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At least 433 records · Page 24

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗

On the use of attachment modes in substructure coupling for dynamic analysis

Substructure coupling or component-mode synthesis may be employed in the solution of dynamics problems for complex structures. Although numerous substructure-coupling methods have been devised, little attention has been devoted to methods employing attachment modes. In the present paper the various mode sets (normal modes, constraint modes, attachment modes) are defined. A generalized substructure-coupling procedure is described. Those substructure-coupling methods which employ attachment modes are described in detail. One of these methods is shown to lead to results (e.g., system natural frequencies) comparable to or better than those obtained by the Hurty (1965) method.

Craig, R. R., Jr.↗

XPS study of interface formation of CVD SiO2 on InSb

The interfacial chemistry of CVD SiO2 films deposited on thin native oxides grown on InSb substrates is examined using X-ray photoemission spectroscopy (XPS) and a relatively benign chemical etching technique for depth profiling. An intensity analysis of XPS spectra is used to derive the compositional structure of the interfaces obtained in the SiO2/native oxide/InSb system. Peak positions in these spectra are used to follow the change in substrate surface potential during the etch sequence, and to establish the chemical nature of the species formed during deposition and subsequent processing. Reaction of the substrate with oxygen resulted in an In-rich native oxide and 1-2 monolayers of excess elemental Sb at the native-oxide/substrate interface, incompletely oxidized silane reduced the native oxide, leaving less than 1 monolayer of elemental In at the SiO2/native oxide interface. Etch removal of this thin In-rich layer leads to a change in the substrate surface potential of 0.06 eV, corresponding to a net increase in positive charge. The results are consistent with simple thermodynamic considerations; they are also compared to previously reported studies of deposited dielectrics on III-V compound semiconductors.

Vasquez, R. P.↗

Understanding the Role of Biology in the Global Environment: NASA'S Mission to Planet Earth

NASA has long used the unique perspective of space as a means of expanding our understanding of how the Earth's environment functions. In particular, the linkages between land, air, water, and life-the elements of the Earth system-are a focus for NASA's Mission to Planet Earth. This approach, called Earth system science, blends together fields like meteorology, biology, oceanography, and atmospheric science. Mission to Planet Earth uses observations from satellites, aircraft, balloons, and ground researchers as the basis for analysis of the elements of the Earth system, the interactions between those elements, and possible changes over the coming years and decades. This information is helping scientists improve our understanding of how natural processes affect us and how we might be affecting them. Such studies will yield improved weather forecasts, tools for managing agriculture and forests, information for fishermen and local planners, and, eventually, an enhanced ability to predict how the climate will change in the future. NASA has designed Mission to Planet Earth to focus on five primary themes: Land Cover and Land Use Change; Seasonal to Interannual Climate Prediction; Natural Hazards; Long-Term Climate Variability; and Atmosphere Ozone.

Townsend, William F.↗

Two-Pendulum Model of Propellant Slosh in Europa Clipper PMD Tank

Model propellant slosh for Europa Clipper using two pendulums such that controls engineers can predict slosh behavior during the mission. Importance of predicting propellant slosh; (1) Sloshing changes CM (center of mass) of spacecraft and exerts forces and torques on spacecraft. (2) Avoid natural frequencies of structures. (3) Size ACS (Attitude Control Systems) thrusters to counteract forces and torques. Can model sloshing fluid as two pendulums with specific parameters (mass, length, damping),

Two-Pendulum Model of Propellant Slosh in Europa C↗

Cooled Gas Turbine and Combined Cycle Analysis for H 2 -CH 4 Fuel Mixes (Up to 100% H 2 )

In this study, a cooled gas turbine analysis was conducted for varying levels of hydrogen (H 2 ) blends with the natural gas. The ultimate goal is to have a gas turbine design that can be used for all the fuel blends (including 100% H 2 ) without any changes to the system. The technological developments in the cooling system, gas turbine design and materials that will be required for H 2 combustion were identified and analyzed in this study to develop an advanced gas turbine design for H 2 fuels. The study includes a combined cycle performance analysis with the H 2 fuel blends using the advanced gas turbine design developed in this study. A techno-economic analysis was conducted for analyzing the impact of the H 2 fuels on the levelized cost of electricity and cost sensitivities to fuel price and capacity factor.

