Characterization of Macaque Pulmonary Fluid Proteome during Monkeypox Infection: DYNAMICS OF HOST RESPONSE
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Characterization of control noise effects in optimal quantum unitary dynamics
Not Available
Hocker, David↗
Lyapunov exponent as a metric for assessing the dynamic content and predictability of large-eddy simulations
Metrics used to assess the quality of large-eddy simulations commonly rely on a statistical assessment of the solution. While these metrics are valuable, a dynamic measure is desirable to further characterize the ability of a numerical simulation for capturing dynamic processes inherent in turbulent flows. To address this issue, a dynamic metric based on the Lyapunov exponent is proposed which assesses the growth rate of the solution separation. Specifically, this metric is applied to two turbulent flow configurations: forced homogeneous isotropic turbulence and a turbulent jet diffusion flame. First, it is shown that, despite the direct numerical simulation (DNS) and large-eddy simulation (LES) being high-dimensional dynamical systems with O(107) degrees of freedom, the separation growth rate qualitatively behaves like a lower-dimensional dynamical system, in which the dimension of the Lyapunov system is substantially smaller than the discretized dynamical system. Second, a grid refinement analysis of each configuration demonstrates that as the LES filter width approaches the smallest scales of the system the Lyapunov exponent asymptotically approaches a plateau. Third, a small perturbation is superimposed onto the initial conditions of each configuration, and the Lyapunov exponent is used to estimate the time required for divergence, thereby providing a direct assessment of the predictability time of simulations. By comparing inert and reacting flows, it is shown that combustion increases the predictability of the turbulent simulation as a result of the dilatation and increased viscosity by heat release. The predictability time is found to scale with the integral time scale in both the reacting and inert jet flows. Fourth, an analysis of the local Lyapunov exponent is performed to demonstrate that this metric can also determine flow-dependent properties, such as regions that are sensitive to small perturbations or conditions of large turbulence within the flow field. Finally, it is demonstrated that the global Lyapunov exponent can be utilized as a metric to determine if the computational domain is large enough to adequately encompass the dynamic nature of the flow.
42 ENGINEERING↗
WE-G-BRD-02: Characterizing Information Loss in a Sparse-Sampling-Based Dynamic MRI Sequence (k-T BLAST) for Lung Motion Monitoring
Purpose: Rapid MRI is an attractive, non-ionizing tool for soft-tissue-based monitoring of respiratory motion in thoracic and abdominal radiotherapy. One big challenge is to achieve high temporal resolution while maintaining adequate spatial resolution. K-t BLAST, sparse-sampling and reconstruction sequence based on a-priori information represents a potential solution. In this work, we investigated how much “true” motion information is lost as a-priori information is progressively added for faster imaging. Methods: Lung tumor motions in superior-inferior direction obtained from ten individuals were replayed into an in-house, MRI-compatible, programmable motion platform (50Hz refresh and 100microns precision). Six water-filled 1.5ml tubes were placed on it as fiducial markers. Dynamic marker motion within a coronal slice (FOV: 32×32cm{sup 2}, resolution: 0.67×0.67mm{sup 2}, slice-thickness: 5mm) was collected on 3.0T body scanner (Ingenia, Philips). Balanced-FFE (TE/TR: 1.3ms/2.5ms, flip-angle: 40degrees) was used in conjunction with k-t BLAST. Each motion was repeated four times as four k-t acceleration factors 1, 2, 5, and 16 (corresponding frame rates were 2.5, 4.7, 9.8, and 19.1Hz, respectively) were compared. For each image set, one average motion trajectory was computed from six marker displacements. Root mean square error (RMS) was used as a metric of spatial accuracy where measured trajectories were compared to original data. Results: Tumor motion was approximately 10mm. The mean(standard deviation) of respiratory rates over ten patients was 0.28(0.06)Hz. Cumulative distributions of tumor motion frequency spectra (0–25Hz) obtained from the patients showed that 90% of motion fell on 3.88Hz or less. Therefore, the frame rate must be a double or higher for accurate monitoring. The RMS errors over patients for k-t factors of 1, 2, 5, and 16 were.10(.04),.17(.04), .21(.06) and.26(.06)mm, respectively. Conclusions: K-t factor of 5 or higher can cover the high frequency component of tumor respiratory motion, while the estimated error of spatial accuracy was approximately.2mm.
