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At least 991 records · Page 55

Characterization of Microgravity Environment on Mir

This paper presents the microgravity analysis results using dynamic response data collected during the first phase of the Mir Structural Dynamics Experiment (MiSDE). Although MiSDE was designed and performed to verify structural dynamic models, it also provided information for determining microgravity characteristics of the structure. This study analyzed ambient responses acquired during orbital day-to-night and night-to-day transitions, crew treadmill and ergometer exercises, and intentional crew activities. Acceleration levels for one-third octave bands were calculated to characterize the microgravity environment of the station. Spectrograms were also used to analyze the time transient nature of the responses. Detailed theoretical background and analysis results will also be included in the final draft.

Kim, Hyoung↗

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

Thompson, Michael C. (ORCID:0000000260992027)↗

Orientational Pair Correlations and Local Structure of Benzonitrile from Molecular Dynamics Simulations with Comparisons to Experiments [plus supplemental information]

Here, we present an experimentally parametrized molecular dynamics study of single-molecule and collective orientational relaxation in neat benzonitrile through the analysis of the reorientational anisotropy and polarizability anisotropy time-correlation function (PA-TCF). The simulations show that the PA-TCF is dominated by collective reorientation after 20 ps. Collective reorientation is found to be slower than single-molecule reorientation by a factor of 1.67, consistent with recent experiments. The simulations provide direct evidence of local antiparallel benzonitrile configurations. These structures, which have been the center of some debate, are responsible for the slower rate of collective vs. single-molecule reorientation in the liquid. Further structural analysis indicates that significant Coulombic interactions between the nitrile group and hydrogen atoms on adjacent molecules play a role in the formation of the antiparallel structures. The single-molecule dynamics reflected in the anisotropy are complex and consist of a ballistic regime, restricted angular diffusion, and spatially anisotropic free diffusion. The principal components of the rotational diffusion tensor are independently obtained and shown to reproduce the free diffusion regime of the anisotropy for each principal axis according to the predictions of a previous theory.

14 SOLAR ENERGY↗

Automated characterization of spatial and dynamical heterogeneity in supercooled liquids via implementation of machine learning

Abstract A computational approach by an implementation of the principle component analysis (PCA) with K -means and Gaussian mixture (GM) clustering methods from machine learning algorithms to identify structural and dynamical heterogeneities of supercooled liquids is developed. In this method, a collection of the average weighted coordination numbers ( W C N s ‾ ) of particles calculated from particles’ positions are used as an order parameter to build a low-dimensional representation of feature (structural) space for K -means clustering to sort the particles in the system into few meso-states using PCA. Nano-domains or aggregated clusters are also formed in configurational (real) space from a direct mapping using associated meso-states’ particle identities with some misclassified interfacial particles. These classification uncertainties can be improved by a co-learning strategy which utilizes the probabilistic GM clustering and the information transfer between the structural space and configurational space iteratively until convergence. A final classification of meso-states in structural space and domains in configurational space are stable over long times and measured to have dynamical heterogeneities. Armed with such a classification protocol, various studies over the thermodynamic and dynamical properties of these domains indicate that the observed heterogeneity is the result of liquid–liquid phase separation after quenching to a supercooled state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Time Varying Compensator Design for Reconfigurable Structures Using Non-Collocated Feedback

Analysis and synthesis tools are developed to improved the dynamic performance of reconfigurable nonminimum phase, nonstrictly positive real-time variant systems. A novel Spline Varying Optimal (SVO) controller is developed for the kinematic nonlinear system. There are several advantages to using the SVO controller, in which the spline function approximates the system model, observer, and controller gain. They are: The spline function approximation is simply connected, thus the SVO controller is more continuous than traditional gain scheduled controllers when implemented on a time varying plant; ft is easier for real-time implementations in storage and computational effort; where system identification is required, the spline function requires fewer experiments, namely four experiments; and initial startup estimator transients are eliminated. The SVO compensator was evaluated on a high fidelity simulation of the Shuttle Remote Manipulator System. The SVO controller demonstrated significant improvement over the present arm performance: (1) Damping level was improved by a factor of 3; and (2) Peak joint torque was reduced by a factor of 2 following Shuttle thruster firings.

Scott, Michael A.↗

High Performance Parallel Analysis of Coupled Problems for Aircraft Propulsion

In order to predict the dynamic response of a flexible structure in a fluid flow, the equations of motion of the structure and the fluid must be solved simultaneously. In this paper, we present several partitioned procedures for time-integrating this focus coupled problem and discuss their merits in terms of accuracy, stability, heterogeneous computing, I/O transfers, subcycling, and parallel processing. All theoretical results are derived for a one-dimensional piston model problem with a compressible flow, because the complete three-dimensional aeroelastic problem is difficult to analyze mathematically. However, the insight gained from the analysis of the coupled piston problem and the conclusions drawn from its numerical investigation are confirmed with the numerical simulation of the two-dimensional transient aeroelastic response of a flexible panel in a transonic nonlinear Euler flow regime.

Felippa, C. A.↗

Box truss antenna technology status

Recent technology development activities for box truss structures and box truss antennas are summarized. Three primary activities are discussed: the development of an integrated analysis system for box truss mesh antennae; dynamic testing to characterize the effect of joint free play on the dynamic behavior of box truss structures; and fabrication of a 4.5 meter diameter offset fed mesh reflector integrated to an all graphite epoxy box truss cube.

