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At least 1,297 records · Page 72

Differentiating densities on smooth manifolds

Lebesgue integration of derivatives of strongly-oscillatory functions is a recurring challenge in computational science and engineering. Integration by parts is an effective remedy for huge computational costs associated with Monte Carlo integration schemes. In case of Lebesgue integrals over a smooth manifold, however, integration by parts gives rise to a derivative of the density implied by charts describing the domain manifold. This paper focuses on the computation of that derivative, which we call the density gradient function, on general smooth manifolds. We analytically derive formulas for the density gradient and present examples of manifolds determined by popular differential equation-driven systems. Furthermore, we highlight the significance of the density gradient by demonstrating a numerical example of Monte Carlo integration involving oscillatory integrands.

97 MATHEMATICS AND COMPUTING↗

Optimizing a detection system for fissile material in nuclear disarmament verification

In arms control treaties, verification plays a crucial role in detecting non-compliance, deterring future violations, and building trust between state parties. Neutron interrogation that induces fission reactions in fissile isotopes and measures the resulting fission neutrons, could be employed for this purpose. This study aims to develop a system which can determine the presence of fissile material while intrinsically protecting information. In this paper, we focus on optimizing the system for discriminating between an enriched uranium block from a depleted uranium (DU) block. The system was built and we report on benchmark measurements with DU and 16% enriched uranium blocks. Furthermore, the Excalibur (Experiment for Calibration with Uranium) neutron source, a neutron spectrometer (redBubble Technology Industries (BTI) N-Probe), and superheated droplet detectors were used for these measurements. MCNP simulations provided insights into detector responses to fissile materials with varying isotopic compositions, confirming that the system functioned as designed.

Active neutron interrogation↗

Evaluating the pressure dependence of PZT structures using a virtual reality environment

Pb–Zr–Ti–O (PZT) perovskites span a large solid-solution range and have found widespread use due to their piezoelectric and ferroelectric properties that also span a large range. Crystal structure analysis via Rietveld refinement facilitates materials analysis via the extraction of the structural parameters. These parameters, often obtained as a function of an additional dimension (e.g., pressure), can help to diagnose materials response within a use environment. Often referred to as “ in-situ ” studies, these experiments provide an abundance of data. Viewing structural changes due to applied pressure conditions can give much-needed insight into materials performance. However, challenges exist for viewing/presenting results when the details are inherently three-dimensional (3D) in nature. For PZT perovskites, the use of polyhedra (e.g., Zr/Ti–O 6 octahedra) to view bonding/connectivity is beneficial; however, the visualization of the octahedra behavior with pressure dependence is less easily demonstrated due to the complexity of the added pressure dimension. We present a more intuitive visualization by projecting structural data into virtual reality (VR). We employ previously published structural data for Pb 0.99 (Zr 0.95 Ti 0.05 ) 0.98 Nb 0.02 O 3 as an exemplar for VR visualization of the PZT R3c crystal structure between ambient and 0.62 GPa pressure. This is accomplished via our in-house CAD2VR™ software platform and the new CrystalVR plugin. The use of the VR environment enables a more intuitive viewing experience, while enabling on-the-fly evaluation of crystal data, to form a detailed and comprehensive understanding of in-situ datasets. Discussion of methodology and tools for viewing are given, along with how recording results in video form can enable the viewing experience.

Rodriguez, Mark A. (ORCID:0000000269405044)↗

Force-Modulated C–C Reductive Elimination from Nickel Bis(polyfluorophenyl) Complexes