60 APPLIED LIFE SCIENCES↗
Wide Area Wind Field Monitoring Status & Results
Volume-scanning elastic has been investigated as a means to derive 3D dynamic wind fields for characterization and monitoring of wind energy sites. An eye-safe volume-scanning lidar system was adapted for volume imaging of aerosol concentrations out to a range of 300m. Reformatting of the lidar data as dynamic volume images was successfully demonstrated. A practical method for deriving 3D wind fields from dynamic volume imagery was identified and demonstrated. However, the natural phenomenology was found to provide insufficient aerosol features for reliable wind sensing. The results of this study may be applicable to wind field measurement using injected aerosol tracers.
17 WIND ENERGY↗
Characterization of Axial Inducer Cavitation Instabilities via High Speed Video Recordings
Sub-scale water tests were undertaken to assess the viability of utilizing high resolution, high frame-rate digital video recordings of a liquid rocket engine turbopump axial inducer to characterize cavitation instabilities. These high speed video (HSV) images of various cavitation phenomena, including higher order cavitation, rotating cavitation, alternating blade cavitation, and asymmetric cavitation, as well as non-cavitating flows for comparison, were recorded from various orientations through an acrylic tunnel using one and two cameras at digital recording rates ranging from 6,000 to 15,700 frames per second. The physical characteristics of these cavitation forms, including the mechanisms that define the cavitation frequency, were identified. Additionally, these images showed how the cavitation forms changed and transitioned from one type (tip vortex) to another (sheet cavitation) as the inducer boundary conditions (inlet pressures) were changed. Image processing techniques were developed which tracked the formation and collapse of cavitating fluid in a specified target area, both in the temporal and frequency domains, in order to characterize the cavitation instability frequency. The accuracy of the analysis techniques was found to be very dependent on target size for higher order cavitation, but much less so for the other phenomena. Tunnel-mounted piezoelectric, dynamic pressure transducers were present throughout these tests and were used as references in correlating the results obtained by image processing. Results showed good agreement between image processing and dynamic pressure spectral data. The test set-up, test program, and test results including H-Q and suction performance, dynamic environment and cavitation characterization, and image processing techniques and results will be discussed.
Arellano, Patrick↗
Characterization of Single Ion Strikes using In-Situ Dynamic Transmission Electron Microscopy.
Abstract not provided.
Monterrosa, Anthony↗
Effectiveness And Nonlinear Characterization Of Energy Harvesting Absorbers With Stoppers In Controlling Dynamical Systems.
Abstract not provided.
Alvis, Tyler↗
Evolution of nano-rheological properties of Nafion{sup ®} thin films during pH modification by strong base treatment: A static and dynamic force spectroscopy study
Addition of a strong base to Nafion{sup ®} proton exchange membranes is a common practice in industry to increase their overall performance in fuel cells. Here, we investigate the evolution of the nano-rheological properties of Nafion thin films as a function of the casting pH, via characterization with static and dynamic, contact and intermittent-contact atomic force microscopy (AFM) techniques. The addition of KOH causes non-monotonic changes in the viscoelastic properties of the films, which behave as highly dissipative, softer materials near neutral pH values, and as harder, more elastic materials at extreme pH values. We quantify this behavior through calculation of the temporal evolution of the compliance and the glassy compliance under static AFM measurements. We complement these observations with dynamic AFM metrics, including dissipated power and virial (for intermittent-contact-mode measurements), and contact resonance frequency and quality factor (for dynamic contact-mode measurements). We explain the non-monotonic material property behavior in terms of the degree of ionic crosslinking and moisture content of the films, which vary with the addition of KOH. This work focuses on the special case study of the addition of strong bases, but the observed mechanical property changes are broadly related to water plasticizing effects and ionic crosslinking, which are also important in other types of films.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Dissecting galaxy formation models with sensitivity analysis—a new approach to constrain the Milky Way formation history
We present an application of a statistical tool known as sensitivity analysis to characterize the relationship between input parameters and observational predictions of semi-analytic models of galaxy formation coupled to cosmological N-body simulations. We show how a sensitivity analysis can be performed on our chemo-dynamical model, ChemTreeN, to characterize and quantify its relationship between model input parameters and predicted observable properties. The result of this analysis provides the user with information about which parameters are most important and most likely to affect the prediction of a given observable. It can also be used to simplify models by identifying input parameters that have no effect on the outputs (i.e., observational predictions) of interest. Conversely, sensitivity analysis allows us to identify what model parameters can be most efficiently constrained by the given observational data set. We have applied this technique to real observational data sets associated with the Milky Way, such as the luminosity function of the dwarf satellites. The results from the sensitivity analysis are used to train specific model emulators of ChemTreeN, only involving the most relevant input parameters. This allowed us to efficiently explore the input parameter space. A statistical comparison of model outputs and real observables is used to obtain a 'best-fitting' parameter set. We consider different Milky-Way-like dark matter halos to account for the dependence of the best-fitting parameter selection process on the underlying merger history of the models. For all formation histories considered, running ChemTreeN with best-fitting parameters produced luminosity functions that tightly fit their observed counterpart. However, only one of the resulting stellar halo models was able to reproduce the observed stellar halo mass within 40 kpc of the Galactic center. On the basis of this analysis, it is possible to disregard certain models, and their corresponding merger histories, as good representations of the underlying merger history of the Milky Way.
