A Critical Assessment of the Performance of Protein-ligand Scoring Functions Based on NMR Chemical Shift Perturbations

PubMed Central

Wang, Bing; Westerhoff, Lance M.; Merz, Kenneth M.

2008-01-01

We have generated docking poses for the FKBP-GPI complex using eight docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby, providing a new tool facilitating the structure-based drug discovery process. PMID:17867664

Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

PubMed Central

Salsbury, Freddie R.; Poole, Leslie B.; Fetrow, Jacquelyn S.

2013-01-01

One of the most popular and simple models for the calculation of pKas from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pKas. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pKas; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pKas. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pKa values (where the calculation should reproduce the pKa within experimental error). Both the general behavior of cysteines in proteins and the perturbed pKa in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pKa should be shifted, and validation of force field parameters for cysteine residues. PMID:22777874

Effect of a Perturbation on the Chemical Equilibrium: Comparison with Le Châtelier's Principle

NASA Astrophysics Data System (ADS)

Martínez Torres, Emilio

2007-03-01

This article develops a general thermodynamic treatment to predict the direction of shift in a chemical equilibrium when it is subjected to a stress. This treatment gives an inequality that relates the change in the perturbed variable and the change that the equilibrium shift produces in the conjugated variable. To illustrate the generality of this approach, it has been applied to predict the direction of shift caused by changes of pressure, volume, and amount of substance. In this last case, the well-known unexpected shift in the ammonia synthesis equilibrium upon addition of nitrogen is easily explained. From the above referred inequality and the stability criteria of thermodynamics some conclusions have been obtained about the direction of shift in terms of extensive and extensive variables. This article is suitable for physical chemistry courses.

Extracting 3D Information from 1D and 2D Diagnostic Systems on the DIII-D Tokamak

NASA Astrophysics Data System (ADS)

Brookman, Michael

2017-10-01

The interpretation of tokamak data often hinges on assumptions of axisymetry and flux surface equilibria, neglecting 3D effects. This work discusses examples on the DIII-D tokamak where this assumption is an insufficient approximation, and explores the diagnostic information available to resolve 3D effects while preserving 1D profiles. Methods for extracting 3D data from the electron cyclotron emission radiometers, density profile reflectometer, and Thomson scattering system are discussed. Coordinating diagnostics around the tokamak shows the significance of 3D features, such as sawteeth[1] and resonant magnetic perturbations. A consequence of imposed 3D perturbations is a shift in major radius of measured profiles between diagnostics at different toroidal locations. Integrating different diagnostics requires a database containing information about their toroidal, poloidal, and radial locations. Through the data analysis framework OMFIT, it is possible to measure the magnitude of the apparent shifts from 3D effects and enforce consistency between diagnostics. Using the existing 1D and 2D diagnostic systems on DIII-D, this process allows the effects of the 3D perturbations on 1D profiles to be addressed. Supported by US DOE contracts DE-FC02-04ER54698, DE-FG03-97ER54415.

Nozzle Aerodynamic Stability During a Throat Shift

NASA Technical Reports Server (NTRS)

Kawecki, Edwin J.; Ribeiro, Gregg L.

2005-01-01

An experimental investigation was conducted on the internal aerodynamic stability of a family of two-dimensional (2-D) High Speed Civil Transport (HSCT) nozzle concepts. These nozzles function during takeoff as mixer-ejectors to meet acoustic requirements, and then convert to conventional high-performance convergent-divergent (CD) nozzles at cruise. The transition between takeoff mode and cruise mode results in the aerodynamic throat and the minimum cross-sectional area that controls the engine backpressure shifting location within the nozzle. The stability and steadiness of the nozzle aerodynamics during this so called throat shift process can directly affect the engine aerodynamic stability, and the mechanical design of the nozzle. The objective of the study was to determine if pressure spikes or other perturbations occurred during the throat shift process and, if so, identify the caused mechanisms for the perturbations. The two nozzle concepts modeled in the test program were the fixed chute (FC) and downstream mixer (DSM). These 2-D nozzles differ principally in that the FC has a large over-area between the forward throat and aft throat locations, while the DSM has an over-area of only about 10 percent. The conclusions were that engine mass flow and backpressure can be held constant simultaneously during nozzle throat shifts on this class of nozzles, and mode shifts can be accomplished at a constant mass flow and engine backpressure without upstream pressure perturbations.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography*

PubMed Central

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N.; Nishida, Clinton R.; de Montellano, Paul R. Ortiz

2015-01-01

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. PMID:25670859

The detection of impending regime shifts from Fisher Information(presentation)

EPA Science Inventory

Resilient systems typically exhibit periodic fluctuations yet are able to withstand perturbations while maintaining functionality. However, it is possible for a system to reach a dynamic threshold and shift to another set of system conditions. These regime shifts have been demon...

Over/Undervoltage and undervoltage shift of hybrid islanding detection method of distributed generation.

PubMed

Yingram, Manop; Premrudeepreechacharn, Suttichai

2015-01-01

The mainly used local islanding detection methods may be classified as active and passive methods. Passive methods do not perturb the system but they have larger nondetection zones, whereas active methods have smaller nondetection zones but they perturb the system. In this paper, a new hybrid method is proposed to solve this problem. An over/undervoltage (passive method) has been used to initiate an undervoltage shift (active method), which changes the undervoltage shift of inverter, when the passive method cannot have a clear discrimination between islanding and other events in the system. Simulation results on MATLAB/SIMULINK show that over/undervoltage and undervoltage shifts of hybrid islanding detection method are very effective because they can determine anti-islanding condition very fast. ΔP/P > 38.41% could determine anti-islanding condition within 0.04 s; ΔP/P < -24.39% could determine anti-islanding condition within 0.04 s; -24.39% ≤ ΔP/P ≤ 38.41% could determine anti-islanding condition within 0.08 s. This method perturbed the system, only in the case of -24.39% ≤ ΔP/P ≤ 38.41% at which the control system of inverter injected a signal of undervoltage shift as necessary to check if the occurrence condition was an islanding condition or not.

Far-infrared self-broadening in methylcyanide - Absorber-perturber resonance

NASA Technical Reports Server (NTRS)

Buffa, G.; Tarrini, O.; De Natale, P.; Inguscio, M.; Pavone, F. S.; Prevedelli, M.; Evenson, K. M.; Zink, L. R.; Schwaab, G. W.

1992-01-01

Using tunable far-infrared spectrometers with high-frequency stability and accuracy, the self-pressure broadening and shift of CH3CN are measured. Evidence of absorber-perturber resonance effects on the collisional line shape are obtained. This tests the theoretical model and its possible improvements and also allows predictions of broadening and shift for a large class of molecules. Moreover, the resonance effect produces a theoretical temperature dependence of self-broadening that is different from what is commonly assumed.

Origin of the pre-tropical storm Debby (2006) African easterly wave-mesoscale convective system

NASA Astrophysics Data System (ADS)

Lin, Yuh-Lang; Liu, Liping; Tang, Guoqing; Spinks, James; Jones, Wilson

2013-05-01

The origins of the pre-Debby (2006) mesoscale convective system (MCS) and African easterly wave (AEW) and their precursors were traced back to the southwest Arabian Peninsula, Asir Mountains (AS), and Ethiopian Highlands (EH) in the vicinity of the ITCZ using satellite imagery, GFS analysis data and ARW model. The sources of the convective cloud clusters and vorticity perturbations were attributed to the cyclonic convergence of northeasterly Shamal wind and the Somali jet, especially when the Mediterranean High shifted toward east and the Indian Ocean high strengthened and its associated Somali jet penetrated farther to the north. The cyclonic vorticity perturbations were strengthened by the vorticity stretching associated with convective cloud clusters in the genesis region—southwest Arabian Peninsula. A conceptual model was proposed to explain the genesis of convective cloud clusters and cyclonic vorticity perturbations preceding the pre-Debby (2006) AEW-MCS system.

The detection and assessment of impending regime shifts from Fisher Information

EPA Science Inventory

Resilient systems typically exhibit periodic fluctuations yet are able to withstand perturbations while maintaining functionality. However, it is possible for a system to reach a dynamic threshold and shift to another set of system conditions. These regime shifts have been demon...

Control of the spin geometric phase in semiconductor quantum rings.

PubMed

Nagasawa, Fumiya; Frustaglia, Diego; Saarikoski, Henri; Richter, Klaus; Nitta, Junsaku

2013-01-01

Since the formulation of the geometric phase by Berry, its relevance has been demonstrated in a large variety of physical systems. However, a geometric phase of the most fundamental spin-1/2 system, the electron spin, has not been observed directly and controlled independently from dynamical phases. Here we report experimental evidence on the manipulation of an electron spin through a purely geometric effect in an InGaAs-based quantum ring with Rashba spin-orbit coupling. By applying an in-plane magnetic field, a phase shift of the Aharonov-Casher interference pattern towards the small spin-orbit-coupling regions is observed. A perturbation theory for a one-dimensional Rashba ring under small in-plane fields reveals that the phase shift originates exclusively from the modulation of a pure geometric-phase component of the electron spin beyond the adiabatic limit, independently from dynamical phases. The phase shift is well reproduced by implementing two independent approaches, that is, perturbation theory and non-perturbative transport simulations.

Sensory-Motor Networks Involved in Speech Production and Motor Control: An fMRI Study

PubMed Central

Behroozmand, Roozbeh; Shebek, Rachel; Hansen, Daniel R.; Oya, Hiroyuki; Robin, Donald A.; Howard, Matthew A.; Greenlee, Jeremy D.W.

2015-01-01

Speaking is one of the most complex motor behaviors developed to facilitate human communication. The underlying neural mechanisms of speech involve sensory-motor interactions that incorporate feedback information for online monitoring and control of produced speech sounds. In the present study, we adopted an auditory feedback pitch perturbation paradigm and combined it with functional magnetic resonance imaging (fMRI) recordings in order to identify brain areas involved in speech production and motor control. Subjects underwent fMRI scanning while they produced a steady vowel sound /a/ (speaking) or listened to the playback of their own vowel production (playback). During each condition, the auditory feedback from vowel production was either normal (no perturbation) or perturbed by an upward (+600 cents) pitch shift stimulus randomly. Analysis of BOLD responses during speaking (with and without shift) vs. rest revealed activation of a complex network including bilateral superior temporal gyrus (STG), Heschl's gyrus, precentral gyrus, supplementary motor area (SMA), Rolandic operculum, postcentral gyrus and right inferior frontal gyrus (IFG). Performance correlation analysis showed that the subjects produced compensatory vocal responses that significantly correlated with BOLD response increases in bilateral STG and left precentral gyrus. However, during playback, the activation network was limited to cortical auditory areas including bilateral STG and Heschl's gyrus. Moreover, the contrast between speaking vs. playback highlighted a distinct functional network that included bilateral precentral gyrus, SMA, IFG, postcentral gyrus and insula. These findings suggest that speech motor control involves feedback error detection in sensory (e.g. auditory) cortices that subsequently activate motor-related areas for the adjustment of speech parameters during speaking. PMID:25623499

Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

PubMed

Salsbury, Freddie R; Poole, Leslie B; Fetrow, Jacquelyn S

2012-11-01

One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pK(a) values (where the calculation should reproduce the pK(a) within experimental error). Both the general behavior of cysteines in proteins and the perturbed pK(a) in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pK(a) should be shifted, and validation of force field parameters for cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

INDEPENDENT SIGNALS FROM THE INFLUENCE OF INTERNAL MAGNETIC LAYERS ON THE FREQUENCIES OF SOLAR p-MODES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foullon, C.; Nakariakov, V. M.

2010-05-01

The discovery that p-mode frequencies of low degree do not follow changes of solar surface activity during the recent solar minimum offers the possibility of a new diagnostic signature of the responsible pressure perturbation in the wave guiding medium, potentially rich of information regarding the structure of the Sun and the cause of the unusually long solar minimum. Magnetic fields, as well as temperature changes, introduce equilibrium pressure deviations that modify the resonant frequencies of p-mode oscillations. Assuming the perturbation to be caused by a horizontal layer of magnetic field located in a plane-stratified model of the Sun, we compilemore » analytical frequency shifts and process them to allow direct comparison with observations. The effect of magnetism itself on the central p-mode frequencies can be neglected in comparison with the thermal effect of a perturbative layer buried in the solar interior. A parametric study shows that a layer as thin as 2100 km at subsurface depths is able to reproduce reported mean anomalous frequency shifts (not correlated with the surface activity), while a layer of size around 4200 km increasing by a small amount at depths near 0.08 R {sub sun} can explain individual low-degree shifts. It is also possible to obtain the mean shifts via the upward motion through depths near 0.03 R {sub sun} of a rising perturbative layer of thickness around 7000 km. Hence, the anomalous frequency shifts are best explained by thermal effects in the upper regions of the convection zone. The effects of latitudinal distribution are not treated here.« less

Perturbations i have Known and Loved

NASA Astrophysics Data System (ADS)

Field, Robert W.

2011-06-01

A spectroscopic perturbation is a disruption of a ^1Σ-^1Σ-like regular pattern that can embody level-shifts, extra lines, and intensity anomalies. Once upon a time, when a band was labeled ``perturbed,'' it was considered worthless because it could at best yield molecular constants unsuited for archival tables. Nevertheless, a few brave spectroscopists, notably Albin Lagerqvist and Richard Barrow, collected perturbations because they knew that the pattern of multiple perturbations formed an intricate puzzle that would eventually reveal the presence and electronic symmetry of otherwise unobservable electronic states. There are many kinds of patterns of broken patterns. In my PhD thesis I showed how to determine absolute vibrational assignments for the perturber from patterns among the observed values of perturbation matrix elements. When a ^3Π state is perturbed, its six (Ω, parity) components capture a pattern of level shifts and intensity anomalies that reveals more about the nature of the perturber than a simple perturbation of the single component of a ^1Σ state. In perturbation-facilitated OODR, a perturbed singlet level acts as a spectroscopic doorway through which the entire triplet manifold may be systematically explored. For polyatomic molecule vibrations, a vibrational polyad (a group of mutually perturbing vibrational levels, among which the perturbation matrix elements are expected to follow harmonic oscillator scaling rules) can contain more components than a ^3Π state and intrapolyad patterns can be exquisitely sensitive not merely to the nature of an interloper within the polyad but also to the eigenvector character of the vibronic state from which the polyad is viewed. Variation of scaled polyad interaction parameters from one polyad to the next, a pattern of patterns, can signal proximity to an isomerization barrier. Everything in Rydberg-land seems to scale as N⋆-3, yet a trespassing valence state causes all scaling and propensity rules go out the window.

Protein dielectric constants determined from NMR chemical shift perturbations.

PubMed

Kukic, Predrag; Farrell, Damien; McIntosh, Lawrence P; García-Moreno E, Bertrand; Jensen, Kristine Steen; Toleikis, Zigmantas; Teilum, Kaare; Nielsen, Jens Erik

2013-11-13

Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatic calculations are essential for this purpose, but their use has been limited by a long-standing discussion on which value to use for the dielectric constants (ε(eff) and ε(p)) required in Coulombic and Poisson-Boltzmann models. The currently used values for ε(eff) and ε(p) are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for ε(eff) and ε(p) by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in 14 proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (ε(eff)) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (ε(p)) ranged from 2 to 5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders and how different it is from the ε(p) of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of ε(p) = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pK(a) values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable ε(p) common to most folded proteins.

Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.

PubMed

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N; Nishida, Clinton R; de Montellano, Paul R Ortiz

2015-04-17

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE PAGES

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; ...

2015-02-10

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Over/Undervoltage and Undervoltage Shift of Hybrid Islanding Detection Method of Distributed Generation

PubMed Central

Premrudeepreechacharn, Suttichai

2015-01-01

The mainly used local islanding detection methods may be classified as active and passive methods. Passive methods do not perturb the system but they have larger nondetection zones, whereas active methods have smaller nondetection zones but they perturb the system. In this paper, a new hybrid method is proposed to solve this problem. An over/undervoltage (passive method) has been used to initiate an undervoltage shift (active method), which changes the undervoltage shift of inverter, when the passive method cannot have a clear discrimination between islanding and other events in the system. Simulation results on MATLAB/SIMULINK show that over/undervoltage and undervoltage shifts of hybrid islanding detection method are very effective because they can determine anti-islanding condition very fast. ΔP/P > 38.41% could determine anti-islanding condition within 0.04 s; ΔP/P < −24.39% could determine anti-islanding condition within 0.04 s; −24.39% ≤ ΔP/P ≤ 38.41% could determine anti-islanding condition within 0.08 s. This method perturbed the system, only in the case of −24.39% ≤ ΔP/P ≤ 38.41% at which the control system of inverter injected a signal of undervoltage shift as necessary to check if the occurrence condition was an islanding condition or not. PMID:25879064

Temporal, thermal, and light stability of continuously tunable cholesteric liquid crystal laser array.

PubMed

Jeong, Mi-Yun; Chung, Ki Soo; Wu, Jeong Weon

2014-11-01

Fine-structured polymerized cholesteric liquid crystal (PCLC) wedge laser devices have been realized, with high fine spatial tunability of the lasing wavelength. With resolution less than 0.3 nm in a broad spectral range, more than one hundred laser lines could be obtained in a PCLC cell without extra devices. For practical device application, we studied the stability of the device in detail over time, and in response to strong external light sources, and thermal perturbation. The PCLC wedge cells had good temporal stability for 1 year and showed good stability for strong perturbations, with the lasing wavelength shifting less than 1 nm, while the laser peak intensities decreased by up to 34%, and the high energy band edge of the photonic band gap (PBG) was red shifted 3 nm by temperature perturbation. However, when we consider the entire lasing spectrum for the PCLC cell, the 1-nm wavelength shift may not matter. Although the laser peak intensities were decreased by up to 34% in total for all of the perturbation cases, the remaining 34% laser peak intensity is considerable extent to make use. This good stability of the PCLC laser device is due to the polymerization of the CLC by UV curing. This study will be helpful for practical CLC laser device development.

Automation of peak-tracking analysis of stepwise perturbed NMR spectra.

PubMed

Banelli, Tommaso; Vuano, Marco; Fogolari, Federico; Fusiello, Andrea; Esposito, Gennaro; Corazza, Alessandra

2017-02-01

We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TINT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered. TINT was applied successfully to several protein systems during a temperature ramp in isotope exchange experiments. A comparison with a state-of-the-art algorithm showed promising results for great numbers of spectra and low signal to noise ratios, when the graduality of the perturbation is appropriate. TINT can be applied to different kinds of high throughput chemical shift mapping experiments, with quasi-continuous variations, in which a quantitative automated recognition is crucial.

Self-organized kilometer-scale shoreline sand wave generation: Sensitivity to model and physical parameters

NASA Astrophysics Data System (ADS)

Idier, Déborah; Falqués, Albert; Rohmer, Jérémy; Arriaga, Jaime

2017-09-01

The instability mechanisms for self-organized kilometer-scale shoreline sand waves have been extensively explored by modeling. However, while the assumed bathymetric perturbation associated with the sand wave controls the feedback between morphology and waves, its effect on the instability onset has not been explored. In addition, no systematic investigation of the effect of the physical parameters has been done yet. Using a linear stability model, we investigate the effect of wave conditions, cross-shore profile, closure depth, and two perturbation shapes (P1: cross-shore bathymetric profile shift, and P2: bed level perturbation linearly decreasing offshore). For a P1 perturbation, no instability occurs below an absolute critical angle θc0≈ 40-50°. For a P2 perturbation, there is no absolute critical angle: sand waves can develop also for low-angle waves. In fact, the bathymetric perturbation shape plays a key role in low-angle wave instability: such instability only develops if the curvature of the depth contours offshore the breaking zone is larger than the shoreline one. This can occur for the P2 perturbation but not for P1. The analysis of bathymetric data suggests that both curvature configurations could exist in nature. For both perturbation types, large wave angle, small wave period, and large closure depth strongly favor instability. The cross-shore profile has almost no effect with a P1 perturbation, whereas large surf zone slope and gently sloping shoreface strongly enhance instability under low-angle waves for a P2 perturbation. Finally, predictive statistical models are set up to identify sites prone to exhibit either a critical angle close to θc0 or low-angle wave instability.

Implications of solar p-mode frequency shifts

NASA Technical Reports Server (NTRS)

Goldreich, Peter; Murray, Norman; Willette, Gregory; Kumar, Pawan

1991-01-01

An expression is derived that relates solar p-mode frequency shifts to changes in the entropy and magnetic field of the sun. The frequency variations result from changes in path length and propagation speed. Path length changes dominate for entropy perturbations, and propagation speed changes dominate for most types of magnetic field peturbations. The p-mode frequencies increased along with solar activity between 1986 and 1989; these frequency shifts exhibited a rapid rise with increasing frequency followed by a precipitous drop. The positive component of the shifts can be accounted for by variations of the mean square magnetic field strength in the vicinity of the photosphere. The magnetic stress perturbation decays above the top of the convection zone on a length scale comparable to the pressure scale height and grows gradually with depth below. The presence of a resonance in the chromospheric cavity means that the transition layer maintains enough coherence to partially reflect acoustic waves even near cycle maximum.

Dynamical patterns and regime shifts in the nonlinear model of soil microorganisms growth

NASA Astrophysics Data System (ADS)

Zaitseva, Maria; Vladimirov, Artem; Winter, Anna-Marie; Vasilyeva, Nadezda

2017-04-01

Dynamical model of soil microorganisms growth and turnover is formulated as a system of nonlinear partial differential equations of reaction-diffusion type. We consider spatial distributions of concentrations of several substrates and microorganisms. Biochemical reactions are modelled by chemical kinetic equations. Transport is modelled by simple linear diffusion for all chemical substances, while for microorganisms we use different transport functions, e.g. some of them can actively move along gradient of substrate concentration, while others cannot move. We solve our model in two dimensions, starting from uniform state with small initial perturbations for various parameters and find parameter range, where small initial perturbations grow and evolve. We search for bifurcation points and critical regime shifts in our model and analyze time-space profile and phase portraits of these solutions approaching critical regime shifts in the system, exploring possibility to detect such shifts in advance. This work is supported by NordForsk, project #81513.

Role of the strange quark in the rho(770) meson

DOE Office of Scientific and Technical Information (OSTI.GOV)

Molina Peralta, Raquel; Guo, Dehua; Hu, B.

2017-03-01

Recently, the GWU lattice group has evaluated high-precision phase-shift data formore » $$\\pi\\pi$$ scattering in the $I = 1$, $J = 1$ channel. Unitary Chiral Perturbation Theory describes these data well around the resonance region and for different pion masses. Moreover, it allows to extrapolate to the physical point and estimate the effect of the missing $$K\\bar{K}$$ channel in the two-flavor lattice calculation. The absence of the strange quark in the lattice data leads to a lower $$\\rho$$ mass, and the analysis with U$$\\chi$$PT shows that the $$K \\bar{K}$$ channel indeed pushes the $$\\pi\\pi$$-scattering phase shift upward, having a surprisingly large effect on the $$\\rho$$-mass. The inelasticity is shown to be compatible with the experimental data. The analysis is then extended to all available two-flavor lattice simulations and similar mass shifts are observed. Chiral extrapolations of $$N_f = 2 + 1$$ lattice simulations for the $$\\rho(770)$$ are also reported.« less

Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675.