We have analyzed the rate of C(sp 2 )–C(sp 2 ) reductive elimination from nickel(II) bis(2,4,6-trifluorophenyl) complex-es (P–P)Ni(2,4,6-C 6 H 2 F 3 ) 2 containing either MeOBiPhep (3a) or macrocyclic bisphosphine ligand (3b-3e) as a func-tion of force applied to the biaryl backbone of these ligands through intramolecular tension generated by a molecular force probe. Nickel complexes 3 were isolated in 22-60% yield from reaction of bisphosphine with the bis(tetrahydrofuranyl) complex (THF) 2 Ni(2,4,6-C 6 H 2 F 3 ) 2 followed by chromatography. Thermolysis of complexes 3 in C 6 D 6 at 68 °C leads to first-order decay through > 3 half-lives to form 2,2',4,4',6,6'-hexaflurorobiphenyl as the exclusive fluorine-containing product in ≥93% yield. Whereas compressive forces up to –65 pN have no significant effect on the rate of reductive elimination, extension forces increase the rate of reductive elimination by a factor of three over a ~230 pN range of restoring forces relative to the strain-free MeOBiphep complex. Furthermore, the rate response of reductive elimination from nickel(II) bis(trifluorophenyl) complexes as a function of extension force is similar to the previously reported 2.8-fold increase in the rate of reductive elimination from platinum diaryl complexes (P–P)Pt(4-C 6 H 4 NMe 2 ) 2 over the same range of forces

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

Mechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using a single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg 2+ and the key tertiary interactions. The absence of Mg 2+ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structures in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations in combination with force distribution analysis. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗

Viscosity in water from first-principles and deep-neural-network simulations

Abstract We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio molecular dynamics (AIMD), based on density-functional theory (DFT). In order to cope with the long simulation times necessary to achieve an acceptable statistical accuracy, our ab initio approach is enhanced with deep-neural-network potentials (NNP). This approach is first validated against AIMD results, obtained by using the Perdew–Burke–Ernzerhof (PBE) exchange-correlation functional and paying careful attention to crucial, yet often overlooked, aspects of the statistical data analysis. Then, we train a second NNP to a dataset generated from the Strongly Constrained and Appropriately Normed (SCAN) functional. Once the error resulting from the imperfect prediction of the melting line is offset by referring the simulated temperature to the theoretical melting one, our SCAN predictions of the shear viscosity of water are in very good agreement with experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of interlayer confinement and hydration on capacitive charge storage in birnessite

Nanostructured birnessite exhibits high specific capacitance and nearly ideal capacitive behaviour in aqueous electrolytes, rendering it an important electrode material for low-cost, high-power energy storage devices. The mechanism of electrochemical capacitance in birnessite has been described as both Faradaic (involving redox) and non-Faradaic (involving only electrostatic interactions). To clarify the capacitive mechanism, we characterized birnessite’s response to applied potential using ex situ X-ray diffraction, electrochemical quartz crystal microbalance, in situ Raman spectroscopy and operando atomic force microscope dilatometry to provide a holistic understanding of its structural, gravimetric and mechanical responses. These observations are supported by atomic-scale simulations using density functional theory for the cation-intercalated structure of birnessite, ReaxFF reactive force field-based molecular dynamics and ReaxFF-based grand canonical Monte Carlo simulations on the dynamics at the birnessite–water–electrolyte interface. We show that capacitive charge storage in birnessite is governed by interlayer cation intercalation. We conclude that the intercalation appears capacitive due to the presence of nanoconfined interlayer structural water, which mediates the interaction between the intercalated cation and the birnessite host and leads to minimal structural changes.

36 MATERIALS SCIENCE↗

GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean

Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are distinctive archaeal membrane-spanning lipids with up to eight cyclopentane rings and/or one cyclohexane ring. The number of rings added to the GDGT core structure can vary as a function of environmental conditions, such as changes in growth temperature. This physiological response enables cyclic GDGTs preserved in sediments to be employed as proxies for reconstructing past global and regional temperatures and to provide fundamental insights into ancient climate variability. Yet, confidence in GDGT-based paleotemperature proxies is hindered by uncertainty concerning the archaeal communities contributing to GDGT pools in modern environments and ambiguity in the environmental and physiological factors that affect GDGT cyclization in extant archaea. To properly constrain these uncertainties, a comprehensive understanding of GDGT biosynthesis is required. Here in this paper, we identify 2 GDGT ring synthases, GrsA and GrsB, essential for GDGT ring formation in Sulfolobus acidocaldarius . Both proteins are radical S-adenosylmethionine proteins, indicating that GDGT cyclization occurs through a free radical mechanism. In addition, we demonstrate that GrsA introduces rings specifically at the C-7 position of the core GDGT lipid, while GrsB cyclizes at the C-3 position, suggesting that cyclization patterns are differentially controlled by 2 separate enzymes and potentially influenced by distinct environmental factors. Finally, phylogenetic analyses of the Grs proteins reveal that marine Thaumarchaeota, and not Euryarchaeota, are the dominant source of cyclized GDGTs in open ocean settings, addressing a major source of uncertainty in GDGT-based paleotemperature proxy applications.

