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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The dark matter haloes of HI selected galaxies

We present the neutral hydrogen mass (M HI) function (HIMF) and velocity width (w 50 ) function (HIWF) based on a sample of 7857 galaxies from the 40 per cent data release of the ALFALFA survey (α.40). The low mass (velocity width) end of the HIMF (HIWF) is dominated by the blue population of galaxies whereas the red population dominates the HIMF (HIWF) at the high mass (velocity width) end. We use a deconvolution method to estimate the HI rotational velocity (V rot ) functions (HIVF) from the HIWF for the total, red, and blue samples. The HIWF and HIVF for the red and blue samples are well separated at the knee of the function compared to their HIMFs. We then use recent stacking results from the ALFALFA survey to constrain the halo mass (M h ) function of HI-selected galaxies. This allows us to obtain various scaling relations between M HI –w 50 –V rot –M h , which we present. The M HI –M h relation has a steep slope ~2.10 at small masses and flattens to ~0.34 at masses larger than a transition halo mass, $\log _{10}(M_{\rm{ht}}h_{70}^2/M_{\odot })=10.62$. Our scaling relation is robust and consistent with a volume-limited sample of α.40. The M HI –M h relation is qualitatively similar to the M star –M h relation but the transition halo mass is smaller by ~1.4 dex compared to that of the M star –M h relation. Our results suggest that baryonic processes like heating and feedback in larger mass haloes suppress HI gas on a shorter time-scale compared to star formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Image feature extraction and galaxy classification: a novel and efficient approach with automated machine learning

ABSTRACT In this work, we explore the possibility of applying machine learning methods designed for 1D problems to the task of galaxy image classification. The algorithms used for image classification typically rely on multiple costly steps, such as the point spread function deconvolution and the training and application of complex Convolutional Neural Networks of thousands or even millions of parameters. In our approach, we extract features from the galaxy images by analysing the elliptical isophotes in their light distribution and collect the information in a sequence. The sequences obtained with this method present definite features allowing a direct distinction between galaxy types. Then, we train and classify the sequences with machine learning algorithms, designed through the platform Modulos AutoML. As a demonstration of this method, we use the second public release of the Dark Energy Survey (DES DR2). We show that we are able to successfully distinguish between early-type and late-type galaxies, for images with signal-to-noise ratio greater than 300. This yields an accuracy of $86{{\ \rm per\ cent}}$ for the early-type galaxies and $93{{\ \rm per\ cent}}$ for the late-type galaxies, which is on par with most contemporary automated image classification approaches. The data dimensionality reduction of our novel method implies a significant lowering in computational cost of classification. In the perspective of future data sets obtained with e.g. Euclid and the Vera Rubin Observatory, this work represents a path towards using a well-tested and widely used platform from industry in efficiently tackling galaxy classification problems at the peta-byte scale.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

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.↗
DOE OSTI2020

Radiation Mapping for an Unmanned Aerial Vehicle: Development and Simulated Testing of Algorithms for Source Mapping and Navigation Path Generation

Image reconstruction algorithms were developed for radiation source mapping and used for generating the search path of a moving radiation detector, such as one onboard an unmanned aerial vehicle. Simulations consisted of first assuming radioactive sources of varying complexity and estimating the radiation fields that would then be produced by that source distribution. Next, the "measurements" that would result from a pair of adjacent spatial locations were computed. A crude estimate of the source distribution likely to have produced such "measurements" was reconstructed based upon the limited measurements. Location of the next "measurement" was then determined as halfway between the location of the estimated source and the current "measurement." With each additional sample, improved source distribution reconstructions were made and used to inform the immediate direction of detector motion. Source reconstruction or mapping was formulated as an inverse problem solved with either maximum a posteriori or least squares (LS) regression deconvolution methods. Different amounts of noise were added to the simulated "measurements," allowing evaluation of the methods' performances as functions of signal-to-noise ratio of the measured map. As expected, methods that promote sparsity were better suited in reconstructing point sources. Reliable prior information of the source distribution also improved the reconstruction results, especially with distributed sources. With a non-negative least square algorithm and the suggested paths it generated, location of sources was successfully estimated to an accuracy of 0.014 m within nine iterations in a single-source scenario and 12 iterations in a two-source scenario, given a 10% error on the integrated counts and a Poisson distribution of the noise associated with the measured counts.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2022

Size Effect of Local Current-Voltage Characteristics of MX 2 Nanoflakes: Local Density of States Reconstruction from Scanning Tunneling Microscopy Experiments

