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At least 469 records · Page 26

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

The aim of this paper is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. Finally, this study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamical regimes of vortex flow in type-II superconductors with parallel twin boundaries

We explore the dynamics of driven magnetic flux lines in disordered type-II superconductors in the presence of twin boundaries oriented parallel to the direction of the applied magnetic field, using a three-dimensional elastic line model simulated with Langevin molecular dynamics. The lines are driven perpendicular to the planes to model the effect of an electric current applied parallel to the planes and perpendicular to the magnetic field. A study of the long-time non-equilibrium steady states for varying sample orientation and thickness reveals a rich collection of dynamical regimes spanning the depinning crossover region that separates the pinned and moving-lattice states of vortex matter. We observe the emergence of a preferred direction for the ordering of the Abrikosov lattice in the free- owing vortex regime due to asymmetric pinning by the planar defects. Furthermore, we have performed novel direct measurements of flux line excitations such as half-loops and double kinks to aid the characterization of the topologically rich flux flow profile.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electronic structure and dynamics of confined atoms

Confined atomic systems are of great importance owing a multitude of possible applications in various areas of science and technology. Of particular interest are atoms encaged in the C 60 molecule, A@C 60 , since the near-spherical symmetry of C 60 simplifies theoretical studies, and the stability of C 60 renders it amenable to experimental examination. Herein a review of investigations of the electronic structure and dynamics of A@C 60 is presented in this manuscript focusing on developments in the last decade. Addressed mainly are how the confinement affects electronic structure properties such as ionization potentials, localization of atomic electrons, Shannon entropy, correlation effects, relativistic interactions, and others. In the area of dynamics, photoionization and e-A@C 60 scattering are reviewed and summarized, and the major effects of confinement on the dynamical properties, e.g., confinement resonances, hybridization, Wigner time delay, are delineated.

74 ATOMIC AND MOLECULAR PHYSICS↗

DYNAMIC - The Nonlinear Dynamical Network Simulator v. 0.1

The purpose of the DYNAMIC software system is to perform simulations to validate a new research concept called “Chaotic Logic” which we recently published. The problem to be solved is to simulate certain networks of nonlinearly-interacting dynamical variables, and collect statistics on their behavior, to show that they can reliably perform useful computations. The dynamical trajectories for such networks are computed by time integration of their Hamilton’s equations.

Frank, MichaelP.↗

Measurement of needle and armature dynamics in a gasoline direct injector by high-speed neutron imaging

In modern spark ignition engines, precise delivery of fuel with gasoline direct injection has become increasingly important in the effort to meet ever stricter efficiency and emissions regulations. Use of multiple small close-coupled injections has become more common in attempt to precisely control fuel distribution in the cylinder, but these strategies are hindered by nonlinear injection effects due to operation in the ballistic region of the solenoid-operated valve and due to armature bounce at the end of injection. Understanding the internal dynamics of the injector is crucial to minimizing and controlling non-linearity and shot-to-shot variation, but the experimental techniques available to date are capable only of tracking the position of either the top of the needle (via laser sensors or by monitoring current and voltage in the solenoid coil) or the bottom of the needle (via transparent nozzles or high-speed x-ray imaging). Furthermore, a complete picture of the axial and radial motion of valve needle has until now remained elusive. In this work, we present high-speed ensemble neutron transmission imaging of an entire 8-hole gasoline direct injector operating at 200 bar, allowing for both visualization and quantification of the actuation dynamics including lift and wobble of the valve ball, oscillation and bending of the valve needle, lift, rocking, and bounce of the armature, compression of the springs, and radial swelling of the solenoid during energization. Because neutrons offer high penetration through the metal injector while also being sensitive to the 1 H nuclei in fuel molecules, it is also possible to simultaneously see the fluid dynamics of the injection process, including filling of the sac volume, emanation of the spray through the nozzle holes and into the downstream gas, and the formation and evolution of fuel films on the tip of the injector and the walls of the spray container.