03 NATURAL GAS↗

Electrolyte-Dependent, “Microscopically Irreversible” H-Atom Transfer Kinetics of Ce-Based Metal–Organic Framework, Ce-MOF-808

Redox reactions at the interface of metal oxides and protic electrolytes almost always involve protons and electrons in equal amounts. Given the stoichiometry, these proton-coupled electron transfer (PCET) reactions are thermochemically equivalent to net H-atom transfer (HAT) reactions. The correlation between the chemical nature of solid catalysts and HAT kinetics has been employed for decades as the design principle for energy-relevant reactions (e.g., reactions of 2H + /H 2 ). More recently, chemists have experimentally determined that a change in liquid electrolytes that alters the microenvironment at the redox-active sites has an equally profound impact on electrocatalysis involving PCET/HAT. Yet, precise correlations between the chemical nature of electrolytes and the PCET kinetics are, to date, rare in the literature. Herein, we report our findings using the Ce-based metal−organic framework, Ce-MOF-808, as a model system. Each Ce 6 (μ 3 −O) 4 (μ 3 − OH) 4 (OH) 6 (H 2 O) 6 node of this MOF undergoes a 1H + /1e − redox reaction. Using chronoamperometry and the Cottrell analysis, we have determined that the PCET hopping kinetics within the pores of Ce-MOF-808 can change by orders of magnitude by altering the buffer species and the proton activity of the electrolyte. Furthermore, in all buffers, reductive reactions were ∼3−10 times faster in kinetics than the reverse oxidative reaction with the same electrochemical driving force, suggesting that the system, at first glance, violates the principle of microscopic reversibility. Isothermal titration calorimetry (ITC) and computational simulations corroborated that the buffer-node binding thermodynamics are quite distinct, depending on the chemical nature of the buffer and the oxidation state of the node. Together, these results suggest that the substrate and the product during the oxidative vs reductive reaction of Ce-MOF-808 are chemically different species, which explains the apparent ‘microscopic irreversibility.’ Thus, the rational modulation of electrolytes can dramatically enhance PCET kinetics, even though the solid electrodes remain identical. Implications of these findings are contrasted with the electrochemical/electrocatalytic behavior of other redox-active MOFs, heterogeneous catalysts, and enzymatic systems at the solid−liquid interface.

Ce-based MOF↗

Is there a planet int he PSR 1620-26 triple system?

The unusually large eccentricity (e(sub 1) = 0.025) of the low-mass binary millisecond pular PSR B1620-26 can be explained naturally as arising from the secular perturbation of a second, more distant companion. Such a triple configuration has been proposed recently as the most likely cause of the anomalous second period derivative of the pulsar. The current timing data are consistent with a second-companion mass m(sub 2) as low as approximately 10(exp -3) solar mass, i.e., comparable to that of Jupiter. However, if the eccentricity is indeed produced by secular perturbations, then the second companion must be another star, most likely of mass m(sub 2) less than or approximately equal to 1 solar mass and in a very eccentric (e(sub 2) greater than or approximately equal to 0.5) orbit of period P(sub 2) approximately equal 10(exp 2) - 10(exp 3) yr. A second companion of planetary mass cannot induce the observed eccentricity. Independent of the mass of the second companion, small changes in the binary pulsar's orbit should become detectable with just a few additional years of timing data. This detection would provide direct confirmation of the triple nature of the system, and an accurate measurement of the effects would place important new constraints on the orbital parameters.

Rasio, Frederic A.↗

Towards Comprehensive Variation Models for Designing Vehicle Monitoring Systems

When designing vehicle vibration monitoring systems for aerospace devices, it is common to use well-established models of vibration features to determine whether failures or defects exist. Most of the algorithms used for failure detection rely on these models to detect significant changes in a flight environment. In actual practice, however, most vehicle vibration monitoring systems are corrupted by high rates of false alarms and missed detections. This crucial roadblock makes their implementation in real vehicles (e.g., helicopter transmissions and aircraft engines) difficult, making their operation costly and unreliable. Research conducted at the NASA Ames Research Center has determined that a major reason for the high rates of false alarms and missed detections is the numerous sources of statistical variations that are not taken into account in the modeling assumptions. In this paper, we address one such source of variations, namely, those caused during the design and manufacturing of rotating machinery components that make up aerospace systems. We present a novel way of modeling the vibration response by including design variations via probabilistic methods. Using such models, we develop a methodology to account for design and manufacturing variations, and explore the changes in the vibration response to determine its stochastic nature. We explore the potential of the methodology using a nonlinear cam-follower model, where the spring stiffness values are assumed to follow a normal distribution. The results demonstrate initial feasibility of the method, showing great promise in developing a general methodology for designing more accurate aerospace vehicle monitoring systems.

