NMR and crystallographic structural studies of the extremely stable monomeric variant of human cystatin C with single amino acid substitution
Abstract not provided
Maszota‐Zieleniak, Martyna↗
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Confidence Calibration Metrics
This technical report serves to summarize a literature search conducted that covered confidence calibration. This report is meant to serve as a solid starting reference for individuals interested in learning more about the confidence calibration domain as well as for individuals more familiar with this work – as a summarizing document for calibration metrics is notably lacking in the literature. This report is not meant to serve as a comprehensive review of everything that has been done in this field – in fact, the reader is encouraged to look further into this domain. We describe confidence and calibration and discuss properties of good calibration metrics. We detail various calibration and calibration-tangential metrics, presenting equations, algorithms, parameters, and an analysis of strengths and weaknesses. We apply a subset of these metrics to eight proxy confidence assessment datasets. We examine the various metrics in the context of model confidence. Finally, we discuss promising future directions and outstanding questions.
99 GENERAL AND MISCELLANEOUS↗
An Examination of Launch Vehicle Loads Reanalysis Techniques
The typical approach to calculating dynamic launch loads in aerospace applications is coupled loads analysis (CLA). A component mode model of the launch vehicle is coupled with a component mode model of a payload, system modes are calculated, forcing functions are applied, and the dynamic responses are computed. This approach requires the explicit knowledge of the component models for the launch vehicle and payload, as well as the forcing functions. In many situations, the launch vehicle and forcing functions do not change from one analysis to the next only the payload is different. For this type of application, a method called reanalysis was developed to compute the response of a modified payload on the same launch vehicle. If the launch forcing functions are also the same, the approach eliminates the need for the launch vehicle model and the forcing functions and dramatically reduces the computation time. This work investigates the application and accuracy of three previously developed reanalysis methods using a typical launch vehicle and two different payloads. All three methods are based on knowledge of system modes from the original CLA, and Hurty/Craig-Bampton (HCB) models of the original and new payloads. The first method was developed at JPL (Jet Propulsion Lab) and is often referred to as substitution. It is a frequency-domain method, which requires transformation of time signals to and from the frequency domain. The other two methods are time-domain methods that more closely mimic the CLA process. The three methods were applied to two simple examples and a more complex one. The results indicate that the time-domain methods are considerably more robust with respect to modal truncation and other numerical errors than the frequency-domain JPL method.
Reanalysis↗
Computer Modeling and Simulation: Increasing Reliability by Disentangling Verification and Validation
Verification and validation (V&V) of computer codes and models used in simulations are two aspects of the scientific practice of high importance that recently have been discussed widely by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to the model’s relation to the real world and its intended use. Because complex simulations are generally opaque to a practitioner, the Duhem problem can arise with verification and validation due to their entanglement; such an entanglement makes it impossible to distinguish whether a coding error or the model’s general inadequacy to its target should be blamed in the case of a failure. I argue that a clear distinction between computer modeling and simulation has to be made to disentangle verification and validation. Drawing on that distinction, I suggest to associate modeling with verification and simulation, which shares common epistemic strategies with experimentation, with validation. To explain the reasons for their entanglement in practice, I propose a Weberian ideal–typical model of modeling and simulation as roles in practice. I examine an approach to mitigate the Duhem problem for verification and validation that is generally applicable in practice and is based on differences in epistemic strategies and scopes. Based on this analysis, I suggest two strategies to increase the reliability of simulation results, namely, avoiding alterations of verified models at the validation stage as well as performing simulations of the same target system using two or more different models. In response to Winsberg’s claim that verification and validation are entangled I argue that deploying the methodology proposed in this work it is possible to mitigate inseparability of V&V in many if not all domains where modeling and simulation are used.
