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At least 487 records · Page 27

Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster

α/β hydrolases make up a large and diverse protein superfamily. In natural product biosynthesis, cis-acting thioesterase α/β hydrolases can terminate biosynthetic assembly lines and release products by hydrolyzing or cyclizing the biosynthetic intermediate. Thioesterases can also act in trans, removing aberrant intermediates and restarting stalled biosynthesis. Knockout of this "editing" function leads to reduced product titers. The borrelidin biosynthetic gene cluster from Streptomyces parvulus Tü4055 contains a hitherto uncharacterized stand-alone thioesterase, borB. In this work, we demonstrate that purified BorB cleaves acyl substrates with a preference for propionate, which supports the hypothesis that it is also an editing thioesterase. The crystal structure of BorB shows a wedgelike hydrophobic substrate binding crevice that limits substrate length. To investigate the structure-function relationship, we made chimeric BorB variants using loop regions from characterized homologues with different specificities. BorB chimeras slightly reduced activity, arguing that the modified region is a not major determinant of substrate preference. Overall, the structure-function relationships described here contribute to the process of elimination for understanding thioesterase specificity and, ultimately, engineering and applying trans-acting thioesterases in biosynthetic assembly lines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Perspectives on van der Waals Density Functionals: The Case of TiS 2

The van der Waals interaction is of foundational importance for a wide variety of physical systems. In particular, van der Waals forces lie at the heart of potential device technologies that may be realized from the functional organization of layered two-dimensional (2D) nanomaterials. Furthermore, for intermediate to large-scale applications modeling, van der Waals density functionals have become the de facto choice for first-principles calculations. In particular, the vdW-DF family of functionals have provided a systematic approach to this theoretically challenging problem. While much progress has been made, there remains room for improvement in the microscopic description of vdW forces from these density functionals. In this work, we compute benchmark results for the binding energy and the electronic density response to binding in TiS2 via accurate diffusion quantum Monte Carlo calculations. We compare these benchmark data to results obtained from local, semilocal, and van der Waals functionals. In particular, we gauge the quality of the original vdW-DF/vdW-DF2 functionals, as well as updated variants such as vdW-DF-C09, vdW-DF-optB88, vdW-DF-optB86b, and vdW-DF2-B86R. We find a close relationship between the accuracy of predicted interlayer separation distances and binding energies for TiS 2 , with the vdW-DF-optB88 functional performing very well in terms of both quantities. In general, the more recently developed functionals are systematic improvements over older ones. However, when considering the response of the electron density to binding, we find that local-density approximation (LDA) and PBEsol generally outperform the vdW-DF functionals in describing the interlayer charge accumulation with vdW-DF-C09 variants performing the best overall.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Critical Assessment of the Thermodynamics of Vacancy Formation in Fe 2 O 3 Using Hybrid Density Functional Theory

Fe 2 O 3 hematite is a technologically important material with applications in energy storage as well as being the key phase formed in the rust of iron-based materials. Despite this central importance, there is much that is still unknown regarding the properties of defects in Fe 2 O 3 and consequently oxide growth. In this work, using screened hybrid density functional theory (HSE06), we consider the thermodynamics of vacancies in Fe 2 O 3 , considering the effects of ionic and electronic chemical potentials on both iron and oxygen vacancy formation. We find that, in the oxygen-rich limit, iron vacancies are easier to form, though the difference in formation energy between the two vacancies is only about 1 eV. In contrast, in the Fe-rich limit, oxygen vacancies have an extremely low formation energy, only 0.07 eV at mid-gap, and would spontaneously form as the Fermi level is reduced, while Fe vacancies require over 5 eV to form. Consistent with experiment, this indicates that Fe 2 O 3 is relatively easily reduced but not oxidized. However, the theoretical picture is very different when considering other exchange–correlation functionals (GGA + U or SCAN), emphasizing the critical role of the exchange–correlation functional in describing this system accurately.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First-Principles Simulations of Liquid Water Using a Dielectric-Dependent Hybrid Functional

