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At least 1,207 records · Page 67

Discovery top-down proteomics in symbiotic soybean root nodules

Proteomic methods have been widely used to study proteins in complex biological samples to understand biological molecular mechanisms. Most well-established methods (known as bottom-up proteomics, BUP) employ an enzymatic digestion step to cleave intact proteins into smaller peptides for liquid chromatography (LC) mass spectrometry (MS) detection. In contrast, top-down proteomics (TDP) directly characterizes intact proteins including all possible post-translational modifications (PTMs), thus offering unique insights into proteoform biology where combinations of individual PTMs may play important roles. We performed TDP on soybean root nodules infected by the symbiotic Bradyrhizobium japonicum in both the wildtype bacterium and a nifH- mutant, which lacks the ability to fix nitrogen in the soybean root nodule. TDP captured 1648 proteoforms derived from 313 bacterial genes and 178 soybean genes. Leghemoglobin, the most abundant protein in the sample, existed in many truncated proteoforms. Interestingly, these truncated proteoforms were considerably more abundant in the wildtype relative to the nifH- mutant, implicating protease activity as an important factor in nitrogen fixation. Proteoforms with various PTMs and combinations thereof were identified using an unrestricted open modification search. This included less common PTMs such as myristoylation, palmitoylation, cyanylation, and sulfation. In parallel, we collected high resolution MS imaging (MSI) data of intact proteins and biopolymers (<20 kDa due to current technical limitations) from sections of the soybean root nodules using matrix-assisted laser desorption/ionization (MALDI) coupled to high resolution Orbitrap. Several detected proteoforms exhibited unique spatial distributions inside the infection zone and cortex, suggesting functional compartmentalization in these regions. A subset of peaks from the MALDI-MSI were assigned to proteoforms detected in TDP LCMS data based on matching accurate masses. Many of the proteins detected in both LCMS and MALDI-MSI are currently uncharacterized in UniProt: the PTM and spatial information presented here will be valuable in understanding their biological functions. Taken together, our study demonstrates how untargeted TDP approach can provide unique insights into plant proteoform biology. On-going technology developments are expected to further improve TDP coverage for more comprehensive high-throughput analysis of proteoforms.

59 BASIC BIOLOGICAL SCIENCES↗

Three-dimension heat transfer program

An IBM 7094, three dimensional, heat transfer program for satellite application is discussed. The program may be applied to all phases of spacecraft life, from launch to orbital quasi-steady state. Launch phase heating includes inputs by radiation from the hot fairing and free molecule flow heating after nose cone ejection. Orbital heat fluxes are accounted for by direct sunlight, earth-reflected sunlight, and earth-emitted input to the satellite. Internal heat exchange by conduction and radiation is determined, provided the appropriate conductances, radiation view factors, and effective emittances are known. A simplified analysis of an active thermal controlled spacecraft is incorporated into the program. One or more surfaces may contain shutter systems which have optical properties specified as a function of shutter opening. The program evaluates the feasibility of any configuration based upon maintaining an internal component within its tolerable temperature limits. The program employs a matrix inversion subroutine (Gauss Elimination Method) to solve the heat balance equations.

COMPUTER PROGRAM↗

Manufacturing in space.

Space, in contrast to earth, offers total gravity control and unequaled vacuum, temperature, pressure, and radiation characteristics. In zero-g molecular forces such as cohesion and adhesion become controlling factors even in the largest bulk processes. The absence of relative mass accelerations eliminates the need for support of solid matter. Stability in liquid-solid, liquid-liquid, or liquid-gas mixtures, and the absence of thermal convection is obtained because there is no relative motion in fluids due to differences in density. Applications of these characteristics include liquid-matrix preparation of composites, fine-grain castings, supersaturated alloys, combinations which exhibit liquid-phase immiscibility, the containerless free suspension of materials, surface-tension casting, surface-tension drawing, adhesion casting, and controlled density casting.