97 MATHEMATICS AND COMPUTING↗
Origin of Phase Separation in Ni-Rich Layered Oxide Cathode Materials During Electrochemical Cycling
In intercalation materials, the kinetics and uniformity of mass transport across the nanocrystalline domains dictate the structural reversibility and transport capability at the macroscopic level. (De)intercalation-induced interlayer disintegrations exhibit anisotropic crystallite size change. Due to the anisotropic mass transport mechanism, separated phases are inherently crystallographically oriented. One such material is LiNi $1–x–y$ Mn $x$ Co $y$ O 2 , which plays a pivotal role in advanced Li-ion batteries but suffers from severe phase inhomogeneities under fast charge or electrochemical aging. Here, using operando synchrotron techniques, we probe the mechanistic origins of the compositional and orientational-dependent phase separations during the electrochemical cycling of LiNi 0.8 Mn 0.1 Co 0.1 O 2 by comprehensive analysis of both in-plane and out-of-plane reflections. In the H2/H3 phase regime, in-plane domain propagation occurs due to increased covalency despite the severe decay of interlayer crystallographic order, resulting in the change of crystalline domain shape from 3D spheres to two-dimensional nanosheets. The crystallographically selective XRD line splitting is linked to the geometry of the facets as mass transfers along the ab plane. In conclusion, this work provides mechanistic insights into crystallographic orientation-dependent phase inhomogeneity under fast charge and extended cycling.
36 MATERIALS SCIENCE↗
Direct observation of magnetic ordering induced via systematic lattice disorder in artificial rhombus spin ices
It is critical to understand the effect of lattice geometry on the order parameter of a condensed matter system, as it controls phase transitions in such systems. Artificial spin ices (ASIs) are two-dimensional lattices of Ising-like nanomagnets that provide an opportunity to explore such phenomena by lithographically controlling the lattice geometry to observe its influence on magnetic ordering and frustration effects. Here we report a systematic approach to studying the effects of disorder in rhombus ASIs generated from combinations of five vertex motifs. We investigate four geometries characterized by a geometric order parameter, with symmetries ranging from periodic to quasiperiodic to random. Lorentz transmission electron microscopy data indicates magnetic domain behavior depends on chains of strongly-coupled islands in the periodic and sixfold-twinned lattices, while the behavior of the disordered lattice is dominated by vertex motifs with large configurational degeneracy. Utilizing micromagnetic simulations, a quantitative analysis of the lattice energetics showed that the experimental rotationally-demagnetized state of the disordered ASI was closer in energy to the idealized ground state compared to other periodic and twinned ASIs. Finally, our work provides a unique pathway for using degeneracy, magnetic frustration, and order to control the magnetization behavior of designer disordered systems.
36 MATERIALS SCIENCE↗
Color glass condensate meets high twist expansion
We establish the correspondence between two well-known frameworks for quantum chromodynamics (QCD) multiple scattering in nuclear media: the color glass condensate (CGC) and the high-twist (HT) expansion formalism. We argue that a consistent matching between both frameworks, in their common domain of validity, is achieved by incorporating the subeikonal longitudinal momentum phase in the CGC formalism, which mediates the transition between coherent and incoherent scattering. We perform a detailed calculation and analysis of direct photon production in proton-nucleus scattering as a concrete example to establish the matching between HT and CGC up to twist-4, including initial- and final-state interactions, as well as their interferences. The techniques developed in this work can be adapted to other processes in electron-nucleus and proton-nucleus collisions, and they provide a potential avenue for a unified picture of dilute-dense dynamics in nuclear media.