We carried out first-principles simulations of liquid water under ambient conditions using a dielectric-dependent hybrid functional, where the fraction of exact exchange is set equal to the inverse of the high-frequency dielectric constant of the liquid. We found excellent agreement with experiment for the oxygen oxygen partial correlation function at the experimental equilibrium density and 311 +/- 3 K. Other structural and dynamical properties, such as the diffusion coefficient, molecular dipole moments, and vibrational spectra, are also in good agreement with experiment. Our results, together with previous findings on electronic properties of the liquid with the same functional, show that the dielectric-dependent hybrid functional accurately describes both the structural and electronic properties of liquid water.

Gaiduk, Alex P.↗

Why Two Metals Are Better Than One for Heterodinuclear Cobalt–Zirconium-Catalyzed Kumada Coupling

Heterodinuclear transition metal complexes with a direct metal–metal interaction offer the potential of unique reactivity compared with mononuclear catalysts. Heterodinuclear Co–Zr complexes with phosphinoamide ligands bridging Co and Zr metal centers are effective precatalysts for Kumada C–C bond coupling reactions between alkyl halides and alkyl Grignards. On the other hand, the analogous mononuclear Co tris(phosphinoamine) complex without Zr provides very inefficient catalysis. Here we describe density functional theory calculations that reveal the mechanistic and reactivity impact of the Co–Zr metal–metal interaction and phosphinoamide ligands on alkyl halide–alkyl Grignard Kumada coupling catalysis. The Co–Zr interaction enables two-electron reduction of the precatalyst to form an active catalyst, which then allows a low-energy electron-transfer alkyl halide oxidative addition mechanism. The Co–Zr interaction and the phosphinoamide ligands bridging the metal centers provide a dialkyl intermediate with a low-energy C–C bond forming reductive elimination route through a phosphine dissociation pathway, which is not viable for an analogous mononuclear Co complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mimicking Microbial Rhodopsin Isomerization in a Single Crystal

Bacteriorhodopsin represents the simplest, and possibly most abundant, phototropic system requiring only a retinal-bound transmembrane protein to convert photons of light to an energy-generating proton gradient. The creation and interrogation of a microbial rhodopsin mimic, based on an orthogonal protein system, would illuminate the design elements required to generate new photoactive proteins with novel function. We describe a microbial rhodopsin mimic, created using a small soluble protein as a template, that specifically photoisomerizes all-trans to 13-cis retinal followed by thermal relaxation to the all-trans isomer, mimicking the bacteriorhodopsin photocycle, in a single crystal. The key element for selective isomerization is a tuned steric interaction between the chromophore and protein, similar to that seen in the microbial rhodopsins. Additionally, it is further demonstrated that a single mutation converts the system to a protein photoswitch without chromophore photoisomerization or conformational change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Single Column Atmosphere Model Version 6 (SCAM6): Not a Scam but a Tool for Model Evaluation and Development

The Single Column Atmosphere Model (SCAM) is a single column model version of the Community Atmosphere Model (CAM). Here we describe the functionality and features of SCAM6, available as part of CAM6 in the Community Earth System Model, version 2 (CESM2). SCAM6 features a wide selection of standard cases, as well as the ability to easily configure a case specified by the user based on a particular point in a CAM 3-D simulation. This work illustrates how SCAM6 reproduces CAM6 results for physical parameterizations, mostly of moisture and clouds. We demonstrate how SCAM6 can be used for model development through different physics selections, as well as with parameter sweep experiments to highlight the sensitivity of cloud properties to the specification of the vapor deposition process in the cloud microphysics. Furthermore, we use SCAM6 to illustrate the sensitivity of CAM6 cloud radiative properties and precipitation to variable drop number (cloud microphysics properties). Finally, we illustrate how SCAM6 can be used to explore critical emergent processes such as cloud feedbacks and show that CAM6 cloud responses to surface warming in stratus and stratocumulus regimes are similar to those in CAM5. CAM6 has a larger response in the shallow cumulus regime than CAM5. CAM6 cloud feedbacks in the shallow cumulus regime are sensitive to turbulence parameters. SCAM6 is thus a valuable tool for model development, evaluation, and scientific analy sis and an important part of the model hierarchy in Community Earth System Model, version 2.

