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At least 595 records · Page 33

Extended Lagrangian Born–Oppenheimer molecular dynamics using a Krylov subspace approximation

It is shown how the electronic equations of motion in extended Lagrangian Born–Oppenheimer molecular dynamics simulations can be integrated using low-rank approximations of the inverse Jacobian kernel. This kernel determines the metric tensor in the harmonic oscillator extension of the Lagrangian that drives the evolution of the electronic degrees of freedom. The proposed kernel approximation is derived from a pseudoinverse of a low-rank estimate of the Jacobian, which is expressed in terms of a generalized set of directional derivatives with directions that are given from a Krylov subspace approximation. The approach allows a tunable and adaptive approximation that can take advantage of efficient preconditioning techniques. The proposed kernel approximation for the integration of the electronic equations of motion makes it possible to apply extended Lagrangian first-principles molecular dynamics simulations to a broader range of problems, including reactive chemical systems with numerically sensitive and unsteady charge solutions. This can be achieved without requiring exact full calculations of the inverse Jacobian kernel in each time step or relying on iterative non-linear self-consistent field optimization of the electronic ground state prior to the force evaluations as in regular direct Born–Oppenheimer molecular dynamics. We note the low-rank approximation of the Jacobian is directly related to Broyden’s class of quasi-Newton algorithms and Jacobian-free Newton–Krylov methods and provides a complementary formulation for the solution of nonlinear systems of equations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Synechocystis sp. PCC 6803 Requires the Bidirectional Hydrogenase to Metabolize Glucose and Arginine Under Oxic Conditions

The cyanobacterium Synechocystis sp.PCC 6803 possesses a bidirectional NiFe-hydrogenase, HoxEFUYH. It functions to produce hydrogen under dark, fermentative conditions and photoproduces hydrogen when dark-adapted cells are illuminated. Unexpectedly, we found that the deletion of the large subunit of the hydrogenase (HoxH) in Synechocystis leads to an inability to grow on arginine and glucose under continuous light in the presence of oxygen. This is surprising, as the hydrogenase is an oxygen-sensitive enzyme. In wild-type (WT) cells, thylakoid membranes largely disappeared, cyanophycin accumulated, and the plastoquinone (PQ) pool was highly reduced, whereas ΔhoxH cells entered a dormant-like state and neither consumed glucose nor arginine at comparable rates to the WT. Hydrogen production was not traceable in the WT under these conditions. We tested and could show that the hydrogenase does not work as an oxidase on arginine and glucose but has an impact on the redox states of photosynthetic complexes in the presence of oxygen. It acts as an electron valve as an immediate response to the supply of arginine and glucose but supports the input of electrons from arginine and glucose oxidation into the photosynthetic electron chain in the long run, possibly via the NDH-1 complex. Despite the data presented in this study, the latter scenario requires further proof. The exact role of the hydrogenase in the presence of arginine and glucose remains unresolved. In addition, a unique feature of the hydrogenase is its ability to shift electrons between NAD(H), NADP(H), ferredoxin, and flavodoxin, which was recently shown in vitro and might be required for fine-tuning. Taken together, our data show that Synechocystis> depends on the hydrogenase to metabolize organic carbon and nitrogen in the presence of oxygen, which might be an explanation for its prevalence in aerobic cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Probabilistic structural analysis of adaptive/smart/intelligent space structures

A three-bay, space, cantilever truss is probabilistically evaluated for adaptive/smart/intelligent behavior. For each behavior, the scatter (ranges) in buckling loads, vibration frequencies, and member axial forces are probabilistically determined. Sensitivities associated with uncertainties in the structure, material and load variables that describe the truss are determined for different probabilities. The relative magnitude for these sensitivities are used to identify significant truss variables that control/classify its behavior to respond as an adaptive/smart/intelligent structure. Results show that the probabilistic buckling loads and vibration frequencies increase for each truss classification, with a substantial increase for intelligent trusses. Similarly, the probabilistic member axial forces reduce for adaptive and intelligent trusses and increase for smart trusses.