quantum chromodynamics↗
Optimizing Error-Bounded Lossy Compression for Scientific Data by Dynamic Spline Interpolation
Today's scientific simulations are producing vast volumes of data that cannot be stored and transferred efficiently because of limited storage capacity, parallel I/O bandwidth, and network bandwidth. The situation is getting worse over time because of the ever-increasing gap between relatively slow data transfer speed and fast-growing computation power in modern supercomputers. Error-bounded lossy compression is becoming one of the most critical techniques for resolving the big scientific data issue, in that it can significantly reduce the scientific data volume while guaranteeing that the reconstructed data is valid for users because of its compression-error-bounding feature. In this paper, we present a novel error-bounded lossy compressor based on a state-of-the-art prediction-based compression framework. Our solution exhibits substantially better compression quality than all of the existing error-bounded lossy compressors, with comparable compression speed. Specifically, our contribution is threefold. (1) We provide an in-depth analysis of why the best-existing prediction-based lossy compressor can only minimally improve the compression quality. (2) We propose a dynamic spline interpolation approach with a series of optimization strategies that can significantly improve the data prediction accuracy, substantially improving the compression quality in turn. (3) We perform a thorough evaluation using six real-world scientific simulation datasets across different science domains to evaluate our solution vs. all other related works. Experiments show that the compression ratio of our solution is higher than that of the second-best lossy compressor by 20%similar to 460% with the same error bound in most of the cases.
Zhao, Kai↗
Propagation of Boundary-Induced Discontinuity in Stationary Radiative Transfer
We consider the boundary value problem of the stationary transport equation in the slab domain of general dimensions. In this paper, we discuss the relation between discontinuity of the incoming boundary data and that of the solution to the stationary transport equation. We introduce two conditions posed on the boundary data so that discontinuity of the boundary data propagates along positive characteristic lines as that of the solution to the stationary transport equation. Our analysis does not depend on the celebrated velocity averaging lemma, which is different from previous works. We also introduce an example in two dimensional case which shows that piecewise continuity of the boundary data is not a sufficient condition for the main result.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Multiphysics modeling of printed surface acoustic wave thermometers
Surface acoustic wave (SAW) transducers are a class of sensors and actuators that operate on the fundamental principle of piezoelectricity. Aerosol jet printing and other additive manufacturing techniques have resulted in the low-cost fabrication of low-power and small-footprint SAW devices that are suitable for sensing in high-temperature and radioactive environments. In this work, we developed a series of temperature-dependent finite element models for a SAW transducer consisting of printed silver interdigitated transducers (IDTs) deposited onto piezoelectric lithium niobate. Modeling accuracy was evaluated experimentally from room temperature to 200 °C using an aerosol-jet-printed SAW thermometer. A time-domain study enabled visualization of the wave propagation and successfully guided the denoising of the scattering parameter measurement. Additionally, frequency-domain models using traditional modal analysis or the unique port boundary condition feature in COMSOL Multiphysics accurately predicted the temperature-driven natural frequency drift in the SAW thermometer. The finite element models developed in this study serve to facilitate the computer-aided design of future SAW transducers for applications in harsh environments.
47 OTHER INSTRUMENTATION↗
A Multi-Harmonic System Identification Method for Internal Circuit Element Monitoring
Many critical infrastructures depend on the reliability of electronic circuits, whose health depends on the values of internal circuit elements that degrade over time. It is therefore important to estimate the values of internal circuit elements from external measurements and monitor them for changes. The challenge to doing so is that, typically, the internal voltages and currents are not accessible for measurement. Prior work on internal circuit element monitoring uses data obtained from sensors placed inside the circuit or requires additional circuitry to be added to the given system, both of which are undesirable. We propose a new multi-harmonic frequency-domain based system identification method that is non-intrusive. It exploits the latent non-idealities already present in the system, specifically harmonics in the measured input and output signals. We show how sensitivity analysis can be used to both assess the accuracy of the method as well as to optimize the choice of harmonics to use. We use as a motivation and illustrative example the problem of determining the equivalent series resistance and capacitance in a class of dc-link capacitance circuits in Adjustable Speed Drives. We assess the performance of this method using simulations, and establish its validity by experimental results.