58 GEOSCIENCES↗

Uniting Surface Properties With Hydrodynamic Roughness in Shallow Overland Flow Models

Describing flow resistance from the properties of an underlying surface is a challenge in surface hydrology. Runoff models must specify a resistance formulation or “roughness scheme”—describing the functional relationship between flow resistance and flow depth/velocity—and its parameters. Uncertainty in runoff predictions derives from both the selected roughness scheme (e.g., Darcy Weisbach, Manning's, or laminar flow equations), and its parameterization with a roughness coefficient (e.g., Manning's n). Both choices are informed by model calibration to data, usually discharge, and, if available, velocity. In this study, a Saint Venant Equation-based runoff model is calibrated to discharge and velocity data from 112 rainfall simulator experiments. The results are used to identify the optimal roughness scheme among four widely-used options for each experiment, and to explore whether surface properties can be used to select the optimal roughness scheme and its coefficient. Among the tested roughness schemes, a transitional flow equation provided the best fit to the plurality of experiments. The most suitable roughness scheme for a given experiment was not related to measured surface properties. Regression models predicted the calibrated roughness coefficients with adjusted values between 0.48 and 0.54, depending on the roughness scheme used. Litter cover was the best predictor of the roughness coefficient, followed by soil cover and average canopy gap size. The results suggest that selection of an optimal roughness scheme based on surface properties alone remains difficult, but that once a scheme is selected, roughness coefficients can be estimated from surface properties.

54 ENVIRONMENTAL SCIENCES↗

Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network

Spin glasses, generally defined as disordered systems with randomized competing interactions, are a widely investigated complex system. Theoretical models describing spin glasses are broadly used in other complex systems, such as those describing brain function, error-correcting codes5 or stock-market dynamics. This wide interest in spin glasses provides strong motivation to generate an artificial spin glass within the framework of artificial spin ice systems. Here we present the experimental realization of an artificial spin glass consisting of dipolar coupled single-domain Ising-type nanomagnets arranged onto an interaction network that replicates the aspects of a Hopfield neural network. Using cryogenic X-ray photoemission electron microscopy (XPEEM), we performed temperature-dependent imaging of thermally driven moment fluctuations within these networks and observed characteristic features of a two-dimensional Ising spin glass. Specifically, the temperature dependence of the spin glass correlation function follows a power-law trend predicted from theoretical models on two-dimensional spin glasses. As a result, we observe clear signatures of the hard-to-observe rugged spin glass free energy in the form of sub-aging, out-of-equilibrium autocorrelations and a transition from stable to unstable dynamics.

36 MATERIALS SCIENCE↗

Modeling polymer crystallisation induced by a moving heat sink

Recent experimental work has shown that polymer crystallisation can be used to “move” and organize nanoparticles (NP). As a first effort at modeling this situation, we consider the classical Stefan problem but with the modification that polymer crystallisation does not occur at a single temperature. Rather, the rate of crystallisation is proportional to its subcooling, and here we employ a form inspired by the classical Avrami model to describe this functional form. Our results for the movement of the polymer crystallisation front, as defined as the point where the crystallinity is 50%, closely track the results of the classical Stefan problem. Thus, at this level of approximation, the crystallisation kinetics of the polymer do not cause qualitative changes to the physics of this situation. Inspired by this fact we study the more interesting situation where the directional recrystallisation of a polymer melt is considered, e.g. , through the application of a moving heat sink over an initially molten polymer, reminiscent of a processing technique termed zone annealing. The polymer crystallisation shows that a steady state exists for a range of sink velocities. The solid–melt interface moves slightly ahead of the sink but at the same velocity. The steady-state distance between the sink and the interface decreases with increasing sink velocity – this is a consequence of the excess cooling provided by the sink over what is required to crystallise the melt. The most interesting new result is that the temperature of the crystal–melt interface decreases with increasing sink velocity. This is in line with the ansatz of Lovinger and Gryte who suggested that larger zone annealing velocities correspond to progressively larger effective undercoolings at which polymer crystallisation occurs.