59 BASIC BIOLOGICAL SCIENCES↗

Autonomous phototaxis of hydrogel swimmers

The design of synthetic soft matter capable of emulating the complex behaviors of living organisms, such as sensing and adapting to their environment, remains an important challenge in developing biomimetic materials. Functionalized hydrogels are ideal candidates for such materials since they are highly responsive to their environment and can be operated in water. In this work, we investigate a hybrid bonding hydrogel composed of peptide amphiphile supramolecular nanofibers covalently attached to a photoresponsive network, in which high-aspect-ratio ferromagnetic nanowires are aligned along the length of the sample, designed to swim under oscillating magnetic fields. This hybrid hydrogel swimmer can autonomously swim toward a light source by utilizing photoinduced interactions between supramolecular and covalent networks reminiscent of phototactic swimming in living systems. Using a combination of experimental techniques and a continuum model incorporating photochemistry, magnetoelasticity, and hydrodynamics, we explain the swimming mechanism and predict phototactic behavior. Our work highlights the potential role of hybrid bonding polymers, which leverage the interplay between supramolecular assemblies and covalent networks. We demonstrate how these polymers can be tailored to react dynamically to their environment, paving the way for developing intelligent and autonomous robotic systems.

Science & Technology - Other Topics↗

How earthquakes organize stress

Stress is not uniform in the Earth. Therefore, we must use natural experiments to measure the distribution of stresses and related quantities, rather than single values. For instance, dynamic triggering shows that faults are uniformly distributed over their loading cycles in Southern California. The probability that a fault ruptures across a barrier measures the in situ energy distribution. Fault roughness reflects the distribution of strength. These natural experiments produce observable distributions that are surprisingly consistent and suggest some degree of self-organization in the Earth’s crust. Once established, the functional form of the distributions can be used to track changes in response to earthquakes as well as to distinguish fundamentally different fault systems. Transient fault locking before stress release in laboratory experiments can be interpreted as a consequence of self-organization of fault stress. The robust self-organization of multiple variables in earthquake systems suggests that the most consequential mechanical outcome of earthquakes may be the redistribution of stress and the strain energy associated with it. The low friction on a fault during seismic slip as inferred by temperature measurements of the Tohoku earthquake is consistent with dissipation playing a secondary role to this redistribution process. Through stress redistribution and interaction, subduction zone faults tend to synchronize, perhaps due to their geometric simplicity, while the continental system of Southern California cannot synchronize, perhaps due to the complexity of the fault network. Earthquakes organize stress in the crust and produce a suite of well-defined, consistent distributions.

earthquakes↗

Quantum critical dynamics of a Josephson junction at the topological transition

We find the admittance Y(ω) of a Josephson junction at or near a topological transition. The dependence of the admittance on frequency and temperature at the critical point is universal and determined by the symmetries of the system. Despite the absence of a spectral gap at the transition, the dissipative response may remain weak at low energies: ReY(ω)∝max(ω,T) 2 . This behavior is strikingly different from the electromagnetic response of a normal metal. Away from the critical point, the scaling functions for the dependence of the admittance on frequency and temperature are controlled by at most two parameters.