PubMed

Konold, Patrick E; Yoon, Eunjin; Lee, Junghwa; Allen, Samantha L; Chapagain, Prem P; Gerstman, Bernard S; Regmi, Chola K; Piatkevich, Kiryl D; Verkhusha, Vladislav V; Joo, Taiha; Jimenez, Ralph

2016-08-04

Far-red fluorescent proteins are critical for in vivo imaging applications, but the relative importance of structure versus dynamics in generating large Stokes-shifted emission is unclear. The unusually red-shifted emission of TagRFP675, a derivative of mKate, has been attributed to the multiple hydrogen bonds with the chromophore N-acylimine carbonyl. We characterized TagRFP675 and point mutants designed to perturb these hydrogen bonds with spectrally resolved transient grating and time-resolved fluorescence (TRF) spectroscopies supported by molecular dynamics simulations. TRF results for TagRFP675 and the mKate/M41Q variant show picosecond time scale red-shifts followed by nanosecond time blue-shifts. Global analysis of the TRF spectra reveals spectrally distinct emitting states that do not interconvert during the S1 lifetime. These dynamics originate from photoexcitation of a mixed ground-state population of acylimine hydrogen bond conformers. Strategically tuning the chromophore environment in TagRFP675 might stabilize the most red-shifted conformation and result in a variant with a larger Stokes shift.

Resummation of divergent perturbation series: Application to the vibrational states of H2CO molecule

NASA Astrophysics Data System (ADS)

Duchko, A. N.; Bykov, A. D.

2015-10-01

Large-order Rayleigh-Schrödinger perturbation theory (RSPT) is applied to the calculation of anharmonic vibrational energy levels of H2CO molecule. We use the model of harmonic oscillators perturbed by anharmonic terms of potential energy. Since the perturbation series typically diverge due to strong couplings, we apply the algebraic approximation technique because of its effectiveness shown earlier by Goodson and Sergeev [J. Chem. Phys. 110, 8205 (1999); ibid. 124, 094111 (2006)] and in our previous articles [A. D. Bykov et al. Opt. Spectrosc. 114, 396 (2013); ibid. 116, 598 (2014)]. To facilitate the resummation of terms contributing to perturbed states, when resonance mixing between states is especially strong and perturbation series diverge very quick, we used repartition of the Hamiltonian by shifting the normal mode frequencies. Energy levels obtained by algebraic approximants were compared with the results of variational calculation. It was found that for low energy states (up to ˜5000 cm-1), algebraic approximants gave accurate values of energy levels, which were in excellent agreement with the variational method. For highly excited states, strong and multiple resonances complicate series resummation, but a suitable change of normal mode frequencies allows one to reduce the resonance mixing and to get accurate energy levels. The theoretical background of the problem of RSPT series divergence is discussed along with its numerical analysis. For these purposes, the vibrational energy is considered as a function of a complex perturbation parameter. Layout and classification of its singularities allow us to model the asymptotic behavior of the perturbation series and prove the robustness of the algorithm.

Resummation of divergent perturbation series: Application to the vibrational states of H2CO molecule.

PubMed

Duchko, A N; Bykov, A D

2015-10-21

Large-order Rayleigh-Schrödinger perturbation theory (RSPT) is applied to the calculation of anharmonic vibrational energy levels of H2CO molecule. We use the model of harmonic oscillators perturbed by anharmonic terms of potential energy. Since the perturbation series typically diverge due to strong couplings, we apply the algebraic approximation technique because of its effectiveness shown earlier by Goodson and Sergeev [J. Chem. Phys. 110, 8205 (1999); ibid. 124, 094111 (2006)] and in our previous articles [A. D. Bykov et al. Opt. Spectrosc. 114, 396 (2013); ibid. 116, 598 (2014)]. To facilitate the resummation of terms contributing to perturbed states, when resonance mixing between states is especially strong and perturbation series diverge very quick, we used repartition of the Hamiltonian by shifting the normal mode frequencies. Energy levels obtained by algebraic approximants were compared with the results of variational calculation. It was found that for low energy states (up to ∼5000 cm(-1)), algebraic approximants gave accurate values of energy levels, which were in excellent agreement with the variational method. For highly excited states, strong and multiple resonances complicate series resummation, but a suitable change of normal mode frequencies allows one to reduce the resonance mixing and to get accurate energy levels. The theoretical background of the problem of RSPT series divergence is discussed along with its numerical analysis. For these purposes, the vibrational energy is considered as a function of a complex perturbation parameter. Layout and classification of its singularities allow us to model the asymptotic behavior of the perturbation series and prove the robustness of the algorithm.

Bernstein wave aided laser third harmonic generation in a plasma

NASA Astrophysics Data System (ADS)

Tyagi, Yachna; Tripathi, Deepak; Kumar, Ashok

2016-09-01

The process of Bernstein wave aided resonant third harmonic generation of laser in a magnetized plasma is investigated. The extra-ordinary mode (X-mode) laser of frequency ω 0 and wave number k → 0 , travelling across the magnetic field in a plasma, exerts a second harmonic ponderomotive force on the electrons imparting them an oscillatory velocity v → 2 ω0 , 2 k → 0 . This velocity beats with the density perturbation due to the Bernstein wave to produce a density perturbation at cyclotron frequency shifted second harmonic. The density perturbation couples with the oscillatory velocity v → ω0 , k → 0 of X-mode of the laser to produce the cyclotron frequency shifted third harmonic current density leading to harmonic radiation. The phase matching condition for the up shifted frequency is satisfied when the Bernstein wave is nearly counter-propagating to the laser. As the transverse wave number of the Bernstein wave is large, it is effective in the phase matched third harmonic generation, when the laser frequency is not too far from the upper hybrid frequency.

Spectro-spatial analysis of wave packet propagation in nonlinear acoustic metamaterials

NASA Astrophysics Data System (ADS)

Zhou, W. J.; Li, X. P.; Wang, Y. S.; Chen, W. Q.; Huang, G. L.

2018-01-01

The objective of this work is to analyze wave packet propagation in weakly nonlinear acoustic metamaterials and reveal the interior nonlinear wave mechanism through spectro-spatial analysis. The spectro-spatial analysis is based on full-scale transient analysis of the finite system, by which dispersion curves are generated from the transmitted waves and also verified by the perturbation method (the L-P method). We found that the spectro-spatial analysis can provide detailed information about the solitary wave in short-wavelength region which cannot be captured by the L-P method. It is also found that the optical wave modes in the nonlinear metamaterial are sensitive to the parameters of the nonlinear constitutive relation. Specifically, a significant frequency shift phenomenon is found in the middle-wavelength region of the optical wave branch, which makes this frequency region behave like a band gap for transient waves. This special frequency shift is then used to design a direction-biased waveguide device, and its efficiency is shown by numerical simulations.

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

PubMed Central

Liu, Jin

2016-01-01

Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2) in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier’s principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery. PMID:27115535

Sensory-motor networks involved in speech production and motor control: an fMRI study.

PubMed

Behroozmand, Roozbeh; Shebek, Rachel; Hansen, Daniel R; Oya, Hiroyuki; Robin, Donald A; Howard, Matthew A; Greenlee, Jeremy D W

2015-04-01

Speaking is one of the most complex motor behaviors developed to facilitate human communication. The underlying neural mechanisms of speech involve sensory-motor interactions that incorporate feedback information for online monitoring and control of produced speech sounds. In the present study, we adopted an auditory feedback pitch perturbation paradigm and combined it with functional magnetic resonance imaging (fMRI) recordings in order to identify brain areas involved in speech production and motor control. Subjects underwent fMRI scanning while they produced a steady vowel sound /a/ (speaking) or listened to the playback of their own vowel production (playback). During each condition, the auditory feedback from vowel production was either normal (no perturbation) or perturbed by an upward (+600 cents) pitch-shift stimulus randomly. Analysis of BOLD responses during speaking (with and without shift) vs. rest revealed activation of a complex network including bilateral superior temporal gyrus (STG), Heschl's gyrus, precentral gyrus, supplementary motor area (SMA), Rolandic operculum, postcentral gyrus and right inferior frontal gyrus (IFG). Performance correlation analysis showed that the subjects produced compensatory vocal responses that significantly correlated with BOLD response increases in bilateral STG and left precentral gyrus. However, during playback, the activation network was limited to cortical auditory areas including bilateral STG and Heschl's gyrus. Moreover, the contrast between speaking vs. playback highlighted a distinct functional network that included bilateral precentral gyrus, SMA, IFG, postcentral gyrus and insula. These findings suggest that speech motor control involves feedback error detection in sensory (e.g. auditory) cortices that subsequently activate motor-related areas for the adjustment of speech parameters during speaking. Copyright © 2015 Elsevier Inc. All rights reserved.

The analysis of harmonic generation coefficients in the ablative Rayleigh-Taylor instability

NASA Astrophysics Data System (ADS)

Lu, Yan; Fan, Zhengfeng; Lu, Xinpei; Ye, Wenhua; Zou, Changlin; Zhang, Ziyun; Zhang, Wen

2017-10-01

In this research, we use the numerical simulation method to investigate the generation coefficients of the first three harmonics and the zeroth harmonic in the Ablative Rayleigh-Taylor Instability. It is shown that the interface shifts to the low temperature side during the ablation process. In consideration of the third-order perturbation theory, the first three harmonic amplitudes of the weakly nonlinear regime are calculated and then the harmonic generation coefficients are obtained by curve fitting. The simulation results show that the harmonic generation coefficients changed with time and wavelength. Using the higher-order perturbation theory, we find that more and more harmonics are generated in the later weakly nonlinear stage, which is caused by the negative feedback of the later higher harmonics. Furthermore, extending the third-order theory to the fifth-order theory, we find that the second and the third harmonics coefficients linearly depend on the wavelength, while the feedback coefficients are almost constant. Further analysis also shows that when the fifth-order theory is considered, the normalized effective amplitudes of second and third harmonics can reach about 25%-40%, which are only 15%-25% in the frame of the previous third-order theory. Therefore, the third order perturbation theory is needed to be modified by the higher-order theory when ηL reaches about 20% of the perturbation wavelength.

Non-Abelian integrable hierarchies: matrix biorthogonal polynomials and perturbations

NASA Astrophysics Data System (ADS)

Ariznabarreta, Gerardo; García-Ardila, Juan C.; Mañas, Manuel; Marcellán, Francisco

2018-05-01

In this paper, Geronimus–Uvarov perturbations for matrix orthogonal polynomials on the real line are studied and then applied to the analysis of non-Abelian integrable hierarchies. The orthogonality is understood in full generality, i.e. in terms of a nondegenerate continuous sesquilinear form, determined by a quasidefinite matrix of bivariate generalized functions with a well-defined support. We derive Christoffel-type formulas that give the perturbed matrix biorthogonal polynomials and their norms in terms of the original ones. The keystone for this finding is the Gauss–Borel factorization of the Gram matrix. Geronimus–Uvarov transformations are considered in the context of the 2D non-Abelian Toda lattice and noncommutative KP hierarchies. The interplay between transformations and integrable flows is discussed. Miwa shifts, τ-ratio matrix functions and Sato formulas are given. Bilinear identities, involving Geronimus–Uvarov transformations, first for the Baker functions, then secondly for the biorthogonal polynomials and its second kind functions, and finally for the τ-ratio matrix functions, are found.

'Constraint consistency' at all orders in cosmological perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nandi, Debottam; Shankaranarayanan, S., E-mail: debottam@iisertvm.ac.in, E-mail: shanki@iisertvm.ac.in

2015-08-01

We study the equivalence of two—order-by-order Einstein's equation and Reduced action—approaches to cosmological perturbation theory at all orders for different models of inflation. We point out a crucial consistency check which we refer to as 'Constraint consistency' condition that needs to be satisfied in order for the two approaches to lead to identical single variable equation of motion. The method we propose here is quick and efficient to check the consistency for any model including modified gravity models. Our analysis points out an important feature which is crucial for inflationary model building i.e., all 'constraint' inconsistent models have higher ordermore » Ostrogradsky's instabilities but the reverse is not true. In other words, one can have models with constraint Lapse function and Shift vector, though it may have Ostrogradsky's instabilities. We also obtain single variable equation for non-canonical scalar field in the limit of power-law inflation for the second-order perturbed variables.« less

Influence of the ac-Stark shift on GPS atomic clock timekeeping

NASA Astrophysics Data System (ADS)

Formichella, V.; Camparo, J.; Tavella, P.

2017-01-01

The ac-Stark shift (or light shift) is a fundamental aspect of the field/atom interaction arising from virtual transitions between atomic states, and as Alfred Kastler noted, it is the real-photon counterpart of the Lamb shift. In the rubidium atomic frequency standards (RAFS) flying on Global Positioning System (GPS) satellites, it plays an important role as one of the major perturbations defining the RAFS' frequency: the rf-discharge lamp in the RAFS creates an atomic signal via optical pumping and simultaneously perturbs the atoms' ground-state hyperfine splitting via the light shift. Though the significance of the light shift has been known for decades, to date there has been no concrete evidence that it limits the performance of the high-quality RAFS flying on GPS satellites. Here, we show that the long-term frequency stability of GPS RAFS is primarily determined by the light shift as a consequence of stochastic jumps in lamplight intensity. Our results suggest three paths forward for improved GPS system timekeeping: (1) reduce the light-shift coefficient of the RAFS by careful control of the lamp's spectrum; (2) operate the lamp under conditions where lamplight jumps are not so pronounced; and (3) employ a light source for optical pumping that does not suffer pronounced light jumps (e.g., a diode laser).

Stark broadening parameter regularities and interpolation and critical evaluation of data for CP star atmospheres research: Stark line shifts

NASA Astrophysics Data System (ADS)

Dimitrijevic, M. S.; Tankosic, D.

1998-04-01

In order to find out if regularities and systematic trends found to be apparent among experimental Stark line shifts allow the accurate interpolation of new data and critical evaluation of experimental results, the exceptions to the established regularities are analysed on the basis of critical reviews of experimental data, and reasons for such exceptions are discussed. We found that such exceptions are mostly due to the situations when: (i) the energy gap between atomic energy levels within a supermultiplet is equal or comparable to the energy gap to the nearest perturbing levels; (ii) the most important perturbing level is embedded between the energy levels of the supermultiplet; (iii) the forbidden transitions have influence on Stark line shifts.

Solution Structure of a Phytocystatin from Ananas comosus and Its Molecular Interaction with Papain

PubMed Central

Irene, Deli; Chung, Tse-Yu; Chen, Bo-Jiun; Liu, Ting-Hang; Li, Feng-Yin; Tzen, Jason T. C.; Wang, Cheng-I; Chyan, Chia-Lin

2012-01-01

The structure of a recombinant pineapple cystatin (AcCYS) was determined by NMR with the RMSD of backbone and heavy atoms of twenty lowest energy structures of 0.56 and 1.11 Å, respectively. It reveals an unstructured N-terminal extension and a compact inhibitory domain comprising a four-stranded antiparallel β-sheet wrapped around a central α-helix. The three structural motifs (G45, Q89XVXG, and W120) putatively responsible for the interaction with papain-like proteases are located in one side of AcCYS. Significant chemical shift perturbations in two loop regions, residues 45 to 48 (GIYD) and residues 89 to 91 (QVV), of AcCYS strongly suggest their involvement in the binding to papain, consistent with studies on other members of the cystatin family. However, the highly conserved W120 appears not to be involved in the binding with papain as no chemical shift perturbation was observed. Chemical shift index analysis further indicates that the length of the α-helix is shortened upon association with papain. Collectively, our data suggest that AcCYS undergoes local secondary structural rearrangements when papain is brought into close contact. A molecular model of AcCYS/papain complex is proposed to illustrate the interaction between AcCYS and papain, indicating a complete blockade of the catalytic triad by AcCYS. PMID:23139757

USING FISHER INFORMATION TO DETECT GRADUAL AND RAPID ECOSYSTEM REGIME SHIFTS

EPA Science Inventory

As ecosystems experience perturbations of varying regularity and intensity, they may either remain within the state space neighborhood of the current regime, or "flip" into the neighborhood of a regime with different characteristics. Although the possibility of such regime shifts...

Regularities And Irregularities Of The Stark Parameters For Single Ionized Noble Gases

NASA Astrophysics Data System (ADS)

Peláez, R. J.; Djurovic, S.; Cirišan, M.; Aparicio, J. A.; Mar S.

2010-07-01

Spectroscopy of ionized noble gases has a great importance for the laboratory and astrophysical plasmas. Generally, spectra of inert gases are important for many physics areas, for example laser physics, fusion diagnostics, photoelectron spectroscopy, collision physics, astrophysics etc. Stark halfwidths as well as shifts of spectral lines are usually employed for plasma diagnostic purposes. For example atomic data of argon krypton and xenon will be useful for the spectral diagnostic of ITER. In addition, the software used for stellar atmosphere simulation like TMAP, and SMART require a large amount of atomic and spectroscopic data. Availability of these parameters will be useful for a further development of stellar atmosphere and evolution models. Stark parameters data of spectral lines can also be useful for verification of theoretical calculations and investigation of regularities and systematic trends of these parameters within a multiplet, supermultiplet or transition array. In the last years, different trends and regularities of Stark parameters (halwidths and shifts of spectral lines) have been analyzed. The conditions related with atomic structure of the element as well as plasma conditions are responsible for regular or irregular behaviors of the Stark parameters. The absence of very close perturbing levels makes Ne II as a good candidate for analysis of the regularities. Other two considered elements Kr II and Xe II with complex spectra present strong perturbations and in some cases an irregularities in Stark parameters appear. In this work we analyze the influence of the perturbations to Stark parameters within the multiplets.

Two approaches for the gravitational self-force in black hole spacetime: Comparison of numerical results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sago, Norichika; Barack, Leor; Detweiler, Steven

2008-12-15

Recently, two independent calculations have been presented of finite-mass ('self-force') effects on the orbit of a point mass around a Schwarzschild black hole. While both computations are based on the standard mode-sum method, they differ in several technical aspects, which makes comparison between their results difficult--but also interesting. Barack and Sago [Phys. Rev. D 75, 064021 (2007)] invoke the notion of a self-accelerated motion in a background spacetime, and perform a direct calculation of the local self-force in the Lorenz gauge (using numerical evolution of the perturbation equations in the time domain); Detweiler [Phys. Rev. D 77, 124026 (2008)] describesmore » the motion in terms a geodesic orbit of a (smooth) perturbed spacetime, and calculates the metric perturbation in the Regge-Wheeler gauge (using frequency-domain numerical analysis). Here we establish a formal correspondence between the two analyses, and demonstrate the consistency of their numerical results. Specifically, we compare the value of the conservative O({mu}) shift in u{sup t} (where {mu} is the particle's mass and u{sup t} is the Schwarzschild t component of the particle's four-velocity), suitably mapped between the two orbital descriptions and adjusted for gauge. We find that the two analyses yield the same value for this shift within mere fractional differences of {approx}10{sup -5}-10{sup -7} (depending on the orbital radius)--comparable with the estimated numerical error.« less

Resummation of divergent perturbation series: Application to the vibrational states of H{sub 2}CO molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duchko, A. N.; V.E. Zuev Institute of Atmospheric Optics, Tomsk; Bykov, A. D., E-mail: adbykov@rambler.ru

2015-10-21

Large-order Rayleigh–Schrödinger perturbation theory (RSPT) is applied to the calculation of anharmonic vibrational energy levels of H{sub 2}CO molecule. We use the model of harmonic oscillators perturbed by anharmonic terms of potential energy. Since the perturbation series typically diverge due to strong couplings, we apply the algebraic approximation technique because of its effectiveness shown earlier by Goodson and Sergeev [J. Chem. Phys. 110, 8205 (1999); ibid. 124, 094111 (2006)] and in our previous articles [A. D. Bykov et al. Opt. Spectrosc. 114, 396 (2013); ibid. 116, 598 (2014)]. To facilitate the resummation of terms contributing to perturbed states, when resonancemore » mixing between states is especially strong and perturbation series diverge very quick, we used repartition of the Hamiltonian by shifting the normal mode frequencies. Energy levels obtained by algebraic approximants were compared with the results of variational calculation. It was found that for low energy states (up to ∼5000 cm{sup −1}), algebraic approximants gave accurate values of energy levels, which were in excellent agreement with the variational method. For highly excited states, strong and multiple resonances complicate series resummation, but a suitable change of normal mode frequencies allows one to reduce the resonance mixing and to get accurate energy levels. The theoretical background of the problem of RSPT series divergence is discussed along with its numerical analysis. For these purposes, the vibrational energy is considered as a function of a complex perturbation parameter. Layout and classification of its singularities allow us to model the asymptotic behavior of the perturbation series and prove the robustness of the algorithm.« less

Reconstructing the metric of the local Universe from number counts observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vallejo, Sergio Andres; Romano, Antonio Enea, E-mail: antonio.enea.romano@cern.ch

Number counts observations available with new surveys such as the Euclid mission will be an important source of information about the metric of the Universe. We compute the low red-shift expansion for the energy density and the density contrast using an exact spherically symmetric solution in presence of a cosmological constant. At low red-shift the expansion is more precise than linear perturbation theory prediction. We then use the local expansion to reconstruct the metric from the monopole of the density contrast. We test the inversion method using numerical calculations and find a good agreement within the regime of validity ofmore » the red-shift expansion. The method could be applied to observational data to reconstruct the metric of the local Universe with a level of precision higher than the one achievable using perturbation theory.« less

Proton polarisability contribution to the Lamb shift in muonic hydrogen at fourth order in chiral perturbation theory

NASA Astrophysics Data System (ADS)

Birse, M. C.; McGovern, J. A.

2012-09-01

We calculate the amplitude T1 for forward doubly virtual Compton scattering in heavy-baryon chiral perturbation theory, to fourth order in the chiral expansion and with the leading contribution of the γ N Δ form factor. This provides a model-independent expression for the amplitude in the low-momentum region, which is the dominant one for its contribution to the Lamb shift. It allows us to significantly reduce the theoretical uncertainty in the proton polarisability contributions to the Lamb shift in muonic hydrogen. We also stress the importance of consistency between the definitions of the Born and structure parts of the amplitude. Our result leaves no room for any effect large enough to explain the discrepancy between proton charge radii as determined from muonic and normal hydrogen.

Principal component analysis of chemical shift perturbation data of a multiple-ligand-binding system for elucidation of respective binding mechanism.

PubMed

Konuma, Tsuyoshi; Lee, Young-Ho; Goto, Yuji; Sakurai, Kazumasa

2013-01-01

Chemical shift perturbations (CSPs) in NMR spectra provide useful information about the interaction of a protein with its ligands. However, in a multiple-ligand-binding system, determining quantitative parameters such as a dissociation constant (K(d) ) is difficult. Here, we used a method we named CS-PCA, a principal component analysis (PCA) of chemical shift (CS) data, to analyze the interaction between bovine β-lactoglobulin (βLG) and 1-anilinonaphthalene-8-sulfonate (ANS), which is a multiple-ligand-binding system. The CSP on the binding of ANS involved contributions from two distinct binding sites. PCA of the titration data successfully separated the CSP pattern into contributions from each site. Docking simulations based on the separated CSP patterns provided the structures of βLG-ANS complexes for each binding site. In addition, we determined the K(d) values as 3.42 × 10⁻⁴ M² and 2.51 × 10⁻³ M for Sites 1 and 2, respectively. In contrast, it was difficult to obtain reliable K(d) values for respective sites from the isothermal titration calorimetry experiments. Two ANS molecules were found to bind at Site 1 simultaneously, suggesting that the binding occurs cooperatively with a partial unfolding of the βLG structure. On the other hand, the binding of ANS to Site 2 was a simple attachment without a significant conformational change. From the present results, CS-PCA was confirmed to provide not only the positions and the K(d) values of binding sites but also information about the binding mechanism. Thus, it is anticipated to be a general method to investigate protein-ligand interactions. Copyright © 2012 Wiley Periodicals, Inc.

Phosphorescence/microwave double-resonance spectra of tryptophan perturbed by methylmercury(II).