McAdams, Daniel A.↗

Assessment of Thin Plastic Scintillation Detectors for Beta-Particle Measurements at the Advanced Test Reactor Critical Facility

The Fission Wire Measurement System is a custom measurement system designed in the 1960s to measure the beta-particle activity of irradiated uranium-aluminum fission wires. This measurement is conducted to determine the fission rate profile of the Advanced Reactor Test Critical facility. The Advanced Test Reactor Critical facility is an open-pool, low-power test reactor used to qualify experiment configurations and verify core models prior to full-power experiment irradiations in the Advanced Test Reactor. Power distribution measurements in ATR-C use uranium-aluminum wires that are distributed throughout the core to validate simulation and modeling results. These measurements require from 340 to 1500 wires to be irradiated and measured within a 12-hour window. The system consists of 4 measurement channels and one reference channel, each with a 2-pi proportional gas flow detector and the measurement channels each have an automated sample changer. The gas flow detectors are of a custom design for this detector system that use methane gas with a large anode wire compared to modern proportional counters. These detectors, which are nearly 60 years old are irreplaceable. The measurements from these gas detectors are affected by the gas flow rate, atmospheric and line pressure, and are very sensitive to the applied high voltage. Recent improvements have been made to the control and data acquisition system, but the detectors have remained the same. The nature of the measurement of the fission product decay activity is such that the energy spectrum of the signal is changing with time. Thin, 250-um thick, plastic scintillators were commercially obtained as a potential replacement for the gas flow detectors. The original calibration of the uranium-aluminum fission wires was conducted in 1965 using a series of irradiations of gold foils and the wires in a well-characterized thermal neutron field. These measurements provided a time-dependent fission rate conversion factor from the gold foil data to calibrate the fission wires based on the response from the 2-pi proportional gas detectors. Transitioning to the new detectors requires qualification and testing. The sensitivity of the scintillators to changes in the energy spectrum of the fission wires and translation of the calibration factor have been completed. These measurements indicated that the sensitivity of the scintillators over time changes at a different rate than the sensitivity of the gas flow detectors. However, the inverse activity of measurements of both detector types is linear with time. Initial results indicate that the scintillator detectors will be a sufficient replacement for the gas detectors with minor adjustments to the fission rate conversion factor. Replacement of the detectors will improve the fission wire measurements and provide a more stable and reliable measurement system.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

Corals from Space

The goal of this research is to monitor the health and vigor of coral reef ecosystems, and their sensitivity to natural and anthropogenic climate changes. To achieve these lofty goals, this research is investigating the feasibility of using spaceborne high-resolution spectrometers (on the US Landsat, French Systeme Probatoire pour l'Observation de la Terre [SPOT] and/or the Indian Resources Satellite [IRS 1C & 1D] spacecraft) to first map the aerial extent of coral reef systems, and second separate the amount of particular corals. If this is successful, we could potentially provide a quantum leap in our understanding of coral reef systems, as well as provide much needed baseline data to measure future changes in global coral reef ecosystems. In collaboration with Tomas Tomascik, Yann Morel, and other colleagues, a series of experiments were planned to coordinate in situ coral observations, high-resolution spaceborne imagery (from Landsat, SPOT, and, possibly, IRS IC spacecraft), and NASA Space Shuttle photographs and digital images. Our eventual goal is to develop "coral health algorithms" that can be used to assess time series of imagery collected from satellite sensors (Landsat since 1972, SPOT since 1986) in concert with in situ observations. The bad news from last year was that from 1997 to mid- 1998, the extreme cloudiness over southeast Asia due to prolonged smoke from El Nino-related fires and the economic chaos in this region frustrated both our space and reef-based data collection activities. When this volatile situation stabilizes, we will restart these activities. The good news was that in collaboration with Al Strong at the National Oceanic and Atmospheric Administration (NOAA) we had an exciting year operationally using the NOAA's Advanced Very High Resolution Radiometer sensor derived sea surface temperature products to warn of coral "bleaching" at many locations throughout the tropics. Data from NOAA's satellites showed that during the El Nino of 1997 and the first half of 1998, more ocean area in the tropics experienced exceptionally high sea surface temperatures, or "hot spots," than have been observed in any fall year since the El Nino of 1982. From January to July, the coral bleaching events were concentrated in the Southern Hemisphere (during its warm season). Since July 1998, the reports of extensive coral bleaching have again spread into regions of the Northern Hemisphere following abnormally high sea surface temperatures, especially around the Philippines and throughout the Caribbean Basin, Bahamas, Bermuda and Florida Keys. These El Nino induced events clearly demonstrated that corals are the "canaries of the marine ecosystem," highly sensitive to short-term natural climate events (El Nino), and should be monitored as measures of longer-term environmental and climate change. Additional information is contained in the original.

