce unique wake flow structures that minimize self-induced vibration and reduce drag. The cause of these wake features are due to the peculiar three-dimensional morphology of the whisker surface. The whisker can be defined as an elliptical cross section with variation in the major and minor axis of the ellipse along the length of the whisker as well as rotation of the elliptical plane with respect to the whisker axis, angle of incidence. While the effects of several dominant parameters of the whisker morphology have been studied, the effect of the rotation of the elliptical plane has not been well understood. This paper will examine the influence of the angle of incidence on the wake flow structure through series of water channel studies. Several models of whisker-like geometries will be tested which isolate the rotation angle as the only variation between models. The wake structure behind each seal whisker model will be measured through particle image velocimetry (PIV). The different models’ wake structures will be compared identifying the effect of angle of incidence on the wake structure. Angle of incidence was found to influence the wake structure through reorganization of velocity patterns, reduction of recovery length and modification of magnitude of Tu. These results help provide a more complete understanding of the seal whisker geometry relationship to wake structure and can provide insight into design practices for application of whisker geometery to various engineering problems.

vortex induced vibration↗

Invasion and rapid adaptation of guppies ( Poecilia reticulata ) across the Hawaiian Archipelago

How much does natural selection, as opposed to genetic drift, admixture, and gene flow, contribute to the evolution of invasive species following introduction to a new environment? Here we assess how evolution can shape biological invasions by examining population genomic variation in non-native guppies (Poecilia reticulata) introduced to the Hawaiian Islands approximately a century ago. By examining 18 invasive populations from four Hawaiian islands and four populations from the native range in northern South America, we reconstructed the history of introductions and evaluated population structure as well as the extent of ongoing gene flow across watersheds and among islands. Patterns of differentiation indicate that guppies have developed significant population structure, with little natural or human-mediated gene flow having occurred among populations following introduction. Demographic modeling and admixture graph analyses together suggest that guppies were initially introduced to O‘ahu and Maui and then translocated to Hawai‘i and Kaua‘i. We detected evidence for only one introduction event from the native range, implying that any adaptive evolution in introduced populations likely utilized the genetic variation present in the founding population. Environmental association tests accounting for population structure identified loci exhibiting signatures of adaptive variation related to predators and landscape characteristics but not nutrient regimes. When paired with high estimates of effective population sizes and detectable population structure, the presence of environment-associated loci supports the role of natural selection in shaping contemporary evolution of Hawaiian guppy populations. Our findings indicate that local adaptation may engender invasion success, particularly in species with life histories that facilitate rapid evolution. Finally, evidence of low gene flow between populations suggests that removal could be an effective approach to control invasive guppies across the Hawaiian archipelago.

59 BASIC BIOLOGICAL SCIENCES↗

The characteristics of atmospheric boundary layer height over the Arctic Ocean during MOSAiC

The important roles that the atmospheric boundary layer (ABL) plays in the central Arctic climate system have been recognized, but the atmospheric boundary layer height (ABLH), defined as the layer of continuous turbulence adjacent to the surface, has rarely been investigated. Using a year-round radiosonde dataset during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition, we improve a Richardson-number-based algorithm that takes cloud effects into consideration and subsequently analyze the characteristics and variability of the ABLH over the Arctic Ocean. The results reveal that the annual cycle is clearly characterized by a distinct peak in May and two respective minima in January and July. This annual variation in the ABLH is primarily controlled by the evolution of the ABL thermal structure. Temperature inversions in the winter and summer are intensified by seasonal radiative cooling and warm-air advection with the surface temperature constrained by melting, respectively, leading to the low ABLH at these times. Meteorological and turbulence variables also play a significant role in ABLH variation, including the near-surface potential temperature gradient, friction velocity, and turbulent kinetic energy (TKE) dissipation rate. In addition, the MOSAiC ABLH is more suppressed than the ABLH during the Surface Heat Budget of the Arctic Ocean (SHEBA) experiment in the summer, which indicates that there is large variability in the Arctic ABL structure during the summer melting season.

54 ENVIRONMENTAL SCIENCES↗

Acoustic fatigue - A Monte Carlo approach

The present paper reviews the basic concepts of nonlinear structural response to surface flow and acoustic pressure inputs. A time domain solution and the Monte Carlo method are utilized to estimate the required statistics of the nonlinear response. Simulation procedures of multi-dimensional and multi-variate random processes are discussed. Application of these procedures to acoustic fatigue of flight structures are considered. Numerical examples are included to illustrate the applicability of this method for the solution of nonlinear problems.

Vaicaitis, R.↗

The formation and structure of iron-dominated planetesimals

Metal-rich asteroids and iron meteorites are considered core remnants of differentiated planetesimals and/or products of oxygen-depleted accretion. Investigating the origins of iron-rich planetesimals could provide key insights into planet formation mechanisms. Using differentiation models, we evaluate the interior structure and composition of representative-sized planetesimals (~200 km diameter), while varying oxygen fugacity and initial bulk meteoritic composition. Under the oxygen-poor conditions that likely existed early in the inner regions of the Solar System and other protoplanetary disks, core fractions remain relatively consistent across a range of bulk compositions (CI, H, EH, and CBa). Some of these cores could incorporate significant amounts of silicon (10–30 weight%) and explain the metal fractions of Fe-rich bodies in the absence of mantle stripping. Conversely, planetesimals forming under more oxidizing conditions, such as beyond snow lines, could exhibit smaller cores, enriched in carbon, sulfur (>1 wt%), and oxides. Sulfur-rich cores, like those formed from EH and H bulk compositions, could remain partly molten, sustain dynamos, and even drive sulfur-rich volcanism. Additionally, bodies with high carbon contents, such as CI compositions, can form graphitic outer layers. These variations highlight the importance of initial formation conditions in shaping planetesimal structures. Future missions, such as NASA’s Psyche mission, offer an opportunity to measure the relative abundances of key elements (Fe, Ni, Si, and S) necessary to distinguish among formation scenarios and structure models for Fe-rich and reduced planetesimals.

meteorites↗

Multiwavelength Monitoring of Active Galactic Nuclei

By intensive monitoring of AGN variability over a large range in wavelength, we can probe the structure and physics of active galactic nuclei on microarcsecond angular scales. For example, multi-wavelength variability data allow us (a) to establish causal relationships between variations in different wavebands, and thus determine which physical processes are primary and which spectral changes are induced by variations at other wavelengths, and (b) through reverberation mapping of the UV/optical emission lines, to determine the structure and kinematics of the line-emitting region, and thus accurately determine the central masses in AGNs. Multiwavelength monitoring is resource-intensive, and is difficult to implement with general-purpose facilities. As a result, virtually all programs undertaken to date have been either sparsely sampled, or short in duration, or both. The potentially high return on this type of investigation, however, argues for dedicated facilities for multiwavelength monitoring programs.

Peterson, Bradley M.↗

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand–protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes

Abstract Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram‐positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase‐mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae , identifying a number of putative β7–β8 loop‐mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1′ position of the substrate motif, underlined in LPXT G , in contrast to the strict P1′ Gly recognition of SrtA from Staphylococcus aureus . However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C‐terminus, and three others of β7–β8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified β7–β8 loop‐mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. A greater understanding of individual SrtA sequence and structural determinants of target selectivity may also facilitate the design or discovery of improved sortagging tools.

Gao, Melody↗