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At least 1,585 records · Page 88

Micro- to macroscale perspectives on space plasmas

The Earth's magnetosphere is the most accessible of natural collisionless plasma environments; an astrophysical plasma 'laboratory'. Magnetospheric physics has been in an exploration phase since its origin 35 years ago but new coordinated, multipoint observations, theory, modeling, and simulations are moving this highly interdisciplinary field of plasma science into a new phase of synthesis and understanding. Plasma systems are ones in which binary collisions are relatively negligible and collective behavior beyond the microscale emerges. Most readily accessible natural plasma systems are collisional and nearest-neighbor classical interactions compete with longer-range plasma effects. Except for stars, most space plasmas are collisionless, however, and the effects of electrodynamic coupling dominate. Basic physical processes in such collisionless plasmas occur at micro-, meso-, and macroscales that are not merely reducible to each other in certain crucial ways as illustrated for the global coupling of the Earth's magnetosphere and for the nonlinear dynamics of charged particle motion in the magnetotail. Such global coupling and coherence makes the geospace environment, the domain of solar-terrestrial science, the most highly coupled of all physical geospheres.

Eastman, Timothy E.↗

Studies on nonequilibrium phenomena in supersonic chemically reacting flows

This study deals with a systematic investigation of nonequilibrium processes in supersonic combustion. The two-dimensional, elliptic Navier-Stokes equations are used to investigate supersonic flows with nonequilibrium chemistry and thermodynamics, coupled with radiation, for hydrogen-air systems. The explicit, unsplit MacCormack finite-difference scheme is used to advance the governing equations in time, until convergence is achieved. For a basic understanding of the flow physics, premixed flows undergoing finite rate chemical reactions are investigated. Results obtained for specific conditions indicate that the radiative interactions vary substantially, depending on reactions involving HO2 and NO species, and that this can have a noticeable influence on the flowfield. The second part of this study deals with premixed reacting flows under thermal nonequilibrium conditions. Here, the critical problem is coupling of the vibrational relaxation process with the radiative heat transfer. The specific problem considered is a premixed expanding flow in a supersonic nozzle. Results indicate the presence of nonequilibrium conditions in the expansion region of the nozzle. This results in reduction of the radiative interactions in the flowfield. Next, the present study focuses on investigation of non-premixed flows under chemical nonequilibrium conditions. In this case, the main problem is the coupled turbulence-chemistry interaction. The resulting formulation is validated by comparison with experimental data on reacting supersonic coflowing jets. Results indicate that the effect of heat release is to lower the turbulent shear stress and the mean density. The last part of this study proposes a new theoretical formulation for the coupled turbulence-radiation interactions. Results obtained for the coflowing jets experiment indicate that the effect of turbulence is to enhance the radiative interactions.

Tiwari, S. N.↗

A new approach to the study of the turbulence layer

Turbulent thermal convection is of considerable importance in fluid dynamical transport phenomena occurring, for example, in the planetary boundary layer of the Earth, the interiors of stars, and accretion disks. In particular, during a significant portion of the evolutionary phase of many stars having convectively unstable cores or outer envelopes, a substantial fraction of energy is transported from the central layers to the outer layers by thermal convection. Moreover, as much of the interior of a star is in highly turbulent motion, a complete theory of stellar structure and evolution requires the explicit consideration of turbulence in order to have expressions for the turbulent quantities arising in the stellar structure equations, and particularly, the turbulent fluxes that appear in the total flux conservation equation, such as the convective flux, kinetic energy flux, etc. A reliable quantification of these fluxes continues to present a challenge in astrophysical fluid dynamics, primarily because astrophysical turbulence is almost always fully-developed and nearly inviscid, and therefore governed by strong nonlinear interactions that distribute the energy among a very wide spectrum of eddies with scales ranging from the characteristic dimension of the flow to those sufficiently small to be affected by viscous dissipation. Furthermore, astrophysical flows are invariably compressible, anisotropic, and inhomogeneous, which requires the consideration of the dynamics of longitudinal modes and their interaction with the transverse modes, as well as complicated boundary conditions. In order to reach a compromise between analytical and numerical tractability and the basic physics of turbulent convection, we have constructed a model of stationary turbulent convection that yields various turbulence statistics, including the convective flux, that are required in stellar evolution models.