Pai, Shantaram S.↗

Probabilistic structural analysis of adaptive/smart/intelligent space structures

A three-bay, space, cantilever truss is probabilistically evaluated for adaptive/smart/intelligent behavior. For each behavior, the scatter (ranges) in buckling loads, vibration frequencies, and member axial forces are probabilistically determined. Sensitivities associated with uncertainties in the structure, material and load variables that describe the truss are determined for different probabilities. The relative magnitude for these sensitivities are used to identify significant truss variables that control/classify its behavior to respond as an adaptive/smart/intelligent structure. Results show that the probabilistic buckling loads and vibration frequencies increase for each truss classification, with a substantial increase for intelligent trusses. Similarly, the probabilistic member axial forces reduce for adaptive and intelligent trusses and increase for smart trusses.

Pai, Shantaram S.↗

In vivo volumetric imaging of calcium and glutamate activity at synapses with high spatiotemporal resolution

Studying neuronal activity at synapses requires high spatiotemporal resolution. For high spatial resolution in vivo imaging at depth, adaptive optics (AO) is required to correct sample-induced aberrations. To improve temporal resolution, Bessel focus has been combined with two-photon fluorescence microscopy (2PFM) for fast volumetric imaging at subcellular lateral resolution. To achieve both high-spatial and high-temporal resolution at depth, we develop an efficient AO method that corrects the distorted wavefront of Bessel focus at the objective focal plane and recovers diffraction-limited imaging performance. Applying AO Bessel focus scanning 2PFM to volumetric imaging of zebrafish larval and mouse brains down to 500 µm depth, we demonstrate substantial improvements in the sensitivity and resolution of structural and functional measurements of synapses in vivo. This enables volumetric measurements of synaptic calcium and glutamate activity at high accuracy, including the simultaneous recording of glutamate activity of apical and basal dendritic spines in the mouse cortex.

59 BASIC BIOLOGICAL SCIENCES↗

Near-field infrared microscopy: A novel analytic mapping technique to nanocharacterize calcium silicate-based cement materials

Infrared imaging via scattering-type scanning near-field optical microscopy (s-SNOM) allows chemical mapping of organic and inorganic materials with nanoscale spatial resolution. However, its potential adaptation to the complex multiphase structure of Portland cement is yet to be explored. Here we demonstrate the successful implementation of s-SNOM to spatially resolve coexisting chemical phases in tricalcium silicate, Portland cement's main compound, with 20-nm resolution. We found that s-SNOM is sensitive to different anhydrous polymorphic phases, revealing nanoscale domains that are ‘invisible’ to other microscopic techniques. Furthermore, s-SNOM's ability to distinguish the unhydrated and hydrated phases signifies its great promise as an analytical tool to study the complex hydration process of cement. The key to s-SNOM's application was nano-modifying the surface roughness of the cement samples, allowing nanoscale infrared imaging without topographical artifacts. Our study opens a window for infrared spectral microscopy in cement and other porous inorganic materials.

36 MATERIALS SCIENCE↗

Graph-based quantum response theory and shadow Born–Oppenheimer molecular dynamics

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born–Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. Further, the proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗

Acclimation and Compensating Metabolite Responses to UV-B Radiation in Natural and Transgenic Populus spp. Defective in Lignin Biosynthesis

Plants have evolved to protect leaf mesophyll tissue from damage caused by UV-B radiation by producing an array of UV-absorbing secondary metabolites. Flavonoids (phenolic glycosides) and sinapate esters (hydroxycinnamates) have been implicated as UV-B protective compounds because of the accumulation in the leaf epidermis and the strong absorption in the wavelengths corresponding to UV. Environmental adaptations by plants also generate a suite of responses for protection against damage caused by UV-B radiation, with plants from high elevations or low latitudes generally displaying greater adaptation or tolerance to UV-B radiation. In an effort to explore the relationships between plant lignin levels and composition, the origin of growth elevation, and the hierarchical synthesis of UV-screening compounds, a collection of natural variants as well as transgenic Populus spp. were examined for sensitivity or acclimation to UV-B radiation under greenhouse and laboratory conditions. Noninvasive, ecophysiological measurements using epidermal transmittance and chlorophyll fluorescence as well as metabolite measurements using UPLC-MS generally revealed that the synthesis of anthocyanins, flavonoids, and lignin precursors are increased in Populus upon moderate to high UV-B treatment. However, poplar plants with genetic modifications that affect lignin biosynthesis, or natural variants with altered lignin levels and compositions, displayed complex changes in phenylpropanoid metabolites. A balance between elevated metabolic precursors to protective phenylpropanoids and increased biosynthesis of these anthocyanins, flavonoids, and lignin is proposed to play a role in the acclimation of Populus to UV-B radiation and may provide a useful tool in engineering plants as improved bioenergy feedstocks.