Coyner, J. V.↗

Box truss antenna technology status

Recent technology development activities for box truss structures and box truss antennas are summarized. Three primary activities are discussed: the development of an integrated analysis system for box truss mesh antennae; dynamic testing to characterize the effect of joint free play on the dynamic behavior of box truss structures; and fabrication of a 4.5 meter diameter offset fed mesh reflector integrated to an all graphite epoxy box truss cube.

Coyner, J. V.↗

Recent Advances in Multidisciplinary Analysis and Optimization, part 1

This three-part document contains a collection of technical papers presented at the Second NASA/Air Force Symposium on Recent Advances in Multidisciplinary Analysis and Optimization, held September 28-30, 1988 in Hampton, Virginia. The topics covered include: helicopter design, aeroelastic tailoring, control of aeroelastic structures, dynamics and control of flexible structures, structural design, design of large engineering systems, application of artificial intelligence, shape optimization, software development and implementation, and sensitivity analysis.

Barthelemy, Jean-Francois M.↗

Recent Advances in Multidisciplinary Analysis and Optimization, part 2

This three-part document contains a collection of technical papers presented at the Second NASA/Air Force Symposium on Recent Advances in Multidisciplinary Analysis and Optimization, held September 28-30, 1988 in Hampton, Virginia. The topics covered include: helicopter design, aeroelastic tailoring, control of aeroelastic structures, dynamics and control of flexible structures, structural design, design of large engineering systems, application of artificial intelligence, shape optimization, software development and implementation, and sensitivity analysis.

Barthelemy, Jean-Francois M.↗

Recent Advances in Multidisciplinary Analysis and Optimization, part 3

This three-part document contains a collection of technical papers presented at the Second NASA/Air Force Symposium on Recent Advances in Multidisciplinary Analysis and Optimization, held September 28-30, 1988 in Hampton, Virginia. The topics covered include: aircraft design, aeroelastic tailoring, control of aeroelastic structures, dynamics and control of flexible structures, structural design, design of large engineering systems, application of artificial intelligence, shape optimization, software development and implementation, and sensitivity analysis.

Barthelemy, Jean-Francois M.↗

Impact of Cross-Axis Structural Dynamics on Validation of Linear Models for Space Launch System

A feasibility study was performed to examine the advisability of incorporating a set of Programmed Test Inputs (PTIs) during the Space Launch System (SLS) vehicle flight. The intent of these inputs is to provide validation to the preflight models for control system stability margins, aerodynamics, and structural dynamics. During October 2009, Ares I-X program was successful in carrying out a series of PTI maneuvers which provided a significant amount of valuable data for post-flight analysis. The resulting data comparisons showed excellent agreement with the preflight linear models across the frequency spectrum of interest. However unlike Ares I-X, the structural dynamics associated with the SLS boost phase configuration are far more complex and highly coupled in all three axes. This presents a challenge when implementing this similar system identification technique to SLS. Preliminary simulation results show noticeable mismatches between PTI validation and analytical linear models in the frequency range of the structural dynamics. An alternate approach was examined which demonstrates the potential for better overall characterization of the system frequency response as well as robustness of the control design.

Pei, Jing↗

Research on the control of large space structures

The research effort on the control of large space structures at the University of Houston has concentrated on the mathematical theory of finite-element models; identification of the mass, damping, and stiffness matrix; assignment of damping to structures; and decoupling of structure dynamics. The objective of the work has been and will continue to be the development of efficient numerical algorithms for analysis, control, and identification of large space structures. The major consideration in the development of the algorithms has been the large number of equations that must be handled by the algorithm as well as sensitivity of the algorithms to numerical errors.

Denman, E. D.↗

Microscopic theory of onset of decaging and bond-breaking activated dynamics in ultradense fluids with strong short-range attractions

We theoretically study thermally activated “in cage” elementary dynamical processes that precede full structural relaxation in ultra-dense particle liquids interacting via strong short range attractive forces. The analysis is based on a microscopic theory formulated at the particle trajectory level built on the dynamic free energy concept and an explicit treatment of how attractive forces control the formation and lifetime of physical bonds. Mean time scales for bond breaking, the early stage of cage escape, and non-Fickian displacement by a fixed amount are analyzed in the repulsive glass, bonded repulsive (attractive) glass, fluid, and dense gel regimes. The theory predicts a strong length-scale-dependent growth of these time scales with attractive force strength at fixed packing fraction, a much weaker slowing down with density at fixed attraction strength, and a strong decoupling of the shorter bond breaking time with the other two time scales that are controlled mainly by perturbed steric caging. All results are in good accord with simulations, and additional testable predictions are made. In conclusion, the classic statistical mechanical projection approximation of replacing all bare attractive and repulsive forces with a single effective force determined by pair structure incurs major errors for describing processes associated with thermally activated escape from transiently localized states.

36 MATERIALS SCIENCE↗

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis

X-ray free electron lasers (XFELs) provide ultrashort intense X-ray pulses suitable to probe electron dynamics but can also induce a multitude of nonlinear excitation processes. These affect spectroscopic measurements and interpretation, particularly for upcoming brighter XFELs. Here we identify and discuss the limits to observing classical spectroscopy, where only one photon is absorbed per atom for a Mn 2+ in a light element (O, C, H) environment. X-ray emission spectroscopy (XES) with different incident photon energies, pulse intensities, and pulse durations is presented. A rate equation model based on sequential ionization and relaxation events is used to calculate populations of multiply ionized states during a single pulse and to explain the observed X-ray induced spectral lines shifts. Furthermore this model provides easy estimation of spectral shifts, which is essential for experimental designs at XFELs and illustrates that shorter X-ray pulses will not overcome sequential ionization but can reduce electron cascade effects.

47 OTHER INSTRUMENTATION↗