36 MATERIALS SCIENCE↗

Effective Action for Relativistic Hydrodynamics from the Crooks Fluctuation Theorem

A new effective theory framework for fluctuating hydrodynamics in the relativistic regime is derived using standard thermodynamical principles and general properties of nonequilibrium stochastic dynamics. For the first time, we establish clear and concise conditions for ensuring that the resulting effective theories are causal, stable, and well-posed within general relativity. Here, these properties are independent of spacetime foliation and are valid in the full nonlinear regime. Out-of-equilibrium fluctuations are constrained by a relativistically covariant version of the Crooks fluctuation theorem, which determines how the entropy production is distributed even when the system is driven by an external force. This leads to an emerging Z 2 symmetry responsible for imposing fluctuation-dissipation relations for n-point correlation functions, which matches the standard constraints for the Schwinger-Keldysh effective action.

Fluctuation theorems↗

Cyanobacterial carboxysomes contain an unique rubisco–activase–like protein

In plants, rubisco activase (Rca) regulates rubisco by removing inhibitory molecules such as ribulose–1,5–bisphosphate (RuBP). In cyanobacteria, a homologous protein (activase–like cyanobacterial protein, ALC), contains a distinctive C–terminal fusion resembling the small–subunit of rubisco. Although cyanobacterial rubisco is believed to be less sensitive to RuBP inhibition, the ALC is widely distributed among diverse cyanobacteria. Using microscopy, biochemistry and molecular biology, the cellular localization of the ALC, its effect on carboxysome/cell ultrastructure in Fremyella diplosiphon, and its function in vitro were studied. Bioinformatic analysis uncovered evolutionary relationships between the ALC and rubisco. ALC localizes to carboxysomes and exhibits ATPase activity. Furthermore, the ALC induces rubisco aggregation in a manner similar to that of another carboxysomal protein, M35, and this activity is affected by ATP. An alc deletion mutant showed modified cell morphology when grown under enriched CO 2 and impaired regulation of carboxysome biogenesis, without affecting growth rate. Carbamylation of Fremyella recombinant rubisco was inhibited by RuBP, but this inhibition was not relieved by the ALC. Here, the ALC does not appear to function like a canonical Rca; instead, it exerts an effect on the response to CO 2 availability at the level of a metabolic module, the carboxysome, through rubisco network formation, and carboxysome organization.

59 BASIC BIOLOGICAL SCIENCES↗

California annual grass phenology and allometry influence ecosystem dynamics and fire regime in a vegetation demography model

Grass-dominated ecosystems cover wide areas of the land surface yet have received far less attention from the Earth System Model (ESM) community. This limits model projections of ecosystem dynamics in response to global change and coupled vegetation–climate dynamics. We used the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a dynamic vegetation demography model, to determine ecosystem sensitivity to alternate, observed grass allometries and biophysical traits, and evaluated model performance in capturing California C 3 annual grasslands structure and fire regimes. Grass allometry, leaf physiology, plant phenology, and plant mortality all drove the seasonal variation in matter and energy exchange and fire dynamics in California annual grasslands. Allometry influenced grassland structure and function mainly through canopy architecture-mediated space and light competition instead of through carbon partitioning strategy. Regional variation in grassland annual burned area was driven by variation in ecosystem productivity. Our study advances the modeling of grassy ecosystems in ESMs by establishing the importance of grass allometry and plant phenology and mortality in driving C 3 annual grassland seasonal dynamics and fire regime. The calibrated annual grass allometry and biophysical traits presented can be applied in future studies to project climate–vegetation–fire feedbacks in annual grass-dominant ecosystems under global change.