59 BASIC BIOLOGICAL SCIENCES↗

Optical Monitoring of Weld Penetration

Robotic welding controlled by reliable, relatively-noise-free optoelectronic unit. Bounding off meniscus of pool of molten metal, laser beam impinges on position-sensitive photodetector. Beam diameter adjusted for width of weld. Optical filters screen out light from arc. Made from small, low-cost components and utilizing optical fibers to conduct signals, system immune to electromagnetic interference common in industrial environments. Aimed for automatic welders, robot welders in particular and also adaptable to other types of welding, including tungsten/inert-gas, laser, and electron-beam techniques.

Maram, J.↗

Light Isotopes and Trace Organics Analysis of Mars Samples with Mass Spectrometry

Precision measurement of light isotopes in Mars surface minerals and comparison of this isotopic composition with atmospheric gas and other, well-mixed reservoirs such as surface dust are necessary to understand the history of atmospheric evolution from a possibly warmer and wetter Martian surface to the present state. Atmospheric sources and sinks that set these ratios are volcanism, solar wind sputtering, photochemical processes, and weathering. Measurement of a range of trace organic species with a particular focus on species such as amino acids that are the building blocks of terrestrial life are likewise important to address the questions of prebiotic and present or past biological activity on Mars. The workshop topics "isotopic mineralogy" and "biology and pre-biotic chemistry" will be addressed from the point of view of the capabilities and limitations of insitu mass spectrometry (MS) techniques such as thermally evolved gas analysis (TEGA) and gas chromatography (GC) surface experiments using MS, in both cases, as a final chemical and isotopic composition detector. Insitu experiments using straightforward adaptations of existing space proven hardware can provide a substantial improvement in the precision and accuracy of our present knowledge of isotopic composition both in molecular and atomic species in the atmosphere and those chemically bound in rocks and soils. Likewise, detection of trace organic species with greatly improved sensitivity from the Viking GCMS experiment is possible using gas enrichment techniques. The limits to precision and accuracy of presently feasible insitu techniques compared to laboratory analysis of returned samples will be explored. The insitu techniques are sufficiently powerful that they can provide a high fidelity method of screening samples obtained from a diverse set of surface locations such as the subsurface or the interior of rocks for selection of those that are the most interesting for return to Earth.

Mahaffy, P.↗

Temperature-Related Death and Illness

Based on present-day sensitivity to heat, an increase of thousands to tens of thousands of premature heat-related deaths in the summer and a decrease of premature cold-related deaths in the winter are projected each year as a result of climate change by the end of the century. Future adaptation will very likely reduce these impacts (see Changing Tolerance to Extreme Heat Finding). The reduction in cold-related deaths is projected to be smaller than the increase in heat-related deaths in most regions. Days that are hotter than usual in the summer or colder than usual in the winter are both associated with increased illness and death. Mortality effects are observed even for small differences from seasonal average temperatures. Because small temperature differences occur much more frequently than large temperature differences, not accounting for the effect of these small differences would lead to underestimating the future impact of climate change. An increase in population tolerance to extreme heat has been observed over time. Changes in this tolerance have been associated with increased use of air conditioning, improved social responses, and or physiological acclimatization, among other factors. Expected future increases in this tolerance will reduce the projected increase in deaths from heat. Older adults and children have a higher risk of dying or becoming ill due to extreme heat. People working outdoors, the socially isolated and economically disadvantaged, those with chronic illnesses, as well as some communities of color, are also especially vulnerable to death or illness.

winter↗

Simulated impact of fill tube geometry on recent high-yield implosions at the National Ignition Facility