PubMed Central

Davis, J M; Maki, A H

1982-01-01

Amplitude-modulated phosphorescence/microwave double-resonance (AM-PMDR) spectra are reported for complexes of methylmercury(II) cation, designated CH3Hg(II), with tryptophan and glyceraldehyde-3-phosphate dehydrogenase (GPDHase; from rabbit muscle). Wavelength shifts are observed in the AM-PMDR spectra of CH3Hg(II)-tryptophan, which are obtained by microwave pumping in distinct zero-field D + E magnetic resonance transitions, demonstrating that AM-PMDR can be used to display selectively the phosphorescence spectra of structurally distinct complexes with different zero-field splittings. The AM-PMDR spectra accurately represent the phosphorescence of CH3Hg(II)-tryptophan. Binding of CH3Hg(II) to a cysteine site of GDPHase perturbs the luminescence of one of the two optically resolved tryptophan. The AM-PMDR spectrum of the perturbed tryptophan is obtained by microwave pumping of the D + E magnetic resonance signal, which can be observed optically only in the presence of a heavy atom perturbation. The resulting spectrum is broadened and shifted to the blue relative to the corresponding tryptophan phosphorescence spectrum of the uncomplexed enzyme. Comparison of the AM-PMDR spectra of CH3Hg(II)-tryptophan and CH3Hg(II)-GPDHase suggests that there are differences in the mechanisms of heavy atom perturbation in these complexes. PMID:6956860

Control of aperture closure during reach-to-grasp movements in parkinson’s disease

PubMed Central

Rand, M. K.; Smiley-Oyen, A. L.; Shimansky, Y. P.; Bloedel, J. R.; Stelmach, G. E.

2007-01-01

This study examined whether the pattern of coordination between arm-reaching toward an object (hand transport) and the initiation of aperture closure for grasping is different between PD patients and healthy individuals, and whether that pattern is affected by the necessity to quickly adjust the reach-to-grasp movement in response to an unexpected shift of target location. Subjects reached for and grasped a vertical dowel, the location of which was indicated by illuminating one of the three dowels placed on a horizontal plane. In control conditions, target location was fixed during the trial. In perturbation conditions, target location was shifted instantaneously by switching the illumination to a different dowel during the reach. The hand distance from the target at which the subject initiated aperture closure (aperture closure distance) was similar for both the control and perturbation conditions within each group of subjects. However, that distance was significantly closer to the target in the PD group than in the control group. The timing of aperture closure initiation varied considerably across the trials in both groups of subjects. In contrast, aperture closure distance was relatively invariant, suggesting that aperture closure initiation was determined by spatial parameters of arm kinematics rather than temporal parameters. The linear regression analysis of aperture closure distance showed that the distance was highly predictable based on the following three parameters: the amplitude of maximum grip aperture, hand velocity, and hand acceleration. This result implies that a control law, the arguments of which include the above parameters, governs the initiation of aperture closure. Further analysis revealed that the control law was very similar between the subject groups under each condition as well as between the control and perturbation conditions for each group. Consequently, the shorter aperture closure distance observed in PD patients apparently is a result of the hypometria of their grip aperture and bradykinesia of hand transport movement, rather than a consequence of a deficit in transport-grasp coordination. It is also concluded that the perturbation of target location does not disrupt the transport-grasp coordination in either healthy individuals or PD patients. PMID:16307233

Control of aperture closure during reach-to-grasp movements in Parkinson's disease.

PubMed

Rand, M K; Smiley-Oyen, A L; Shimansky, Y P; Bloedel, J R; Stelmach, G E

2006-01-01

This study examined whether the pattern of coordination between arm-reaching toward an object (hand transport) and the initiation of aperture closure for grasping is different between PD patients and healthy individuals, and whether that pattern is affected by the necessity to quickly adjust the reach-to-grasp movement in response to an unexpected shift of target location. Subjects reached for and grasped a vertical dowel, the location of which was indicated by illuminating one of the three dowels placed on a horizontal plane. In control conditions, target location was fixed during the trial. In perturbation conditions, target location was shifted instantaneously by switching the illumination to a different dowel during the reach. The hand distance from the target at which the subject initiated aperture closure (aperture closure distance) was similar for both the control and perturbation conditions within each group of subjects. However, that distance was significantly closer to the target in the PD group than in the control group. The timing of aperture closure initiation varied considerably across the trials in both groups of subjects. In contrast, aperture closure distance was relatively invariant, suggesting that aperture closure initiation was determined by spatial parameters of arm kinematics rather than temporal parameters. The linear regression analysis of aperture closure distance showed that the distance was highly predictable based on the following three parameters: the amplitude of maximum grip aperture, hand velocity, and hand acceleration. This result implies that a control law, the arguments of which include the above parameters, governs the initiation of aperture closure. Further analysis revealed that the control law was very similar between the subject groups under each condition as well as between the control and perturbation conditions for each group. Consequently, the shorter aperture closure distance observed in PD patients apparently is a result of the hypometria of their grip aperture and bradykinesia of hand transport movement, rather than a consequence of a deficit in transport-grasp coordination. It is also concluded that the perturbation of target location does not disrupt the transport-grasp coordination in either healthy individuals or PD patients.

Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift.

PubMed

Kukić, Predrag; Farrell, Damien; Søndergaard, Chresten R; Bjarnadottir, Una; Bradley, John; Pollastri, Gianluca; Nielsen, Jens Erik

2010-03-01

pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural transitions in bovine beta-lactoglobulin (betaLG) by analyzing its NMR pH-titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in betaLG. The results show that around 20% of the amide nuclei CSPs in betaLG originate exclusively from "through-space" electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH-dependent structural transitions in betaLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH-dependent conformational change. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Rapid Ecological Change in Two Contrasting Lake Ecosystems: Evidence of Threshold Responses, Altered Species Dynamics, and Perturbed Patterns of Variability

NASA Astrophysics Data System (ADS)

Simpson, G. L.

2015-12-01

Studying threshold responses to environmental change is often made difficult due to the paucity of monitoring data prior to and during change. Progress has been made via theoretical models of regime shifts or experimental manipulation but natural, real world, examples of threshold change are limited and in many cases inconclusive. Lake sediments provide the potential to examine abrupt ecological change by directly observing how species, communities, and biogeochemical proxies responded to environmental perturbation or recorded ecosystem change. These records are not problem-free; age uncertainties, uneven and variable temporal resolution, and time-consuming taxonomic work all act to limit the scope and scale of the data or complicate its analysis. Here I use two annually laminated records 1. Kassjön, a seasonally anoxic mesotrophic lake in N Sweden, and2. Baldeggersee, a nutrient rich, hardwater lake on the central Swiss Plateau to investigate lake ecosystem responses to abrupt environmental change using ideal paleoecological time series. Rapid cooling 2.2kyr ago in northern Sweden significantly perturbed the diatom community of Kassjön. Using wavelet analysis, this amelioration in climate also fundamentally altered patterns of variance in diatom abundances, suppressing cyclicity in species composition that required several hundred years to reestablish. Multivariate wavelet analysis of the record showed marked switching between synchronous and asynchronous species dynamics in response to rapid climatic cooling and subsequent warming. Baldeggersee has experienced a long history of eutrophication and the diatom record has been used as a classic illustration of a regime shift in response to nutrient loading. Time series analysis of the record identified some evidence of a threshold-like response in the diatoms. A stochastic volatility model identified increasing variance in composition prior to the threshold, as predicted from theory, and a switch from compensatory to synchronous species dynamics, concomitant with eutrophication, was observed. These results document in high resolution how two aquatic systems reacted to abrupt change and demonstrate that under ideal conditions sediments can preserve valuable evidence of rapid ecological change.

Theoretical, Experimental, and Computational Evaluation of Several Vane-Type Slow-Wave Structures

NASA Technical Reports Server (NTRS)

Wallett, Thomas M.; Qureshi, A. Haq

1994-01-01

Several types of periodic vane slow-wave structures were fabricated. The dispersion characteristics were found by theoretical analysis, experimental testing, and computer simulation using the MAFIA code. Computer-generated characteristics agreed to approximately within 2 percent of the experimental characteristics for all structures. The theoretical characteristics, however, deviated increasingly as the width to height ratio became smaller. Interaction impedances were also computed based on the experimental and computer-generated resonance frequency shifts due to the introduction of a perturbing dielectric rod.

¹H NMR-based metabolic profiling of naproxen-induced toxicity in rats.

PubMed

Jung, Jeeyoun; Park, Minhwa; Park, Hye Jin; Shim, Sun Bo; Cho, Yang Ha; Kim, Jinho; Lee, Ho-Sub; Ryu, Do Hyun; Choi, Donwoong; Hwang, Geum-Sook

2011-01-15

The dose-dependent perturbations in urinary metabolite concentrations caused by naproxen toxicity were investigated using ¹H NMR spectroscopy coupled with multivariate statistical analysis. Histopathologic evaluation of naproxen-induced acute gastrointestinal damage in rats demonstrated a significant dose-dependent effect. Furthermore, principal component analysis (PCA) of ¹H NMR from rat urine revealed a dose-dependent metabolic shift between the vehicle-treated control rats and rats treated with low-dose (10 mg/kg body weight), moderate-dose (50 mg/kg), and high-dose (100 mg/kg) naproxen, coinciding with their gastric damage scores after naproxen administration. The resultant metabolic profiles demonstrate that the naproxen-induced gastric damage exhibited energy metabolism perturbations that elevated their urinary levels of citrate, cis-aconitate, creatine, and creatine phosphate. In addition, naproxen administration decreased choline level and increased betaine level, indicating that it depleted the main protective constituent of the gastric mucosa. Moreover, naproxen stimulated the decomposition of tryptophan into kynurenate, which inhibits fibroblast growth factor-1 and delays ulcer healing. These findings demonstrate that ¹H NMR-based urinary metabolic profiling can facilitate noninvasive and rapid diagnosis of drug side effects and is suitable for elucidating possible biological pathways perturbed by drug toxicity. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

The Role of Perturbations in the B-X UV Spectrum of S_{2} in a Temperature-Dependent Mechanism for Sulfur Mass Independent Fractionation

NASA Astrophysics Data System (ADS)

Hull, Alexander W.; Field, Robert W.; Ono, Shuhei

2017-06-01

Sulfur mass independent fractionation (S-MIF) describes anomalous sulfur isotope ratios commonly found in sedimentary rocks older than 2.45 billion years. These anomalies likely originate from photochemistry of small, sulfur-containing molecules in the atmosphere, and their sudden disappearance from rock samples younger than 2.45 years is thought to be correlated with a sharp rise in atmospheric oxygen levels. The emergence of atmospheric oxygen is an important milestone in the development of life on Earth, but the mechanism for sulfur MIF in an anoxic atmosphere is not well understood. In this context, we present an analysis of the B-X UV spectrum of S_{2}, an extension of work presented last year. The B state of S_{2} is strongly perturbed by the nearby B" state, as originally described by Green and Western (1996). Our analysis suggests that a doorway-mediated transfer mechanism shifts excited state population from the short-lifetime B state to the longer-lifetime B" state. Furthermore, access to the perturbed doorway states is strongly dependent on the population distribution in the ground state. This suggests that the temperature of the Achaean atmosphere may have played a significant role in determining the extent of S-MIF.

Computation of deuterium isotope perturbation of 13C NMR chemical shifts of alkanes: a local mode zero-point level approach.

PubMed

Yang, Kin S; Hudson, Bruce

2010-11-25

Replacement of H by D perturbs the (13)C NMR chemical shifts of an alkane molecule. This effect is largest for the carbon to which the D is attached, diminishing rapidly with intervening bonds. The effect is sensitive to stereochemistry and is large enough to be measured reliably. A simple model based on the ground (zero point) vibrational level and treating only the C-H(D) degrees of freedom (local mode approach) is presented. The change in CH bond length with H/D substitution as well as the reduction in the range of the zero-point level probability distribution for the stretch and both bend degrees of freedom are computed. The (13)C NMR chemical shifts are computed with variation in these three degrees of freedom, and the results are averaged with respect to the H and D distribution functions. The resulting differences in the zero-point averaged chemical shifts are compared with experimental values of the H/D shifts for a series of cycloalkanes, norbornane, adamantane, and protoadamantane. Agreement is generally very good. The remaining differences are discussed. The proton spectrum of cyclohexane- is revisited and updated with improved agreement with experiment.

Exciton diamagnetic shift and optical properties in CdSe nanocrystal quantum dots in magnetic fields

NASA Astrophysics Data System (ADS)

Wu, Shudong; Cheng, Liwen

2018-04-01

The magnetic field dependence of the optical properties of CdSe nanocrystal quantum dots (NQDs) is investigated theoretically using a perturbation method within the effective-mass approximation. The results show that the magnetic field lifts the degeneracy of the electron (hole) states. A blue-shift in the absorption spectra of m ≥ 0 exciton states is observed while the absorption peak of m < 0 exciton states is first red-shifted and then blue-shifted with increasing the magnetic field strength B. This is attributed to the interplay of the orbital Zeeman effect and the additive confinement induced by the magnetic field. The excitonic absorption coefficient is almost independent of B in the strong confinement regime. The applied magnetic field causes the splitting of degenerated exciton states, resulting in the new absorption peaks. Based on the first-order perturbation theory, we propose the analytical expressions for the exciton binding energy, exciton transition energy and exciton diamagnetic shift of 1s, 1p-1, 1p0, 1p1, 1d-2, 1d-1, 1d0, 1d1, 1d2 and 2s exciton states on the applied magnetic field in the strong confinement regime.

SU-F-T-192: Study of Robustness Analysis Method of Multiple Field Optimized IMPT Plans for Head & Neck Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Y; Wang, X; Li, H

Purpose: Proton therapy is more sensitive to uncertainties than photon treatments due to protons’ finite range depending on the tissue density. Worst case scenario (WCS) method originally proposed by Lomax has been adopted in our institute for robustness analysis of IMPT plans. This work demonstrates that WCS method is sufficient enough to take into account of the uncertainties which could be encountered during daily clinical treatment. Methods: A fast and approximate dose calculation method is developed to calculate the dose for the IMPT plan under different setup and range uncertainties. Effects of two factors, inversed square factor and range uncertainty,more » are explored. WCS robustness analysis method was evaluated using this fast dose calculation method. The worst-case dose distribution was generated by shifting isocenter by 3 mm along x,y and z directions and modifying stopping power ratios by ±3.5%. 1000 randomly perturbed cases in proton range and x, yz directions were created and the corresponding dose distributions were calculated using this approximated method. DVH and dosimetric indexes of all 1000 perturbed cases were calculated and compared with the result using worst case scenario method. Results: The distributions of dosimetric indexes of 1000 perturbed cases were generated and compared with the results using worst case scenario. For D95 of CTVs, at least 97% of 1000 perturbed cases show higher values than the one of worst case scenario. For D5 of CTVs, at least 98% of perturbed cases have lower values than worst case scenario. Conclusion: By extensively calculating the dose distributions under random uncertainties, WCS method was verified to be reliable in evaluating the robustness level of MFO IMPT plans of H&N patients. The extensively sampling approach using fast approximated method could be used in evaluating the effects of different factors on the robustness level of IMPT plans in the future.« less

Probing the independence of formant control using altered auditory feedback

PubMed Central

MacDonald, Ewen N.; Purcell, David W.; Munhall, Kevin G.

2011-01-01

Two auditory feedback perturbation experiments were conducted to examine the nature of control of the first two formants in vowels. In the first experiment, talkers heard their auditory feedback with either F1 or F2 shifted in frequency. Talkers altered production of the perturbed formant by changing its frequency in the opposite direction to the perturbation but did not produce a correlated alteration of the unperturbed formant. Thus, the motor control system is capable of fine-grained independent control of F1 and F2. In the second experiment, a large meta-analysis was conducted on data from talkers who received feedback where both F1 and F2 had been perturbed. A moderate correlation was found between individual compensations in F1 and F2 suggesting that the control of F1 and F2 is processed in a common manner at some level. While a wide range of individual compensation magnitudes were observed, no significant correlations were found between individuals’ compensations and vowel space differences. Similarly, no significant correlations were found between individuals’ compensations and variability in normal vowel production. Further, when receiving normal auditory feedback, most of the population exhibited no significant correlation between the natural variation in production of F1 and F2. PMID:21361452

Anthropogenic Sulfur Perturbations on Biogenic Oxidation: SO2 Additions Impact Gas-Phase OH Oxidation Products of α- and β-Pinene.

PubMed

Friedman, Beth; Brophy, Patrick; Brune, William H; Farmer, Delphine K

2016-02-02

In order to probe how anthropogenic pollutants can impact the atmospheric oxidation of biogenic emissions, we investigated how sulfur dioxide (SO2) perturbations impact the oxidation of two monoterpenes, α-and β-pinene. We used chemical ionization mass spectrometry to examine changes in both individual molecules and gas-phase bulk properties of oxidation products as a function of SO2 addition. SO2 perturbations impacted the oxidation systems of α-and β-pinene, leading to an ensemble of products with a lesser degree of oxygenation than unperturbed systems. These changes may be due to shifts in the OH:HO2 ratio from SO2 oxidation and/or to SO3 reacting directly with organic molecules. Van Krevelen diagrams suggest a shift from gas-phase functionalization by alcohol/peroxide groups to functionalization by carboxylic acid or carbonyl groups, consistent with a decreased OH:HO2 ratio. Increasing relative humidity dampens the impact of the perturbation. This decrease in oxygenation may impact secondary organic aerosol formation in regions dominated by biogenic emissions with nearby SO2 sources. We observed sulfur-containing organic compounds following SO2 perturbations of monoterpene oxidation; whether these are the result of photochemistry or an instrumental artifact from ion-molecule clustering remains uncertain. However, our results demonstrate that the two monoterpene isomers produce unique suites of oxidation products.

Thermal anomalies and magmatism due to lithospheric doubling and shifting

NASA Astrophysics Data System (ADS)

Vlaar, N. J.

1983-11-01

We present some thermal and magmatic consequences of the processes of lithospheric doubling and lithospheric shifting. Lithospheric doubling concerns the obduction of a cold continental or old oceanic lithospheric plate over a young and hot oceanic lithosphere/upper mantle system, including an oceanic ridge. Lithospheric shifting concerns the translation and rotation of a lithospheric plate relative to the upper mantle. In both cases the resulting thermal state of the upper mantle below the obducting or shifting lithosphere may be perturbed relative to a "normal" continental or oceanic geothermal situation. The perturbed geothermal state gives rise to a density inversion at depth and thus induces a vertical gravitational instability which favours magmatism. We speculate about the magmatic consequences of this situation and infer that in the case of lithospheric doubling our model may account for the petrology and geochemistry of the resulting magma. The original layering and composition of the overridden young oceanic lithosphere may strongly influence magmatic processes. We dwell shortly on the genesis of kimberlites within the framework of our lithospheric doubling model and on magmatism in general. Lithospheric recycling is inherent to the mechanism of lithospheric doubling.

The Early Cretaceous Sulfur Isotope Record: New Data, Revised Ages, and Updated Modeling

NASA Astrophysics Data System (ADS)

Kristall, B.; Hurtgen, M.; Sageman, B. B.; Jacobson, A. D.

2015-12-01

The Early Cretaceous is a time of significant transformation with the continued break-up of Pangea, the emplacement of several LIPs, and a climatic shift from a cool greenhouse to a warm greenhouse. The timing of these major events and their relationship to seawater geochemistry (as recorded in isotope records) is critical for understanding changes in global biogeochemical cycles during this time. Within this context, recent revisions to the Cretaceous portion of the geologic timescale necessitate a reevaluation of the Cretaceous S isotope record as recorded in marine barite (Paytan et al., 2004). We present a revised Early Cretaceous S isotope record and present new δ34Sbarite data that extend the record further back in time and provide more detail during two major S isotope shifts of the Early Cretaceous. The new data maintain the major ~5‰ negative shift but raise questions on the timing and structure of this perturbation. Furthermore, recently updated estimates for global rates of marine microbial sulfate reduction (MSR) (Bowles et al., 2014) and sulfate burial during the Phanerozoic (Halevy et al., 2012) require notable revisions in the fluxes and isotopic values used to model the global S cycle. We present a revised global S cycle box model and reconstruct the evolution of the Early Cretaceous S isotope record primarily through perturbations in volcanic and hydrothermal fluxes (e.g., submarine LIPs). Changes to the weathering and pyrite burial fluxes and the global integrated fractionation factor for MSR are also used to modulate, balance, and smooth the LIP-driven perturbation. The massive evaporite burial during the Late Aptian post dates the major -5‰ shift and has little affect on the modeled S isotope composition of seawater sulfate, despite causing a major drop in sulfate concentration. The S cycle box model is coupled to a Sr cycle box model to provide additional constraints on the magnitude and timing of perturbations within the S isotope record.

Nonperturbative Quantum Physics from Low-Order Perturbation Theory.

PubMed

Mera, Héctor; Pedersen, Thomas G; Nikolić, Branislav K

2015-10-02

The Stark effect in hydrogen and the cubic anharmonic oscillator furnish examples of quantum systems where the perturbation results in a certain ionization probability by tunneling processes. Accordingly, the perturbed ground-state energy is shifted and broadened, thus acquiring an imaginary part which is considered to be a paradigm of nonperturbative behavior. Here we demonstrate how the low order coefficients of a divergent perturbation series can be used to obtain excellent approximations to both real and imaginary parts of the perturbed ground state eigenenergy. The key is to use analytic continuation functions with a built-in singularity structure within the complex plane of the coupling constant, which is tailored by means of Bender-Wu dispersion relations. In the examples discussed the analytic continuation functions are Gauss hypergeometric functions, which take as input fourth order perturbation theory and return excellent approximations to the complex perturbed eigenvalue. These functions are Borel consistent and dramatically outperform widely used Padé and Borel-Padé approaches, even for rather large values of the coupling constant.

Perturbation analyses of intermolecular interactions

NASA Astrophysics Data System (ADS)

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Perturbation analyses of intermolecular interactions.

PubMed

Koyama, Yohei M; Kobayashi, Tetsuya J; Ueda, Hiroki R

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, B.; Molina, R.; Döring, M.

Recentmore » $$N_f=2+1$$ lattice data for meson-meson scattering in $p$-wave and isospin $I=1$ are analyzed using a unitarized model inspired by Chiral Perturbation Theory in the inverse-amplitude formulation for two and three flavors. We perform chiral extrapolations that postdict phase shifts extracted from experiment quite well. Additionally, the low-energy constants are compared to the ones from a recent analysis of $$N_f=2$$ lattice QCD simulations to check for the consistency of the hadronic model used here. Some inconsistencies are detected in the fits to $$N_f=2+1$$ data, in contrast to the previous analysis of $$N_f=2$$ data.« less

Instabilities in a nonstationary model of self-gravitating disks. III. The phenomenon of lopsidedness and a comparison of perturbation modes

NASA Astrophysics Data System (ADS)

Mirtadjieva, K. T.; Nuritdinov, S. N.; Ruzibaev, J. K.; Khalid, Muhammad

2011-06-01

This is an examination of the gravitational instability of the major large-scale perturbation modes for a fixed value of the azimuthal wave number m = 1 in nonlinearly nonstationary disk models with isotropic and anisotropic velocity diagrams for the purpose of explaining the displacement of the nucleus away from the geometric center (lopsidedness) in spiral galaxies. Nonstationary analogs of the dispersion relations for these perturbation modes are obtained. Critical diagrams of the initial virial ratio are constructed from the rotation parameters for the models in each case. A comparative analysis is made of the instability growth rates for the major horizontal perturbation modes in terms of two models, and it is found that, on the average, the instability growth rate for the m = 1 mode with a radial wave number N = 3 almost always has a clear advantage relative to the other modes. An analysis of these results shows that if the initial total kinetic energy in an isotropic model is no more than 12.4% of the initial potential energy, then, regardless of the value of the rotation parameter Ω, an instability of the radial motions always occurs and causes the nucleus to shift away from the geometrical center. This instability is aperiodic when Ω = 0 and is oscillatory when Ω ≠ 0 . For the anisotropic model, this kind of structure involving the nucleus develops when the initial total kinetic energy in the model is no more than 30.6% of the initial potential energy.

Graphene-induced band gap renormalization in polythiophene: a many-body perturbation study

NASA Astrophysics Data System (ADS)

Marsusi, F.; Fedorov, I. A.; Gerivani, S.