33 ADVANCED PROPULSION SYSTEMS↗

Collaborative Research. Damage and Burst Dynamics in Failure of Complex Geomaterials. A Statistical Physics Approach to Understanding the Complex Emergent Dynamics in Near Mean-Field Geological Materials

We have carried out research to determine the dynamics of failure in complex geomaterials, specifically focusing on the role of defects, damage and asperities in the catastrophic failure processes (now popularly termed “Black Swan events”). We have examined fracture branching and flow processes using models for invasion percolation, focusing particularly on the dynamics of bursts in the branching process. We have achieved a fundamental understanding of the dynamics of nucleation in complex geomaterials, specifically in the presence of inhomogeneous structures.

58 GEOSCIENCES↗

Probing the Structure and Dynamics of Fluid Mixtures in Porous Materials Through Ultrafast Vibrational Spectro-Microscopy and Many-Body Molecular Dynamics

This research program focused on the characterization of both molecular structure and dynamics of aqueous solutions in various metal-organic frameworks (MOFs) and organic polymers that have recently been proposed for applications in water treatment technologies. This was accomplished by integrating ultrafast vibrational spectroscopy and microscopy, which are sensitive to local environments, molecular orientation, and dynamical couplings, with many-body molecular dynamics (MB-MD) simulations, which enable realistic modeling of aqueous systems and porous materials under different thermodynamic conditions. Our studies allowed for identifying the physical mechanisms and characterizing the underlying molecular interactions between water and host materials that determine the adsorption and transport processes of water in various MOFs and β-cyclodextrin polymers – prototypical examples of porous materials and polymers, that have recently been proposed for technological applications in water purification. By combining bulk- and surface-sensitive, spatially resolved ultrafast vibrational spectroscopy with MB-MD simulations, it was possible to gain broad insight into the structure and mobility of water under heterogeneous confinement at various length scales. In particular, measurements of surface- and bulk-sensitive vibrational spectra at single crystal level, integrated with MB-MD simulations were used to characterize domain-specific, structure–binding affinity relationships. Besides providing specific information about the behavior of aqueous solutions in prototypical MOFs and organic polymers for potential applications in water treatment technologies, our studies also provided fundamental insights into the properties of aqueous solutions in confined heterogeneous environments, which have broad implications in many areas, ranging from heterogeneous catalysis to oil recovery, ion transport processes, and reaction-diffusion processes in crowded systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Silicalite is an important nanoporous material that finds applications in several industries, including gas separation and catalysis. While the sorption, structure, and dynamics of several molecules confined in the pores of silicalite have been reported, most of these studies have been restricted to low pressures. Here we report a comparative study of sorption, structure, and dynamics of CO2 and ethane in silicalite at high pressures (up to 100 bar) using a combination of Monte Carlo (MC) and molecular dynamics (MD) simulations. The behavior of the two fluids is studied in terms of the simulated sorption isotherms, the positional and orientational distribution of sorbed molecules in silicalite, and their translational diffusion, vibrational spectra, and rotational motion. Both CO2 and ethane are found to exhibit orientational ordering in silicalite pores; however, at high pressures, while CO2 prefers to reside in the channel intersections, ethane molecules reside mostly in the sinusoidal channels. While CO2 exhibits a higher self-diffusion coefficient than ethane at low pressures, at high pressures, it becomes slower than ethane. Both CO2 and ethane exhibit rotational motion at two time scales. At both time scales, the rotational motion of ethane is faster. The differences observed here in the behavior of CO2 and ethane in silicalite pores can be seen as a consequence of an interplay of the kinetic diameter of the two molecules and the quadrupole moment of CO2.

Gautam, Siddharth (ORCID:0000000314435382)↗

Applications of dynamic stability parameters to problems in aircraft dynamics

The application and analysis of dynamic stability parameters were examined. The effects of wing leading edge modifications on the stalling and spinning characteristics of a single engine general aviation research airplane are evaluated. It is illustrated how dynamic stability parameters measured in wind tunnel tests are used to predict the spin resistance of this class of aircraft, and that autorotation criteria are derived from the relationships which exist between static and dynamic aerodynamic characteristics.

Chambers, J. R.↗

Applications of dynamic stability parameters to problems in aircraft dynamics

The paper presents highlights of a recent study which illustrates the application and analysis of dynamic stability parameters. More specifically, the investigation consisted of an evaluation of the effects of wing leading-edge modifications on the stalling and spinning characteristics of a single-engine general aviation research airplane. The results of the investigation illustrate how dynamic stability parameters measured in wind-tunnel tests are used to predict the spin resistance of this class of aircraft; and that autorotation criteria can be derived from the relationships which exist between static and dynamic aerodynamic characteristics.