Inertial confinement fusion capsules fielded at the National Ignition Facility are filled with deuterium and tritium fuel by means of a fill tube. The fill tube introduces a low-density pathway into the fuel region of the capsule that allows high Z contaminant to invade the hot spot during the course of the implosion. A recent series of nominally identical high-yield implosions on the NIF has exhibited significant variability in performance. We evaluate the impact of the fill tube in these implosions computationally to determine whether variations in fill tube geometry could have contributed to this variability. The main contrast between the fill tube geometry in the six shots was the outer diameter of the capsule bore hole, a conical hole into which the fill tube is inserted. In our simulations, the geometry of the bore hole can play a significant role in the development of nonlinear flows seeded by the fill tube. Additionally, we find that the amount of space between the bore hole and the fill tube is the primary factor that determines the amount of contaminant jetted into the hot spot by the fill tube and, in turn, the level of yield reduction due to the fill tube in our simulations. As a consequence, some capsules with 5 μm fill tubes are predicted to outperform capsules with 2 μm fill tubes. We also find that micrometer-scale changes to bore hole size can impact fusion yields by up to four times near the ignition threshold. Nevertheless, simulation trends do not reproduce experimental yield trends, suggesting that the fill tube geometry was not the primary factor contributing to the observed variability in performance and that the fill tube could be masking sensitivity to other asymmetries such as other micrometer-scale capsule defects like voids that were not included in our simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Flow separation in shear-layer-driven cavities

A study of the shear-layer flow over a range of open-top cavity configurations is reported. Emphasis is placed on the effect that altering the cavity's span length and aspect ratio has on the development of the shear layer. Computational results are obtained using an interactive method which adapts the compressible boundary-layer model for the flow above the cavity and incompressible Navier-Stokes equations within the enclosure. Interaction of this composite model with the outer, inviscid supersonic flow is also considered in one case. The results show that the location of the stagnation points is sensitive primarily to the variation of the span. When the span was fixed and the aspect ratio varied, the shear layer was nearly unaffected except at aspect ratios less than 0.5. Interaction with the outer flow had a smoothing effect on the shape of the dividing streamline but did not significantly affect the location of the stagnation points.

Brandeis, J.↗

A stochastic model for photon noise induced by charged particles in multiplier phototubes of the space telescope fine guidance sensors

The Space Telescope (ST) is subjected to charged particle strikes in its space environment. ST's onboard fine guidance sensors utilize multiplier phototubes (PMT) for attitude determination. These tubes, when subjected to charged particle strikes, generate spurious photons in the form of Cerenkov radiation and fluorescence which give rise to unwanted disturbances in the pointing of the telescope. A stochastic model for the number of these spurious photons which strike the photocathode of the multiplier phototube which in turn produce the unwanted photon noise are presented. The model is applicable to both galactic cosmic rays and charged particles trapped in the Earth's radiation belts. The model which was programmed allows for easy adaption to a wide range of particles and different parameters for the phototube of the multiplier. The probability density functions for photons noise caused by protons, alpha particles, and carbon nuclei were using thousands of simulated strikes. These distributions are used as part of an overall ST dynamics simulation. The sensitivity of the density function to changes in the window parameters was also investigated.

Howell, L. W.↗

Stochastic model for photon noise induced by charged particles in multiplier phototubes of the Hubble Space Telescope fine guidance sensors

The Space Telescope (ST) is subjected to charged particle strikes in its space environment. ST's onboard fine guidance sensors utilize multiplier phototubes (PMT) for attitude determination. These tubes, when subjected to charged particle strikes, generate spurious photons in the form of Cerenkov radiation and fluorescence which give rise to unwanted disturbances in the pointing of the telescope. A stochastic model for the number of these spurious photons which strike the photocathodes of the multiplier phototube which in turn produce the unwanted photon noise are presented. The model is applicable to both galactic cosmic rays and charged particles trapped in the earth's radiation belts. The model which was programmed allows for easy adaption to a wide range of particles and different parameters for the phototube of the multiplier. The probability density functions for photons noise caused by protons, alpha particles, and carbon nuclei were using thousands of simulated strikes. These distributions are used as part of an overall ST dynamics simulation. The sensitivity of the density function to changes in the window parameters was also investigated.