2018-01-01

Density functional theory and many-body perturbation theory at the G0W0 level are employed to study the electronic properties of polythiophene (PT) adsorbed on the graphene surface. Analysis of the charge density difference shows that substrate-adsorbate interaction leads to a strong physisorption and interfacial electric dipole moment formation. The electrostatic potential displays a  -0.19 eV shift in the graphene work function from its initial value of 4.53 eV, as the result of the interaction. The LDA band gap of the polymer does not show any change. However, the band structure exhibits weak orbital hybridizations resulting from slight overlapping between the polymer and graphene states wave functions. The interfacial polarization effects on the band gap and levels alignment are investigated at the G0W0 level and show a notable reduction of PT band gap compared to that of the isolated chain.

A comprehensive analysis of surface acoustic wave reflections

NASA Astrophysics Data System (ADS)

Robinson, H.; Hahn, Y.; Gau, J. N.

1989-06-01

A thorough study of the perturbative and variational approaches is carried out for the surface acoustic wave reflection problem. We have shown that the perturbation treatment by Datta and Hunsinger and potentially powerful variational formulation by Chen and Haus [IEEE Trans. Sonics Ultrason. SU-32, 395 (1985)] are mutually consistent. In their common region of validity, these two approaches yield nearly identical results for the reflection coefficients and velocity shifts due to metal finger and groove overlays. Term-by-term comparison of the mass- and stress-loading effects, and also the electric shorting effect, is carried out to provide a coherent picture of the reflection phenomena. The on- and off-resonance behavior of the reflection coefficient can be described correctly using either one of these theories, with proper inclusion of the overlay shape dependence. A new term for electric shorting is derived for groove overlays.

Investigation of Bose-Einstein Condensates in q-Deformed Potentials with First Order Perturbation Theory

NASA Astrophysics Data System (ADS)

Nutku, Ferhat; Aydıner, Ekrem

2018-02-01

The Gross-Pitaevskii equation, which is the governor equation of Bose-Einstein condensates, is solved by first order perturbation expansion under various q-deformed potentials. Stationary probability distributions reveal one and two soliton behavior depending on the type of the q-deformed potential. Additionally a spatial shift of the probability distribution is found for the dark soliton solution, when the q parameter is changed.

Scale interaction and arrangement in a turbulent boundary layer perturbed by a wall-mounted cylindrical element

NASA Astrophysics Data System (ADS)

Tang, Zhanqi; Jiang, Nan

2018-05-01

This study reports the modifications of scale interaction and arrangement in a turbulent boundary layer perturbed by a wall-mounted circular cylinder. Hot-wire measurements were executed at multiple streamwise and wall-normal wise locations downstream of the cylindrical element. The streamwise fluctuating signals were decomposed into large-, small-, and dissipative-scale signatures by corresponding cutoff filters. The scale interaction under the cylindrical perturbation was elaborated by comparing the small- and dissipative-scale amplitude/frequency modulation effects downstream of the cylinder element with the results observed in the unperturbed case. It was obtained that the large-scale fluctuations perform a stronger amplitude modulation on both the small and dissipative scales in the near-wall region. At the wall-normal positions of the cylinder height, the small-scale amplitude modulation coefficients are redistributed by the cylinder wake. The similar observation was noted in small-scale frequency modulation; however, the dissipative-scale frequency modulation seems to be independent of the cylindrical perturbation. The phase-relationship observation indicated that the cylindrical perturbation shortens the time shifts between both the small- and dissipative-scale variations (amplitude and frequency) and large-scale fluctuations. Then, the integral time scale dependence of the phase-relationship between the small/dissipative scales and large scales was also discussed. Furthermore, the discrepancy of small- and dissipative-scale time shifts relative to the large-scale motions was examined, which indicates that the small-scale amplitude/frequency leads the dissipative scales.

Collisional perturbation of radio-frequency E1 transitions in an atomic beam of dysprosium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cingoez, A.; Lapierre, Alain; Nguyen, A.-T.

2005-12-15

We have studied collisional perturbations of radio-frequency (rf) electric-dipole (E1) transitions between the nearly degenerate opposite-parity levels in atomic dysprosium (Dy) in the presence of 10 to 80 {mu}Torr of H{sub 2}, N{sub 2}, He, Ar, Ne, Kr, and Xe. Collisional broadening and shift of the resonance, as well as the attenuation of the signal amplitude are observed to be proportional to the foreign-gas density with the exception of H{sub 2} and Ne, for which no shifts were observed. Corresponding rates and cross sections are presented. In addition, rates and cross sections for O{sub 2} are extracted from measurements usingmore » air as foreign gas. The primary motivation for this study is the need for accurate determination of the shift rates, which are needed in a laboratory search for the temporal variation of the fine-structure constant [A. T. Nguyen, D. Budker, S. K. Lamoreaux, and J. R. Torgerson, Phys. Rev. A 69, 22105 (2004)].« less

Quantitative analysis of intrinsic and extrinsic factors in the aggregation mechanism of Alzheimer-associated Aβ-peptide

NASA Astrophysics Data System (ADS)

Meisl, Georg; Yang, Xiaoting; Frohm, Birgitta; Knowles, Tuomas P. J.; Linse, Sara

2016-01-01

Disease related mutations and environmental factors are key determinants of the aggregation mechanism of the amyloid-β peptide implicated in Alzheimer's disease. Here we present an approach to investigate these factors through acquisition of highly reproducible data and global kinetic analysis to determine the mechanistic influence of intrinsic and extrinsic factors on the Aβ aggregation network. This allows us to translate the shift in macroscopic aggregation behaviour into effects on the individual underlying microscopic steps. We apply this work-flow to the disease-associated Aβ42-A2V variant, and to a variation in pH as examples of an intrinsic and an extrinsic perturbation. In both cases, our data reveal a shift towards a mechanism in which a larger fraction of the reactive flux goes via a pathway that generates potentially toxic oligomeric species in a fibril-catalyzed reaction. This is in agreement with the finding that Aβ42-A2V leads to early-onset Alzheimer’s disease and enhances neurotoxicity.

Spectral stability of shifted states on star graphs

NASA Astrophysics Data System (ADS)

Kairzhan, Adilbek; Pelinovsky, Dmitry E.

2018-03-01

We consider the nonlinear Schrödinger (NLS) equation with the subcritical power nonlinearity on a star graph consisting of N edges and a single vertex under generalized Kirchhoff boundary conditions. The stationary NLS equation may admit a family of solitary waves parameterized by a translational parameter, which we call the shifted states. The two main examples include (i) the star graph with even N under the classical Kirchhoff boundary conditions and (ii) the star graph with one incoming edge and N  -  1 outgoing edges under a single constraint on coefficients of the generalized Kirchhoff boundary conditions. We obtain the general counting results on the Morse index of the shifted states and apply them to the two examples. In the case of (i), we prove that the shifted states with even N ≥slant 4 are saddle points of the action functional which are spectrally unstable under the NLS flow. In the case of (ii), we prove that the shifted states with the monotone profiles in the N  -  1 edges are spectrally stable, whereas the shifted states with non-monotone profiles in the N  -  1 edges are spectrally unstable, the two families intersect at the half-soliton states which are spectrally stable but nonlinearly unstable under the NLS flow. Since the NLS equation on a star graph with shifted states can be reduced to the homogeneous NLS equation on an infinite line, the spectral instability of shifted states is due to the perturbations breaking this reduction. We give a simple argument suggesting that the spectrally stable shifted states in the case of (ii) are nonlinearly unstable under the NLS flow due to the perturbations breaking the reduction to the homogeneous NLS equation.

Nonlinear Bayesian cue integration explains the dynamics of vocal learning

NASA Astrophysics Data System (ADS)

Zhou, Baohua; Sober, Samuel; Nemenman, Ilya

The acoustics of vocal production in songbirds is tightly regulated during both development and adulthood as birds progressively refine their song using sensory feedback to match an acoustic target. Here, we perturb this sensory feedback using headphones to shift the pitch (fundamental frequency) of song. When the pitch is shifted upwards (downwards), birds eventually learn to compensate and sing lower (higher), bringing the experienced pitch closer to the target. Paradoxically, the speed and amplitude of this motor learning decrease with increases in the introduced error size, so that birds respond rapidly to a small sensory perturbation, while seemingly never correcting a much bigger one. Similar results are observed broadly across the animal kingdom, and they do not derive from a limited plasticity of the adult brain since birds can compensate for a large error as long as the error is imposed gradually. We develop a mathematical model based on nonlinear Bayesian integration of two sensory modalities (one perturbed and the other not) that quantitatively explains all of these observations. The model makes predictions about the structure of the probability distribution of the pitches sung by birds during the pitch shift experiments, which we confirm using experimental data. This work was supported in part by James S. McDonnell Foundation Grant # 220020321, NSF Grant # IOS/1208126, NSF Grant # IOS/1456912 and NIH Grants # R01NS084844.

Influence of geometric and material properties on artifacts generated by interventional MRI devices: Relevance to PRF-shift thermometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tatebe, Ken, E-mail: Ken.Tatebe@gmail.com; Ramsay, Elizabeth; Kazem, Mohammad

2016-01-15

Purpose: Magnetic resonance imaging (MRI) is capable of providing valuable real-time feedback during medical procedures, partly due to the excellent soft-tissue contrast available. Several technical hurdles still exist to seamless integration of medical devices with MRI due to incompatibility of most conventional devices with this imaging modality. In this study, the effect of local perturbations in the magnetic field caused by the magnetization of medical devices was examined using finite element analysis modeling. As an example, the influence of the geometric and material characteristics of a transurethral high-intensity ultrasound applicator on temperature measurements using proton resonance frequency (PRF)-shift thermometry wasmore » investigated. Methods: The effect of local perturbations in the magnetic field, caused by the magnetization of medical device components, was examined using finite element analysis modeling. The thermometry artifact generated by a transurethral ultrasound applicator was simulated, and these results were validated against analytic models and scans of an applicator in a phantom. Several parameters were then varied to identify which most strongly impacted the level of simulated thermometry artifact, which varies as the applicator moves over the course of an ablative high-intensity ultrasound treatment. Results: Key design parameters identified as having a strong influence on the magnitude of thermometry artifact included the susceptibility of materials and their volume. The location of components was also important, particularly when positioned to maximize symmetry of the device. Finally, the location of component edges and the inclination of the device relative to the magnetic field were also found to be important factors. Conclusions: Previous design strategies to minimize thermometry artifact were validated, and novel design strategies were identified that substantially reduce PRF-shift thermometry artifacts for a variety of device orientations. These new strategies are being incorporated into the next generation of applicators. The general strategy described in this study can be applied to the design of other interventional devices intended for use with MRI.« less

Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tanping, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu; Kumar, Revati, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu

2015-11-07

We explore the connection between the solvation dynamics of a chromophore upon photon excitation and equilibrium fluctuations of the solvent. Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. When the perturbed and unperturbed surfaces exhibit different solvent equilibrium fluctuations, the linear response approach on the former surface shows agreement with the nonequilibrium process. This agreement is excellent when the perturbed surface exhibits Gaussian statistics and qualitative in the case of an isomerization induced non-Gaussian statistics. However, the linear response theory on the unperturbed surface breaksmore » down even in the presence of Gaussian fluctuations. Experiments also provide evidence of the connection between the excited state solvent fluctuations and the total fluorescence shift. These observations indicate that the equilibrium statistics on the excited state surface characterize the relaxation dynamics of the fluorescence Stokes shift. Our studies specifically analyze the Gaussian fluctuations of the solvent in the complex protein environment and further confirm the role of solvent fluctuations on the excited state surface. The results are consistent with previous investigations, found in the literature, of solutes dissolved in liquids.« less

H2-broadening, shifting and mixing coefficients of the doublets in the ν2 and ν4 bands of PH3 at room temperature

NASA Astrophysics Data System (ADS)

Salem, Jamel; Blanquet, Ghislain; Lepère, Muriel; Younes, Rached ben

2018-05-01

The broadening, shifting and mixing coefficients of the doublet spectral lines in the ν2 and ν4 bands of PH3 perturbed by H2 have been determined at room temperature. Indeed, the collisional spectroscopic parameters: intensities, line widths, line shifts and line mixing parameters, are all grouped together in the collisional relaxation matrix. To analyse the collisional process and physical effects on spectra of phosphine (PH3), we have used the measurements carried out using a tunable diode-laser spectrometer in the ν2 and ν4 bands of PH3 perturbed by hydrogen (H2) at room temperature. The recorded spectra are fitted by the Voigt profile and the speed-dependent uncorrelated hard collision model of Rautian and Sobelman. These profiles are developed in the studies of isolated lines and are modified to account for the line mixing effects in the overlapping lines. The line widths, line shifts and line mixing parameters are given for six A1 and A2 doublet lines with quantum numbers K = 3n, (n = 1, 2, …) and overlapped by collisional broadening at pressures of less than 50 mbar.

Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding

PubMed Central

Fenley, Andrew T.; Muddana, Hari S.; Gilson, Michael K.

2012-01-01

Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a torsion angle or interresidue distance, can select for occupancy of one or another conformational state. These results establish the basis for a mechanism that we term entropy–enthalpy transduction (EET), in which the thermodynamic character of a local perturbation, such as enthalpic binding of a small molecule, is camouflaged by the thermodynamics of a global conformational change induced by the perturbation, such as a switch into a high-entropy conformational state. It is noted that EET could occur in many systems, making measured entropies and enthalpies of folding and binding unreliable indicators of actual thermodynamic driving forces. The same mechanism might also account for the high experimental variance of measured enthalpies and entropies relative to free energies in some calorimetric studies. Finally, EET may be the physical mechanism underlying many cases of entropy–enthalpy compensation. PMID:23150595

Taking Systems Medicine to Heart.

PubMed

Trachana, Kalliopi; Bargaje, Rhishikesh; Glusman, Gustavo; Price, Nathan D; Huang, Sui; Hood, Leroy E

2018-04-27

Systems medicine is a holistic approach to deciphering the complexity of human physiology in health and disease. In essence, a living body is constituted of networks of dynamically interacting units (molecules, cells, organs, etc) that underlie its collective functions. Declining resilience because of aging and other chronic environmental exposures drives the system to transition from a health state to a disease state; these transitions, triggered by acute perturbations or chronic disturbance, manifest as qualitative shifts in the interactions and dynamics of the disease-perturbed networks. Understanding health-to-disease transitions poses a high-dimensional nonlinear reconstruction problem that requires deep understanding of biology and innovation in study design, technology, and data analysis. With a focus on the principles of systems medicine, this Review discusses approaches for deciphering this biological complexity from a novel perspective, namely, understanding how disease-perturbed networks function; their study provides insights into fundamental disease mechanisms. The immediate goals for systems medicine are to identify early transitions to cardiovascular (and other chronic) diseases and to accelerate the translation of new preventive, diagnostic, or therapeutic targets into clinical practice, a critical step in the development of personalized, predictive, preventive, and participatory (P4) medicine. © 2018 American Heart Association, Inc.

Single exosome detection in serum using microtoroid optical resonators (Conference Presentation)

NASA Astrophysics Data System (ADS)

Su, Judith

2016-03-01

Recently exosomes have attracted interest due to their potential as cancer biomarkers. We report the real time, label-free sensing of single exosomes in serum using microtoroid optical resonators. We use this approach to assay the progression of tumors implanted in mice by specifically detecting low concentrations of tumor-derived exosomes. Our approach measures the adsorption of individual exosomes onto a functionalized silica microtoroid by tracking changes in the optical resonant frequency of the microtoroid. When exosomes land on the microtoroid, they perturb its refractive index in the evanescent field and thus shift its resonance frequency. Through digital frequency locking, we are able to rapidly track these shifts with accuracies of better than 10 attometers (one part in 10^11). Samples taken from tumor-implanted mice from later weeks generated larger frequency shifts than those from earlier weeks. Control samples taken from a mouse with no tumor generated no such increase in signal between subsequent weeks. Analysis of shifts from tumor-implanted mouse samples show a distribution of unitary steps, with the maximum step having a height of ~1.2 fm, corresponding to an exosome size of 44 ± 4.8 nm. This size range corresponds to that found by performing nanoparticle tracking analysis on the same samples. Our results demonstrate development towards a minimally-invasive tumor "biopsy" that eliminates the need to find and access a tumor.

A synergetic combination of small and large neighborhood schemes in developing an effective procedure for solving the job shop scheduling problem.

PubMed

Amirghasemi, Mehrdad; Zamani, Reza

2014-01-01

This paper presents an effective procedure for solving the job shop problem. Synergistically combining small and large neighborhood schemes, the procedure consists of four components, namely (i) a construction method for generating semi-active schedules by a forward-backward mechanism, (ii) a local search for manipulating a small neighborhood structure guided by a tabu list, (iii) a feedback-based mechanism for perturbing the solutions generated, and (iv) a very large-neighborhood local search guided by a forward-backward shifting bottleneck method. The combination of shifting bottleneck mechanism and tabu list is used as a means of the manipulation of neighborhood structures, and the perturbation mechanism employed diversifies the search. A feedback mechanism, called repeat-check, detects consequent repeats and ignites a perturbation when the total number of consecutive repeats for two identical makespan values reaches a given threshold. The results of extensive computational experiments on the benchmark instances indicate that the combination of these four components is synergetic, in the sense that they collectively make the procedure fast and robust.

Accurate calculation of dynamic Stark shifts and depopulation rates of Rydberg energy levels induced by blackbody radiation. Hydrogen, helium, and alkali-metal atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farley, J.W.; Wing, W.H.

1981-05-01

A highly excited (Rydberg) atom bathed in blackbody radiation is perturbed in two ways. A dynamic Stark shift is induced by the off-resonant components of the blackbody radiation. Additionally, electric-dipole transitions to other atomic energy levels are induced by the resonant components of the blackbody radiation. This depopulation effect shortens the Rydberg-state lifetime, thereby broadening the energy level. Calculations of these two effects in many states of hydrogen, helium, and the alkali-metal atoms Li, Na, K, Rb, and Cs are presented for T = 300 K. Contributions from the entire blackbody spectrum and from both discrete and continuous perturbing statesmore » are included. The accuracy is considerably greater than that of previous estimates.« less

A numerical scheme for singularly perturbed reaction-diffusion problems with a negative shift via numerov method

NASA Astrophysics Data System (ADS)

Dinesh Kumar, S.; Nageshwar Rao, R.; Pramod Chakravarthy, P.

2017-11-01

In this paper, we consider a boundary value problem for a singularly perturbed delay differential equation of reaction-diffusion type. We construct an exponentially fitted numerical method using Numerov finite difference scheme, which resolves not only the boundary layers but also the interior layers arising from the delay term. An extensive amount of computational work has been carried out to demonstrate the applicability of the proposed method.

Probing Structural Perturbation in a Bent Molecular Crystal with Synchrotron Infrared Microspectroscopy and Periodic Density Functional Theory Calculations.

PubMed

Pejov, Ljupčo; Panda, Manas K; Moriwaki, Taro; Naumov, Panče

2017-02-15

The range of unit cell orientations generated at the kink of a bent single crystal poses unsurmountable challenges with diffraction analysis and limits the insight into the molecular-scale mechanism of bending. On a plastically bent crystal of hexachlorobenzene, it is demonstrated here that spatially resolved microfocus infrared spectroscopy using synchrotron radiation can be applied in conjunction with periodic density functional theory calculations to predict spectral changes or to extract information on structural changes that occur as a consequence of bending. The approach reproduces well the observed trends, such as the wall effects, and provides estimations of the vibrational shifts, unit cell deformations, and intramolecular parameters. Generally, expansion of the lattice induces red-shift while compression induces larger blue-shift of the characteristic ν(C-C) and ν(C-Cl) modes. Uniform or non-uniform expansion or contraction of the unit cell of 0.1 Å results in shifts of several cm -1 , whereas deformation of the cell of 0.5° at the unique angle causes shifts of <0.5 cm -1 . Since this approach does not include parameters related to the actual stimulus by which the deformation has been induced, it can be generalized and applied to other mechanically, photochemically, or thermally bent crystals.

Modification of response functions of cat visual cortical cells by spatially congruent perturbing stimuli.

PubMed

Kabara, J F; Bonds, A B

2001-12-01

Responses of cat striate cortical cells to a drifting sinusoidal grating were modified by the superimposition of a second, perturbing grating (PG) that did not excite the cell when presented alone. One consequence of the presence of a PG was a shift in the tuning curves. The orientation tuning of all 41 cells exposed to a PG and the spatial frequency tuning of 83% of the 23 cells exposed to a PG showed statistically significant dislocations of both the response function peak and center of mass from their single grating values. As found in earlier reports, the presence of PGs suppressed responsiveness. However, reductions measured at the single grating optimum orientation or spatial frequency were on average 1.3 times greater than the suppression found at the peak of the response function modified by the presence of the PG. Much of the loss in response seen at the single grating optimum is thus a result of a shift in the tuning function rather than outright suppression. On average orientation shifts were repulsive and proportional (approximately 0.10 deg/deg) to the angle between the perturbing stimulus and the optimum single grating orientation. Shifts in the spatial frequency response function were both attractive and repulsive, resulting in an overall average of zero. For both simple and complex cells, PGs generally broadened orientation response function bandwidths. Similarly, complex cell spatial frequency response function bandwidths broadened. Simple cell spatial frequency response functions usually did not change, and those that did broadened only 4% on average. These data support the hypothesis that additional sinusoidal components in compound stimuli retune cells' response functions for orientation and spatial frequency.

Do kinematic metrics of walking balance adapt to perturbed optical flow?

PubMed

Thompson, Jessica D; Franz, Jason R

2017-08-01

Visual (i.e., optical flow) perturbations can be used to study balance control and balance deficits. However, it remains unclear whether walking balance control adapts to such perturbations over time. Our purpose was to investigate the propensity for visuomotor adaptation in walking balance control using prolonged exposure to optical flow perturbations. Ten subjects (age: 25.4±3.8years) walked on a treadmill while watching a speed-matched virtual hallway with and without continuous mediolateral optical flow perturbations of three different amplitudes. Each of three perturbation trials consisted of 8min of prolonged exposure followed by 1min of unperturbed walking. Using 3D motion capture, we analyzed changes in foot placement kinematics and mediolateral sacrum motion. At their onset, perturbations elicited wider and shorter steps, alluding to a more cautious, general anticipatory balance control strategy. As perturbations continued, foot placement tended toward values seen during unperturbed walking while step width variability and mediolateral sacrum motion concurrently increased. Our findings suggest that subjects progressively shifted from a general anticipatory balance control strategy to a reactive, task-specific strategy using step-to-step adjustments. Prolonged exposure to optical flow perturbations may have clinical utility to reinforce reactive, task-specific balance control through training. Copyright © 2017 Elsevier B.V. All rights reserved.

Integration of auditory and somatosensory error signals in the neural control of speech movements.

PubMed

Feng, Yongqiang; Gracco, Vincent L; Max, Ludo

2011-08-01

We investigated auditory and somatosensory feedback contributions to the neural control of speech. In task I, sensorimotor adaptation was studied by perturbing one of these sensory modalities or both modalities simultaneously. The first formant (F1) frequency in the auditory feedback was shifted up by a real-time processor and/or the extent of jaw opening was increased or decreased with a force field applied by a robotic device. All eight subjects lowered F1 to compensate for the up-shifted F1 in the feedback signal regardless of whether or not the jaw was perturbed. Adaptive changes in subjects' acoustic output resulted from adjustments in articulatory movements of the jaw or tongue. Adaptation in jaw opening extent in response to the mechanical perturbation occurred only when no auditory feedback perturbation was applied or when the direction of adaptation to the force was compatible with the direction of adaptation to a simultaneous acoustic perturbation. In tasks II and III, subjects' auditory and somatosensory precision and accuracy were estimated. Correlation analyses showed that the relationships 1) between F1 adaptation extent and auditory acuity for F1 and 2) between jaw position adaptation extent and somatosensory acuity for jaw position were weak and statistically not significant. Taken together, the combined findings from this work suggest that, in speech production, sensorimotor adaptation updates the underlying control mechanisms in such a way that the planning of vowel-related articulatory movements takes into account a complex integration of error signals from previous trials but likely with a dominant role for the auditory modality.