79 ASTRONOMY AND ASTROPHYSICS↗
Interactions of anesthetics with the water-hexane interface. A molecular dynamics study
The free energy profiles characterizing the transfer of nine solutes across the liquid-vapor interfaces of water and hexane and across the water-hexane interface were calculated from molecular dynamics simulations. Among the solutes were n-butane and three of its halogenated derivatives, as well as three halogenated cyclobutanes. The two remaining molecules, dichlorodifluoromethane and 1,2-dichloroperfluoroethane, belong to series of halo-substituted methanes and ethanes, described in previous studies (J. Chem. Phys. 1996, 104, 3760; Chem. Phys. 1996, 204, 337). Each series of molecules contains structurally similar compounds that differ greatly in anesthetic potency. The accuracy of the simulations was tested by comparing the calculated and the experimental free energies of solvation of all nine compounds in water and in hexane. In addition. the calculated and the measured surface excess concentrations of n-butane at the water liquid-vapor interface were compared. In all cases, good agreement with experimental results was found. At the water-hexane interface, the free energy profiles for polar molecules exhibited significant interfacial minima, whereas the profiles for nonpolar molecules did not. The existence of these minima was interpreted in terms of a balance between the free energy contribution arising from solute-solvent interactions and the work to form a cavity that accommodates the solute. These two contributions change monotonically, but oppositely, across the interface. The interfacial solubilities of the solutes, obtained from the free energy profiles, correlate very well with their anesthetic potencies. This is the case even when the Meyer-Overton hypothesis, which predicts a correlation between anesthetic potency and solubility in oil, fails.
NASA Center ARC↗
Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations
The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 μs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electrothermal Modeling and Analysis of Gallium Oxide Power Switching Devices: Preprint
Gallium oxide is an emerging wide band-gap material that has the potential to penetrate the power electronics market in the near future. In this paper, a finite-element gallium oxide semiconductor model is presented that can predict the electrical and thermal characteristics of the device. The finite element model of the two-dimensional device architecture is developed inside the Sentaurus environment. A vertical FinFET device architecture is employed to assess the device's behavior and its static and dynamic behavior. Enhancement-mode device operation is realized with this type of device architecture without the need for any selective area doping. The dynamic thermal behavior of the device is characterized through its short-circuit behavior. Based on the device static and dynamic behavior, it is envisioned that reliable vertical transistors can be fabricated for the power electronics applications.