Howell, L. W.↗

Zonal winds near Venus' cloud top level - A model study of the interaction between the zonal mean circulation and the semidiurnal tide

The Holton (1982) wave-mean flow interaction model's primitive equation is presently adapted in order to clarify the interaction between the semidiurnal tide and the thermally driven mean meridional circulation near cloud top level. The model is found to produce midlatitude jets whose structure is insensitive to vertical shear of the background angular velocity, both above and below cloud top level; a sensitivity to background angular velocity at cloud top level, however, is noted. Agreement between the model tide and either the observed one or that generated by the more detailed calculations of Pechmann and Ingersoll (1984) is found to be greatest when the background angular velocity at the jet level is of the order of 30 percent larger than that which is observed.

Baker, Nancy L.↗

Feature Acquisition with Imbalanced Training Data

This work considers cost-sensitive feature acquisition that attempts to classify a candidate datapoint from incomplete information. In this task, an agent acquires features of the datapoint using one or more costly diagnostic tests, and eventually ascribes a classification label. A cost function describes both the penalties for feature acquisition, as well as misclassification errors. A common solution is a Cost Sensitive Decision Tree (CSDT), a branching sequence of tests with features acquired at interior decision points and class assignment at the leaves. CSDT's can incorporate a wide range of diagnostic tests and can reflect arbitrary cost structures. They are particularly useful for online applications due to their low computational overhead. In this innovation, CSDT's are applied to cost-sensitive feature acquisition where the goal is to recognize very rare or unique phenomena in real time. Example applications from this domain include four areas. In stream processing, one seeks unique events in a real time data stream that is too large to store. In fault protection, a system must adapt quickly to react to anticipated errors by triggering repair activities or follow- up diagnostics. With real-time sensor networks, one seeks to classify unique, new events as they occur. With observational sciences, a new generation of instrumentation seeks unique events through online analysis of large observational datasets. This work presents a solution based on transfer learning principles that permits principled CSDT learning while exploiting any prior knowledge of the designer to correct both between-class and withinclass imbalance. Training examples are adaptively reweighted based on a decomposition of the data attributes. The result is a new, nonparametric representation that matches the anticipated attribute distribution for the target events.

Thompson, David R.↗

Geometrically Flexible and Efficient Flow Analysis of High Speed Vehicles Via Domain Decomposition, Part 1: Unstructured-Grid Solver for High Speed Flows

The ability to solve the equations governing the hypersonic turbulent flow of a real gas on unstructured grids using a spatially-elliptic, 2nd-order accurate, cell-centered, finite-volume method has been recently implemented in the VULCAN-CFD code. This paper describes the key numerical methods and techniques that were found to be required to robustly obtain accurate solutions to hypersonic flows on non-hex-dominant unstructured grids. The methods and techniques described include: an augmented stencil, weighted linear least squares, cell-average gradient method, a robust multidimensional cell-average gradient-limiter process that is consistent with the augmented stencil of the cell-average gradient method and a cell-face gradient method that contains a cell skewness sensitive damping term derived using hyperbolic diffusion based concepts. A data-parallel matrix-based symmetric Gauss-Seidel point-implicit scheme, used to solve the governing equations, is described and shown to be more robust and efficient than a matrix-free alternative. In addition, a y+ adaptive turbulent wall boundary condition methodology is presented. This boundary condition methodology is deigned to automatically switch between a solve-to-the-wall and a wall-matching-function boundary condition based on the local y+ of the 1st cell center off the wall. The aforementioned methods and techniques are then applied to a series of hypersonic and supersonic turbulent flat plate unit tests to examine the efficiency, robustness and convergence behavior of the implicit scheme and to determine the ability of the solve-to-the-wall and y+ adaptive turbulent wall boundary conditions to reproduce the turbulent law-of-the-wall. Finally, the thermally perfect, chemically frozen, Mach 7.8 turbulent flow of air through a scramjet flow-path is computed and compared with experimental data to demonstrate the robustness, accuracy and convergence behavior of the unstructured-grid solver for a realistic 3-D geometry on a non-hex-dominant grid.

White, Jeffery A.↗