Chambers, J. R.↗

Dynamic Modeling of Solar Dynamic Components and Systems

The purpose of this grant was to support NASA in modeling efforts to predict the transient dynamic and thermodynamic response of the space station solar dynamic power generation system. In order to meet the initial schedule requirement of providing results in time to support installation of the system as part of the initial phase of space station, early efforts were executed with alacrity and often in parallel. Initially, methods to predict the transient response of a Rankine as well as a Brayton cycle were developed. Review of preliminary design concepts led NASA to select a regenerative gas-turbine cycle using a helium-xenon mixture as the working fluid and, from that point forward, the modeling effort focused exclusively on that system. Although initial project planning called for a three year period of performance, revised NASA schedules moved system installation to later and later phases of station deployment. Eventually, NASA selected to halt development of the solar dynamic power generation system for space station and to reduce support for this project to two-thirds of the original level.

Hochstein, John I.↗

Approximations for inclusion of rotor lag dynamics in helicopter flight dynamics models

Approximate forms are suggested for augmenting linear rotor/body response models to include rotor lag dynamics. Use of an analytically linearized rotor/body model has shown that the primary effect comes from the additional angular rate contributions of the lag inertial response. Addition of lag dynamics may be made assuming these dynamics are represented by an isolated rotor with no shaft motion. Implications of such an approximation are indicated through comparison with flight test data and sensitivity of stability levels with body rate feedback.

Mckillip, Robert, Jr.↗

Dynamic model testing of the X-31 configuration for high-angle-of-attack flight dynamics research

High-angle-of-attack flight dynamics of the X-31 configuration were studied using dynamic model test techniques. These tests identified phenomena including wing rock, spins, and departures that could dominate the high-alpha behavior of the configuration and restrict its usable flight envelope. Results of these tests have been used to design flight control concepts and configuration modifications to minimize adverse effects of these phenomena. The conclusion of the high-alpha envelope expansion flight tests of the X-31 aircraft will complete the database against which the dynamic model results can be correlated.

Croom, Mark A.↗

Automated Technique for the Detection of Step-Like Solar Wind Dynamic Pressure Changes: Application to the Response of the Transpolar Potential to Solar Wind Dynamic Pressure Fronts

The input from the solar wind (SW) and the accompanying Interplanetary Magnetic Field (IMF) is the defining feature of the solar wind-magnetosphere interactions. One of the most important SW drivers is the solar wind dynamic pressure, and most significantly its sharp changes known as pressure fronts. Sudden enhancements in solar wind dynamic pressure, SWP, have been shown to lead to intensification of the auroral electrojets (and Region 1 field-aligned currents), increase in auroral emissions, and significant enhancement in ionospheric convection and the transpolar potential. Case studies of the interaction between pressure fronts and the terrestrial space environment shed great light on their importance to the structure and dynamics of the system. However, thorough understanding of the interaction requires fully statistical investigations. These statistical studies require a large number of suitable pressure front events. In the past these have been obtained through laborious manual inspection of solar wind data. We present an automated procedure that identifies sudden step enhancements in SWP that satisfy a desired set of limiting step-like characteristics, such as magnitude of the change, sign of the change (positive/negative), and rate of change. The procedure yields a list of suitable events, along with their step features within minutes. The technique is tested for missed events and false positives by direct comparison to manual inspection of the data. Its utility is illustrated by application to the statistical effect of pressure fronts to the transpolar potential as measured by the Assimilative Mapping of Ionospheric Electrodynamics (AMIE) technique.

A. Boudouridis↗

Coupling Power System Dynamics and Building Dynamics to Enable Building-to-Grid Integration

The interactions between power system dynamics and building dynamics are usually ignored or over-simplified in existing power systems and building modeling and simulation tools, which limits how system modeling can sup-port Building-to-Grid integration. This paper discusses a new approach to consider those interactions by model-ing motor-driven building devices or systems. The motor-driven model is based on simplified mechanical rotation equations and allows us to study the coupling relationship between frequency/voltage in the power system and motor-driven device operation. This model is validated by performing one proof-of-concept case study with Modelica. The simulation results suggest that the proposed model can yield better representations of these interactions than the existing simplified models, especially the ones with the fast transient dynamics.