Impact of basic angle variations on the parallax zero point for a scanning astrometric satellite

NASA Astrophysics Data System (ADS)

Butkevich, Alexey G.; Klioner, Sergei A.; Lindegren, Lennart; Hobbs, David; van Leeuwen, Floor

2017-07-01

Context. Determination of absolute parallaxes by means of a scanning astrometric satellite such as Hipparcos or Gaia relies on the short-term stability of the so-called basic angle between the two viewing directions. Uncalibrated variations of the basic angle may produce systematic errors in the computed parallaxes. Aims: We examine the coupling between a global parallax shift and specific variations of the basic angle, namely those related to the satellite attitude with respect to the Sun. Methods: The changes in observables produced by small perturbations of the basic angle, attitude, and parallaxes were calculated analytically. We then looked for a combination of perturbations that had no net effect on the observables. Results: In the approximation of infinitely small fields of view, it is shown that certain perturbations of the basic angle are observationally indistinguishable from a global shift of the parallaxes. If these kinds of perturbations exist, they cannot be calibrated from the astrometric observations but will produce a global parallax bias. Numerical simulations of the astrometric solution, using both direct and iterative methods, confirm this theoretical result. For a given amplitude of the basic angle perturbation, the parallax bias is smaller for a larger basic angle and a larger solar aspect angle. In both these respects Gaia has a more favourable geometry than Hipparcos. In the case of Gaia, internal metrology is used to monitor basic angle variations. Additionally, Gaia has the advantage of detecting numerous quasars, which can be used to verify the parallax zero point.

The I=2 ππ S-wave Scattering Phase Shift from Lattice QCD

DOE PAGES

Beane, S. R.; Chang, E.; Detmold, W.; ...

2012-02-16

The π +π + s-wave scattering phase-shift is determined below the inelastic threshold using Lattice QCD. Calculations were performed at a pion mass of m π ≈ 390 MeV with an anisotropic n f = 2+1 clover fermion discretization in four lattice volumes, with spatial extent L ≈ 2.0, 2.5, 3.0 and 3.9 fm, and with a lattice spacing of b s ≈ 0.123 fm in the spatial direction and b t b s/3.5 in the time direction. The phase-shift is determined from the energy-eigenvalues of π +π + systems with both zero and non-zero total momentum in the latticemore » volume using Luscher's method. Our calculations are precise enough to allow for a determination of the threshold scattering parameters, the scattering length a, the effective range r, and the shape-parameter P, in this channel and to examine the prediction of two-flavor chiral perturbation theory: m π 2 a r = 3+O(m π 2/Λ χ 2). Chiral perturbation theory is used, with the Lattice QCD results as input, to predict the scattering phase-shift (and threshold parameters) at the physical pion mass. Our results are consistent with determinations from the Roy equations and with the existing experimental phase shift data.« less

Application of adenosine triphosphate affinity probe and scheduled multiple-reaction monitoring analysis for profiling global kinome in human cells in response to arsenite treatment.

PubMed

Guo, Lei; Xiao, Yongsheng; Wang, Yinsheng

2014-11-04

Phosphorylation of cellular components catalyzed by kinases plays important roles in cell signaling and proliferation. Quantitative assessment of perturbation in global kinome may provide crucial knowledge for elucidating the mechanisms underlying the cytotoxic effects of environmental toxicants. Here, we utilized an adenosine triphosphate (ATP) affinity probe coupled with stable isotope labeling by amino acids in cell culture (SILAC) to assess quantitatively the arsenite-induced alteration of global kinome in human cells. We constructed a SILAC-compatible kinome library for scheduled multiple-reaction monitoring (MRM) analysis and adopted on-the-fly recalibration of retention time shift, which provided better throughput of the analytical method and enabled the simultaneous quantification of the expression of ∼300 kinases in two LC-MRM runs. With this improved analytical method, we conducted an in-depth quantitative analysis of the perturbation of kinome of GM00637 human skin fibroblast cells induced by arsenite exposure. Several kinases involved in cell cycle progression, including cyclin-dependent kinases (CDK1 and CDK4) and Aurora kinases A, B, and C, were found to be hyperactivated, and the altered expression of CDK1 was further validated by Western analysis. In addition, treatment with a CDK inhibitor, flavopiridol, partially restored the arsenite-induced growth inhibition of human skin fibroblast cells. Thus, sodium arsenite may confer its cytotoxic effect partly through the aberrant activation of CDKs and the resultant perturbation of cell cycle progression. Together, we developed a high-throughput, SILAC-compatible, and MRM-based kinome profiling method and demonstrated that the method is powerful in deciphering the molecular modes of action of a widespread environmental toxicant. The method should be generally applicable for uncovering the cellular pathways triggered by other extracellular stimuli.

Application of Adenosine Triphosphate Affinity Probe and Scheduled Multiple-Reaction Monitoring Analysis for Profiling Global Kinome in Human Cells in Response to Arsenite Treatment

PubMed Central

2015-01-01

Phosphorylation of cellular components catalyzed by kinases plays important roles in cell signaling and proliferation. Quantitative assessment of perturbation in global kinome may provide crucial knowledge for elucidating the mechanisms underlying the cytotoxic effects of environmental toxicants. Here, we utilized an adenosine triphosphate (ATP) affinity probe coupled with stable isotope labeling by amino acids in cell culture (SILAC) to assess quantitatively the arsenite-induced alteration of global kinome in human cells. We constructed a SILAC-compatible kinome library for scheduled multiple-reaction monitoring (MRM) analysis and adopted on-the-fly recalibration of retention time shift, which provided better throughput of the analytical method and enabled the simultaneous quantification of the expression of ∼300 kinases in two LC-MRM runs. With this improved analytical method, we conducted an in-depth quantitative analysis of the perturbation of kinome of GM00637 human skin fibroblast cells induced by arsenite exposure. Several kinases involved in cell cycle progression, including cyclin-dependent kinases (CDK1 and CDK4) and Aurora kinases A, B, and C, were found to be hyperactivated, and the altered expression of CDK1 was further validated by Western analysis. In addition, treatment with a CDK inhibitor, flavopiridol, partially restored the arsenite-induced growth inhibition of human skin fibroblast cells. Thus, sodium arsenite may confer its cytotoxic effect partly through the aberrant activation of CDKs and the resultant perturbation of cell cycle progression. Together, we developed a high-throughput, SILAC-compatible, and MRM-based kinome profiling method and demonstrated that the method is powerful in deciphering the molecular modes of action of a widespread environmental toxicant. The method should be generally applicable for uncovering the cellular pathways triggered by other extracellular stimuli. PMID:25301106

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voigt, Aiko; Pincus, Robert; Stevens, Bjorn

Previous modeling work showed that aerosol can affect the position of the tropical rain belt, i.e., the intertropical convergence zone (ITCZ). Yet it remains unclear which aspects of the aerosol impact are robust across models, and which are not. Here we present simulations with seven comprehensive atmosphere models that study the fast and slow impacts of an idealized anthropogenic aerosol on the zonal-mean ITCZ position. The fast impact, which results from aerosol atmospheric heating and land cooling before sea-surface temperature (SST) has time to respond, causes a northward ITCZ shift. Yet the fast impact is compensated locally by decreased evaporationmore » over the ocean, and a clear northward shift is only found for an unrealistically large aerosol forcing. The local compensation implies that while models differ in atmospheric aerosol heating, this does not contribute to model differences in the ITCZ shift. The slow impact includes the aerosol impact on the ocean surface energy balance and is mediated by SST changes. The slow impact is an order of magnitude more effective than the fast impact and causes a clear southward ITCZ shift for realistic aerosol forcing. Models agree well on the slow ITCZ shift when perturbed with the same SST pattern. However, an energetic analysis suggests that the slow ITCZ shifts would be substantially more model-dependent in interactive-SST setups due to model differences in clear-sky radiative transfer and clouds. In conclusion, we also discuss implications for the representation of aerosol in climate models and attributions of recent observed ITCZ shifts to aerosol.« less

Fluorescence spectral shift of QD films with electron injection: Dependence on counterion proximity

NASA Astrophysics Data System (ADS)

Lu, Meilin; Li, Bo; Zhang, Yaxin; Liu, Weilong; Yang, Yanqiang; Wang, Yuxiao; Yang, Qingxin

2017-05-01

Due to the promising application of quantum dot (QD) films in solar cells, LEDs and environmental detectors, the fluorescence of charged QD films has achieved much attention during recent years. In this work, we observe the spectral shift of photoluminescence (PL) in charged CdSe/ZnS QD films controlled by electrochemical potential. The spectral center under negative bias changes from red-shift to blue-shift while introducing smaller inorganic counterions (potassium ions) into the electrolyte. This repeatable effect is attributed to the enhanced electron injection with smaller cations and the electronic perturbations of QD luminescence by these excess charges.

Analysis of the fluctuations of a laser beam due to thermal turbulence

NASA Astrophysics Data System (ADS)

Ndlovu, Sphumelele C.; Chetty, Naven

2014-07-01

A laser beam propagating in air and passing through a point diffraction interferometer (PDI) produces stable interferograms that can be used to extract wavefront data such as major atmospheric characteristics: turbulence strength, inner scale and outer scale of the refractive index. These parameters need to be taken into consideration when developing defense laser weapons since they can be affected by thermal fluctuations that are due to the changes in temperature in close proximity to the propagating beam and results in phase shifts that can be used to calculate the temperature which causes wavefront perturbations on a propagating beam.

Light-Front Hamiltonian Approach to the Bound-State Problem in Quantum Electrodynamics

NASA Astrophysics Data System (ADS)

Jones, Billy D.

1997-10-01

Why is the study of the Lamb shift in hydrogen, which at the level of detail found in this paper was largely completed by Bethe in 1947, of any real interest today? While completing such a calculation using new techniques may be very interesting for formal and academic reasons, our primary motivation is to lay groundwork for precision bound-state calculations in QCD. The Lamb shift provides an excellent pedagogical tool for illustrating light-front Hamiltonian techniques, which are not widely known; but more importantly it presents three of the central dynamical and computational problems that we must face to make these techniques useful for solving QCD: How does a constituent picture emerge in a gauge field theory? How do bound-state energy scales emerge non-perturbatively? How does rotational symmetry emerge in a non-perturbative light-front calculation?

Shifts in Methanogenic Subpopulations Measured with Antibody Probes in a Fixed-Bed Loop Anaerobic Bioreactor Treating Sulfite Evaporator Condensate

PubMed Central

Macario, Alberto J. L.; de Macario, Everly Conway; Ney, Ulrich; Schoberth, Siegfried M.; Sahm, Hermann

1989-01-01

A fixed-bed loop, high-rate anaerobic bioreactor treating sulfite evaporator condensate was sampled when it reached steady state and afterwards following perturbations during a 14-month period. By using immunotechnology, it was observed that shifts in methanogenic subpopulations occurred in association with perturbations, such as restarting and relocating the biomass into a different tank. Methanogens related to Methanobacterium bryantii MoHG and Methanobrevibacter smithii ALI were numerous throughout the observation period, while Methanosarcina mazei S6 and Methanosarcina thermophila TM1 were found in the early and late samples, respectively. Also, Methanobacterium formicicum was more numerous at the top portion of the bioreactor, while Methanobrevibacter arboriphilus AZ and DC were at the bottom. Sample formalinization required for prolonged storage proved suitable for antigen preservation. Images PMID:16347990

Shifts in methanogenic subpopulations measured with antibody probes in a fixed-bed loop anaerobic bioreactor treating sulfite evaporator condensate.

PubMed

Macario, A J; Conway de Macario, E; Ney, U; Schoberth, S M; Sahm, H

1989-08-01

A fixed-bed loop, high-rate anaerobic bioreactor treating sulfite evaporator condensate was sampled when it reached steady state and afterwards following perturbations during a 14-month period. By using immunotechnology, it was observed that shifts in methanogenic subpopulations occurred in association with perturbations, such as restarting and relocating the biomass into a different tank. Methanogens related to Methanobacterium bryantii MoHG and Methanobrevibacter smithii ALI were numerous throughout the observation period, while Methanosarcina mazei S6 and Methanosarcina thermophila TM1 were found in the early and late samples, respectively. Also, Methanobacterium formicicum was more numerous at the top portion of the bioreactor, while Methanobrevibacter arboriphilus AZ and DC were at the bottom. Sample formalinization required for prolonged storage proved suitable for antigen preservation.

Audio-vocal system regulation in children with autism spectrum disorders.

PubMed

Russo, Nicole; Larson, Charles; Kraus, Nina

2008-06-01

Do children with autism spectrum disorders (ASD) respond similarly to perturbations in auditory feedback as typically developing (TD) children? Presentation of pitch-shifted voice auditory feedback to vocalizing participants reveals a close coupling between the processing of auditory feedback and vocal motor control. This paradigm was used to test the hypothesis that abnormalities in the audio-vocal system would negatively impact ASD compensatory responses to perturbed auditory feedback. Voice fundamental frequency (F(0)) was measured while children produced an /a/ sound into a microphone. The voice signal was fed back to the subjects in real time through headphones. During production, the feedback was pitch shifted (-100 cents, 200 ms) at random intervals for 80 trials. Averaged voice F(0) responses to pitch-shifted stimuli were calculated and correlated with both mental and language abilities as tested via standardized tests. A subset of children with ASD produced larger responses to perturbed auditory feedback than TD children, while the other children with ASD produced significantly lower response magnitudes. Furthermore, robust relationships between language ability, response magnitude and time of peak magnitude were identified. Because auditory feedback helps to stabilize voice F(0) (a major acoustic cue of prosody) and individuals with ASD have problems with prosody, this study identified potential mechanisms of dysfunction in the audio-vocal system for voice pitch regulation in some children with ASD. Objectively quantifying this deficit may inform both the assessment of a subgroup of ASD children with prosody deficits, as well as remediation strategies that incorporate pitch training.

Exciton-phonon system on a star graph: A perturbative approach.

PubMed

Yalouz, Saad; Pouthier, Vincent

2016-05-01

Based on the operatorial formulation of the perturbation theory, the properties of an exciton coupled with optical phonons on a star graph are investigated. Within this method, the dynamics is governed by an effective Hamiltonian, which accounts for exciton-phonon entanglement. The exciton is dressed by a virtual phonon cloud whereas the phonons are clothed by virtual excitonic transitions. In spite of the coupling with the phonons, it is shown that the energy spectrum of the dressed exciton resembles that of a bare exciton. The only differences originate in a polaronic mechanism that favors an energy shift and a decay of the exciton hopping constant. By contrast, the motion of the exciton allows the phonons to propagate over the graph so that the dressed normal modes drastically differ from the localized modes associated to bare phonons. They define extended vibrations whose properties depend on the state occupied by the exciton that accompanies the phonons. It is shown that the phonon frequencies, either red shifted or blue shifted, are very sensitive to the model parameter in general, and to the size of the graph in particular.

Fast and slow shifts of the zonal-mean intertropical convergence zone in response to an idealized anthropogenic aerosol

DOE PAGES

Voigt, Aiko; Pincus, Robert; Stevens, Bjorn; ...

2017-04-03

Previous modeling work showed that aerosol can affect the position of the tropical rain belt, i.e., the intertropical convergence zone (ITCZ). Yet it remains unclear which aspects of the aerosol impact are robust across models, and which are not. Here we present simulations with seven comprehensive atmosphere models that study the fast and slow impacts of an idealized anthropogenic aerosol on the zonal-mean ITCZ position. The fast impact, which results from aerosol atmospheric heating and land cooling before sea-surface temperature (SST) has time to respond, causes a northward ITCZ shift. Yet the fast impact is compensated locally by decreased evaporationmore » over the ocean, and a clear northward shift is only found for an unrealistically large aerosol forcing. The local compensation implies that while models differ in atmospheric aerosol heating, this does not contribute to model differences in the ITCZ shift. The slow impact includes the aerosol impact on the ocean surface energy balance and is mediated by SST changes. The slow impact is an order of magnitude more effective than the fast impact and causes a clear southward ITCZ shift for realistic aerosol forcing. Models agree well on the slow ITCZ shift when perturbed with the same SST pattern. However, an energetic analysis suggests that the slow ITCZ shifts would be substantially more model-dependent in interactive-SST setups due to model differences in clear-sky radiative transfer and clouds. In conclusion, we also discuss implications for the representation of aerosol in climate models and attributions of recent observed ITCZ shifts to aerosol.« less

Infrasonic waves in the ionosphere generated by a weak earthquake

NASA Astrophysics Data System (ADS)

Krasnov, V. M.; Drobzheva, Ya. V.; Chum, J.

2011-08-01

A computer code has been developed to simulate the generation of infrasonic waves (frequencies considered ≤80 Hz) by a weak earthquake (magnitude ˜3.6), their propagation through the atmosphere and their effects in the ionosphere. We provide estimates of the perturbations in the ionosphere at the height (˜160 km) where waves at the sounding frequency (3.59 MHz) of a continuous Doppler radar reflect. We have found that the pressure perturbation is 5.79×10-7 Pa (0.26% of the ambient value), the temperature perturbation is 0.088 K (0.015% of the ambient value) and the electron density perturbation is 2×108 m-3 (0.12% of the ambient value). The characteristic perturbation is found to be a bipolar pulse lasting ˜25 s, and the maximum Doppler shift is found to be ˜0.08 Hz, which is too small to be detected by the Doppler radar at the time of the earthquake.

Longitudinal quasi-static stability predicts changes in dog gait on rough terrain

PubMed Central

Reeve, Michelle A.; Haynes, G. Clark; Revzen, Shai; Koditschek, Daniel E.; Spence, Andrew J.

2017-01-01

ABSTRACT Legged animals utilize gait selection to move effectively and must recover from environmental perturbations. We show that on rough terrain, domestic dogs, Canis lupus familiaris, spend more time in longitudinal quasi-statically stable patterns of movement. Here, longitudinal refers to the rostro-caudal axis. We used an existing model in the literature to quantify the longitudinal quasi-static stability of gaits neighbouring the walk, and found that trot-like gaits are more stable. We thus hypothesized that when perturbed, the rate of return to a stable gait would depend on the direction of perturbation, such that perturbations towards less quasi-statically stable patterns of movement would be more rapid than those towards more stable patterns of movement. The net result of this would be greater time spent in longitudinally quasi-statically stable patterns of movement. Limb movement patterns in which diagonal limbs were more synchronized (those more like a trot) have higher longitudinal quasi-static stability. We therefore predicted that as dogs explored possible limb configurations on rough terrain at walking speeds, the walk would shift towards trot. We gathered experimental data quantifying dog gait when perturbed by rough terrain and confirmed this prediction using GPS and inertial sensors (n=6, P<0.05). By formulating gaits as trajectories on the n-torus we are able to make tractable the analysis of gait similarity. These methods can be applied in a comparative study of gait control which will inform the ultimate role of the constraints and costs impacting locomotion, and have applications in diagnostic procedures for gait abnormalities, and in the development of agile legged robots. PMID:28264903

Longitudinal quasi-static stability predicts changes in dog gait on rough terrain.

PubMed

Wilshin, Simon; Reeve, Michelle A; Haynes, G Clark; Revzen, Shai; Koditschek, Daniel E; Spence, Andrew J

2017-05-15

Legged animals utilize gait selection to move effectively and must recover from environmental perturbations. We show that on rough terrain, domestic dogs, Canis lupus familiaris , spend more time in longitudinal quasi-statically stable patterns of movement. Here, longitudinal refers to the rostro-caudal axis. We used an existing model in the literature to quantify the longitudinal quasi-static stability of gaits neighbouring the walk, and found that trot-like gaits are more stable. We thus hypothesized that when perturbed, the rate of return to a stable gait would depend on the direction of perturbation, such that perturbations towards less quasi-statically stable patterns of movement would be more rapid than those towards more stable patterns of movement. The net result of this would be greater time spent in longitudinally quasi-statically stable patterns of movement. Limb movement patterns in which diagonal limbs were more synchronized (those more like a trot) have higher longitudinal quasi-static stability. We therefore predicted that as dogs explored possible limb configurations on rough terrain at walking speeds, the walk would shift towards trot. We gathered experimental data quantifying dog gait when perturbed by rough terrain and confirmed this prediction using GPS and inertial sensors ( n =6, P <0.05). By formulating gaits as trajectories on the n -torus we are able to make tractable the analysis of gait similarity. These methods can be applied in a comparative study of gait control which will inform the ultimate role of the constraints and costs impacting locomotion, and have applications in diagnostic procedures for gait abnormalities, and in the development of agile legged robots. © 2017. Published by The Company of Biologists Ltd.

Elastic pion-nucleon scattering in chiral perturbation theory: A fresh look

NASA Astrophysics Data System (ADS)

Siemens, D.; Bernard, V.; Epelbaum, E.; Gasparyan, A.; Krebs, H.; Meißner, Ulf-G.

2016-07-01

Elastic pion-nucleon scattering is analyzed in the framework of chiral perturbation theory up to fourth order within the heavy-baryon expansion and a covariant approach based on an extended on-mass-shell renormalization scheme. We discuss in detail the renormalization of the various low-energy constants and provide explicit expressions for the relevant β functions and the finite subtractions of the power-counting breaking terms within the covariant formulation. To estimate the theoretical uncertainty from the truncation of the chiral expansion, we employ an approach which has been successfully applied in the most recent analysis of the nuclear forces. This allows us to reliably extract the relevant low-energy constants from the available scattering data at low energy. The obtained results provide clear evidence that the breakdown scale of the chiral expansion for this reaction is related to the Δ resonance. The explicit inclusion of the leading contributions of the Δ isobar is demonstrated to substantially increase the range of applicability of the effective field theory. The resulting predictions for the phase shifts are in an excellent agreement with the predictions from the recent Roy-Steiner-equation analysis of pion-nucleon scattering.

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

PubMed

Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

2011-10-01

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Frequency-comb referenced spectroscopy of v₄₋ and v₅₋excited hot bands in the 1.5 and μm spectrum of C₂H₂

DOE PAGES

Twagirayezu, Sylvestre; Cich, Matthew J.; Sears, Trevor J.; ...

2015-07-14

Doppler-free transition frequencies for v₄₋ and v₅₋excited hot bands have been measured in the v₁ + v₃ band region of the spectrum of acetylene using saturation dip spectroscopy with an extended cavity diode laser referenced to a frequency comb. The frequency accuracy of the measured transitions, as judged from line shape model fits and comparison to known frequencies in the v₁ + v₃ band itself, is between 3 and 22 kHz. This is some three orders of magnitude improvement on the accuracy and precision of previous line position estimates that were derived from the analysis of high-resolution Fourier transform infraredmore » absorption spectra. Comparison to transition frequencies computed from constants derived from published Fourier transform infrared spectra shows that some upper rotational energy levels suffer specific perturbations causing energy level shifts of up to several hundred MHz. These perturbations are due to energy levels of the same rotational quantum number derived from nearby vibrational levels that become degenerate at specific energies. Future identification of the perturbing levels will provide accurate relative energies of excited vibrational levels of acetylene in the 7100–7600 cm⁻¹ energy region.« less

Turbulence, transport, and zonal flows in the Madison symmetric torus reversed-field pinch

NASA Astrophysics Data System (ADS)

Williams, Z. R.; Pueschel, M. J.; Terry, P. W.; Hauff, T.