Local current-voltage characteristics for low-dimensional transition-metal dichalcogenides (LDTMD), as well as the reconstruction of their local density of states (LDOS) from scanning tunneling microscopy (STM) experiments, are of fundamental interest and can be useful for advanced applications. Most of the existing models either have limited applicability for complex-shaped LDTMDs (e.g., those based on the Simmons approach) or require solving of an ill-defined integral equation to deconvolute the unknown LDOS (e.g., those based on the Tersoff approach). Using a serial expansion of the Tersoff formulas, we propose a flexible method to reconstruct the LDOS from local current-voltage characteristics measured in STM experiments. We establish a set of key physical parameters, which characterize the tunneling current of a STM-probe–sample contact and the sample LDOS expanded in Gaussian functions. Using a direct variational method coupled with probabilistic analysis, we determine these parameters from the STM experiments for MoS2 nanoflakes with different numbers of layers. The main result is the reconstruction of the LDOS in a relatively wide energy range around the Fermi level, which allows us to gain insight into the local band structure of LDTMDs. The reconstructed LDOS reveal pronounced size effects for the single-layer, two-layer, and three-layer MoS 2 nanoflakes, which we relate to the low dimensionality and strong bending or corrugation of the nanoflakes. We hope that the proposed elaboration of the Tersoff approach, allowing LDOS reconstruction, will be of critical interest for the quantitative description of STM experiments and also of use to better understand the microscopic physical aspects of the surface, strain, and bending contributions to the LDTMDs’ electronic properties.

42 ENGINEERING↗
DOE OSTI2020

Mixed-strategy approach to band-edge analysis and modeling in semiconductors

In semiconductor physics, the Urbach rule describes an exponential dependence of the UV-Vis absorption coefficient on photon energy at the band edge. The rule is so ubiquitously applied that a single common mechanism, variability in the local potential, is generally considered to be the cause of exponential band edges. Variability in the local potential may be caused by alloy inhomogeneity, structural defects, impurities, thermal excitation, or any other mechanism that interrupts ideal crystallinity and creates disorder. A crucial point of the Urbach rule is its development for band edges which approach linearity when plotted on a logarithmic scale. The rule was not developed in the context of nonlinear band edges with complex fine structure. Even so, this model has been applied extensively to band edges with such features. Using differential analysis and deconvolution, we develop an analytical technique capable of separating the components responsible for the fine structure observed. This approach reduces challenging signal-artifact convolution problems to a simple linear combination. Furthermore, we develop a model that can be applied to the nonlinear band-edge signals extracted. In this work, we show that in the limiting case of linearity, our model is consistent with and produces the same results as the linear Urbach model. Our model is capable of bypassing “tailing” as an indirect measure of the spread in the local potential and gives a direct measure of this quantity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Solid state core-exciton dynamics in NaCl observed by tabletop attosecond four-wave mixing spectroscopy

Nonlinear wave mixing in solids with ultrafast x-rays can provide insight into complex electronic dynamics of materials. Here, tabletop-based attosecond noncollinear four-wave mixing (FWM) spectroscopy using one extreme ultraviolet (XUV) pulse from high harmonic generation and two separately timed few-cycle near-infrared (NIR) pulses characterizes the dynamics of the Na + L 2,3 edge core-excitons in NaCl around 33.5 eV. An inhomogeneous distribution of core-excitons underlying the well-known doublet absorption of the Na+ Γ point core-exciton spectrum is deconvoluted by the resonance-enhanced nonlinear wave mixing spectroscopy. In addition, other dark excitonic states that are coupled to the XUV-allowed levels by the NIR pulses are characterized spectrally and temporally. Approximately <10fs coherence lifetimes of the core-exciton states are observed. Furthermore, the core-excitonic properties are discussed in the context of strong electron-hole exchange interactions, electron-electron correlation, and electron-phonon broadening. This investigation successfully indicates that tabletop attosecond FWM spectroscopies represent a viable technique for time-resolved solid state measurements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Landau-Ginzburg theory of charge density wave formation accompanying lattice and electronic long-range ordering