Deshpande, Ankit Vivek↗
Development and Application of an Integrated Approach toward NASA Airspace Systems Research
The National Aeronautics and Space Administration's (NASA) Airspace Systems Program is contributing air traffic management research in support of the 2025 Next Generation Air Transportation System (NextGen). Contributions support research and development needs provided by the interagency Joint Planning and Development Office (JPDO). These needs generally call for integrated technical solutions that improve system-level performance and work effectively across multiple domains and planning time horizons. In response, the Airspace Systems Program is pursuing an integrated research approach and has adapted systems engineering best practices for application in a research environment. Systems engineering methods aim to enable researchers to methodically compare different technical approaches, consider system-level performance, and develop compatible solutions. Systems engineering activities are performed iteratively as the research matures. Products of this approach include a demand and needs analysis, system-level descriptions focusing on NASA research contributions, system assessment and design studies, and common systemlevel metrics, scenarios, and assumptions. Results from the first systems engineering iteration include a preliminary demand and needs analysis; a functional modeling tool; and initial system-level metrics, scenario characteristics, and assumptions. Demand and needs analysis results suggest that several advanced concepts can mitigate demand/capacity imbalances for NextGen, but fall short of enabling three-times current-day capacity at the nation s busiest airports and airspace. Current activities are focusing on standardizing metrics, scenarios, and assumptions, conducting system-level performance assessments of integrated research solutions, and exploring key system design interfaces.
Barhydt, Richard↗
3D face analysis for demographic biometrics
Despite being increasingly easy to acquire, 3D data is rarely used for face-based biometrics applications beyond identification. Recent work in image-based demographic biometrics has enjoyed much success, but these approaches suffer from the well-known limitations of 2D representations, particularly variations in illumination, texture, and pose, as well as a fundamental inability to describe 3D shape. This paper shows that simple 3D shape features in a face-based coordinate system are capable of representing many biometric attributes without problem-specific models or specialized domain knowledge. The same feature vector achieves impressive results for problems as diverse as age estimation, gender classification, and race classification.
Tokola, Ryan A↗
Colloidal Synthesis of Palladium Nanocluster‐Decorated Cs 3 Sb 2 Cl 9 Perovskite Heterostructural Nanorods for Enhanced CO 2 Photoreduction
Developing efficient and sustainable photocatalysts for CO 2 reduction remains a significant challenge, particularly with environmentally benign materials. Here, in this study, we report the first one-step synthesis of metal–lead-free perovskite heterostructural nanocrystals by decorating Cs 3 Sb 2 Cl 9 perovskite nanorods with size-controlled Pd nanoclusters via a one-step hot-injection method. The resulting Pd-Cs 3 Sb 2 Cl 9 heteronanorods (HNRs) exhibit strong interfacial electronic coupling, enhanced charge separation, and excellent colloidal stability. Transient absorption spectroscopy and DFT calculations reveal a built-in electric field that drives directional electron transfer from the perovskite host to the Pd domains. Under UV irradiation, the Pd-Cs 3 Sb 2 Cl 9 HNRs demonstrate excellent CO 2 photoreduction activity with high CH 4 selectivity, achieving a record apparent quantum yield (AQY) of 2.62% among halide perovskite nanocrystal-based systems with a large electronic yield of 689.3 ± 12.2 µmol·g cat −1 . In situ spectroscopic monitoring and Gibbs free energy analysis further unveil a Pd-facilitated reaction pathway involving stabilization of key intermediates. This work introduces a new class of lead-free perovskite-based heterostructures through a facile one-step synthesis strategy and offers a new design principle for next-generation photocatalysts for solar fuel production.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Chd1p recognizes H3K36Ac to maintain nucleosome positioning near the transcription start site
In Saccharomyces cerevisiae, the ATP-dependent chromatin remodeler, Chd1p, globally affects nucleosome positioning at coding regions, where nucleosomes are specifically and directionally aligned with respect to the transcription start site (TSS). Various auxiliary domains of remodelers play critical roles by performing specialized functions that are unique to the type of remodeler. Here, we report that yeast Chd1p directly binds to acetylated histone H3K36 (H3K36Ac) via its chromodomain, and that H3K36Ac stimulates the nucleosome sliding activity of Chd1p in vitro. Furthermore, we use genome-wide analysis to demonstrate that H3K36Ac promotes the remodeling activity of Chd1p to maintain chromatin stability at the 5′ ends of genes in vivo. Our work linking Chd1p with H3K36Ac provides novel insights into how the nucleosome remodeling activity of Chd1p is controlled near the TSS.