Levenson, Ruth A.↗

A test of a vortex method for the computation of flap side edge noise

Upon approach to landing, a major source location of airframe noise occurs at the side edges of the part span, trailing edge flaps. In the vicinity of these flaps, a complex arrangement of spanwise flow with primary and secondary tip vortices may form. Each of these vortices is observed to become fully three-dimensional. In the present study, a numerical model is developed to investigate the noise radiated from the side edge of a flap. The inherent three-dimensionality of this flow forces us to carefully consider a numerical scheme which will be both accurate in its prediction of the flow acoustics and also computationally efficient. Vortex methods have offered a fast and efficient means of simulating many two and three-dimensional, vortex dominated flows. In vortex methods, the time development of the flow is tracked by following exclusively the vorticity containing regions. Through the Biot-Savart law, knowledge of the vorticity field enables one to obtain flow quantities at any desired location during the flow evolution. In the present study, a numerical procedure has been developed which incorporates the Lagrangian approach of vortex methods into a calculation for the noise radiated by a flow-surface interaction. In particular, the noise generated by a vortex in the presence of a flat half plane is considered. This problem serves as a basic model of flap edge flow. It also permits the direct comparison between our computed results and previous acoustic analyses performed for this problem. In our numerical simulations, the mean flow is represented by the complex potential W(z) = Aiz(exp l/2), which is obtained through conformal mapping techniques. The magnitude of the mean flow is controlled by the parameter A. This mean flow has been used in the acoustic analysis by Hardin and is considered a reasonable model of the flow field in the vicinity of the edge and away from the leading and trailing edges of the flap. To represent the primary vortex which occurs near the flap, a point vortex is introduced just below the flat half plane. Using a technique from panel methods, boundary conditions on the flap surface are satisfied by the introduction of a row of stationary point vortices along the extent of the flap. At each time step in the calculation, the strength of these vortices is chosen to eliminate the normal velocity at intermediary collocation points. The time development of the overall flow field is then tracked using standard techniques from vortex methods. Vortex trajectories obtained through this computation are in good agreement with those predicted by the analytical solution given by Hardin, thus verifying the viability of this procedure for more complex flow arrangements. For the flow acoustics, the Ffowcs Williams-Hawkings equation is numerically integrated. This equation supplies the far field acoustic pressure based upon pressures occurring along the flap surface. With our vortex method solution, surface pressures may be obtained with exceptional resolution. The Ffowcs Williams-Hawkings equation is integrated using a spatially fourth order accurate Simpson's rule. Rational function interpolation is used to obtain the surface pressures at the appropriate retarded times. Comparisons between our numerical results for the acoustic pressure and those predicted by the Hardin analysis have been made. Preliminary results indicate the need for an improved integration technique. In the future, the numerical procedure developed in this study will be applied to the case of a rectangular flap of finite thickness and ultimately modified for application to the fully three-dimensional problem.

Martin, James E.↗

A Comparison of Three-Dimensional Simulations of Traveling-Wave Tube Cold-Test Characteristics Using CST MICROWAVE STUDIO and MAFIA

Previously, it was shown that MAFIA (solutions of Maxwell's equations by the Finite Integration Algorithm), a three-dimensional simulation code, can be used to produce accurate cold-test characteristics including frequency-phase dispersion, interaction impedance, and attenuation for traveling-wave tube (TWT) slow-wave structures. In an effort to improve user-friendliness and simulation time, a model was developed to compute the cold-test parameters using the electromagnetic field simulation software package CST MICROWAVE STUDIO (MWS). Cold-test parameters were calculated for several slow-wave circuits including a ferruled coupled-cavity, a folded waveguide, and a novel finned-ladder circuit using both MWS and MAFIA. Comparisons indicate that MWS provides more accurate cold-test data with significantly reduced simulation times. Both MAFIA and MWS are based on the finite integration (FI) method; however, MWS has several advantages over MAFIA. First, it has a Windows based interface for PC operation, making it very user-friendly, whereas MAFIA is UNIX based. MWS uses a new Perfect Boundary Approximation (PBA), which increases the accuracy of the simulations by avoiding stair step approximations associated with MAFIA's representation of structures. Finally, MWS includes a Visual Basic for Applications (VBA) compatible macro language that enables the simulation process to be automated and allows for the optimization of user-defined goal functions, such as interaction impedance.