Here we propose an analytical Landau-Ginzburg (LG) theory of the charge density waves coupled with lattice and electronic long-range order parameters. Examples of long-range order include the electronic wave function of superconducting Cooper pairs, structural distortions, electric polarization, and magnetization. We formulate the LG free energy density as a power expansion with respect to the charge density and other long-range order parameters as well as their spatial gradients and biquadratic coupling terms. We introduced a biquadratic coupling between the charge density gradient and long-range order parameters as well as nonlinear higher gradients of the long-range order parameters. The biquadratic gradient coupling is critical to the appearance of different spatially modulated phases in charge-ordered ferroics and high-temperature superconductors. We derived the thermodynamic conditions for the stability of the spatially modulated phases, which are the intertwined spatial waves of charge density and lattice/electronic long-range order. The analytical expressions for the energies of different phases, corresponding order parameters, charge density waves amplitudes, and modulation periods obtained in this paper can be employed to guide the comprehensive physical explanation, deconvolution, and Bayesian analysis of experimental data on quantum materials ranging from charge-ordered ferroics to high-temperature superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Determination of β -decay feeding patterns of 88 Rb and 88 Kr using the Modular Total Absorption Spectrometer at ORNL HRIBF

We report precise determination of ground-state feeding in the β decay of fission products is an important but challenging component in modeling reactor antineutrino flux and reactor decay heat. The Modular Total Absorption Spectrometer (MTAS) is a versatile NaI(Tl) detector array that determines the true β-decay pattern free from the pandemonium effect, including precise ground-state feeding intensities. In this paper, we report MTAS results of the β feeding intensities of 88 Rb and 88 Kr, fission products with large cumulative yields in nuclear reactors. By comparing MTAS results with previous measurements, 88 Rb provides a validation of MTAS's ability to determine ground-state feedings in β decays, while the precision of 88 Kr ground-state feeding is improved when compared with the Evaluated Nuclear Structure Data File (ENSDF). The investigation of sources that contribute to β feeding branching uncertainties in MTAS experiments is discussed in detail. Lastly, the deconvolution of 88 Rb decay spectra suggests that MTAS can distinguish an allowed β spectral shape from a first forbidden unique β spectral shape.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Detailed study of quark-hadron duality in spin structure functions of the proton and neutron

Background: The response of hadrons, the bound states of the strong force (QCD), to external probes can be described in two different, complementary frameworks: as direct interactions with their fundamental constituents, quarks and gluons, or alternatively as elastic or inelastic coherent scattering that leaves the hadrons in their ground state or in one of their excited (resonance) states. The former picture emerges most clearly in hard processes with high momentum transfer, where the hadron response can be described by the perturbative expansion of QCD, while at lower energy and momentum transfers, the resonant excitations of the hadrons dominate the cross section. The overlap region between these two pictures, where both yield similar predictions, is referred to as quark-hadron duality and has been extensively studied in reactions involving unpolarized hadrons. Some limited information on this phenomenon also exists for polarized protons, deuterons, and 3 He nuclei, but not yet for neutrons. Purpose: In this paper, we present comprehensive and detailed results on the correspondence between the extrapolated deep inelastic structure function g 1 of both the proton and the neutron with the same quantity measured in the nucleon resonance region. Thanks to the fine binning and high precision of our data, and using a well-controlled perturbative QCD (pQCD) fit for the partonic prediction, we can make quantitative statements about the kinematic range of applicability of both local duality and global duality. Method: We use the most updated QCD global analysis results at high x from the Jefferson Lab Angular Momentum Collaboration to extrapolate the spin structure function g 1 into the nucleon resonance region and then integrate over various intervals in the scaling variable x. We compare the results with the large data set collected in the quark-hadron transition region by the CLAS Collaboration, including, for the first time, deconvoluted neutron data, integrated over the same intervals. We present this comparison as a function of the momentum transfer Q 2 . Results: We find that, depending on the integration interval and the minimum momentum transfer chosen, a clear transition to quark-hadron duality can be observed in both nucleon species. Furthermore, we show, for the first time, the approach to scaling behavior for g 1 measured in the resonance region at sufficiently high momentum transfer. Conclusions: Here, our results can be used to quantify the deviations from the applicability of pQCD for data taken at moderate energies and can help with extraction of quark distribution functions from such data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

String-based parametrization of nucleon GPDs at any skewness: A comparison to lattice QCD

We introduce a string-based parametrization for nucleon quark and gluon generalized parton distributions (GPDs) valid at all skewness values. The conformal moments of the GPDs are expressed as sums of the spin-j nucleon A-form factor and the skewness-dependent spin-j nucleon D-form factor. This representation, which fulfills the polynomiality condition (due to Lorentz invariance) and does not rely on model-specific assumptions, is derived from t-channel string exchanges in anti-de Sitter spaces. The spin-j nucleon D-form factor is closely related to the spin-j nucleon A-form factor. We use the Mellin moments from empirical parton distributions to model the spin-j nucleon A-form factors. Using only five Regge slope parameters, fixed from the electromagnetic and gravitational form factors, our string-based parametrization generates accurate singlet, nonsinglet, isovector, and flavor-separated nucleon quark GPDs, along with symmetric nucleon gluon GPDs from their Mellin-Barnes integral representations. Our isovector nucleon quark GPD is in agreement with existing lattice data. Our string-based parametrization should facilitate the empirical extraction and global analysis of nucleon GPDs in exclusive processes, bypassing the deconvolution challenge.