36 MATERIALS SCIENCE↗

False metals, real insulators, and degenerate gapped metals

This paper deals with a significant family of compounds predicted by simplistic electronic structure theory to be metals but are, in fact, insulators. This false metallic state has been traditionally attributed in the literature to reflect the absence of proper treatment of electron-electron correlation (“Mott insulators”) whereas, in fact, even mean-field like density functional theory describes the insulating phase correctly if the restrictions posed on the simplistic theory are avoided. Such unwarranted restrictions included different forms of disallowing symmetry breaking described in this article. As the science and technology of conductors have transitioned from studying simple elemental metals such as Al or Cu to compound conductors such as binary or ternary oxides and pnictides, a special class of degenerate but gapped metals has been noticed. Their presumed electronic configurations show the Fermi level inside the conduction band or valence band, yet there is an “internal band gap” between the principal band edges. The significance of this electronic configuration is that it might be unstable toward the formation of states inside the internal band gap when the formation of such states costs less energy than the energy gained by transferring carriers from the conduction band to these lower energy acceptor states, changing the original (false) metal to an insulator. The analogous process also exists for degenerate but gapped metals with the Fermi level inside the valence band, where the energy gain is defined by transfer of electrons from the donor level to the unoccupied part of the valence band. We focus here on the fact that numerous electronic structure methodologies have overlooked some physical factors that could stabilize the insulating alternative, predicting instead false metals that do not really exist (note that this is in general not a physical phase transition, but a correction of a previous error in theory that led to a false prediction of a metal). Such errors include: (i) ignoring spin symmetry breaking, such as disallowing magnetic spin ordering in CuBi2O4 or disallowing the formation of polymorphous spin networks in paramagnetic LaTiO 3 and YTiO 3 ; (ii) ignoring structural symmetry breaking, e.g., not enabling energy-lowering bond disproportionation (Li-doped TiO 2 , SrBiO 3 , and rare-earth nickelates), or not exploring pseudo-Jahn–Teller-like distortions in LaMnO 3 , or disallowing spontaneous formation of ordered vacancy compounds in Ba 4 As 3 and Ag 3 Al 22 O 34 ; and (iii) ignoring spin–orbit coupling forcing false metallic states in CaIrO 3 and Sr 2 IrO 4 . The distinction between false metals vs real insulators is important because (a) predicting theoretically that a given compound is metal even though it is found to be an insulator often creates the temptation to invoke high order novel physical effects (such as correlation in d-electron Mott insulators) to explain what was in effect caused by a more mundane artifact in a lower-level mean-field band theory, (b) recent prediction of exotic physical effects such as topological semimetals were unfortunately based on the above compounds that were misconstrued by theory to be metal, but are now recognized to be stable insulators not hosting exotic effects, and (c) practical technological applications based on stable degenerate but gapped metals such as transparent conductors or electrides for catalysis must rely on the systematically correct and reliable theoretical classification of metals vs insulators.