2017-12-01

The robustness and the effect of zonal flows in trapped electron mode (TEM) turbulence and Ion Temperature Gradient (ITG) turbulence in the reversed-field pinch (RFP) are investigated from numerical solutions of the gyrokinetic equations with and without magnetic external perturbations introduced to model tearing modes. For simulations without external magnetic field perturbations, zonal flows produce a much larger reduction of transport for the density-gradient-driven TEM turbulence than they do for the ITG turbulence. Zonal flows are studied in detail to understand the nature of their strong excitation in the RFP and to gain insight into the key differences between the TEM- and ITG-driven regimes. The zonal flow residuals are significantly larger in the RFP than in tokamak geometry due to the low safety factor. Collisionality is seen to play a significant role in the TEM zonal flow regulation through the different responses of the linear growth rate and the size of the Dimits shift to collisionality, while affecting the ITG only minimally. A secondary instability analysis reveals that the TEM turbulence drives zonal flows at a rate that is twice that of the ITG turbulence. In addition to interfering with zonal flows, the magnetic perturbations are found to obviate an energy scaling relation for fast particles.

Chiral extrapolations of the ρ ( 770 ) meson in N f = 2 + 1 lattice QCD simulations

DOE PAGES

Hu, B.; Molina, R.; Döring, M.; ...

2017-08-24

Recentmore » $$N_f=2+1$$ lattice data for meson-meson scattering in $p$-wave and isospin $I=1$ are analyzed using a unitarized model inspired by Chiral Perturbation Theory in the inverse-amplitude formulation for two and three flavors. We perform chiral extrapolations that postdict phase shifts extracted from experiment quite well. Additionally, the low-energy constants are compared to the ones from a recent analysis of $$N_f=2$$ lattice QCD simulations to check for the consistency of the hadronic model used here. Some inconsistencies are detected in the fits to $$N_f=2+1$$ data, in contrast to the previous analysis of $$N_f=2$$ data.« less

Frequency dependence of p-mode frequency shifts induced by magnetic activity in Kepler solar-like stars

NASA Astrophysics Data System (ADS)

Salabert, D.; Régulo, C.; Pérez Hernández, F.; García, R. A.

2018-04-01

The variations of the frequencies of the low-degree acoustic oscillations in the Sun induced by magnetic activity show a dependence on radial order. The frequency shifts are observed to increase towards higher-order modes to reach a maximum of about 0.8 μHz over the 11-yr solar cycle. A comparable frequency dependence is also measured in two other main sequence solar-like stars, the F-star HD 49933, and the young 1 Gyr-old solar analog KIC 10644253, although with different amplitudes of the shifts of about 2 μHz and 0.5 μHz, respectively. Our objective here is to extend this analysis to stars with different masses, metallicities, and evolutionary stages. From an initial set of 87 Kepler solar-like oscillating stars with known individual p-mode frequencies, we identify five stars showing frequency shifts that can be considered reliable using selection criteria based on Monte Carlo simulations and on the photospheric magnetic activity proxy Sph. The frequency dependence of the frequency shifts of four of these stars could be measured for the l = 0 and l = 1 modes individually. Given the quality of the data, the results could indicate that a physical source of perturbation different from that in the Sun is dominating in this sample of solar-like stars.

Perturbation measurement of waveguides for acoustic thermometry

NASA Astrophysics Data System (ADS)

Lin, H.; Feng, X. J.; Zhang, J. T.

2013-09-01

Acoustic thermometers normally embed small acoustic transducers in the wall bounding a gas-filled cavity resonator. At high temperature, insulators of transducers loss electrical insulation and degrade the signal-to-noise ratio. One essential solution to this technical trouble is to couple sound by acoustic waveguides between resonator and transducers. But waveguide will break the ideal acoustic surface and bring perturbations(Δf+ig) to the ideal resonance frequency. The perturbation model for waveguides was developed based on the first-order acoustic theory in this paper. The frequency shift Δf and half-width change g caused by the position, length and radius of waveguides were analyzed using this model. Six different length of waveguides (52˜1763 mm) were settled on the cylinder resonator and the perturbation (Δf+ig) were measured at T=332 K and p=250˜500 kPa. The experiment results agreed with the theoretical prediction very well.

Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole

NASA Astrophysics Data System (ADS)

McDowell, Sean A. C.

2017-04-01

An MP2 computational study of model hydrogen-bonded pyrrole⋯YZ (YZ = NH3, NCH, BF, CO, N2, OC, FB) complexes was undertaken in order to examine the variation of the Nsbnd H bond length change and its associated vibrational frequency shift. The chemical hardness of Y, as well as the YZ dipole moment, were found to be important parameters in modifying the bond length change/frequency shift. The basis set effect on the computed properties was also assessed. A perturbative model, which accurately reproduced the ab initio Nsbnd H bond length changes and frequency shifts, was useful in rationalizing the observed trends.

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

PubMed Central

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-01-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy. PMID:27666199

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments.

PubMed

Kearns, Patrick J; Angell, John H; Howard, Evan M; Deegan, Linda A; Stanley, Rachel H R; Bowen, Jennifer L

2016-09-26

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

NASA Astrophysics Data System (ADS)

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-09-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

Solution structural ensembles of substrate-free cytochrome P450(cam).

PubMed

Asciutto, Eliana K; Young, Matthew J; Madura, Jeffry; Pochapsky, Susan Sondej; Pochapsky, Thomas C

2012-04-24

Removal of substrate (+)-camphor from the active site of cytochrome P450(cam) (CYP101A1) results in nuclear magnetic resonance-detected perturbations in multiple regions of the enzyme. The (1)H-(15)N correlation map of substrate-free diamagnetic Fe(II) CO-bound CYP101A permits these perturbations to be mapped onto the solution structure of the enzyme. Residual dipolar couplings (RDCs) were measured for (15)N-(1)H amide pairs in two independent alignment media for the substrate-free enzyme and used as restraints in solvated molecular dynamics (MD) simulations to generate an ensemble of best-fit structures of the substrate-free enzyme in solution. Nuclear magnetic resonance-detected chemical shift perturbations reflect changes in the electronic environment of the NH pairs, such as hydrogen bonding and ring current shifts, and are observed for residues in the active site as well as in hinge regions between secondary structural features. RDCs provide information about relative orientations of secondary structures, and RDC-restrained MD simulations indicate that portions of a β-rich region adjacent to the active site shift so as to partially occupy the vacancy left by removal of the substrate. The accessible volume of the active site is reduced in the substrate-free enzyme relative to the substrate-bound structure calculated using the same methods. Both symmetric and asymmetric broadening of multiple resonances observed upon substrate removal as well as localized increased errors in RDC fits suggest that an ensemble of enzyme conformations are present in the substrate-free form.

Interactions between gaze-evoked blinks and gaze shifts in monkeys.

PubMed

Gandhi, Neeraj J

2012-02-01

Rapid eyelid closure, or a blink, often accompanies head-restrained and head-unrestrained gaze shifts. This study examines the interactions between such gaze-evoked blinks and gaze shifts in monkeys. Blink probability increases with gaze amplitude and at a faster rate for head-unrestrained movements. Across animals, blink likelihood is inversely correlated with the average gaze velocity of large-amplitude control movements. Gaze-evoked blinks induce robust perturbations in eye velocity. Peak and average velocities are reduced, duration is increased, but accuracy is preserved. The temporal features of the perturbation depend on factors such as the time of blink relative to gaze onset, inherent velocity kinematics of control movements, and perhaps initial eye-in-head position. Although variable across animals, the initial effect is a reduction in eye velocity, followed by a reacceleration that yields two or more peaks in its waveform. Interestingly, head velocity is not attenuated; instead, it peaks slightly later and with a larger magnitude. Gaze latency is slightly reduced on trials with gaze-evoked blinks, although the effect was more variable during head-unrestrained movements; no reduction in head latency is observed. Preliminary data also demonstrate a similar perturbation of gaze-evoked blinks during vertical saccades. The results are compared with previously reported effects of reflexive blinks (evoked by air-puff delivered to one eye or supraorbital nerve stimulation) and discussed in terms of effects of blinks on saccadic suppression, neural correlates of the altered eye velocity signals, and implications on the hypothesis that the attenuation in eye velocity is produced by a head movement command.

Sub-Doppler rotationally resolved spectroscopy of lower vibronic bands of benzene with Zeeman effects

NASA Astrophysics Data System (ADS)

Doi, Atsushi; Kasahara, Shunji; Katô, Hajime; Baba, Masaaki

2004-04-01

Sub-Doppler high-resolution excitation spectra and the Zeeman effects of the 601, 101601, and 102601 bands of the S1 1B2u←S0 1A1g transition of benzene were measured by crossing laser beam perpendicular to a collimated molecular beam. 1593 rotational lines of the 101601 band and 928 lines of the 102601 band were assigned, and the molecular constants of the excited states were determined. Energy shifts were observed for the S1 1B2u(v1=1,v6=1,J,Kl=-11) levels, and those were identified as originating from a perpendicular Coriolis interaction. Many energy shifts were observed for the S1 1B2u(v1=2,v6=1,J,Kl) levels. The Zeeman splitting of a given J level was observed to increase with K and reach the maximum at K=J, which demonstrates that the magnetic moment lies perpendicular to the molecular plane. The Zeeman splittings of the K=J levels were observed to increase linearly with J. From the analysis, the magnetic moment is shown to be originating mostly from mixing of the S1 1B2u and S2 1B1u states by the J-L coupling (electronic Coriolis interaction). The number of perturbations was observed to increase as the excess energy increases, and all the perturbing levels were found to be a singlet state from the Zeeman spectra.

Near-infrared absorption in symmetric squarylium and croconate dyes: a comparative study using symmetry-adapted cluster-configuration interaction methods.

PubMed

Prabhakar, Ch; Yesudas, K; Krishna Chaitanya, G; Sitha, Sanyasi; Bhanuprakash, K; Rao, V Jayathirtha

2005-09-29

Symmetric croconate (CR) and squarylium dyes (SQ) are well-known near-infrared (NIR) dyes and, in general, are considered to be donor-acceptor-donor type molecules. It is established in the literature that CR dyes absorb in a longer wavelength region than the corresponding SQ dyes. This has been attributed to the CR ring being a better acceptor than the SQ ring. Thus increasing the donor capacity should lead to a bathochromic shift in both SQ and CR. On the other hand, some experiments reported in the literature have revealed that increasing the conjugation in the donor part of the SQ molecule leads first to red shift, which upon a further increase of the conjugation changes to a blue shift. Hence, to understand the role of the central ring and the substitutions in the absorption of these dyes, we carried out high-level symmetry-adapted cluster-configuration interaction (SAC-CI) calculations of some substituted SQ and CR dyes and compare the absorption energy with the existing experimental data. We found that there is very good agreement. We also carried out SAC-CI calculations of some smaller model molecules, which contain the main oxyallyl substructure. We varied the geometry (angle) of the oxyallyl subgroup and the substitution in these model molecules to establish a correlation with the bathochromic shift. We found that the charge transfer is very small and does not play the key role in the red shift, but on the other hand, the perturbation of the HOMO-LUMO gap (HLG) from both the geometry and substitution seems to be responsible for this shift. We suggest as a design principle that increasing the donor capacity of the groups may not help in the red shift, but introducing groups which perturb the HLG and decrease it without changing the MO character should lead to a larger bathochromic shift.

Identification of the WW domain-interaction sites in the unstructured N-terminal domain of EBV LMP 2A.

PubMed

Seo, Min-Duk; Park, Sung Jean; Kim, Hyun-Jung; Lee, Bong Jin

2007-01-09

Epstein-Barr virus latency is maintained by the latent membrane protein (LMP) 2A, which mimics the B-cell receptor (BCR) and perturbs BCR signaling. The cytoplasmic N-terminal domain of LMP2A is composed of 119 amino acids. The N-terminal domain of LMP2A (LMP2A NTD) contains two PY motifs (PPPPY) that interact with the WW domains of Nedd4 family ubiquitin-protein ligases. Based on our analysis of NMR data, we found that the LMP2A NTD adopts an overall random-coil structure in its native state. However, the region between residues 60 and 90 was relatively ordered, and seemed to form the hydrophobic core of the LMP2A NTD. This region resides between two PY motifs and is important for WW domain binding. Mapping of the residues involved in the interaction between the LMP2A NTD and WW domains was achieved by chemical shift perturbation, by the addition of WW2 and WW3 peptides. Interestingly, the binding of the WW domains mainly occurred in the hydrophobic core of the LMP2A NTD. In addition, we detected a difference in the binding modes of the two PY motifs against the two WW peptides. The binding of the WW3 peptide caused the resonances of five residues (Tyr(60), Glu(61), Asp(62), Trp(65), and Gly(66)) just behind the N-terminal PY motif of the LMP2A NTD to disappear. A similar result was obtained with WW2 binding. However, near the C-terminal PY motif, the chemical shift perturbation caused by WW2 binding was different from that due to WW3 binding, indicating that the residues near the PY motifs are involved in selective binding of WW domains. The present work represents the first structural study of the LMP2A NTD and provides fundamental structural information about its interaction with ubiquitin-protein ligase.

Plasma Perturbations in High-Speed Probing of Hall Thruster Discharge Chambers: Quantification and Mitigation

NASA Technical Reports Server (NTRS)

Jorns, Benjamin A.; Goebel, Dan M.; Hofer, Richard R.

2015-01-01

An experimental investigation is presented to quantify the effect of high-speed probing on the plasma parameters inside the discharge chamber of a 6-kW Hall thruster. Understanding the nature of these perturbations is of significant interest given the importance of accurate plasma measurements for characterizing thruster operation. An array of diagnostics including a high-speed camera and embedded wall probes is employed to examine in real time the changes in electron temperature and plasma potential induced by inserting a high-speed reciprocating Langmuir probe into the discharge chamber. It is found that the perturbations onset when the scanning probe is downstream of the electron temperature peak, and that along channel centerline, the perturbations are best characterized as a downstream shift of plasma parameters by 15-20% the length of the discharge chamber. A parametric study is performed to investigate techniques to mitigate the observed probe perturbations including varying probe speed, probe location, and operating conditions. It is found that the perturbations largely disappear when the thruster is operated at low power and low discharge voltage. The results of this mitigation study are discussed in the context of recommended methods for generating unperturbed measurements of the discharge chamber plasma.

Blue and red shifted temperature dependence of implicit phonon shifts in graphene

NASA Astrophysics Data System (ADS)

Mann, Sarita; Jindal, V. K.

2017-07-01

We have calculated the implicit shift for various modes of frequency in a pure graphene sheet. Thermal expansion and Grüneisen parameter which are required for implicit shift calculation have already been studied and reported. For this calculation, phonon frequencies are obtained using force constants derived from dynamical matrix calculated using VASP code where the density functional perturbation theory (DFPT) is used in interface with phonopy software. The implicit phonon shift shows an unusual behavior as compared to the bulk materials. The frequency shift is large negative (red shift) for ZA and ZO modes and the value of negative shift increases with increase in temperature. On the other hand, blue shift arises for all other longitudinal and transverse modes with a similar trend of increase with increase in temperature. The q dependence of phonon shifts has also been studied. Such simultaneous red and blue shifts in transverse or out plane modes and surface modes, respectively leads to speculation of surface softening in out of plane direction in preference to surface melting.

Electronic structure and vibrational analysis of AHA⋯HX complexes

NASA Astrophysics Data System (ADS)

Joshi, Kaustubh A.; Gejji, Shridhar P.

2005-10-01

Electronic structures of the binary complexes of acetohydroxamic acid (AHA) and hydrogen halides, HX (X = F, Cl, Br) have been investigated using the second order perturbation theory. In the lowest energy structure of AHA⋯HF complex, hydrogen fluoride acts as a proton-donor with carbonyl oxygen and simultaneously as a proton-acceptor with the hydroxyl group. For chloro- and bromo-substituted derivatives, however, the lowest minimum possesses hydrogen-bonded interactions with the carbonyl oxygen in addition to those from the methyl proton of AHA. Frequency shifts of NH and CN stretching vibrations enable one to distinguish different conformers of AHA⋯HX complexes.

Second-Order Moller-Plesset Perturbation Theory for Molecular Dirac-Hartree-Fock Wave Functions

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Arnold, James O. (Technical Monitor)

1994-01-01

Moller-Plesset perturbation theory is developed to second order for a selection of Kramers restricted Dirac-Hartree-Fock closed and open-shell reference wave functions. The open-shell wave functions considered are limited to those with no more than two electrons in open shells, but include the case of a two-configuration SCF reference. Denominator shifts are included in the style of Davidson's OPT2 method. An implementation which uses unordered integrals with labels is presented, and results are given for a few test cases.

Effects of the finite size of the ion (dd{mu}){sup +} on the energy levels of the molecules (dd{mu})e and (dd{mu})dee

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harston, M.R.; Hara, S.; Kino, Y.

1997-10-01

The energy shift due to the finite size of the pseudonucleus (dd{mu}){sub 11}{sup +} in the molecules (dd{mu}){sub 11}e and (dd{mu}){sub 11}dee, the subscripts indicating the first excited state with total angular momentum of one unit, is of importance in the theoretical estimation of the rate of d-d fusion catalyzed by negative muons. The energy shift in the molecule (dd{mu}){sub 11}e is calculated using perturbation theory up to second order. The finite-size shift is found to be 1.46 meV. This is significantly larger than the value of 0.7 meV for this energy shift calculated by Bakalov [Muon Catalyzed Fusion {boldmore » 3}, 321 (1988)] by a method similar to the present method; recently found excellent agreement of theory with experimental results for the formation rate of the molecule (dd{mu}){sub 11}dee was based on Bakalov{close_quote}s value with some modifications. The results of a direct calculation of the finite-size energy shifts in (dd{mu}){sub 11}dee using first-order perturbation theory are presented. The contribution from the quadrupole component of the (dd{mu}){sub 11} charge distribution, which is not taken into account in the conventional scaling procedure based on the finite-size energy shifts of (dd{mu}){sub 11}e, is found to be of the order of 1 meV and to depend on the angular-momentum states of (dd{mu}){sub 11}dee. Sources of uncertainty in the current theoretical estimates are also discussed. {copyright} {ital 1997} {ital The American Physical Society}« less

Two stages and three components of the postural preparation to action.

PubMed

Krishnan, Vennila; Aruin, Alexander S; Latash, Mark L

2011-07-01

Previous studies of postural preparation to action/perturbation have primarily focused on anticipatory postural adjustments (APAs), the changes in muscle activation levels resulting in the production of net forces and moments of force. We hypothesized that postural preparation to action consists of two stages: (1) Early postural adjustments (EPAs), seen a few hundred ms prior to an expected external perturbation and (2) APAs seen about 100 ms prior to the perturbation. We also hypothesized that each stage consists of three components, anticipatory synergy adjustments seen as changes in covariation of the magnitudes of commands to muscle groups (M-modes), changes in averaged across trials levels of muscle activation, and mechanical effects such as shifts of the center of pressure. Nine healthy participants were subjected to external perturbations created by a swinging pendulum while standing in a semi-squatting posture. Electrical activity of twelve trunk and leg muscles and displacements of the center of pressure were recorded and analyzed. Principal component analysis was used to identify four M-modes within the space of muscle activations using indices of integrated muscle activation. This analysis was performed twice, over two phases, 400-700 ms prior to the perturbation and over 200 ms just prior to the perturbation. Similar robust results were obtained using the data from both phases. An index of a multi-M-mode synergy stabilizing the center of pressure displacement was computed using the framework of the uncontrolled manifold hypothesis. The results showed high synergy indices during quiet stance. Each of the two stages started with a drop in the synergy index followed by a change in the averaged across trials activation levels in postural muscles. There was a very long electromechanical delay during the early postural adjustments and a much shorter delay during the APAs. Overall, the results support our main hypothesis on the two stages and three components of the postural preparation to action/perturbation. This is the first study to document anticipatory synergy adjustments in whole-body tasks. We interpret the results within the referent configuration hypothesis (an extension of the equilibrium-point hypothesis): The early postural adjustment is based primarily on changes in the coactivation command, while the APAs involve changes in the reciprocal command. The results fit an earlier hypothesis that whole-body movements are controlled by a neuromotor hierarchy where each level involves a few-to-many mappings organized to stabilize its overall output.

Navigating the Neural Space in Search of the Neural Code.

PubMed

Jazayeri, Mehrdad; Afraz, Arash

2017-03-08

The advent of powerful perturbation tools, such as optogenetics, has created new frontiers for probing causal dependencies in neural and behavioral states. These approaches have significantly enhanced the ability to characterize the contribution of different cells and circuits to neural function in health and disease. They have shifted the emphasis of research toward causal interrogations and increased the demand for more precise and powerful tools to control and manipulate neural activity. Here, we clarify the conditions under which measurements and perturbations support causal inferences. We note that the brain functions at multiple scales and that causal dependencies may be best inferred with perturbation tools that interface with the system at the appropriate scale. Finally, we develop a geometric framework to facilitate the interpretation of causal experiments when brain perturbations do or do not respect the intrinsic patterns of brain activity. We describe the challenges and opportunities of applying perturbations in the presence of dynamics, and we close with a general perspective on navigating the activity space of neurons in the search for neural codes. Copyright © 2017 Elsevier Inc. All rights reserved.

Emerging technological and cultural shifts advancing drylands research and management

USDA-ARS?s Scientific Manuscript database

Sustainable provisioning of ecosystem services in dryland landscapes is complicated by extreme conditions that constrain biological responses to perturbation, vast spatial and temporal complexity, and uncertainty regarding the resilience of these ecosystems to management practices and climate change...

Deep Space Spaceflight Hazards Effects on Cognition, Behavioral Health, and Behavioral Biomarkers in Humans

NASA Astrophysics Data System (ADS)

Williams, T. J.; Norsk, P.; Zwart, S.; Crucian, B.; Simonsen, L. C.; Antonsen, E.

2018-02-01

Deep Space Gateway missions provide testing grounds to identify the risk of both behavioral performance and cognitive perturbations caused by stressors of spaceflight such as radiation, fluid shifts, sleep deprivation, chronic stress, and others.

Autobalanced Ramsey Spectroscopy

NASA Astrophysics Data System (ADS)

Sanner, Christian; Huntemann, Nils; Lange, Richard; Tamm, Christian; Peik, Ekkehard

2018-01-01

We devise a perturbation-immune version of Ramsey's method of separated oscillatory fields. Spectroscopy of an atomic clock transition without compromising the clock's accuracy is accomplished by actively balancing the spectroscopic responses from phase-congruent Ramsey probe cycles of unequal durations. Our simple and universal approach eliminates a wide variety of interrogation-induced line shifts often encountered in high precision spectroscopy, among them, in particular, light shifts, phase chirps, and transient Zeeman shifts. We experimentally demonstrate autobalanced Ramsey spectroscopy on the light shift prone Yb+ 171 electric octupole optical clock transition and show that interrogation defects are not turned into clock errors. This opens up frequency accuracy perspectives below the 10-18 level for the Yb+ system and for other types of optical clocks.

Influence of Surface Processes over Africa on the Atlantic Marine ITCZ and South American Precipitation.

NASA Astrophysics Data System (ADS)

Hagos, Samson M.; Cook, Kerry H.

2005-12-01

Previous studies show that the climatological precipitation over South America, particularly the Nordeste region, is influenced by the presence of the African continent. Here the influence of African topography and surface wetness on the Atlantic marine ITCZ (AMI) and South American precipitation are investigated.Cross-equatorial flow over the Atlantic Ocean introduced by north south asymmetry in surface conditions over Africa shifts the AMI in the direction of the flow. African topography, for example, introduces an anomalous high over the southern Atlantic Ocean and a low to the north. This results in a northward migration of the AMI and dry conditions over the Nordeste region.The implications of this process on variability are then studied by analyzing the response of the AMI to soil moisture anomalies over tropical Africa. Northerly flow induced by equatorially asymmetric perturbations in soil moisture over northern tropical Africa shifts the AMI southward, increasing the climatological precipitation over northeastern South America. Flow associated with an equatorially symmetric perturbation in soil moisture, however, has a very weak cross-equatorial component and very weak influence on the AMI and South American precipitation. The sensitivity of the AMI to soil moisture perturbations over certain regions of Africa can possibly improve the skill of prediction.