Patzert, William C.↗

The Computing and Data Grid Approach: Infrastructure for Distributed Science Applications

With the advent of Grids - infrastructure for using and managing widely distributed computing and data resources in the science environment - there is now an opportunity to provide a standard, large-scale, computing, data, instrument, and collaboration environment for science that spans many different projects and provides the required infrastructure and services in a relatively uniform and supportable way. Grid technology has evolved over the past several years to provide the services and infrastructure needed for building 'virtual' systems and organizations. We argue that Grid technology provides an excellent basis for the creation of the integrated environments that can combine the resources needed to support the large- scale science projects located at multiple laboratories and universities. We present some science case studies that indicate that a paradigm shift in the process of science will come about as a result of Grids providing transparent and secure access to advanced and integrated information and technologies infrastructure: powerful computing systems, large-scale data archives, scientific instruments, and collaboration tools. These changes will be in the form of services that can be integrated with the user's work environment, and that enable uniform and highly capable access to these computers, data, and instruments, regardless of the location or exact nature of these resources. These services will integrate transient-use resources like computing systems, scientific instruments, and data caches (e.g., as they are needed to perform a simulation or analyze data from a single experiment); persistent-use resources. such as databases, data catalogues, and archives, and; collaborators, whose involvement will continue for the lifetime of a project or longer. While we largely address large-scale science in this paper, Grids, particularly when combined with Web Services, will address a broad spectrum of science scenarios. both large and small scale.

Johnston, William E.↗

Shape‐Evolving Structured Liquids

Migration, division, and reconfiguration - functions essential to living systems - are driven by active processes. Developing synthetic mimics is an outstanding challenge. Lipid bilayers that bound natural systems are locally deformed by active species, e.g., microtubules, but the resulting non-equilibrium shapes relax when active species motion ceases, and the shape changes lack immediate control. A fully synthetic system is described, driven by active particles encapsulated by a reconfigurable nanoparticle-surfactant membrane that undergoes shape fluctuations reminiscent of living cells. These shape changes are preserved after particle activity stops. Surfactant concentration tunes the interfacial tension over three orders of magnitude, making on-demand shape evolution possible. Directional migration, division, and reconfiguration across multiple scales are possible, leading to a new class of biomimetic, reconfigurable, and responsive materials, paving the way for autonomous synthetic machines.

Kim, Paul Y↗

Tomographic Volumetric Additive Manufacturing of Silica Glass with In Situ Error Calculation and Projection Tiling

The optical, thermal, and chemical properties of glass make it an ideal material for use in a wide range of applications, from optics and chemistry reactionware to consumer products. Tomographic volumetric additive manufacturing (tVAM) creates 3D objects by selectively gelling material within a rotating vial of photo-sensitive material by exposure to a series of tomographically-determined images. Here, in this study, tVAM is investigated for fabrication of complex, centimeter-scale, 3D silica glass parts. By optimizing the post-processing procedure, fully-dense glass parts with up to 2 cm 2 cross sectional area are achieved. The changes in optical properties during printing are leveraged for in situ metrology during printing, and the non-Newtonian nature of the glass-filled photoresin system to facilitate larger fabrication volumes via tiled projections. Printed structures are finally demonstrated for applications as MEMS components, optics, fluidics, and consumer products.