Chevalier, C. T.↗

Prototype Videodisk-Based Part-Task Thermal Imaging Trainer

Thermal images, or infrared images, are representations of the world based on heat, instead of visible light. Research has shown that the resulting thermal image results in perceptual differences leading to difficulties in interpretation (e.g., the determination of slope angle, concavity/convexity), or increased identification latencies. A joint research project between the United States (NASA and U.S. Army) and Israel (Ministry of Defense and Israel Air Force) has resulted in the development of a prototype part-task trainer for the acquisition of perceptual skills associated with thermal imaging usage. This prototype system is videodisk-based under computer control, using recordings of thermal images. A lesson section introduces declarative knowledge, in which the basic physics and heuristics of thermal imagery are taught. An exercise section teaches procedural knowledge, with the user viewing dynamic, actual imagery, with an interactive detection/location determination task. The general philosophy and design of the trainer will be demonstrated.

Brickner, Michael S.↗

Comparative Ecology of H2 Cycling in Organotrophic and Phototrophic Ecosystems

The simple biochemistry of H2 is critical to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. The sensitivity of these many processes to H2 can be described quantitatively, at a basic thermodynamic level. This shared dependence on H2 may provide a means for interpreting the ecology and system-level biogeochemistry of widely variant microbial ecosystems on a common (and quantitative) level. Understanding the factors that control H2 itself is a critical prerequisite. Here, we examine two ecosystems that vary widely with respect to H2 cycling. In anoxic, 'organotrophic' sediments from Cape Lookout Bight (North Carolina, USA), H2 partial pressures are strictly maintained at low, steady-state levels by H2-consuming organisms, in a fashion that can be quantitatively predicted by simple thermodynamic calculations. In phototrophic microbial mats from Baja, Mexico, H2 partial pressures are instead controlled by the activity of light-sensitive H2-producing organisms. In consequence, H2 partial pressures within the system fluctuate by orders of magnitude on hour-long time scales. The differences in H2 cycling subsequently impact H2-sensitive microbial processes, such as methanogenesis. For example, the presence of sulfate in the organotrophic system always yielded low levels of H2 that were inhibitory to methanogenesis; however, the elevated levels of H2 in the phototrophic system favored methane production at significant levels, even in the presence of high sulfate concentrations. The myriad of other H2-sensitive microbial processes are expected to exhibit similar behavior.

Hoehler, Tori M.↗

A Cognitive-System Model for En Route Air Traffic Management

NASA Ames Research Center has been engaged in the development of advanced air traffic management technologies whose basic form is cognitive aiding systems for air traffic controller and flight deck operations. In the design and evaluation of such systems the dynamic interaction between the airborne aiding system and the ground-based aiding systems forms a critical coupling for control. The human operator is an integral control element in the system and the optimal integration of human decision and performance parameters with those of the automation aiding systems offers a significant challenge to cognitive engineering. This paper presents a study in full mission simulation and the development of a predictive computational model of human performance. We have found that this combination of methodologies provide a powerful design-aiding process. We have extended the computational model Man Machine Integrated Design and Analysis System (N13DAS) to include representation of multiple cognitive agents (both human operators and intelligent aiding systems), operating aircraft airline operations centers and air traffic control centers in the evolving airspace. The demands of this application require the representation of many intelligent agents sharing world-models, and coordinating action/intention with cooperative scheduling of goals and actions in a potentially unpredictable world of operations. The operator's activity structures have been developed to include prioritization and interruption of multiple parallel activities among multiple operators, to provide for anticipation (knowledge of the intention and action of remote operators), and to respond to failures of the system and other operators in the system in situation-specific paradigms. We have exercised this model in a multi-air traffic sector scenario with potential conflict among aircraft at and across sector boundaries. We have modeled the control situation as a multiple closed loop system. The inner and outer loop alerting structure of air traffic management has many implications that need to be investigated to assure adequate design. First, there are control and stability factors implicit in the design. As the inner loop response time approaches that of the outer loop, system stability may be compromised in that controllers may be solving a problem the nature of which has already been changed by pilot action. Second, information exchange and information presentation for both air and ground must be designed to complement as opposed to compete with each other. Third, the level of individual and shared awareness in trajectory modification and flight conformance needs to be defined. Fourth, the level of required awareness and performance impact of mixed fleet operations and failed-mode recovery must be explored.