Electron-ion collisions↗
DOE OSTI2022

Non-Boussinesq subgrid-scale model with dynamic tensorial coefficients

A major drawback of Boussinesq-type subgrid-scale stress models used in large-eddy simulations is the inherent assumption of alignment between large-scale strain rates and filtered subgrid-stresses. A priori analyses using direct numerical simulation (DNS) data have shown that this assumption is invalid locally as subgrid-scale stresses are poorly correlated with the large-scale strain rates [J. Bardina, J. Ferziger, and W. Reynolds, Improved subgrid-scale models for large-eddy simulation, in Proceedings of the 13th Fluid and Plasmadynamics Conference, AIAA (1980); C. Meneveau and K. Katz, Scale-invariance and turbulence models for large-eddy simulation, Ann. Rev. Fluid Mech. 32, 1 (2000)]. In the present work, a new, non-Boussinesq subgrid-scale model is presented where the model coefficients are computed dynamically. Some previous non-Boussinesq models have observed issues in providing adequate dissipation of turbulent kinetic energy [e.g., Bardina et al., Proceedings of the 13th Fluid and Plasmadynamics Conference (1980); R. A. Clark, J. Ferziger, and W.C. Reynolds. Evaluation of subgrid-scale models using an accurately simulated turbulent flow, J. Fluid Mech. 91, 1 (1979); S. Stolz and N. A. Adams, An approximate deconvolution procedure for large-eddy simulation, Phys. Fluids 11, 1699 (1999)]; however, the present model is shown to provide sufficient dissipation using dynamic coefficients. Modeled subgrid-scale Reynolds stresses satisfy the consistency requirements of the governing equations for large-eddy simulation (LES), vanish in laminar flow and at solid boundaries, and have the correct asymptotic behavior in the near-wall region of a turbulent boundary layer. The new model, referred to as the dynamic tensor-coefficient Smagorinsky model (DTCSM), has been tested in simulations of canonical flows: decaying and forced homogeneous isotropic turbulence, and wall-modeled turbulent channel flow at high Reynolds numbers. The results show favorable agreement with DNS data. It has been shown that DTCSM offers similar predictive capabilities as the dynamic Smagorinsky model for canonical flows. In order to assess the performance of DTCSM in more complex flows, wall-modeled simulations of high Reynolds number flow over a Gaussian bump (Boeing speed bump) exhibiting smooth-body flow separation are performed. Predictions of surface pressure and skin friction, compared against DNS and experimental data, show improved accuracy from DTCSM in comparison to existing static coefficient (Vreman) and dynamic Smagorinsky model. The computational cost of performing LES with this model is up to 15% higher than the dynamic Smagorinsky model.

42 ENGINEERING↗
DOE OSTI2024

Parametrization of Generalized Parton Distributions from 𝑡-Channel String Exchange in AdS Spaces

We introduce a string-based parametrization for nucleon quark and gluon generalized parton distributions (GPDs) that is valid for all skewness. Our approach leverages conformal moments, representing them as the sum of spin-𝑗 nucleon 𝐴-form factor and skewness-dependent spin-𝑗 nucleon 𝐷-form factor, derived from 𝑡-channel string exchange in AdS spaces consistent with Lorentz invariance and unitarity. This model-independent framework, satisfying the polynomiality condition due to Lorentz invariance, uses Mellin moments from empirical data to estimate these form factors. With just five Regge slope parameters, our method accurately produces various nucleon quark GPD types and symmetric nucleon gluon GPDs through pertinent Mellin-Barnes integrals. Our isovector nucleon quark GPD is in agreement with existing lattice data, promising to improve the empirical extraction and global analysis of nucleon GPDs in exclusive processes, by avoiding the deconvolution problem at any skewness, for the first time.

