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At least 1,549 records · Page 86

Flipped GUT inflation

We analyse the prospects for constructing hybrid models of inflation that provide a dynamical realisation of the apparent closeness between the supersymmetric GUT scale and the possible scale of cosmological inflation. In the first place, we consider models based on the flipped SU(5)×U(1) gauge group, which has no magnetic monopoles. In one model, the inflaton is identified with a sneutrino field, and in the other model it is a gauge singlet. In both cases we find regions of the model parameter spaces that are compatible with the experimental magnitudes of the scalar perturbations, A{sub s}, and the tilt in the scalar perturbation spectrum, n{sub s}, as well as with an indicative upper limit on the tensor-to-scalar perturbation ratio, r. We also discuss embeddings of these models into SO(10), which is broken at a higher scale so that its monopoles are inflated away.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Bi{sub 1−x}Nb{sub x}O{sub 1.5+x} (x=0.0625, 0.12) fast ion conductors: Structures, stability and oxide ion migration pathways

A combined experimental and computational study of Bi{sub 1−x}Nb{sub x}O{sub 1.5+x} (x=0.0625 and 0.12) has been carried out using laboratory X-ray, neutron and electron diffraction, impedance measurements and ab-initio molecular dynamics. We demonstrate that Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625}, previously reported to adopt a cubic fluorite-type superstructure, can form two different polymorphs depending on the synthetic method: a metastable cubic phase is produced by quenching; while slower cooling yields a stable material with a tetragonal √2×√2×1 superstructure, which undergoes a reversible phase transition into the cubic form at ~680 °C on subsequent reheating. Neutron diffraction reveals that the tetragonal superstructure arises mainly from ordering in the oxygen sublattice, with Bi and Nb remaining disordered, although structured diffuse scattering observed in the electron diffraction patterns suggests a degree of short-range ordering. Both materials are oxide ion conductors. On thermal cycling, Bi{sub 0.88}Nb{sub 0.12}O{sub 1.62} exhibits a decrease in conductivity of approximately an order of magnitude due to partial transformation into the tetragonal phase, but still exhibits conductivity comparable to yttria-stabilised zirconia (YSZ). Ab-initio molecular dynamics simulations performed on Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} show that oxide ion diffusion occurs by O{sup 2−} jumps between edge- and corner-sharing OM{sub 4} groups (M=Bi, Nb) via tetrahedral □M{sub 4} and octahedral □M{sub 6} vacancies. - Graphical abstract: Oxide ion migration in tetragonal Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} occurs by O{sup 2−} jumps between edge- and corner-sharing OM{sub 4} groups (M=Bi, Nb) via tetrahedral M{sub 4} and octahedral M{sub 6} vacancies. - Highlights: • Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} adopts a tetragonal √2×√2×1 fluorite superstructure. • Superstructure is due to ordering in the O-sublattice, with Bi/Nb disordered. • Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} is a good oxide ion conductor. • O{sup 2−} jump between OM{sub 4} groups (M=Bi, Nb) via tetrahedral and octahedral vacancies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Abstract Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

59 BASIC BIOLOGICAL SCIENCES↗

Scaling CFB risers: Beyond the data using microstructure similarity

Scaling circulating fluidized bed risers has been a point of contention for nearly a century. There have been numerous attempts to define various methodologies. These have all fallen short of providing a robust approach, primarily due to a lack of maintaining microstructure dynamics – a key factor in maintaining interphase heat and mass transfer. Recent work by the author put forward an approach based upon preserving dynamic similarity at different scales by ensuring that the microstructure remained similar by maintaining statistical and chaotic parameters across the scale. That work relied on a dimensionless regime map in which the x-axis was defined by the ratio of the solids flux to the saturation carrying capacity. This latter property was only good within the range of the data, and it became evident that extrapolation beyond the limits of the data could induce unrealistic conditions. Therefore, literature was reviewed to develop a better correlation for the saturation carrying capacity. In doing so, a critical riser diameter concept was developed and applied to the correlations for both Geldart Group A and B materials. The critical diameter for Geldart Group A and B materials is 0.2 m and 0.3 m, respectively. Here the paper then gives three examples on how to use the scaling approach to maintain dynamic similarity across the scales.