Wuenscher, H. F.↗

Avionics/crew station integration

The U.S. Navy has been encouraging advanced development concepts aimed at increasing the aircraft instrumentation performance for multi-platform applications of 1990's weapons systems. The three areas covered by the Navy's research and development effort are: System Integration, Technology, and Human Factors. The System Integration objectives are to produce a system architecture easily adaptable to many platforms. Technology objectives are to determine the state of the art for displays, electronics, and controls. The Human Factors objectives are to determine the proper human-machine interfaces so that the ultimate crew station will be capable of providing the pilot with the proper display and controls performance to satisfy the diverse requirements of a fighter, attack, ASW, fixed-wing, rotary-wing, and V/STOL platforms in both a one-man crew or two-man crew matrix. All data/control interface among units of this crew station and other platform subsystems will be via digital data buses and video multiplex buses. No individual discrete signal, data, or control lines will be needed. This paper discusses the six interfaces necessary to ensure the optimum development of this crew station, the predicted platform mission improvements, and the requisite life-cycle cost considerations. This concept will serve as a basis for planning the integration of the necessary hardware and software features in current and future weapons systems.

Mulley, W. G.↗

Linearization of manipulator dynamics using spatial operators

Linearized dynamics models for manipulators are useful in robot analysis, motion planning, and control applications. Techniques from the spatial operator algebra are used to obtain closed form operator expressions for two types of linearized dynamics models, the linearized inverse and forward dynamics models. Spatially recursive algorithms of O(n) and O(n-squared) complexity for the computation of the perturbation vector and coefficient matrices for the linearized inverse dynamics model are developed first. Subsequently, operator factorization and inversion identities are used to develop corresponding closed-form expressions for the linearized forward dynamics model (LFDM). Once again, these are used to develop algorithms of O(n) and O(n-squared) complexity for the computation of the perturbation vector and the coefficient matrices. The algorithms for the LFDM do not require the explicit computation of the mass matrix nor its numerical inversion and are also of lower complexity than the conventional O(n-cubed) algorithms.

Jain, A.↗

High-Time-Resolution Study of Magnetic Holes in the Solar Wind

The objectives of this investigation are to determine the internal plasma structure of kinetic-scale and larger scale magnetic holes, and to determine their stability, their source mechanism(s), and their spatial extent. It is also of importance to determine the relationship between kinetic-scale holes and long-duration holes. As smaller and smaller magnetic depressions are investigated in order to make this a complete study, a robust criterion is necessary for distinguishing magnetic holes from random or unresolvable fluctuations in the interplanetary magnetic field. In order to resolve this ambiguity, we obtained from the MFI experiments magnetic field measurements from the WIND spacecraft at a time resolution of 46 to 184 ms over certain periods. We have also devised a measure of certainty for magnetic hole detections. The certainty factor, q, is defined as the difference between the mean magnetic field in the hole and the local magnetic field, in units of the local standard deviation of the field strength. For fullest generality, it is necessary to calculate this q over the range of available scales of interest, from 60 ms up to 300 s. This technique establishes a two dimensional matrix of relative probabilities that a hole of some duration (d) might exist in the data set at a given time (t). In identifying q-peaks in time and duration, we also come upon a natural method for distinguishing holes with internal structure from multiple holes in close proximity or holes nested inside of others. If two q-peaks are more than a half-width apart, they are simply said to be separate events.

Lazarus, Alan↗

Scaling of Imbibition Front Dynamics in Heterogeneous Porous Media

Here we report a quantitative study on the dynamics of countercurrent imbibition in fractured rock samples with the application of CO 2 geosequestration, as the rock matrix is saturated with CO 2 and brine exists in the adjacent microfracture. Direct pore-scale simulations of spontaneous and forced imbibition in a three-dimensional heterogeneous porous matrix enable us to capture the effect of microscopic properties on the imbibition dynamics as these pore-level descriptions are ignored in the existing coarse-grained models. We have established new scaling classes for the propagation of the center of mass of the imbibition front and fluid-fluid interface broadening. It has become evident that the wettability is a major factor which leads to anomalies in these scaling laws. While the governing capillarity under the water-wet condition induces fast roughening dynamics of the interface, the adverse effect of capillary pressure under the intermediate-wet condition leads to a damping effect on the imbibition front fluctuations.