Corker, Kevin M.↗

EngineSim: Turbojet Engine Simulator Adapted for High School Classroom Use

EngineSim is an interactive educational computer program that allows users to explore the effect of engine operation on total aircraft performance. The software is supported by a basic propulsion web site called the Beginner's Guide to Propulsion, which includes educator-created, web-based activities for the classroom use of EngineSim. In addition, educators can schedule videoconferencing workshops in which EngineSim's creator demonstrates the software and discusses its use in the educational setting. This software is a product of NASA Glenn Research Center's Learning Technologies Project, an educational outreach initiative within the High Performance Computing and Communications Program.

Petersen, Ruth A.↗

Interface Anywhere: Development of a Voice and Gesture System for Spaceflight Operations

The Interface Anywhere Project was funded through Innovation Charge Account (ICA) at NASA JSC in the Fall of 2012. The project was collaboration between human factors and engineering to explore the possibility of designing an interface to control basic habitat operations through gesture and voice control; (a) Current interfaces require the users to be physically near an input device in order to interact with the system; and (b) By using voice and gesture commands, the user is able to interact with the system anywhere they want within the work environment.

Thompson, Shelby↗

A Semantic Basis for Proof Queries and Transformations

We extend the query language PrQL, designed for inspecting machine representations of proofs, to also allow transformation of proofs. PrQL natively supports hiproofs which express proof structure using hierarchically nested labelled trees, which we claim is a natural way of taming the complexity of huge proofs. Query-driven transformations enable manipulation of this structure, in particular, to transform proofs produced by interactive theorem provers into forms that assist their understanding, or that could be consumed by other tools. In this paper we motivate and define basic transformation operations, using an abstract denotational semantics of hiproofs and queries. This extends our previous semantics for queries based on syntactic tree representations.We define update operations that add and remove sub-proofs, and manipulate the hierarchy to group and ungroup nodes. We show that

Proof Queries↗

Structures of Bacterial Biosynthetic Arginine Decarboxylases

Biosynthetic arginine decarboxylase (ADC; also known as SpeA) plays an important role in the biosynthesis of polyamines from arginine in bacteria and plants. SpeA is a pyridoxal-5'-phosphate (PLP)-dependent enzyme and shares weak sequence homology with several other PLP-dependent decarboxylases. Here, the crystal structure of PLP-bound SpeA from Campylobacter jejuni is reported at 3.0 {angstrom} resolution and that of Escherichia coli SpeA in complex with a sulfate ion is reported at 3.1 {angstrom} resolution. The structure of the SpeA monomer contains two large domains, an N-terminal TIM-barrel domain followed by a {beta}-sandwich domain, as well as two smaller helical domains. The TIM-barrel and {beta}-sandwich domains share structural homology with several other PLP-dependent decarboxylases, even though the sequence conservation among these enzymes is less than 25%. A similar tetramer is observed for both C. jejuni and E. coli SpeA, composed of two dimers of tightly associated monomers. The active site of SpeA is located at the interface of this dimer and is formed by residues from the TIM-barrel domain of one monomer and a highly conserved loop in the {beta}-sandwich domain of the other monomer. The PLP cofactor is recognized by hydrogen-bonding, {pi}-stacking and van der Waals interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of CO2 behavior on rutile TiO2 (110) surface