02 PETROLEUM↗

Libration of hydroxyl groups in layered aluminum (oxy)hydroxides and other material analogs: insights from inelastic neutron scattering and theory

We analyzed the hydroxyl librational signatures of five structurally related aluminum (oxy)hydroxides, using inelastic neutron scattering (INS) and plane-wave lattice dynamics simulations. A clear trend across these aluminum-containing phases illustrates the relationship between hydrogen bonding, local atomic structure, and the spectral location and profile of the librational bands. The INS spectra have been compared to previous optical spectroscopy and computational studies, highlighting the complementary nature of the INS technique. Taking into account other structurally or chemically related material analogs, we have identified a correlation between a blueshift (to higher energy) of the upper librational band edge and the geometry of the hydrogen bond interactions, mirroring (with opposite correlation) the well-known redshift in the intramolecular O–H stretching energy with increasing hydrogen bond strength. For hydroxyl groups that do not participate in hydrogen bonding effectively, the bending librations occur at lower energies and hybridize with metal–oxygen lattice modes. Standard density functional theory approximations, including dispersion corrections, struggle to correctly predict vibrational frequencies of motions dominated by H but perform well for metal–oxygen modes, allowing us to make detailed mode assignments in several cases, including a demonstration of how layer-to-layer disorder in boehmite hydrogen bond orientations is reflected in the sharp but minor low energy peaks (at ∼70–80 meV) of the INS spectrum.

Wang, Hsiu-Wen [Oak Ridge National Laboratory (ORN↗

Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

Abstract Background Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4′ ether bonds and C–C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4′ ether bonds and of C–C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme. Results Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4% at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% β-O-4′ ether bond cleavage, 27.0% C α -C 1 carbon bond cleavage, and 3.6% C α -oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4′ bonds. Conclusion These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved in lignin depolymerization should include targeting stability at low pH.

09 BIOMASS FUELS↗

A numerically exact description of ultrafast vibrational decoherence in vibration-coupled electron transfer

Broadband pump–probe spectroscopy has been widely used to measure vibrational decoherence associated with the reaction coordinate in photoinduced ultrafast vibration-coupled electron transfer (VCET) reactions. These experiments provide insight into the interplay of intramolecular coordinates along the reaction coordinate. However, a general theoretical foundation for analyzing, and even for explaining rigorously, these data is lacking. In this work, we study vibrational decoherence in a model VCET reaction using the nearly exact time-dependent density matrix renormalization group simulation method. We explore how analyzing the density matrix with quantum information measures can help elucidate the evolution of vibrational coherence in simulations of dynamics. We examine how vibrational coherence is affected by electron transfer on the timescale of approximately 100 femtoseconds. Our results suggest that electron transfer, in the nonadiabatic model, changes the vibrational equilibrium position abruptly—an example of a “quantum quench” event. This explains the concomitant vibrational decoherence. We find that abrupt vibrational decoherence can be mitigated by wavepacket motion occurring on the timescale of the electron transfer.

Science & Technology - Other Topics↗

Rational design of a carboxylic esterase Rh Est1 based on computational analysis of substrate binding

A new carboxylic esterase RhEst1 which catalyzes the hydrolysis of (S)-(+)-2,2-dimethylcyclopropanecarboxylate (S-DmCpCe), the key chiral building block of cilastatin, was identified and subsequently crystallized in our previous work. Mutant Rh Est 1A147I/V148F/G254A was found to show a 5-fold increase in the catalytic activity. In this work, molecular dynamic simulations were performed to elucidate the molecular determinant of the enzyme activity. Our simulations show that the substrate binds much more strongly in the A147I/V148F/G254A mutant than in wild type, with more hydrogen bonds formed between the substrate and the catalytic triad and the oxyanion hole. The OH group of the catalytic residue Ser101 in the mutant is better positioned to initiate the nucleophilic attack on S-DmCpCe. Interestingly, the "170-179" loop which is involved in shaping the catalytic sites and facilitating the product release shows remarkable dynamic differences in the two systems. Based on the simulation results, six residues were identified as potential "hot-spots" for further experimental testing. Consequently, the G126S and R133L mutants show higher catalytic efficiency as compared with the wild type. In conclusion, this work provides molecular-level insights into the substrate binding mechanism of carboxylic esterase Rh Est1, facilitating future experimental efforts toward developing more efficient Rh Est1 variants for industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗

Pressure, temperature, and orientation dependent thermal conductivity of pentaerythritol tetranitrate (PETN)

We use reverse non-equilibrium molecular dynamics to determine the thermal conductivity tensor, κ, of tetragonal pentaerythritol tetranitrate (PETN). The most stable form under standard ambient conditions (PETN I, with space group P4¯2 1 c) is considered in the temperature and pressure intervals 200–500 K and 0–8 GPa, which covers approximately the stability range for this polymorph. We compute κ along the [100] and [001] directions, which is enough to construct the full thermal conductivity tensor for a system with tetragonal symmetry. In addition, we also determine κ along the [010] direction and confirm that κ 100 ~ κ 010 , with less than 4% average absolute error between the two quantities. We observe an anisotropic response for κ, with κ 100 > κ 001 across the whole (T,P) interval, and 37% difference at 300 K, 0 GPa. Furthermore, we provide analytical functions to interpolate κ(P,T) within the fitting interval and serve as input for continuum-scale simulations.