Rosetta at comet 67P/Churyumov-Gerasimenko: Spacecraft orbit modeling

NASA Astrophysics Data System (ADS)

Hahn, Matthias; Paetzold, Martin; Tellmann, Silvia; Haeusler, Bernd; Andert, Thomas

The Rosetta spacecraft has been successfully launched on 2nd March 2004 to its target comet 67P/Churyumov-Gerasimenko. The science objectives of the Rosetta Radio Science Investiga-tions (RSI) experiment addresses fundamental aspects of cometary science such as the deter-minations of the nucleus mass and bulk density, its size and shape, its gravity field and internal structure, and its perturbed interplanetary orbit. The radio carrier links at X-band (8.4 GHz) and S-band (2.3 GHz) between the Rosetta spacecraft and the Earth will be used for these investigations. The motion of the spacecraft will be perturbed near the comet nucleus. The Doppler frequency shifts of the transmitted radio signals can be used to reconstruct the flown orbit. In order to extract small changes of the Doppler frequency, a prediction of the orbit is needed which includes best known estimates for all forces acting on the spacecraft. These forces are the nucleus gravity field, third body perturbations, the solar radiation pressure, the solar wind pressure, the cometary outgassing, etc. It is then possible to determine iteratively low degree and order harmonic coefficients of the nucleus gravity field or the gas pressure force and the gas production rate from outgassing from the differences between the predicted and the observed frequency shifts.

Fluid and microfluidic dielectric measurement using a cavity perturbation method at microwave C-band

NASA Astrophysics Data System (ADS)

Asghari, Aref

The utilization of cavity perturbation technique in dielectric property measurement of fluid and micro-fluid is investigated in this thesis to better assist the ever-growing needs of science and technology for analysis and characterization of such materials in various applications from genetics, MEMS devices, to consumer product industry. Development of different techniques for measuring complex dielectric properties of fluid and micro-fluids at Giga (10 9)-Hz frequencies is of significant importance as their usage is increasingly coupled with infrared and microwave electromagnetic wavelengths. Conventional cavity perturbation method could provide a sensitive and convenient system for measuring fluids of low (e.g., epsilonr <10) permittivity that meets the assumptions of negligible perturbation to the electromagnetic field distribution in the cavity. Developing a methodology that uses conventional cavity perturbation method that is however suitable for a sensitive, accurate, and reliable measurement of high permittivity polar liquids at microwave C-band is the goal in the current work. Systematic studies are carried out, using de-ionic (DI) water as test specimens, to evaluate the influence of sample's container, volume, dimension, and temperature on the sensitivity and reliability of microwave dielectric measurement. The cavity perturbation measurement of DI water in a 1 mm diameter capillary tube showed well-defined temperature dependence of dielectric permittivity and loss coefficients of water. Observation of a permittivity peak in temperature range tested at 4GHz around -10 °C implies an important relaxation in low temperatures at microwave C-band, which corresponds to a critical slowing down of polarization reorientation in crystallized (icy) H2O. Numerical simulations using Finite Element Analysis (FEA) COMSOL suites were conducted to established the optimum amount of liquid water for cavity perturbation testing at microwave C-band (in perfectly conducting condition). The results showed at TE103 mode the tube D4= 4mm diameter (272 muL liquid volume capacity) provides the best measurement sensitivity in terms of resonant shift and low loss while for TE105 the 2mm 68 (muL liquid volume capacity) tube is the most promising. The experimental results yielded a shape factor of around 2 and 1 for epsilon' and epsilon", respectively. The examination of epsilon' and epsilon" interdependence using Kramers-Kronig concept showed the permittivity loss values is 4 times more dependent to the quality factor of resonant peak than permittivity. On the other hand, the dielectric permittivity dependence to resonant frequency was calculated around 2 times bigger than dielectric loss which signifies the importance of epsilon" in high loss liquid measurement by the cavity resonant perturbation method.

Is the Lamb shift chemically significant?

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

2001-01-01

The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

A bilateral cortical network responds to pitch perturbations in speech feedback

PubMed Central

Kort, Naomi S.; Nagarajan, Srikantan S.; Houde, John F.

2014-01-01

Auditory feedback is used to monitor and correct for errors in speech production, and one of the clearest demonstrations of this is the pitch perturbation reflex. During ongoing phonation, speakers respond rapidly to shifts of the pitch of their auditory feedback, altering their pitch production to oppose the direction of the applied pitch shift. In this study, we examine the timing of activity within a network of brain regions thought to be involved in mediating this behavior. To isolate auditory feedback processing relevant for motor control of speech, we used magnetoencephalography (MEG) to compare neural responses to speech onset and to transient (400ms) pitch feedback perturbations during speaking with responses to identical acoustic stimuli during passive listening. We found overlapping, but distinct bilateral cortical networks involved in monitoring speech onset and feedback alterations in ongoing speech. Responses to speech onset during speaking were suppressed in bilateral auditory and left ventral supramarginal gyrus/posterior superior temporal sulcus (vSMG/pSTS). In contrast, during pitch perturbations, activity was enhanced in bilateral vSMG/pSTS, bilateral premotor cortex, right primary auditory cortex, and left higher order auditory cortex. We also found speaking-induced delays in responses to both unaltered and altered speech in bilateral primary and secondary auditory regions, the left vSMG/pSTS and right premotor cortex. The network dynamics reveal the cortical processing involved in both detecting the speech error and updating the motor plan to create the new pitch output. These results implicate vSMG/pSTS as critical in both monitoring auditory feedback and initiating rapid compensation to feedback errors. PMID:24076223

Resummation of Goldstone infrared divergences: A proof to all orders

NASA Astrophysics Data System (ADS)

Espinosa, J. R.; Konstandin, T.

2018-03-01

The perturbative effective potential calculated in Landau gauge suffers from infrared problems due to Goldstone boson loops. These divergences are spurious and can be removed by a resummation procedure that amounts to a shift of the mass of soft Goldstones. We prove this to all loops using an effective theory approach, providing a compact recipe for the shift of the Goldstone mass that relies on the use of the method of regions to split soft and hard Goldstone contributions.

Evolution in action: Climate change, biodiversity dynamics and emerging infectious disease

USDA-ARS?s Scientific Manuscript database

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographic and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in clim...

Theoretical study of the NMR chemical shift of Xe in supercritical condition.

PubMed

Lacerda, Evanildo G; Sauer, Stephan P A; Mikkelsen, Kurt V; Coutinho, Kaline; Canuto, Sylvio

2018-02-20

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129 Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129 Xe chemical shift depends under supercritical conditions on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xe n clusters (n = 2 - 8 depending on the density). The analysis of the relativistic effects is made at the level of 4-component Hartree-Fock calculations (4c-HF) and electron correlation effects are considered using second order Møller-Plesset perturbation theory (MP2). To simplify the calculations of the relativistic and electron correlation effects we adopted an additive scheme, where the calculations on the Xe n clusters are carried out at the non-relativistic Hartree-Fock (HF) level, while electron correlation and relativistic corrections are added for all the pairs of Xe atoms in the clusters. Using this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129 Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects.

Hyperfine structure of the MnH X 7Sigma + state: A large gas-to-matrix shift in the Fermi contact interaction

NASA Astrophysics Data System (ADS)

Varberg, Thomas D.; Field, Robert W.; Merer, Anthony J.

1990-06-01

Sub-Doppler spectra of the A 7Π-X 7Σ+ (0,0) band of gas phase MnH near 5680 Å were recorded by intermodulated fluorescence spectroscopy. The spectra reveal hyperfine splittings arising from both the 55Mn and 1H nuclear spins. Internal hyperfine perturbations have been observed between the different spin components of the ground state at low N`. From a preliminary analysis of several rotational lines originating from the isolated and unperturbed F1(J`=3) spin component of the X 7Σ+(N`=0) level, the 55Mn Fermi contact interaction in the ground state has been measured as bF=Aiso =276(1) MHz. This value is 11% smaller than the value obtained by Weltner et al. from an electron-nuclear double resonance (ENDOR) study of MnH in an argon matrix at 4 K. This unprecedented gas-to-matrix shift in the Fermi contact parameter is discussed.

Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock.

PubMed

Parnell, J Jacob; Callister, Stephen J; Rompato, Giovanni; Nicora, Carrie D; Paša-Tolić, Ljiljana; Williamson, Ashley; Pfrender, Michael E

2011-01-01

Shewanellae are microbial models for environmental stress response; however, the sequential expression of mechanisms in response to stress is poorly understood. Here we experimentally determine the response mechanisms of Shewanella amazonensis SB2B during sodium chloride stress using a novel liquid chromatography and accurate mass-time tag mass spectrometry time-course proteomics approach. The response of SB2B involves an orchestrated sequence of events comprising increased signal transduction associated with motility and restricted growth. Following a metabolic shift to branched chain amino acid degradation, motility and cellular replication proteins return to pre-perturbed levels. Although sodium chloride stress is associated with a change in the membrane fatty acid composition in other organisms, this is not the case for SB2B as fatty acid degradation pathways are not expressed and no change in the fatty acid profile is observed. These findings suggest that shifts in membrane composition may be an indirect physiological response to high NaCl stress.

Conditional heteroscedasticity as a leading indicator of ecological regime shifts.

PubMed

Seekell, David A; Carpenter, Stephen R; Pace, Michael L

2011-10-01

Regime shifts are massive, often irreversible, rearrangements of nonlinear ecological processes that occur when systems pass critical transition points. Ecological regime shifts sometimes have severe consequences for human well-being, including eutrophication in lakes, desertification, and species extinctions. Theoretical and laboratory evidence suggests that statistical anomalies may be detectable leading indicators of regime shifts in ecological time series, making it possible to foresee and potentially avert incipient regime shifts. Conditional heteroscedasticity is persistent variance characteristic of time series with clustered volatility. Here, we analyze conditional heteroscedasticity as a potential leading indicator of regime shifts in ecological time series. We evaluate conditional heteroscedasticity by using ecological models with and without four types of critical transition. On approaching transition points, all time series contain significant conditional heteroscedasticity. This signal is detected hundreds of time steps in advance of the regime shift. Time series without regime shifts do not have significant conditional heteroscedasticity. Because probability values are easily associated with tests for conditional heteroscedasticity, detection of false positives in time series without regime shifts is minimized. This property reduces the need for a reference system to compare with the perturbed system.

Astronomical constraints on global carbon-cycle perturbation during Oceanic Anoxic Event 2 (OAE2)

NASA Astrophysics Data System (ADS)

Li, Yong-Xiang; Montañez, Isabel P.; Liu, Zhonghui; Ma, Lifeng

2017-03-01

Oceanic Anoxic Event 2 (OAE2) was a major disturbance in global carbon cycling and transient climate disruption, triggered by a pulse of volcanic CO2. Although this well-studied perturbation to the ocean-atmosphere system offers a unique opportunity to better understand abrupt climate change in response to CO2-forcing, the origin, evolution and duration of the event are still debated due in large part to the temporal resolution of existing OAE2 records and uncertainty over the duration of the overall perturbation and C cycle shifts within it. Here we report coupled magnetic susceptibility (MS) and carbon-isotope time-series of ∼2.5 to 5 ± 0.5kyr resolution from an expanded OAE2 interval from southern Tibet, China. MS cyclicity indicates short eccentricity modulation, permitting the construction of a high-precision orbital timescale which, when integrated with the high resolution δ13Ccarb record, fully constrains the timing and nature of onset through recovery of OAE2, revealing finer-scale structure than previously recognized. Abrupt coupled shifts in δ13Ccarb and MS, and changing phase relationships in-step with transitions between high and low long eccentricity, indicate orbitally linked changes in marine carbon cycling and monsoon dynamics superimposed on repeated wholesale oceanographic changes. In particular, the high-resolution Tibetan record reveals dynamic shifts in the phasing relationship of MS and δ13 C, which suggests that the initiation of ocean anoxia was probably not orbitally forced. This finding is in sharp contrast with the paradigm of orbitally forced ocean anoxia. Conversely, the new record suggests that termination of anoxia was likely orbitally forced and superimposed on a dramatic oceanographic change.

Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the redox active analogue for humic substances.

PubMed

Dantas, Joana M; Ferreira, Marisa R; Catarino, Teresa; Kokhan, Oleksandr; Raj Pokkuluri, P; Salgueiro, Carlos A

2018-05-16

The bacterium Geobacter sulfurreducens can transfer electrons to the quinone moieties of humic substances or to anthraquinone-2,6-disulfonate (AQDS), a model for the humic acids. The reduced form of AQDS (AH 2 QDS) can also be used as energy source G. sulfurreducens. Such bi-directional utilization of humic substances confers competitive advantages to these bacteria in Fe(III) enriched environments. Previous studies have shown that the triheme cytochrome PpcA from G. sulfurreducens has a bi-functional behavior toward the humic substance analogue. It can reduce AQDS but the protein can also be reduced by AH 2 QDS. Using stopped-flow measurements we were able to demonstrate that other periplasmic members of the PpcA-family in G. sulfurreducens (PpcB, PpcD and PpcE) also showed the same bi-functional behavior. The extent of the electron transfer is thermodynamically controlled favoring the reduction of the cytochromes. NMR spectra recorded for 13 C, 15 N-enriched samples in the presence increasing amounts of AQDS showed perturbations in the chemical shift signals of the cytochromes. The chemical shift perturbations on cytochromes backbone NH and 1 H heme methyl group signals were used to map their interaction regions with AQDS, showing that each protein forms a low-affinity binding complex with AQDS through well-defined positive surface regions in the vicinity of heme IV (PpcB, PpcD and PpcE) and I (PpcE). Docking calculations performed using NMR chemical shift perturbations allowed modeling the interactions between AQDS and each cytochrome at a molecular level. Overall, the results obtained provided important structural-functional relationships to rationalize the microbial respiration of humic substances in G. sulfurreducens. Copyright © 2018. Published by Elsevier B.V.

Investigation into the propagation of Omega very low frequency signals and techniques for improvement of navigation accuracy including differential and composite omega

NASA Technical Reports Server (NTRS)

1973-01-01

An analysis of Very Low Frequency propagation in the atmosphere in the 10-14 kHz range leads to a discussion of some of the more significant causes of phase perturbation. The method of generating sky-wave corrections to predict the Omega phase is discussed. Composite Omega is considered as a means of lane identification and of reducing Omega navigation error. A simple technique for generating trapezoidal model (T-model) phase prediction is presented and compared with the Navy predictions and actual phase measurements. The T-model prediction analysis illustrates the ability to account for the major phase shift created by the diurnal effects on the lower ionosphere. An analysis of the Navy sky-wave correction table is used to provide information about spatial and temporal correlation of phase correction relative to the differential mode of operation.

Early Detection of Regime Shifts in Complex Systems from Fisher Information

EPA Science Inventory

The central goal of sustainability is the maintenance of environmental conditions, which are favorable to human existence. A critically important element then is the resilience of the dynamic regime that one wishes to sustain. Resilient systems are able to withstand perturbations...

Precise Determination of the 1s Lamb Shift in Hydrogen-Like Lead and Gold Using Microcalorimeters

NASA Technical Reports Server (NTRS)

Kraft-Bermuth, S.; Andrianov, V.; Bleile, A.; Echler, A.; Egelhof, P.; Grabitz, P.; Ilieva, S.; Kiselev, O.; Kilbourne, C.; McCammon, D.;

Nonlinear evolution of baryon acoustic oscillations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crocce, Martin; Institut de Ciencies de l'Espai, IEEC-CSIC, Campus UAB, Facultat de Ciencies, Torre C5 par-2, Barcelona 08193; Scoccimarro, Roman

2008-01-15

We study the nonlinear evolution of baryon acoustic oscillations in the dark matter power spectrum and the correlation function using renormalized perturbation theory. In a previous paper we showed that renormalized perturbation theory successfully predicts the damping of acoustic oscillations; here we extend our calculation to the enhancement of power due to mode coupling. We show that mode coupling generates additional oscillations that are out of phase with those in the linear spectrum, leading to shifts in the scales of oscillation nodes defined with respect to a smooth spectrum. When Fourier transformed, these out-of-phase oscillations induce percent-level shifts in themore » acoustic peak of the two-point correlation function. We present predictions for these shifts as a function of redshift; these should be considered as a robust lower limit to the more realistic case that includes, in addition, redshift distortions and galaxy bias. We show that these nonlinear effects occur at very large scales, leading to a breakdown of linear theory at scales much larger than commonly thought. We discuss why virialized halo profiles are not responsible for these effects, which can be understood from basic physics of gravitational instability. Our results are in excellent agreement with numerical simulations, and can be used as a starting point for modeling baryon acoustic oscillations in future observations. To meet this end, we suggest a simple physically motivated model to correct for the shifts caused by mode coupling.« less

Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases.

PubMed

Grimm, Lena Lisbeth; Weissbach, Sophie; Flügge, Friedemann; Begemann, Nora; Palcic, Monica M; Peters, Thomas

2017-07-04

Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H, 15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H, 15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[ 13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

UV Spectra of Tris(2,2'-bipyridine)-M(II) Complex Ions in Vacuo (M = Mn, Fe, Co, Ni, Cu, Zn).

PubMed

Xu, Shuang; Smith, James E T; Weber, J Mathias

2016-11-21

We present electronic spectra in the π-π* region of a series of tris(bpy)-M(II) complex ions (bpy = 2,2'-bipyridine; M = Mn, Fe, Co, Ni, Cu, Zn) in vacuo for the first time. By applying photodissociation spectroscopy to cryogenically cooled and mass selected [M II (bpy) 3 ] 2+ ions, we obtain the intrinsic spectra of these ions at low temperature without perturbation by solvent interaction or crystal lattice shifts. This allows spectroscopic analysis of these complex ions in greater detail than possible in the condensed phase. We interpret our experimental data by comparison with time-dependent density functional theory.

Small Scale Response and Modeling of Periodically Forced Turbulence

NASA Technical Reports Server (NTRS)

Bos, Wouter; Clark, Timothy T.; Rubinstein, Robert

2007-01-01

The response of the small scales of isotropic turbulence to periodic large scale forcing is studied using two-point closures. The frequency response of the turbulent kinetic energy and dissipation rate, and the phase shifts between production, energy and dissipation are determined as functions of Reynolds number. It is observed that the amplitude and phase of the dissipation exhibit nontrivial frequency and Reynolds number dependence that reveals a filtering effect of the energy cascade. Perturbation analysis is applied to understand this behavior which is shown to depend on distant interactions between widely separated scales of motion. Finally, the extent to which finite dimensional models (standard two-equation models and various generalizations) can reproduce the observed behavior is discussed.

H0LiCOW – II. Spectroscopic survey and galaxy-group identification of the strong gravitational lens system HE 0435-1223

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sluse, D.; Sonnenfeld, A.; Rumbaugh, N.

Galaxies located in the environment or on the line of sight towards gravitational lenses can significantly affect lensing observables, and can lead to systematic errors on the measurement of H 0 from the time-delay technique. We present the results of a systematic spectroscopic identi cation of the galaxies in the field of view of the lensed quasar HE0435-1223 using the W. M. Keck, Gemini and ESO-Very Large telescopes. Our new catalog triples the number of known galaxy redshifts in the direct vicinity of the lens, expanding to 102 the number of measured redshifts for galaxies separated by less than 30more » from the lens. We complement our catalog with literature data to gather redshifts up to 150 from the lens, and search for galaxy groups or clusters projected towards HE0435-1223. We con rm that the lens is a member of a small group that includes at least 12 galaxies, and nd 8 other group candidates near the line of sight of the lens. The flexion shift, namely the shift of lensed images produced by high order perturbation of the lens potential, is calculated for each galaxy/group and used to identify which objects produce the largest perturbation of the lens potential. This analysis demonstrates that i) at most three of the five brightest galaxies projected within 1200 of the lens need to be explicitly used in the lens models, and ii) the groups can be treated in the lens model as an external tidal field (shear) contribution.« less

Asymptotic analysis of the local potential approximation to the Wetterich equation

NASA Astrophysics Data System (ADS)

Bender, Carl M.; Sarkar, Sarben

2018-06-01

This paper reports a study of the nonlinear partial differential equation that arises in the local potential approximation to the Wetterich formulation of the functional renormalization group equation. A cut-off-dependent shift of the potential in this partial differential equation is performed. This shift allows a perturbative asymptotic treatment of the differential equation for large values of the infrared cut-off. To leading order in perturbation theory the differential equation becomes a heat equation, where the sign of the diffusion constant changes as the space-time dimension D passes through 2. When D  <  2, one obtains a forward heat equation whose initial-value problem is well-posed. However, for D  >  2 one obtains a backward heat equation whose initial-value problem is ill-posed. For the special case D  =  1 the asymptotic series for cubic and quartic models is extrapolated to the small infrared-cut-off limit by using Padé techniques. The effective potential thus obtained from the partial differential equation is then used in a Schrödinger-equation setting to study the stability of the ground state. For cubic potentials it is found that this Padé procedure distinguishes between a -symmetric theory and a conventional Hermitian theory (g real). For an theory the effective potential is nonsingular and has a stable ground state but for a conventional theory the effective potential is singular. For a conventional Hermitian theory and a -symmetric theory (g  >  0) the results are similar; the effective potentials in both cases are nonsingular and possess stable ground states.

H0LiCOW – II. Spectroscopic survey and galaxy-group identification of the strong gravitational lens system HE 0435-1223

DOE PAGES

Sluse, D.; Sonnenfeld, A.; Rumbaugh, N.; ...

2017-06-15

Galaxies located in the environment or on the line of sight towards gravitational lenses can significantly affect lensing observables, and can lead to systematic errors on the measurement of H 0 from the time-delay technique. We present the results of a systematic spectroscopic identi cation of the galaxies in the field of view of the lensed quasar HE0435-1223 using the W. M. Keck, Gemini and ESO-Very Large telescopes. Our new catalog triples the number of known galaxy redshifts in the direct vicinity of the lens, expanding to 102 the number of measured redshifts for galaxies separated by less than 30more » from the lens. We complement our catalog with literature data to gather redshifts up to 150 from the lens, and search for galaxy groups or clusters projected towards HE0435-1223. We con rm that the lens is a member of a small group that includes at least 12 galaxies, and nd 8 other group candidates near the line of sight of the lens. The flexion shift, namely the shift of lensed images produced by high order perturbation of the lens potential, is calculated for each galaxy/group and used to identify which objects produce the largest perturbation of the lens potential. This analysis demonstrates that i) at most three of the five brightest galaxies projected within 1200 of the lens need to be explicitly used in the lens models, and ii) the groups can be treated in the lens model as an external tidal field (shear) contribution.« less

Compensation for pitch-shifted auditory feedback during the production of Mandarin tone sequences

NASA Astrophysics Data System (ADS)

Xu, Yi; Larson, Charles R.; Bauer, Jay J.; Hain, Timothy C.

2004-08-01

Recent research has found that while speaking, subjects react to perturbations in pitch of voice auditory feedback by changing their voice fundamental frequency (F0) to compensate for the perceived pitch-shift. The long response latencies (150-200 ms) suggest they may be too slow to assist in on-line control of the local pitch contour patterns associated with lexical tones on a syllable-to-syllable basis. In the present study, we introduced pitch-shifted auditory feedback to native speakers of Mandarin Chinese while they produced disyllabic sequences /ma ma/ with different tonal combinations at a natural speaking rate. Voice F0 response latencies (100-150 ms) to the pitch perturbations were shorter than syllable durations reported elsewhere. Response magnitudes increased from 50 cents during static tone to 85 cents during dynamic tone productions. Response latencies and peak times decreased in phrases involving a dynamic change in F0. The larger response magnitudes and shorter latency and peak times in tasks requiring accurate, dynamic control of F0, indicate this automatic system for regulation of voice F0 may be task-dependent. These findings suggest that auditory feedback may be used to help regulate voice F0 during production of bi-tonal Mandarin phrases.

On the Coriolis effect in acoustic waveguides.