QCD phenomenology↗
DOE OSTI2024

Three Photon Excited Image Scanning Microscopy for in-Depth Super-Resolution Studies of Biological Samples

Multiphoton laser scanning microscopy is a powerful tool for deep imaging of thick biological samples. Image scanning microscopy (ISM) has demonstrated significant improvements in the signal-to-noise ratio in confocal laser scanning microscopy, while at the same time improving upon the effectively attainable resolution. Two-photon excitation (2PE), combined with ISM, has been shown to allow for deep tissue imaging with enhanced resolution compared to 2PE microscopy. Three-photon excitation (3PE) has enabled record imaging depth and contrast for multiphoton imaging, due to the superior suppression of out-of-focus signal generation. In this paper, we demonstrate super-resolution 3PE ISM. This is achieved using a single-photon avalanche detector array, and 1040-nm pulses for 3PE of blue fluorescence. This method enables subdiffraction limited resolution imaging of biological samples stained with blue fluorescent markers, such as mouse myocardial and spinal cord tissues stained with 4 ′ , 6 -diamidino-2-phenylindole. Deconvolution improves the resolving power further and allows for imaging with better than λ / 8 resolution with respect to the 3PE wavelength λ . With the ISM pixel reassignment procedure, we demonstrate a resolution enhancement of ∼ 1.6 laterally, compared to the resolution attained using a photomultiplier tube in a non-descanned detection arrangement, and a factor of ∼ 1.8 enhancement in axial resolution. The experimentally measured three-dimensional point spread function volume is shrunk ∼ 4.4 -fold, which is close to the theoretically expected enhancement. Published by the American Physical Society 2024

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

BioXTAS RAW 2 : new developments for a free open-source program for small-angle scattering data reduction and analysis

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI ; updated automated Guinier fitting and D max finding algorithms; automated series ( e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares ( REGALS ); creation of electron-density reconstructions using electron density via solution scattering ( DENSS ); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Surrogate Model for Distribution Networks Influenced by Weather

Here, we propose a method for generating reduced representations of time series and for constructing low dimensional surrogate models for time dependent calculations of power and voltage in distribution networks. We employ Fourier polynomials. The surrogate model strategy is aimed at reducing the computational cost of time dependent simulations, albeit, at the expense of fidelity. The reduced representation is achieved by identifying a small and most consequential subset of degrees of freedom. In power and voltage distribution networks dynamics that are heavily influenced by strong cyclic weather events, e.g., the hourly, diurnal and seasonal cycles, the weather/climate time series spectrum exposes these most energetic components. Once the degrees of freedom are identified their amplitudes are optimized using training data. The key challenge in using spectral methods in power network surrogates is addressing the computation of quotients. For this we propose a numerically-stable deconvolution strategy.

Weather events↗
DOE OSTI2022

Binary pseudo-random array standards for calibration of 3D optical surface profilers used for metrology with aspheric x-ray optics

High-accuracy surface metrology is vitally important in manufacturing ultra-high-quality free-form mirrors designed to manipulate x-ray light with nanometer-scale wavelengths. The current and potential capabilities of x˗ray mirror manufacturing are limited by inherent imperfections of the integrated metrology tools. Metrology tools are currently calibrated with super-polished flat test-standard/reference mirrors. This is acceptable for fabrication of slightly curved x-ray optics. However, for even moderately curved aspherical x-ray mirrors the flat-reference calibration is not sufficiently accurate. For micro-stitching interferometry developed for surface measurements with curved x-ray mirrors, the tool aberration errors are known to be transferred into the optical surface topography of x-ray mirrors. Our approach to improving metrology is to thoroughly calibrate the measuring tool and apply the results of the calibration to deconvolution of the measured data. Here we explore the application of a recently developed technique for calibrating the instrument transfer function (ITF) of 3D optical surface profilers to metrology with significantly curved x-ray optics. The technique, based on test standards patterned with two-dimensional (2D) binary pseudo-random arrays (BPRAs), employs the unique properties of the BPRA patterns in the spatial frequency domain. The inherent 2D power spectral density of the pattern has a deterministic white-noise-like character that allows direct determination of the ITF with uniform sensitivity over the entire spatial frequency range and field of view of an instrument. The high efficacy of the technique has been previously demonstrated in application to metrology with flat and slightly curved optics. Here, we concentrate on development of an efficient fabrication process for production of highly randomized (HR) BPRA test standards on flat and 500-mm spherical optical substrates. We also compare and discuss the results of the ITF calibration of an interferometric microscope when using the HR BPRA standards on flat and curved substrates.

Munechika, Keiko↗
DOE OSTI2022

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