58 GEOSCIENCES↗

Intrinsic quality factor extraction of multi-port cavity with arbitrary coupling

In this work, we derived S-parameter based expressions for the intrinsic quality factor of an arbitrary coupled multiport microwave cavity and a non-ideal test fixture. Practical accuracy limitations of the obtained expressions specifically for superconducting accelerator cavities were evaluated both analytically and with the simulation software. The resulting formulas can be used to extract the intrinsic quality factor of normal-conducting and superconducting cavities directly from the calibrated S-parameter measurements.

43 PARTICLE ACCELERATORS↗

Bottomonium suppression from the three-loop QCD potential

We compute the suppression of bottomonium in the quark-gluon plasma using the three-loop QCD static potential. The potential describes the spin-averaged bottomonium spectrum below threshold with a less than 1% error. Within potential nonrelativistic quantum chromodynamics and an open quantum systems framework, we compute the evolution of the bottomonium density matrix. The values of the quarkonium transport coefficients are obtained from lattice QCD measurements of the bottomonium in-medium width and thermal mass shift; we additionally include for the first time a vacuum contribution to the dispersive coefficient γ . Using the three-loop potential and the values of the heavy quarkonium transport coefficients, we find that the resulting bottomonium nuclear modification factor is consistent with experimental observations, while at the same time reproducing the lattice measurements of the in-medium width. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Fracture and crack growth in orthotropic laminates

An approximate solution is developed for the determination of the interlaminar normal and shear stresses in the vicinity of a crack in a three dimensional composite containing unidirectional linearly elastic fibers in an infinite linearly elastic matrix. In order to reduce the complexity of the formulation, certain assumptions are made as to the physically significant stresses to be retained. These simplifications reduce the partial differential equations of elasticity to differential-difference equations which are tractable using Fourier transform techniques. The potential for damaged or debonded zones to be generated by an embedded crack is discussed, and stress concentration factors for fibers near the crack are given. Detailed comparisons are made between the present solution, the analogous two dimensional problem, and corresponding shear-lag models.

Goree, J. G.↗

HITCAN for actively cooled hot-composite thermostructural analysis

A computer code, high temperature composite analyzer (HITCAN), was developed to analyze/design hot metal matrix composite structures. HITCAN is a general purpose code for predicting the global structural and local stress-strain response of multilayered (arbitrarily oriented) metal matrix structures both at the constituent (fiber, matrix, and interphase) and the structural level, including the fabrication process effects. The thermomechanical properties of the constituents are considered to be nonlinearly dependent on several parameters, including temperature, stress, and stress rate. The computational procedure employs an incremental iterative nonlinear approach utilizing a multifactor-interaction material behavior model, i.e., the material properties are expressed in terms of a product of several factors that affect the properties. HITCAN structural analysis capabilities (static, load stepping - a multistep static analysis with material properties updated at each step, modal, and buckling) for cooled hot structures are demonstrated through a specific example problem.

Chamis, C. C.↗

HITCAN for actively cooled hot-composite thermostructural analysis

A computer code, high temperature composite analyzer (HITCAN), was developed to analyze/design hot metal matrix composite structures. HITCAN is a general purpose code for predicting the global structural and local stress-strain response of multilayered (arbitrarily oriented) metal matrix structures both at the constituent (fiber, matrix, and interphase) and the structural level, including the fabrication process effects. The thermomechanical properties of the constituents are considered to be nonlinearly dependent on several parameters, including temperature, stress, and stress rate. The computational procedure employs an incremental iterative nonlinear approach utilizing a multifactor-interaction material behavior model, i.e., the material properties are expressed in terms of a product of several factors that affect the properties. HITCAN structural analysis capabilities (static, load stepping - a multistep static analysis with material properties updated at each step, modal, and buckling) for cooled hot structures are demonstrated through a specific example problem.