33 ADVANCED PROPULSION SYSTEMS↗
Energy Transfer Networks within Upconverting Nanoparticles Are Complex Systems with Collective, Robust, and History-Dependent Dynamics
Applications of photon upconverting nanoparticles (UCNPs) in biological imaging and solar energy conversion demand that their anti-Stokes luminescence be both tunable and efficient. Rational design of more efficient UCNPs requires an understanding of energy transfer (ET) between their lanthanide dopants, dynamics that are typically characterized by measuring luminescence lifetimes. Existing knowledge, however, cannot explain basic observations in lifetime experiments, such as their dependence on excitation power, significantly limiting the generality and reliability of lifetime measurements. Here in this paper, we elucidate the origins of the ET dynamics and luminescence lifetimes of Yb 3+ -, Er 3+ -co-doped NaYF 4 UCNPs using time-resolved luminescence and novel applications of rate equations and stochastic simulations. Experiments and calculations consistently show that at high concentrations of Er 3+ , the luminescence lifetimes of UCNPs decrease as much as six-fold when excitation power densities are increased over 6 orders of magnitude. Since power-dependent lifetimes cannot be explained by intrinsic relaxation rates of individual transitions, we analyze lifetime data by treating each UCNP as a complex ET network. We find that UCNP ET networks exhibit four distinguishing characteristics of complex systems: collectivity, nonlinear feedback, robustness, and history dependence. We conclude that power-dependent lifetimes are the consequence of thousands of minor relaxation pathways that act collectively to depopulate and repopulate Er 3+ emitting levels. These ET pathways are dependent on past excitation power because they originate from excited donors and excited acceptors; however, each transition has an unexpectedly small impact on lifetimes due to negative feedback in the network. This robustness is determined by systematically “knocking out”, or disabling, ET transitions in kinetic models. Our classification of UCNP ET networks as complex systems explains why UCNP luminescence lifetimes do not match the intrinsic lifetimes of emitting states. In the future, UCNP networks may be engineered to rival the complexity of biological networks that pattern features with unmatched precision.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Diffusive dynamics during the high-to-low density transition in amorphous ice
Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distribution function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. In conclusion, the diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid–liquid transition in the ultraviscous regime.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Response of vibrational properties and thermal conductivity of perovskites to pressure
We study the response of SrTiO 3 and KTaO 3 's vibrational properties and thermal conductivity to pressurization. Our goal is to improve the understanding of the relationship between crystal structure, vibrational dynamics, and thermal conductivity in perovskites. We measure the thermal conductivity of SrTiO 3 and KTaO 3 up to 28 GPa by time-domain thermoreflectance. We also perform Raman scattering and stimulated Brillouin scattering measurements of SrTiO 3 and KTaO 3 to characterize changes in vibrational dynamics with pressure. The thermal conductivity of SrTiO 3 increases under pressure with a slope comparable to that of other perovskites whose thermal conductivity has been measured versus pressure. Alternatively, the thermal conductivity of KTaO 3 has a stronger pressure dependence than that of other materials with similar crystal structure. We correlate pressure-induced changes in Raman and Brillouin spectra with pressure-induced changes in thermal conductivity. We show that pressure-induced changes in phonon lifetimes dominate the pressure dependence of thermal conductivity. This study provides benchmark knowledge of why depends on pressure and improves understanding of structure/thermal-property relationships.
36 MATERIALS SCIENCE↗
Self-assembly of the full-length amyloid Aβ42 protein in dimers
The self-assembly of amyloid (Aβ) proteins into nano-aggregates is a hallmark of Alzheimer’s disease (AD) development, yet the mechanism of how disordered monomers assemble into aggregates remains elusive. Here, we applied long-time molecular dynamics simulations to fully characterize the assembly of Aβ42 monomers into dimers. Monomers undergo conformational changes during their interaction, but the resulting dimer structures do not resemble those found in fibril structures. Further, to identify natural conformations of dimers among a set of simulated ones, validation approaches were developed and applied, and a subset of dimer conformations were characterized. These dimers do not contain long β-strands that are usually found in fibrils. The dimers are stabilized primarily by interactions within the central hydrophobic regions and the C-terminal regions, with a contribution from local hydrogen bonding. The dimers are dynamic, as evidenced by the existence of a set of conformations and by the quantitative analyses of the dimer dissociation process.
59 BASIC BIOLOGICAL SCIENCES↗
Estimation of Unsteady Aerodynamic Models from Dynamic Wind Tunnel Data
Demanding aerodynamic modelling requirements for military and civilian aircraft have motivated researchers to improve computational and experimental techniques and to pursue closer collaboration in these areas. Model identification and validation techniques are key components for this research. This paper presents mathematical model structures and identification techniques that have been used successfully to model more general aerodynamic behaviours in single-degree-of-freedom dynamic testing. Model parameters, characterizing aerodynamic properties, are estimated using linear and nonlinear regression methods in both time and frequency domains. Steps in identification including model structure determination, parameter estimation, and model validation, are addressed in this paper with examples using data from one-degree-of-freedom dynamic wind tunnel and water tunnel experiments. These techniques offer a methodology for expanding the utility of computational methods in application to flight dynamics, stability, and control problems. Since flight test is not always an option for early model validation, time history comparisons are commonly made between computational and experimental results and model adequacy is inferred by corroborating results. An extension is offered to this conventional approach where more general model parameter estimates and their standard errors are compared.
Murphy, Patrick↗