36 MATERIALS SCIENCE↗

A New Compendium of Unsteady Aerodynamic Test Cases for CFD: Summary of AVT WG-003 Activities

With the continuous progress in hardware and numerical schemes, Computational Unsteady Aerodynamics (CUA), that is, the application of Computational Fluid Dynamics (CFD) to unsteady flowfields, is slowly finding its way as a useful and reliable tool (turbulence and transition modeling permitting) in the aircraft, helicopter, engine and missile design and development process. Before a specific code may be used with confidence it is essential to validate its capability to describe the physics of the flow correctly, or at least to the level of approximation required, for which purpose a comparison with accurate experimental data is needed. Unsteady wind tunnel testing is difficult and expensive; two factors which dramatically limit the number of organizations with the capability and/or resources to perform it. Thus, unsteady experimental data is scarce, often classified and scattered in diverse documents. Additionally, access to the reports does not necessarily assure access to the data itself. The collaborative effort described in this paper was conceived with the aim of collecting into a single easily accessible document as much quality data as possible. The idea is not new. In the early 80's NATO's AGARD (Advisory Group for Aerospace Research & Development) Structures and Material Panel (SMP) produced AGARD Report No. 702 "Compendium of Unsteady Aerodynamic Measurements", which has found and continues to find extensive use within the CUA Community. In 1995 AGARD's Fluid Dynamics Panel (FDP) decided to update and expand the former database with new geometries and physical phenomena, and launched Working Group WG-22 on "Validation Data for Computational Unsteady Aerodynamic Codes". Shortly afterwards AGARD was reorganized as the RTO (Research and Technology Organization) and the WG was renamed as AVT (Applied Vehicle Technolology) WG-003. Contributions were received from AEDC, BAe, DLR, DERA, Glasgow University, IAR, NAL, NASA, NLR, and ONERA. The final publication with the results of the exercise is expected in the second part of 1999. The aim of the present paper is to announce and present the new database to the Aeroelasticity community. It is also intended to identify, together with one of the groups of end users it targets, deficiencies in the compendium that should be addressed by means of new wind tunnel tests or by obtaining access to additionally existing data.

Ruiz-Calavera, Luis P.↗

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗

( Suzaku Suzaku) X-ray observations of the nearest non-cool core cluster, Antlia: dynamically young but with remarkably relaxed outskirts

We present the results of seven Suzaku mosaic observations (>200 ks in total) of the nearest non-cool core cluster, the Antlia Cluster (or Group), beyond its degree-scale virial radius in its eastern direction. The temperature is consistent with the scaled profiles of many other clusters. Its pressure follows the universal profile. The density slope in its outskirts is significantly steeper than that of the nearest cool core cluster (Virgo) with a similar temperature as Antlia, but shallower than those of the massive clusters. The entropy increases all the way out to R {sub 200}, which is consistent in value with the baseline model predicted by a gravity heating-only mechanism in the outskirts. Antlia is quite relaxed in this direction. However, the entropy inside ∼R {sub 500} is significantly higher than the baseline model, which is similar to many other nearby low mass clusters or groups. The enclosed gas-mass fraction does not exceed the cosmic value out to 1.3R{sub 200}. Thus, there is no evidence of significant gas clumping, electron-ion non-equipartition, or departure from the hydrostatic equilibrium approximation that are suggested to explain the entropy and gas fraction anomalies found in the outskirts of some massive clusters. We also present scaling relations for the gas fraction (f{sub gas,200}), entropy (K {sub 200}), and temperature (T {sub 500}) using 22 groups and clusters with published data in the literature. The enclosed baryon fraction at R {sub 200} is broadly consistent with the cosmic value. The power law slope of the K {sub 200}–T {sub 500} relation is 0.638 ± 0.205. The entropy deficit at R {sub 200} cannot be fully accounted for by the bias or deviation in the gas fraction.

79 ASTRONOMY AND ASTROPHYSICS↗

Advanced and Nontraditional Concepts Working Group Report

Advanced and nontraditional concepts relating to future space power requirements were examined with special emphasis on the requirements for the space station. Key findings in the following ares are outlined: dynamic radiation concepts, space nuclear reactors, energy conversion cycles, beam power transmission, electrodynamic tethers and advanced photovoltaics.