Chamis, C. C.↗

The effects of stress and physical aging on the creep compliance of a polymeric composite

An experimental study was performed to determine the effects of stress and physical aging on the matrix dominated viscoelastic properties of IM7/8320, a high temperature fiber reinforced thermoplastic composite. Established creep/aging test techniques developed for polymers were adapted for testing of the composite material. The transverse and shear compliance for an orthotropic plate were found from creep compliance measurements at constant, sub-Tg temperatures. These compliance terms were shown to be effected by physical aging. Aging time shift factors and shift rates were found to be a function of applied stress.

Gates, Thomas E.↗

Humans to Mars, but How Many? Trade Space Analyses for Mars Mission Crew Size

Missions to Mars will differ from previous human spaceflight missions in that the crew of astronauts will be required to operate in an Earth-independent manner due to the long communication delays. Without a systematic, repeatable process to determine the number and composition of crew necessary to successfully accomplish these missions, NASA increases the risk that crew sizes may be too small to meet primary mission objectives under nominal conditions and, more consequentially, that crewmembers may not have the expertise needed to successfully respond to unforeseen failures without the real-time expertise of the Mission Control Central (MCC) team NASA currently relies upon. The NASA Engineering and Safety Center (NESC) developed a methodology for assessing the trade space of factors that affect the number of crew for Mars missions based on human performance and expertise modeling. This methodology includes the consideration of results from three human performance models developed using the Improved Performance Research and Integration Tool (IMPRINT) modeling platform as well as a custom-built model on expertise trained within the crew based on NASA’s crew qualification and responsibilities matrix (CQRM). We present example model results and discuss implications on trade space analyses for Mars mission crew size.

Mars Mission↗

Development of Segregated Thermal-Hydraulics Solvers in MOOSE

The simulation of fluid flows is an essential part of the design and analysis of nuclear systems. Algorithms able to simulate flows at different fidelity levels are available in the Multiphysics Object-Oriented Simulation Environment (MOOSE) and MOOSE-based applications such as Pronghorn \cite{novak2018pronghorn}, Pronghorn-Subchannel, RELAP-7, and SAM. Currently, significant effort is being invested in the development of coarse-mesh Computational Fluid Dynamics (CFD) capabilities within MOOSE and Pronghorn for the simulation of Generation IV nuclear reactors. Traditionally, the solution algorithms in MOOSE have relied on Newton or quasi-Newton methods (such as the preconditioned Jacobian-free Newton-Krylov method) where residuals and Jacobians (or approximations thereof) are constructed. Both Newton and quasi-Newton methods require the solution of a linear system at each nonlinear Newton iteration with the Jacobian as the system matrix. The Jacobian contains blocks originating from all variables in the problem (i.e., for thermal-hydraulics at least pressure, velocities, and temperature). Due to the formulation of the problem in a general multiphysics setting on unstructured mesh, creating a good preconditioner for the linear system can be challenging, thus many fluid applications have utilized direct solver-based methods such as LU factorization. However, with increasing system size and complexity in multi-dimensional problems, the direct solution of linear systems becomes computationally expensive both in execution time and and memory. For this reason, recent effort has focused on adapting segregated solution algorithms for CFD problems in MOOSE. These algorithms use fixed-point iteration between segregated systems whose assembly and preconditioning are easier those of the monolithic system. Initial results show that the segregated solution algorithm outperforms the monolithic approach in terms of memory usage and for large 3D problems in terms of CPU time as well.