60 APPLIED LIFE SCIENCES↗
Copper-dependent halogenase catalyses unactivated C−H bond functionalization
Carbon–hydrogen (C–H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp 3 )−H bond. In recent years, metalloenzymes have been found to perform C(sp 3 )−H bond functionalization. Despite substantial progresses in the past two decades, enzymatic halogenation and pseudohalogenation of unactivated C(sp 3 )−H—providing a functional handle for further modification—have been achieved with only non-haem iron/α-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes. Here, in this work, we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp 3 )−H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp 3 )−H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs—one interchain and two intrachain—of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp 3 )−H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.
biocatalysis↗
Practical guidelines for workload assessment
The practical problems that might be encountered in carrying out workload evaluations in work settings have been outlined. Different approaches have been distinguished that may determine the type of research design used and provide assistance in the difficult choice between workload assessment techniques. One approach to workload assessment is to examine the short-term consequences of combining various tasks. Theoretical models of attention allocation will underpin specific studies of interference and the consequences of task demand and task conflict for performance. A further approach with a different temporal orientation may lead us to a better understanding of the relationships between work demands and strain through the analysis of individual differences in cognitive control processes. The application of these processes may depend on individual differences in long term styles and short term strategies, but may be used to prevent decrements in work performance under difficult conditions. However, control may attract costs as well as benefits in terms of changes in effective state and physiological activity. Thus, strain associated with work demands may only be measurable in the form of tradeoffs between performance and other domains of individual activity. The methodological implications are to identify patterns of adjustment to workload variations using repeated measures and longitudinal sampling of performance as well as subjective and physiological measures. Possible enhancements to workplace design must take into account these human factors considerations of workload in order to avoid potential decrements in individual performance and associated organizational problems.
Tattersall, Andrew J.↗
Sensitivity analysis of simulated SOA loadings using a variance-based statistical approach: SENSITIVITY ANALYSIS OF SOA
We investigate the sensitivity of secondary organic aerosol (SOA) loadings simulated by a regional chemical transport model to 7 selected tunable model parameters: 4 involving emissions of anthropogenic and biogenic volatile organic compounds, anthropogenic semi-volatile and intermediate volatility organics (SIVOCs), and NOx, 2 involving dry deposition of SOA precursor gases, and one involving particle-phase transformation of SOA to low volatility. We adopt a quasi-Monte Carlo sampling approach to effectively sample the high-dimensional parameter space, and perform a 250 member ensemble of simulations using a regional model, accounting for some of the latest advances in SOA treatments based on our recent work. We then conduct a variance-based sensitivity analysis using the generalized linear model method to study the responses of simulated SOA loadings to the tunable parameters. Analysis of SOA variance from all 250 simulations shows that the volatility transformation parameter, which controls whether particle-phase transformation of SOA from semi-volatile SOA to non-volatile is on or off, is the dominant contributor to variance of simulated surface-level daytime SOA (65% domain average contribution). We also split the simulations into 2 subsets of 125 each, depending on whether the volatility transformation is turned on/off. For each subset, the SOA variances are dominated by the parameters involving biogenic VOC and anthropogenic SIVOC emissions. Furthermore, biogenic VOC emissions have a larger contribution to SOA variance when the SOA transformation to non-volatile is on, while anthropogenic SIVOC emissions have a larger contribution when the transformation is off. NOx contributes less than 4.3% to SOA variance, and this low contribution is mainly attributed to dominance of intermediate to high NOx conditions throughout the simulated domain. The two parameters related to dry deposition of SOA precursor gases also have very low contributions to SOA variance. This study highlights the large sensitivity of SOA loadings to the particle-phase transformation of SOA volatility, which is neglected in most previous models.
Shrivastava, Manish↗