36 MATERIALS SCIENCE↗

Nonlinear fluorescence spectroscopy of layered perovskite quantum wells

Interest in layered organohalide perovskites is motivated by their potential for use in optoelectronic devices. In these systems, the smallest and largest quantum wells are primarily concentrated near the glass and air interfaces of a film, thereby establishing a gradient in the average values of the bandgaps. It has been suggested that this layered architecture promotes the funneling of electronic excitations through space in a manner similar to light-harvesting processes in photosynthetic antennae. Whereas energy and charge transfer are difficult to distinguish by conventional transient absorption techniques, it has recently been shown that these competing relaxation mechanisms may be separately targeted with nonlinear fluorescence (NLFL) and photocurrent “action spectroscopies.” Here, we present perturbative rate functions to describe NLFL experiments conducted on layered perovskite systems. The formulas reproduce the patterns of resonances observed in experimental measurements and show how signatures of energy transfer manifest in two-dimensional spectra. Overall, this work suggests that NLFL spectroscopy may be used to fully reveal the trajectories of electronic excitations by correlating ultrafast energy transfer pathways to fluorescence emission from the thickest quantum wells.

Ouyang, Zhenyu↗

Analysis and optimization of seismic monitoring networks with Bayesian optimal experimental design

SUMMARY Monitoring networks increasingly aim to assimilate data from a large number of diverse sensors covering many sensing modalities. Bayesian optimal experimental design (OED) seeks to identify data, sensor configurations or experiments which can optimally reduce uncertainty and hence increase the performance of a monitoring network. Information theory guides OED by formulating the choice of experiment or sensor placement as an optimization problem that maximizes the expected information gain (EIG) about quantities of interest given prior knowledge and models of expected observation data. Therefore, within the context of seismo-acoustic monitoring, we can use Bayesian OED to configure sensor networks by choosing sensor locations, types and fidelity in order to improve our ability to identify and locate seismic sources. In this work, we develop the framework necessary to use Bayesian OED to optimize a sensor network’s ability to locate seismic events from arrival time data of detected seismic phases at the regional-scale. This framework requires five elements: (i) A likelihood function that describes the distribution of detection and traveltime data from the sensor network, (ii) A prior distribution that describes a priori belief about seismic events, (iii) A Bayesian solver that uses a prior and likelihood to identify the posterior distribution of seismic events given the data, (iv) An algorithm to compute EIG about seismic events over a data set of hypothetical prior events, (v) An optimizer that finds a sensor network which maximizes EIG. Once we have developed this framework, we explore many relevant questions to monitoring such as: how to trade off sensor fidelity and earth model uncertainty; how sensor types, number and locations influence uncertainty; and how prior models and constraints influence sensor placement.

58 GEOSCIENCES↗

A Bayesian Monte Carlo inversion of spatial auto-correlation (SPAC) for near-surface Vs structure applied to both broad-band and geophone data

SUMMARY We propose a new Bayesian method to reveal the Vs structure of the near surface of the earth using spatial autocorrelation (SPAC) functions and apply this new method to synthetic, broad-band and geophone data sets. The principle of SPAC is introduced, and an implementation of the Bayesian Monte Carlo inversion (BMCI) for modelling SPAC coherency functions is described. To demonstrate its effectiveness, BMCI is applied to synthetic tests, data from 14 SPAC array sites in the Salt Lake Valley (SLV), Utah, and two arrays (one broad-band and one geophone) located in south central Utah. The Vs models derived from previous SPAC analysis of the 14 SLV sites differ by 10 per cent at most from those determined by BMCI and lie within uncertainties determined for the BMCI models. These agreements demonstrate the effectiveness of the BMCI method. The synthetic tests and applications to the SLV SPAC data show BMCI has great potential to resolve Vs structure down to at least 400 m. To achieve resolution for deeper Vs structure, longer duration deployments, wider array apertures, and additional seismometers or geophones can be used. Additionally, when the target frequencies are greater than 0.1 Hz, there is no apparent disadvantage in using geophone data for BMCI compared to broad-band data. Most significantly, BMCI places a quantifiable constraint on the uncertainties of the Vs models as well as Vs30.