Materials science↗

Harnessing Ocean Thermal Gradients Using Thermoelectric Based Submersibles for Ocean Power Applications

The urgent need for energy solutions in marine environments has accelerated the development of innovative technologies capable of leveraging natural resources for power generation. This study introduces a buoyancy-driven submersible system designed to harness ocean thermal gradients using thermoelectric generators (TEGs) and phase change materials (PCMs). The technology aims to provide autonomous power to offshore aquaculture farms, unmanned underwater vehicles (UUVs), offshore platform illumination, and ocean sensors, significantly reducing dependence on fossil fuels. Ocean thermal gradients, especially prevalent in mid-latitude regions, exhibit temperature differences between surface and deep waters ranging from 7 degrees Celsius to 30 degrees Celsius depending on seasonal variations. The proposed submersible technology utilizes TEGs to convert thermal energy from these gradients into electrical power, generating between 0.2 and 0.5 watts, while PCMs are employed to store and regulate this energy, ensuring a stable and continuous power supply. The buoyancy-driven mechanism of the submersible enhances its capability to navigate through varying depths, optimizing its exposure to different thermal gradients and maximizing energy harvesting. The performance of this submersible system is analyzed through detailed thermodynamic assessments and computational fluid dynamics (CFD) modeling focused on heat transfer. These analyzes consider real-world ocean temperature profiles and seek to refine the interaction between TEGs and PCMs to optimize energy extraction. The evaluation encompasses several key performance metrics, including power output and energy efficiency. Results confirm the potential of this innovative technology to provide a continuous and reliable power source for marine applications. By demonstrating the feasibility of using ocean thermal gradients for energy generation, this study contributes to the broader efforts of innovation in energy technologies for harsh, remote marine environments. The implementation of such promises is significant advancements in the autonomy of marine operations. The ongoing research will further investigate scalability ensuring that the system can be effectively adapted to various marine settings and operational demands.

16 TIDAL AND WAVE POWER↗

Core Model Proposal #368: Adding fugitive CO2 emissions from fossil resources

This Core Model Proposal adds fugitive CO2 emissions from coal, crude oil, and natural gas resources to the data system. It also includes an improved method to replace outlier emissions factors for fossil resources. Lastly, it makes some minor changes to the data system and Model Interface headers to fix some inconsistencies in how resource technologies are named in the XMLs.

core model proposal↗

Central Atlantic regional ecological test site: A prototype regional environmental information system

The author has identified the following significant results. A comparison of photomorphic regions from an uncontrolled ERTS-1 mosaic of CARETS to land use areas on a map published in the National Atlas revealed close correlations in non-urban regions. Such regional scale analysis of ERTS-1 data has the potential for providing an economical sampling strategy for selecting sites for more detailed field measurements if other environmental variables can be correlated with patterns on ERTS-1 imagery. ERTS-1 imagery has also revealed for the first time the appearance of CARETS during the winter months. Investigators have identified extensive areas of conifers, which have previously been indistinguishable from deciduous vegetation. Imagery has also shown very clearly the extent of snow cover at a particular time over the region. The evaluation of ERTS-1 imagery used for the land use mapping of the shore zone of CARETS, has shown that the presence or absence of elements of an hierarchal system of shoreline landforms can help identify areas of potential rapid change. Changes in land use class distributions on the Barrier Islands signify the environmental response to natural and man-caused processes. Both environmental vulnerability and sensitivity can be estimated from the repetitive ERTS-1 coverage of long reaches of the CARETS coast. Results indicate potential applications to land use planning, management, and regional environmental quality analysis.

Alexander, R. H.↗

Structural Analysis of the Support System for a Large Compressor Driven by a Synchronous Electric Motor

For economic reasons, the steam drive for a large compressor was replaced by a large synchronous electric motor. Due to the resulting large increase in mass and because the unit was mounted on a steel frame approximately 18 feet above ground level, it was deemed necessary to determine if a steady state or transient vibration problem existed. There was a definite possibility that a resonant or near resonant condition could be encountered. The ensuing analysis, which led to some structural changes as the analysis proceeded, did not reveal any major steady state vibration problems. However, the analysis did indicate that the system would go through several natural frequencies of the support structure during start-up and shutdown. This led to the development of special start-up and shutdown procedures to minimize the possibility of exciting any of the major structural modes. A coast-down could result in significant support structure and/or equipment damage, especially under certain circumstances. In any event, dynamic field tests verified the major analytical results. The unit has now been operating for over three years without any major vibration problems.

Winter, J. R.↗