42 ENGINEERING↗

Development of Segregated Thermal-Hydraulics Solvers in MOOSE

The simulation of fluid flows is an essential part of the design and analysis of nuclear systems. Algorithms able to simulate flows at different fidelity levels are available in the Multiphysics Object-Oriented Simulation Environment (MOOSE) and MOOSE-based applications such as Pronghorn \cite{novak2018pronghorn}, Pronghorn-Subchannel, RELAP-7, and SAM. Currently, significant effort is being invested in the development of coarse-mesh Computational Fluid Dynamics (CFD) capabilities within MOOSE and Pronghorn for the simulation of Generation IV nuclear reactors. Traditionally, the solution algorithms in MOOSE have relied on Newton or quasi-Newton methods (such as the preconditioned Jacobian-free Newton-Krylov method) where residuals and Jacobians (or approximations thereof) are constructed. Both Newton and quasi-Newton methods require the solution of a linear system at each nonlinear Newton iteration with the Jacobian as the system matrix. The Jacobian contains blocks originating from all variables in the problem (i.e., for thermal-hydraulics at least pressure, velocities, and temperature). Due to the formulation of the problem in a general multiphysics setting on unstructured mesh, creating a good preconditioner for the linear system can be challenging, thus many fluid applications have utilized direct solver-based methods such as LU factorization. However, with increasing system size and complexity in multi-dimensional problems, the direct solution of linear systems becomes computationally expensive both in execution time and and memory. For this reason, recent effort has focused on adapting segregated solution algorithms for CFD problems in MOOSE. These algorithms use fixed-point iteration between segregated systems whose assembly and preconditioning are easier those of the monolithic system. Initial results show that the segregated solution algorithm outperforms the monolithic approach in terms of memory usage and for large 3D problems in terms of CPU time as well.

42 ENGINEERING↗

The response of accident tolerant fuel cladding to LOCA burst testing: A comparative study of leading concepts

Accident tolerant fuel claddings seek to improve safety margins during loss-of-coolant accident (LOCA) scenarios by reducing cladding steam oxidation rates, hydrogen production, delaying or mitigating cladding burst, and reducing cladding deformation. After rapid and extensive progress in recent years, Cr coated Zr-based alloys, ferritic FeCrAl, and SiC/SiC ceramic matrix composites (CMCs) have emerged as the most promising cladding concepts, but there are few studies comparing the accident tolerance of all three concepts simultaneously. Here, in this study, LOCA burst testing has been conducted on Cr high impulse power magnetron sputtered Zry-4 (Cr/Zry-4), C26M (FeCrAl), and SiC/SiC SiGA (CMC). Experimental observations indicate Cr/Zry-4 burst at higher temperatures than Zry-4 however the effectiveness of the coating on mitigating ZrO 2 formation via Cr 2 O 3 formation depended on physical proximity to the burst opening. No dramatic improvement in diametrical strain nor opening geometry was observed. C26M burst at higher temperatures than Zry-4 at lower pressures, exhibiting small amounts of strain and smaller openings, and formed slow-growing Al 2 O 3 regardless of location. The CMCs did not burst or show any macroscopic signs of deformation, all the way up to an internal cladding pressure of 15.2 MPa. High temperature expanding Nb plug testing indicated that CMC room temperature strength may persist up to 1650°C, with an approximately 40% loss of strength at 1900°C. CMC steam oxidation was also compared to reference chemically vapor deposited SiC up to 1700°C, and CMCs were found to oxidize at slightly accelerated rates that were still orders of magnitude lower than bare Zry-4. Projected H 2 generation during LOCA burst testing showed that when accounting for cladding burst exposing inner diameters to steam, Cr coated Zry-4 reduced H 2 generation by a factor of two compared with bare Zry-4, while both C26M and SiC/SiC reduced H 2 generation by orders of magnitude relative to bare Zry-4.

36 MATERIALS SCIENCE↗

Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis

Pulmonary alveolar microlithiasis is an autosomal recessive lung disease caused by a deficiency in the pulmonary epithelial Npt2b sodium-phosphate co-transporter that results in accumulation of phosphate and formation of hydroxyapatite microliths in the alveolar space. The single cell transcriptomic analysis of a pulmonary alveolar microlithiasis lung explant showing a robust osteoclast gene signature in alveolar monocytes and the finding that calcium phosphate microliths contain a rich protein and lipid matrix that includes bone resorbing osteoclast enzymes and other proteins suggested a role for osteoclast-like cells in the host response to microliths. While investigating the mechanisms of microlith clearance, we found that Npt2b modulates pulmonary phosphate homeostasis through effects on alternative phosphate transporter activity and alveolar osteoprotegerin, and that microliths induce osteoclast formation and activation in a receptor activator of nuclear factor-κB ligand and dietary phosphate dependent manner. This work reveals that Npt2b and pulmonary osteoclast-like cells play key roles in pulmonary homeostasis and suggest potential new therapeutic targets for the treatment of lung disease.

59 BASIC BIOLOGICAL SCIENCES↗