58 GEOSCIENCES↗

Real-space atomic dynamics in liquid gallium studied by inelastic neutron scattering

Gallium is a prototypical liquid metal and has gained renewed attention because of its unique properties. Characterizing and elucidating its atomic dynamics remains elusive despite numerous studies, primarily because of the challenges in quantifying atomic-scale dynamics in liquids. Recent developments in inelastic neutron scattering enable us to measure the Van Hove correlation function that describes the real-space motion of liquid atoms. Here, in this work, we use this approach to reveal the dynamics in gallium liquids and find the co-existence of two dynamical medium-range orders (MROs), which have a dynamical behavior distinct from that of the short-range order (SRO). We propose that these MROs are driven by global forces in the form of two density waves, as a direct consequence of the underlying competition between ionic core repulsion and valence electron cohesion. We suggest that the density wave approach is not only applicable to other metallic liquids exhibiting similar structural anomalies, but also offers a promising direction for elucidating the dynamics of complex liquids and glasses by linking electronic-state fluctuations to atomic dynamics.

Hua, Chengyun [Oak Ridge National Laboratory (ORNL↗

Dominant effect of anharmonicity on the equation of state and thermal conductivity of MgO under extreme conditions

Understanding heat transfer in the earth mantle region is of great scientific interest but highly challenging due to dissimilar conditions from our daily lives. Thermal conductivity of highly pressured and thermally activated materials can be completely different from that at ambient condition. In this study we calculate the equation of state and thermal conductivity of cubic crystalline MgO, a major component of the mantle, in such an environment. It is shown that the material properties are not accurately captured unless rigorous treatment of anharmonicity of phonon vibrational motion is explicitly applied. To predict renormalized phonon dispersion relations, interatomic force constants of high-order expansion are required, especially at elevated temperature. The anharmonicity plays an increasingly substantial role for regulating volume expansion as temperature rises, because the Gibbs free energy of MgO considerably deviates from what was predicted by the quasiharmonic approximation. We find that the lattice thermal conductivity of MgO and the heat transfer of the earth's mantle are reliably estimated only when both the temperature-dependent renormalization of phonon frequencies and four-phonon scattering effects are taken into consideration. We map the characteristics at Geotherm into contour diagrams in which equilibrium volumes and the thermal conductivities are described as functions of temperature and pressure. Furthermore, the thermal conductivity values of MgO in this study are smaller than those in previous theoretical studies due to the additional incorporation of four-phonon scatterings in the calculations. Specifically, deviation between the values in previous studies and in this study becomes larger as thermodynamic variables reach those near the core-mantle boundary. For instance, thermal conductivities of 52.15 and 23.67 Wm -1 K -1 are estimated at ambient and extreme conditions (T = 4000K and P = 135 GPa), respectively.

36 MATERIALS SCIENCE↗

Origin of single transverse-spin asymmetries in high-energy collisions

In this paper, we perform the first simultaneous QCD global analysis of data from semi-inclusive deep inelastic scattering, Drell-Yan, e + e - annihilation into hadron pairs, and proton-proton collisions. Consequently, we are able to extract a universal set of nonperturbative functions that describes the observed asymmetries in these reactions. The outcome of our analysis indicates single transverse-spin asymmetries in high-energy collisions have a common origin. Furthermore, we achieve the first phenomenological agreement with lattice QCD on the up and down quark tensor charges.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Medium-range atomic correlation in simple liquids. I. Distinction from short-range order

Physical properties of liquids and glasses are controlled not only by the short-range order (SRO) in the nearest-neighbor atoms but also by the medium-range order (MRO) observed for atoms beyond the nearest neighbors. In this article the nature of the MRO as the descriptor of point-to-set atomic correlation is discussed focusing on simple liquids, such as metallic liquids. Through the results of x-ray diffraction and simulation with classical potentials we show that the third peak of the pair-distribution function, which describes the MRO, shows a distinct change in temperature dependence at the glass transition, whereas the first peak, which represents the SRO, changes smoothly through the glass transition. Finally, the result suggests that the glass transition is induced by the freezing of the MRO rather than that of the SRO, implying a major role of the MRO on the viscosity of supercooled liquid.

74 ATOMIC AND MOLECULAR PHYSICS↗