Buildings-to-grid integration, motor, coupling sim↗

New insights into the mechanism governing the elasticity of calcium silicate hydrate gels exposed to high temperature: A molecular dynamics study

When exposed to fire, the integrity of cement-based materials is governed by thermally-induced changes in the mechanical properties of their binding phase, i.e., the calcium–silicate–hydrate (C–S–H) gel. However, the effect of temperature on the structure, density, and mechanical properties of C–S–H remains only partially known. Here, based on reactive molecular dynamics simulations, we reveal the nature of thermally-induced damage in C–S–H gels. In general, we show that, at the atomic scale, exposure to high temperature results in partial dehydration, volumetric shrinkage, disordering, and stiffening in the C–S–H grains. However, we show that the thermal response of C–S–H strongly depends on its chemical composition, wherein C–S–H systems associated with lower Ca/Si molar ratios are able to undergo higher temperatures before amorphization. Based on these results, we demonstrate that the stiffness of C–S–H gels (i.e., including porosity—as probed by nanoindentation) is governed by a competition between the stiffening of the grains and the decrease in packing density—wherein the latter eventually become predominant.

36 MATERIALS SCIENCE↗

Coupling computational fluid dynamics with the high resolution rapid refresh model for forecasting dynamic line ratings

This study looks at forecasted dynamic line ratings in southern Idaho by using data from the High Resolution Rapid Refresh (HRRR) model for forecasted weather conditions. The HRRR model can provide accurate 18- hour forecasts with a 15-minute temporal resolution. Typical static ratings used for over head transmission lines use overly conservative assumptions for local weather conditions, such as using the maximum solar irradiance or temperature measured during the summer combined with low wind speed for an entire season. The HRRR forecast model used here has a high spatial resolution to provide local forecast conditions along the entire length of a transmission line. The area that is of interest in this study is in southern Idaho spanning a total of 15,000 square kilometers. The forecasted weather data is coupled with a computational fluid dynamics model of the wind in the region to improve the resolution to an even finer scale for resolving local convective cooling rates on each individual transmission line midpoint span. This high fidelity approach can be used to find the minimum ampacity limit across all given midpoints of a transmission line to determine the absolute minimum to be used for the line rating. The ability to increase the line rating above the conservative static approach with the forecasted weather data provides a large potential to alleviate congestion and provide data for the utility market transactions. Furthermore, this study shows that for the region of interest, using forecasted weather data coupled with CFD modeling will calculate DLR ampacity rating above static about 90% of the time, with only a small relative error in the forecasted ampacity over time.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Computational Fluid Dynamics Modeling of Bacillus anthracis Spore Deposition in Rabbit and Human Respiratory Airways

Three-dimensional computational fluid dynamics and Lagrangian particle deposition models were developed to compare the deposition of aerosolized Bacillus anthracis spores in the respiratory airways of a human with that of the rabbit, a species commonly used in the study of anthrax disease. The respiratory airway geometries for each species were derived from computed tomography (CT) or µCT images. Both models encompassed airways that extended from the external nose to the lung with a total of 272 outlets in the human model and 2878 outlets in the rabbit model. All simulations of spore deposition were conducted under transient, inhalation-exhalation breathing conditions using average species-specific minute volumes. The highest exposure concentration was modeled in the rabbit based upon prior acute inhalation studies. For comparison, human simulation was also conducted at the same concentration. Results demonstrated that regional spore deposition patterns were sensitive to airway geometry and ventilation profiles. Due to the complex airway geometries in the rabbit nose, higher spore deposition efficiency was predicted in the upper conducting airways compared to the human at the same air concentration of anthrax spores. As a result, higher particle deposition was predicted in the conducting airways and deep lung of the human compared to the rabbit lung due to differences in airway branching pattern. This information can be used to refine published and ongoing biokinetic models of inhalation anthrax spore exposures, which currently estimate deposited spore concentrations based solely upon exposure concentrations and inhaled doses that do not factor in species-specific anatomy and physiology.

bacillus anthracis↗