Hertzberg, A.↗

Gamma radiation effects on the dynamic fatigue measurements of glass discs

Circular specimens of low iron soda lime silicate glass were blasted with grit after having a circular notch etched into their centers. After separation into two groups, one group was exposed to gamma radiation. The fracture strengths of all samples were then tested by the biaxial technique, i.e., specimens were balanced on three balls and loaded in the center by a piston. The irradiated samples had received a 140,000 Gy dose from a Co-60 source. An enhanced interaction between the ambient moisture and the grit-blasted central notch was observed in the irradiated samples, which displayed accelerated corrosion.

Ananaba, T. O. J.↗

A dynamic melting model for the origin of Apollo 15 olivine-normative and quartz-normative mare basalts

Early studies of mare basalts from the Apollo 15 site established that two distinct groups are represented: the olivine-normative basalts (ONB) and the quartz-normative basalts (QNB). The ONB and QNB suites are distinguished petrographically by their phenocryst assemblages (the ONB's are olivine-phyric, the QNB's are generally pyroxene-phyric) and chemically by their major element compositions: the QNB's are higher in SiO2 and MgO/FeO, and lower in FeO and TiO2 than ONB's with similar MgO contents. Experimental data show that the QNB suite is derived from a more magnesian, olivine-normative parent magma, a conclusion which is supported by the recent discovery of high-SiO2 olivine-normative basalt clasts in breccia 15498. The high-SiO2 ONB's fall on olivine control lines with primitive QNB's, and least-squares mixing calculations are consistent with the high-SiO2 ONB's being parental to the more evolved QNB suite. These high-SiO2 ONB's are included as part of the 'QNB suite'. Our major element modeling results also are consistent with the conclusions of earlier studies which showed that the ONB and QNB suites cannot be related to one another by low pressure crystal fractionation. The combination of high Mg#, high SiO2, and low TiO2 in the QNB suite precludes a relationship to the ONB suite by simple removal of liquidus minerals (olivine and pigeonite). Despite these significant differences in petrography and major element composition, both groups have nearly identical trace element concentrations and chondrite-normalized abundance patterns. The major question to be addressed by any petrogenetic model for Apollo 15 mare basalts is how to form mare basalt suites with distinctly different major element characteristics but nearly identical trace element compositions. The similarity in trace element concentrations imply compositionally similar source regions and similar percent melting, but these conclusions are not easily reconciled with the observed differences in major element compositions, which require sources with distinct mineralogies or large differences in percent melt.

Vetter, Scott K.↗

A Multireference Approach to Electron and Electron–Nuclear Dynamics in Nanomaterials (Final Report)

Many important chemical and physical phenomena involve dynamics on large number of electronic states. Thus, there is a critical need to develop methods to simulate dynamics in dense manifolds of states. Towards this end, we have: a) developed the multiple cloning in dense manifolds of states (MCDMS) method, which is capable of accurately modeling the quantum mechanical coherence between populations on a large number of electronic states, b) implemented MCDMS into the free, open-source PySpawn software package, c) developed graphics processing unit-accelerated algorithms modeling electron dynamics in light fields via Floquet time-dependent configuration interaction (F-TDCI), and d) critically compared different orbital bases in order to achieve an accurate and efficient F-TDCI expansion. This grant ended in August 2020, when our group moved to from Michigan State University to Stony Brook University, where this project continues under grant number DE-SC0021643.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

Thompson, Michael C. (ORCID:0000000260992027)↗

Computational Studies of [Bmim][PF6]/n-Alcohol Interfaces with Many-Body Potentials

In this paper, we present the results from molecular-dynamics simulations of the equilibrium properties of liquid/liquid interfaces of room temperature ionic liquid [bmim][PF6] and simple alcohols (i.e., methanol, 1-butanol, and 1-hexanol) at room temperature. Polarizable potential models are employed to describe the interactions among species. Results from our simulations show stable interfaces between the ionic liquid and n-alcohols, and we found that the interfacial widths decrease from methanol to 1-butanol systems, and then increase for 1-hexanol interfaces. Angular distribution analysis reveals that the interface induces a strong orientational order of [bmim] and n-alcohol molecules near the interface, with [bmim] extending its butyl group into the alcohol phase while the alcohol has the OH group pointing into the ion liquid region, which is consistent with the recent sum-frequency-generation experiments. We found the interface to have a significant influence on the dynamics of ionic liquids and n-alcohols. The orientational autocorrelation functions illustrate that [bmim] rotate more freely near the interface than in the bulk, while the rotation of n-alcohol is hindered at the interface. Additionally, the time scale associated with the diffusion along the interfacial direction is found to be faster for [bmim] but slowed down for n-alcohols approaching the interface. We also calculate the dipole moment of n-alcohols as a function of the distance normal to the interface. We found that, even though methanol and 1-butanol have different dipole moments in bulk phase, they reach a similar value at the interface. This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for the Department of Energy by Battelle. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.

Chang, Tsun-Mei↗