54 ENVIRONMENTAL SCIENCES↗

Internal Standards for Quantitative Analysis of Chemical Warfare Agents by the GC/MS Method: Nerve Agents

General conditions and requirements for an internal standard useful in the determination of chemical warfare agents (CWAs) by the method of gas chromatography coupled with mass detection (GC/MS) were defined. The determination is based on a GC/MS analysis of a mixture of a CWA with an internal standard, conversion of the TIC chromatogram to a chromatogram extracted at a particular m / z ratio, and calculation of the CWA concentration from the internal standard concentration, response factor, and chromatographic peak areas. Available internal standards were identified, and they were verified for seven organophosphorus nerve-paralysing agents. Corresponding response factors were determined as a ratio of gradients of the linear functions of the peak area and compound concentration. Linearity, repeatability, and accuracy of the measurements were evaluated. The determination can be performed on all GC/MS systems of the Fire Rescue Service of the Czech Republic (FRS), where no CWA standards are available.

Capoun, Tomas↗

guideline36_conformance_test 0.1

The American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE) has established a set of standardized high performance sequences of operation for Heating, Ventilation and Air Conditioning (HVAC) systems in buildings through their "Guideline 36". In order to achieve the intended performance, these sequences must be translated and programmed accurately in the Building Automation System (BAS) controllers. Standardizing these sequences will allow for a more efficient product delivery mechanism where the sequences are programmed and tested centrally by each manufacturer, and then distributed to their dealers/engineering contractors. This approach would minimize the need for each installer to re-interpret and program the sequences, reduces risk of errors, and reduces the time required for commissioning in the field. To achieve this goal, a performance validation method is needed to provide independent confirmation that each manufacturer has programmed the Guideline 36 sequences accurately. A standardized method of test would also avoid the need for manual interpretation (and the associated human variability) that is required with typical functional testing approaches by automating the inputs and the range of expected responses. This software "guideline36_conformance_test" has been developed to conduct standardized, repeatable and manufacturer independent tests to validate that a BAS controller has been programmed in conformance with Guideline 36. Manufacturers would provide the controller (or the control program) and the software would run a suite of tests by setting a set of inputs to the controller and verifying the output signals from the controller matches the expected output as set by Guideline 36.

Pritoni, Marco↗

Best Practices for Measuring the Modulation Transfer Function of Video Endoscopes

Endoscopes are crucial for assisting in surgery and disease diagnosis, including the early detection of cancer. The effective use of endoscopes relies on their optical performance, which can be characterized with a series of metrics such as resolution, vital for revealing anatomical details. The modulation transfer function (MTF) is a key metric for evaluating endoscope resolution. However, the 2020 version of the ISO 8600-5 standard, while introducing an endoscope MTF measurement method, lacks empirical validation and excludes opto-electronic video endoscopes, the largest family of endoscopes. Measuring the MTF of video endoscopes requires tailored standards that address their unique characteristics. This paper aims to expand the scope of ISO 8600-5:2020 to include video endoscopes, by optimizing the MTF test method and addressing parameters affecting measurement accuracy. We studied the effects of intensity and uniformity of image luminance, chart modulation compensation, linearity of image digital values, auto gain control, image enhancement, image compression and the region of interest dimensions on images of slanted-edge test charts, and thus the MTF based on these images. By analyzing these effects, we provided recommendations for setting and controlling these factors to obtain accurate MTF curves. Our goal is to enhance the standard’s relevance and effectiveness for measuring the MTF of a broader range of endoscopic devices, with potential applications in the MTF measurement of other digital imaging devices.

47 OTHER INSTRUMENTATION↗

Artificial Intelligence for Smart Transportation

There are more than 7,000 public transit agencies in the U.S. (and many more private agencies), and together, they are responsible for serving 60 billion passenger miles each year. A well-functioning transit system fosters the growth and expansion of businesses, distributes social and economic benefits, and links the capabilities of community members, thereby enhancing what they can accomplish as a society. Since affordable public transit services are the backbones of many communities, this work investigates ways in which Artificial Intelligence (AI) can improve efficiency and increase utilization from the perspective of transit agencies. This book chapter discusses the primary requirements, objectives, and challenges related to the design of AI-driven smart transportation systems. We focus on three major topics. First, we discuss data sources and data. Second, we provide an overview of how AI can aid decision-making with a focus on transportation. Lastly, we discuss computational problems in the transportation domain and AI approaches to these problems.

Wilbur, Michael↗