The dynamic behavior of carbon dioxide (CO2) adsorbed on the rutile TiO2 (110) surface is studied by dispersion-corrected density functional theory (DFT) and combined ab initio molecular dynamics (AIMD). Understanding he behavior of CO2 is important regarding possible applications for treating CO2 in current environmental problems along with the consideration as a renewable energy source. Concerning the ability as a redusible support of TiO2 surface, a fundamental understanding of the interaction between CO2 and TiO2 surface will help extending the possibile applications. In the current study, CO2 interaction and dynamics behavior on the TiO2 surface is characterized including he effect of the oxygen vacancy (OV) defect. Also the coverage dependence of CO2 behavior is investigated since more contribution of the intermolecular interaction among CO2 molecules can be expected as the coverage increasing. This work is supported by the US Department of Energy (DOE), Office of Basic Science, Division of Chemical Sciences, Geosicences and Biosciences. Pacific Northwest National Laboratory (PNNL) is multiprogram national laboratory operated for DOE by Battelle. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

ab initio molecular dynamics↗

Three-Beam Instabilily in the LHC

In the LHC, a transverse instability has been regularly observed at 4 TeV right after the beta-squeeze, when the beams are separated by ten transverse rms sizes, and only one of the two beams is seen as oscillating. According to the author, only a single hypothesis appeared to be consistent with all the observations and basic concepts, one about a third beam - an electron cloud, generated by the two proton beams in the high-beta areas of the interaction regions. The instability results from a combined action of the cloud nonlinear focusing and impedance.

43 PARTICLE ACCELERATORS↗

Speculations about e-cloud instabilities in the LHC

In the LHC, a transverse instability is regularly observed at 4TeV right after the beta-squeeze, when the beams are separated by about their ten transverse rms sizes [1-3], and only one of the two beams is seen as oscillating. So far only a single hypothesis is consistent with all the observations and basic concepts, one about a third beam - an electron cloud, generated by the two proton beams in the high-beta areas of the interaction regions.

Burov, Alexey↗

Targeting diverse protein–protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold

Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. In this paper, we describe a strategy for designing oligomers containing both α- and β-amino acid residues (“α/β-peptides”) that mimic several peptides derived from the three-helix bundle “Z-domain” scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF 165 -induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain–mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Finally, such reagents would be useful for diagnostic and therapeutic applications.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput small-angle X-ray scattering reveals effective structure factor transitions linked to high-concentration antibody viscosity

High-concentration monoclonal antibody (mAb) formulations are often constrained by elevated viscosity, largely driven by protein–protein interactions, which complicates manufacturing and limits subcutaneous delivery. Early viscosity risk assessment is essential during discovery, yet traditional measurements require large sample volumes, and lack high-throughput capability. Here, we develop a high-throughput small-angle X-ray scattering (SAXS) protocol to detect mAb self-association at dilute concentrations, enabling early predictive insights into high-concentration viscosity. Synchrotron SAXS measurements were conducted for 21 mAbs formulated in a histidine buffer at pH 6.0. An initial subset of 10 mAbs analyzed across 1–150 mg/mL revealed that effective structure factor transitions in the low-q region, indicative of interparticle interactions, consistently emerged below 25 mg/mL. Subsequently, 11 additional mAbs were analyzed at 1–25 mg/mL using automated liquid handling and flow cells to enable high-throughput screening. High-viscosity mAbs exhibited detectable low-q upturns at concentrations ≤10 mg/mL, whereas low-viscosity mAbs showed downturns. A classification criterion based on effective structure factor transitions accurately classified all high- and low-viscosity mAbs at 150 mg/mL, offering a scalable, sample-efficient alternative to conventional methods. These results extend recent findings on the concentration-dependent sensitivity of SAXS to short-range attractions, demonstrating that they can emerge at lower concentrations than previously reported. This study presents the most comprehensive and diverse SAXS dataset for mAbs reported to date within a single formulation, providing a valuable resource for developing and validating coarse-grained models that can more accurately capture intermolecular interactions governing high-concentration solution behavior, thereby enabling rational antibody engineering and improved developability.

36 MATERIALS SCIENCE↗

Structures of Coxsackievirus, Rhinovirus, and Poliovirus Polymerase Elongation Complexes Solved by Engineering RNA Mediated Crystal Contacts

RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2–2.9 Å resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight base-pairs of the nascent duplex, a fully prepositioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.

59 BASIC BIOLOGICAL SCIENCES↗