PubMed

Wegert, Henry; Reindl, Leonard M; Ruile, Werner; Mayer, Andreas P

2012-05-01

Rotation of an elastic medium gives rise to a shift of frequency of its acoustic modes, i.e., the time-period vibrations that exist in it. This frequency shift is investigated by applying perturbation theory in the regime of small ratios of the rotation velocity and the frequency of the acoustic mode. In an expansion of the relative frequency shift in powers of this ratio, upper bounds are derived for the first-order and the second-order terms. The derivation of the theoretical upper bounds of the first-order term is presented for linear vibration modes as well as for stable nonlinear vibrations with periodic time dependence that can be represented by a Fourier series.

Directional constraint of endpoint force emerges from hindlimb anatomy.

PubMed

Bunderson, Nathan E; McKay, J Lucas; Ting, Lena H; Burkholder, Thomas J

2010-06-15

Postural control requires the coordination of force production at the limb endpoints to apply an appropriate force to the body. Subjected to horizontal plane perturbations, quadruped limbs stereotypically produce force constrained along a line that passes near the center of mass. This phenomenon, referred to as the force constraint strategy, may reflect mechanical constraints on the limb or body, a specific neural control strategy or an interaction among neural controls and mechanical constraints. We used a neuromuscular model of the cat hindlimb to test the hypothesis that the anatomical constraints restrict the mechanical action of individual muscles during stance and constrain the response to perturbations to a line independent of perturbation direction. In a linearized neuromuscular model of the cat hindlimb, muscle lengthening directions were highly conserved across 10,000 different muscle activation patterns, each of which produced an identical, stance-like endpoint force. These lengthening directions were closely aligned with the sagittal plane and reveal an anatomical structure for directionally constrained force responses. Each of the 10,000 activation patterns was predicted to produce stable stance based on Lyapunov stability analysis. In forward simulations of the nonlinear, seven degree of freedom model under the action of 200 random muscle activation patterns, displacement of the endpoint from its equilibrium position produced restoring forces, which were also biased toward the sagittal plane. The single exception was an activation pattern based on minimum muscle stress optimization, which produced destabilizing force responses in some perturbation directions. The sagittal force constraint increased during simulations as the system shifted from an inertial response during the acceleration phase to a viscoelastic response as peak velocity was obtained. These results qualitatively match similar experimental observations and suggest that the force constraint phenomenon may result from the anatomical arrangement of the limb.

Succession in the petroleum reservoir microbiome through an oil field production lifecycle.

PubMed

Vigneron, Adrien; Alsop, Eric B; Lomans, Bartholomeus P; Kyrpides, Nikos C; Head, Ian M; Tsesmetzis, Nicolas

2017-09-01

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H 2 S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.

Directional constraint of endpoint force emerges from hindlimb anatomy

PubMed Central

Bunderson, Nathan E.; McKay, J. Lucas; Ting, Lena H.; Burkholder, Thomas J.

2010-01-01

Postural control requires the coordination of force production at the limb endpoints to apply an appropriate force to the body. Subjected to horizontal plane perturbations, quadruped limbs stereotypically produce force constrained along a line that passes near the center of mass. This phenomenon, referred to as the force constraint strategy, may reflect mechanical constraints on the limb or body, a specific neural control strategy or an interaction among neural controls and mechanical constraints. We used a neuromuscular model of the cat hindlimb to test the hypothesis that the anatomical constraints restrict the mechanical action of individual muscles during stance and constrain the response to perturbations to a line independent of perturbation direction. In a linearized neuromuscular model of the cat hindlimb, muscle lengthening directions were highly conserved across 10,000 different muscle activation patterns, each of which produced an identical, stance-like endpoint force. These lengthening directions were closely aligned with the sagittal plane and reveal an anatomical structure for directionally constrained force responses. Each of the 10,000 activation patterns was predicted to produce stable stance based on Lyapunov stability analysis. In forward simulations of the nonlinear, seven degree of freedom model under the action of 200 random muscle activation patterns, displacement of the endpoint from its equilibrium position produced restoring forces, which were also biased toward the sagittal plane. The single exception was an activation pattern based on minimum muscle stress optimization, which produced destabilizing force responses in some perturbation directions. The sagittal force constraint increased during simulations as the system shifted from an inertial response during the acceleration phase to a viscoelastic response as peak velocity was obtained. These results qualitatively match similar experimental observations and suggest that the force constraint phenomenon may result from the anatomical arrangement of the limb. PMID:20511528

Evidence for inflation in an axion landscape

NASA Astrophysics Data System (ADS)

Nath, Pran; Piskunov, Maksim

2018-03-01

We discuss inflation models within supersymmetry and supergravity frameworks with a landscape of chiral superfields and one U(1) shift symmetry which is broken by non-perturbative symmetry breaking terms in the superpotential. We label the pseudo scalar component of the chiral fields axions and their real parts saxions. Thus in the models only one combination of axions will be a pseudo-Nambu-Goldstone-boson which will act as the inflaton. The proposed models constitute consistent inflation for the following reasons: the inflation potential arises dynamically with stabilized saxions, the axion decay constant can lie in the sub-Planckian region, and consistency with the Planck data is achieved. The axion landscape consisting of m axion pairs is assumed with the axions in each pair having opposite charges. A fast roll-slow roll splitting mechanism for the axion potential is proposed which is realized with a special choice of the axion basis. In this basis the 2 m coupled equations split into 2 m - 1 equations which enter in the fast roll and there is one unique linear combination of the 2 m fields which controls the slow roll and thus the power spectrum of curvature and tensor perturbations. It is shown that a significant part of the parameter space exists where inflation is successful, i.e., N pivot = [50, 60], the spectral index n s of curvature perturbations, and the ratio r of the power spectrum of tensor perturbations and curvature perturbations, lie in the experimentally allowed regions given by the Planck experiment. Further, it is shown that the model allows for a significant region of the parameter space where the effective axion decay constant can lie in the sub-Planckian domain. An analysis of the tensor spectral index n t is also given and the future experimental data which constraints n t will further narrow down the parameter space of the proposed inflationary models. Topics of further interest include implications of the model for gravitational waves and non-Gaussianities in the curvature perturbations. Also of interest is embedding of the model in strings which are expected to possess a large axionic landscape.

Kinetic and Thermodynamic Characterization of Dihydrotestosterone-Induced Conformational Perturbations in Androgen Receptor Ligand-Binding Domain

PubMed Central

Jasuja, Ravi; Ulloor, Jagadish; Yengo, Christopher M.; Choong, Karen; Istomin, Andrei Y.; Livesay, Dennis R.; Jacobs, Donald J.; Swerdloff, Ronald S.; Mikšovská, Jaroslava; Larsen, Randy W.; Bhasin, Shalender

2009-01-01

Ligand-induced conformational perturbations in androgen receptor (AR) are important in coactivator recruitment and transactivation. However, molecular rearrangements in AR ligand-binding domain (AR-LBD) associated with agonist binding and their kinetic and thermodynamic parameters are poorly understood. We used steady-state second-derivative absorption and emission spectroscopy, pressure and temperature perturbations, and 4,4′-bis-anilinonaphthalene 8-sulfonate (bis-ANS) partitioning to determine the kinetics and thermodynamics of the conformational changes in AR-LBD after dihydrotestosterone (DHT) binding. In presence of DHT, the second-derivative absorption spectrum showed a red shift and a change in peak-to-peak distance. Emission intensity increased upon DHT binding, and center of spectral mass was blue shifted, denoting conformational changes resulting in more hydrophobic environment for tyrosines and tryptophans within a more compact DHT-bound receptor. In pressure perturbation calorimetry, DHT-induced energetic stabilization increased the Gibbs free energy of unfolding to 8.4 ± 1.3 kcal/mol from 3.5 ± 1.6 kcal/mol. Bis-ANS partitioning studies revealed that upon DHT binding, AR-LBD underwent biphasic rearrangement with a high activation energy (13.4 kcal/mol). An initial, molten globule-like burst phase (k ∼30 sec−1) with greater solvent accessibility was followed by rearrangement (k ∼0.01 sec−1), leading to a more compact conformation than apo-AR-LBD. Molecular simulations demonstrated unique sensitivity of tyrosine and tryptophan residues during pressure unfolding with rearrangement of residues in the coactivator recruitment surfaces distant from the ligand-binding pocket. In conclusion, DHT binding leads to energetic stabilization of AR-LBD domain and substantial rearrangement of residues distant from the ligand-binding pocket. DHT binding to AR-LBD involves biphasic receptor rearrangement including population of a molten globule-like intermediate state. PMID:19443608

Duration of and decoupling between carbon isotope excursions during the end-Triassic mass extinction and Central Atlantic Magmatic Province emplacement

NASA Astrophysics Data System (ADS)

Yager, Joyce A.; West, A. Joshua; Corsetti, Frank A.; Berelson, William M.; Rollins, Nick E.; Rosas, Silvia; Bottjer, David J.

2017-09-01

Changes in δ13Ccarb and δ13Corg from marine strata occur globally in association with the end-Triassic mass extinction and the emplacement of the Central Atlantic Magmatic Province (CAMP) during the break up of Pangea. As is typical in deep time, the timing and duration of these isotopic excursions has remained elusive, hampering attempts to link carbon cycle perturbations to specific processes. Here, we report δ13Ccarb and δ13Corg from Late Triassic and Early Jurassic strata near Levanto, Peru, where intercalated dated ash beds permit temporal calibration of the carbon isotope record. Both δ13Ccarb and δ13Corg exhibit a broad positive excursion through the latest Triassic into the earliest Jurassic. The first order positive excursion in δ13Corg is interrupted by a negative shift noted in many sections around the world coincident with the extinction horizon. Our data indicate that the negative excursion lasts 85 ± 25 kyrs, longer than inferred by previous studies based on cyclostratigraphy. A 260 ± 80 kyr positive δ13Corg shift follows, during which the first Jurassic ammonites appear. The overall excursion culminates in a return to pre-perturbation carbon isotopic values over the next 1090 ± 70 kyrs. Via chronologic, isotopic, and biostratigraphic correlation to other successions, we find that δ13Ccarb and δ13Corg return to pre-perturbation values as CAMP volcanism ceases and in association with the recovery of pelagic and benthic biota. However, the initiation of the carbon isotope excursion at Levanto predates the well-dated CAMP sills from North America, indicating that CAMP may have started earlier than thought based on these exposures, or that the onset of carbon cycle perturbations was not related to CAMP.

Increased sensory noise and not muscle weakness explains changes in non-stepping postural responses following stance perturbations in healthy elderly.

PubMed

Afschrift, Maarten; De Groote, Friedl; Verschueren, Sabine; Jonkers, Ilse

2018-01-01

The response to stance perturbations changes with age. The shift from an ankle to a hip strategy with increasing perturbation magnitude occurs at lower accelerations in older than in young adults. This strategy shift has been related to age-related changes in muscle and sensory function. However, the effect of isolated changes in muscle or sensory function on the responses following stance perturbations cannot be determined experimentally since changes in muscle and sensory function occur simultaneously. Therefore, we used predictive simulations to estimate the effect of isolated changes in (rates of change in) maximal joint torques, functional base of support, and sensory noise on the response to backward platform translations. To evaluate whether these modeled changes in muscle and sensory function could explain the observed changes in strategy; simulated postural responses with a torque-driven double inverted pendulum model controlled using optimal state feedback were compared to measured postural responses in ten healthy young and ten healthy older adults. The experimentally observed peak hip angle during the response was significantly larger (5°) and the functional base of support was smaller (0.04m) in the older than in the young adults but peak joint torques and rates of joint torque were similar during the recovery. The addition of noise to the sensed states in the predictive simulations could explain the observed increase in peak hip angle in the elderly, whereas changes in muscle function could not. Hence, our results suggest that strength training alone might be insufficient to improve postural control in elderly. Copyright © 2017 Elsevier B.V. All rights reserved.

Computation of the free energy due to electron density fluctuation of a solute in solution: A QM/MM method with perturbation approach combined with a theory of solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suzuoka, Daiki; Takahashi, Hideaki, E-mail: hideaki@m.tohoku.ac.jp; Morita, Akihiro

2014-04-07

We developed a perturbation approach to compute solvation free energy Δμ within the framework of QM (quantum mechanical)/MM (molecular mechanical) method combined with a theory of energy representation (QM/MM-ER). The energy shift η of the whole system due to the electronic polarization of the solute is evaluated using the second-order perturbation theory (PT2), where the electric field formed by surrounding solvent molecules is treated as the perturbation to the electronic Hamiltonian of the isolated solute. The point of our approach is that the energy shift η, thus obtained, is to be adopted for a novel energy coordinate of the distributionmore » functions which serve as fundamental variables in the free energy functional developed in our previous work. The most time-consuming part in the QM/MM-ER simulation can be, thus, avoided without serious loss of accuracy. For our benchmark set of molecules, it is demonstrated that the PT2 approach coupled with QM/MM-ER gives hydration free energies in excellent agreements with those given by the conventional method utilizing the Kohn-Sham SCF procedure except for a few molecules in the benchmark set. A variant of the approach is also proposed to deal with such difficulties associated with the problematic systems. The present approach is also advantageous to parallel implementations. We examined the parallel efficiency of our PT2 code on multi-core processors and found that the speedup increases almost linearly with respect to the number of cores. Thus, it was demonstrated that QM/MM-ER coupled with PT2 deserves practical applications to systems of interest.« less

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome.

PubMed

Raymann, Kasie; Bobay, Louis-Marie; Moran, Nancy A

2018-04-01

The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated. To address this gap, we used amplicon sequencing of protein-coding genes to assess effects of antibiotics on fine-scale genetic diversity of the honeybee gut microbiota. We followed the population dynamics of alleles within two dominant core species of the bee gut community, Gilliamella apicola and Snodgrassella alvi, following antibiotic perturbation. Whereas we observed a large reduction in genetic diversity in G. apicola, S. alvi diversity was mostly unaffected. The reduction in G. apicola diversity accompanied an increase in the frequency of several alleles, suggesting resistance to antibiotic treatment. We find that antibiotic perturbation can cause major shifts in diversity and that the extent of these shifts can vary substantially across species. Thus, antibiotics impact not only species composition, but also allelic diversity within species, potentially affecting hosts if variants with particular functions are reduced or eliminated. Overall, we show that amplicon sequencing of protein-coding genes, without clustering into operational taxonomic units, provides an accurate picture of the fine-scale dynamics of microbial communities over time. © 2017 John Wiley & Sons Ltd.

Changes in Head Stability Control in Response to a Lateral Perturbation while Walking in Older Adults

NASA Technical Reports Server (NTRS)

Buccello, Regina R.; Cromwell, Ronita L.; Bloomberg, Jacob J.

2008-01-01

Falling is a main contributor of injury in older adults. The decline in sensory systems associated with aging limits information needed to successfully compensate for unexpected perturbations. Therefore, sensory changes result in older adults having problems maintaining balance stability when experiencing an unexpected lateral perturbation (e.g. slip) in the environment. The goal of this study was to determine head stability movement strategies used by older adults when experiencing an unexpected lateral perturbation during walking. A total of 16 healthy adults, aged 66-81 years, walked across a foam pathway 6 times. One piece of the foam pathway covered a movable platform that translated to the left when the subject stepped on the foam. Three trials were randomized in which the platform shifted. Angular rate sensors were placed on the center of mass for the head and trunk segments to collect head and trunk movement in all three planes of motion. The predominant movement strategies for maintaining head stability were determined from the results of the cross-correlation analyses between the head and trunk segments. The Chi square test of independence was used to evaluate the movement pattern distributions of head-trunk coordination during perturbed and non-perturbed walking. When perturbed, head stabilization was significantly challenged in the yaw and roll planes of motion. Subjects demonstrated a movement pattern of the head leading the trunk in an effort to stabilize the head. The older adult subjects used this head stabilization movement pattern to compensate for sensory changes when experiencing the unexpected lateral perturbation.

Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method

NASA Astrophysics Data System (ADS)

Fukui, H.; Miura, K.; Hirai, A.

A gauge-invariant INDO method based on the coupled Hartree-Fuck perturbation theory is presented and applied to the calculation of 1H and 13C chemical shifts of hydrocarbons including ring compounds. Invariance of the diamagnetic and paramagnetic shieldings with respect to displacement of the coordinate origin is discussed. Comparison between calculated and experimental results exhibits fairly good agreement, provided that the INDO parameters of Ellis et al. (J. Am. Chem. Soc.94, 4069 (1972)) are used with the inclusion of all multicenter one-electron integrals.

The Adverse Outcome Pathway: A conceptual framework to support toxicity testing in the 21st century

EPA Science Inventory

The field of regulatory toxicity testing is at a turning point. The U.S. National Research Council (NRC) envisioned a shift away from traditional toxicity testing and towards a focused effort to explore and understand pathways perturbed by biologically active substances or their ...

A finite-element-based perturbation model for the rotordynamic analysis of shrouded pump impellers: Part 1: Model development and applications

NASA Technical Reports Server (NTRS)

Baskharone, Erian A.

1993-01-01

This study concerns the rotor dynamic characteristics of fluid-encompassed rotors, with special emphasis on shrouded pump impellers. The core of the study is a versatile and categorically new finite-element-based perturbation model, which is based on a rigorous flow analysis and what we have generically termed the 'virtually' deformable finite-element approach. The model is first applied to the case of a smooth annular seal for verification purposes. The rotor excitation components, in this sample problem, give rise to a purely cylindrical, purely conical, and a simultaneous cylindrical/conical rotor whirl around the housing centerline. In all cases, the computed results are compared to existing experimental and analytical data involving the same seal geometry and operating conditions. Next, two labyrinth-seal configurations, which share the same tooth-to-tooth chamber geometry but differ in the total number of chambers, were investigated. The results, in this case, are compared to experimental measurements for both seal configurations. The focus is finally shifted to the shrouded-impeller problem, where the stability effects of the leakage flow in the shroud-to-housing secondary passage are investigated. To this end, the computational model is applied to a typical shrouded-impeller pump stage, fabricated and rotor dynamically tested by Sulzer Bros., and the results compared to those of a simplified 'bulk-flow' analysis and Sulzer Bros.' test data. In addition to assessing the computed rotor dynamic coefficients, the shrouded-impeller study also covers a controversial topic, namely that of the leakage-passage inlet swirl, which was previously cited as the origin of highly unconventional (resonance-like) trends of the fluid-exerted forces. In order to validate this claim, a 'microscopic' study of the fluid/shroud interaction mechanism is conducted, with the focus being on the structure of the perturbed flow field associated with the impeller whirl. The conclusions of this study were solidified by the outcome of a numerical-certainty exercise, where the grid dependency of the numerical results is objectively examined. The final phase of the shrouded-impeller investigation involves the validation of a built-in assumption, in all other perturbation models, whereby single-harmonic tangential distributions of all the flow thermophysical properties are imposed. The last phase of the investigation course is aimed at verifying the fine details of the perturbed flow field in light of recent set of detailed LDA measurements in a smooth annular seal. Grid dependency of the fluid-induced forces is also investigated, and specific recommendations are made.

Following The Money: Characterizing the Dynamics of Microbial Ecosystems and Labile Organic Matter in Grassland Soils

NASA Astrophysics Data System (ADS)

Herbert, B. E.; McNeal, K. S.

2006-12-01

The dynamics of soil microbial ecosystems and labile fractions of soil organic matter in grasslands have important implications for the response of these critical ecosystems to perturbations. Organic, inorganic and genetic biomarkers in the solid (e.g. lipids, microbial DNA), liquid (e.g. porewater ions) or gaseous phases (e.g. carbon dioxide) have been used to characterize carbon cycling and soil microbial ecology. These proxies are generally limited in the amount of temporal information that they can provide (i.e., solid-phase proxies) or the amount of specific information they can provide about carbon sources or microbial community processes (e.g. inorganic gases). It is the aim of this research to validate the use of soil volatile organic carbon emissions (VOCs) as useful indicators of subsurface microbial community shifts and processes as a function of ecosystem perturbations. We present results of method validation using laboratory microcosm, where VOC metabolites as characterized by gas chromatography and mass spectrometry (GC-MS), were related to other proxies including carbon dioxide (CO2) via infra-red technology, and microbial community shifts as measured by Biolog© and fatty acid methyl ester (FAME) techniques. Experiments with soil collected from grasslands along the coastal margin region in southern Texas were preformed where environmental factors such as soil water content, soil type, and charcoal content are manipulated. Results indicate that over fifty identifiable VOC metabolites are produced from the soils, where many (~15) can be direct indicators of microbial ecology. Principle component analysis (PCA) evidences these trends through similar cluster patterns for the VOC results, the Biolog© results, and FAME. Regression analysis further shows that VOCs are significant (p < 0.05) indicators of microbial stress. Our results are encouraging that characterizing VOCs production in grassland soils are easy to measure, relatively inexpensive method, and useful proxies of subsurface microbial ecosystems and the dynamics of labile carbon in these systems.

A possible new test of general relativity with Juno

NASA Astrophysics Data System (ADS)

Iorio, L.

2013-10-01

The expansion in multipoles Jℓ, ℓ = 2, … of the gravitational potential of a rotating body affects the orbital motion of a test particle orbiting it with long-term perturbations both at a classical and at a relativistic level. In this preliminary sensitivity analysis, we show that, for the first time, the J2c-2 effects could be measured by the ongoing Juno mission in the gravitational field of Jupiter during its nearly yearlong science phase (10 November 2016-5 October 2017), thanks to its high eccentricity (e = 0.947) and to the huge oblateness of Jupiter (J2 = 1.47 × 10-2). The semimajor axis a and the perijove ω of Juno are expected to be shifted by Δa ≲ 700-900 m and Δω ≲ 50-60 milliarcseconds (mas), respectively, over 1-2 yr. A numerical analysis shows also that the expected J2c-2 range-rate signal for Juno should be as large as ≈280 microns per second (μm s-1) during a typical 6 h pass at its closest approach. Independent analyses previously performed by other researchers about the measurability of the Lense-Thirring effect showed that the radio science apparatus of Juno should reach an accuracy in Doppler range-rate measurements of ≈1-5 μm s-1 over such passes. The range-rate signature of the classical even zonal perturbations is different from the first post-Newtonian (1PN) one. Thus, further investigations, based on covariance analyses of simulated Doppler data and dedicated parameters estimation, are worth of further consideration. It turns out that the J2c-2 effects cannot be responsible of the flyby anomaly in the gravitational field of the Earth. A dedicated spacecraft in a 6678 km × 57103 km polar orbit would experience a geocentric J2c-2 range-rate shift of ≈0.4 mm s-1.

Strategies and methodologies to develop techniques for computer-assisted analysis of gas phase formation during altitude decompression

NASA Technical Reports Server (NTRS)

Powell, Michael R.; Hall, W. A.

1993-01-01

It would be of operational significance if one possessed a device that would indicate the presence of gas phase formation in the body during hypobaric decompression. Automated analysis of Doppler gas bubble signals has been attempted for 2 decades but with generally unfavorable results, except with surgically implanted transducers. Recently, efforts have intensified with the introduction of low-cost computer programs. Current NASA work is directed towards the development of a computer-assisted method specifically targeted to EVA, and we are most interested in Spencer Grade 4. We note that Spencer Doppler Grades 1 to 3 have increased in the FFT sonogram and spectrogram in the amplitude domain, and the frequency domain is sometimes increased over that created by the normal blood flow envelope. The amplitude perturbations are of very short duration, in both systole and diastole and at random temporal positions. Grade 4 is characteristic in the amplitude domain but with modest increases in the FFT sonogram and spectral frequency power from 2K to 4K over all of the cardiac cycle. Heart valve motion appears to characteristic display signals: (1) the demodulated Doppler signal amplitude is considerably above the Doppler-shifted blow flow signal (even Grade 4); and (2) demodulated Doppler frequency shifts are considerably greater (often several kHz) than the upper edge of the blood flow envelope. Knowledge of these facts will aid in the construction of a real-time, computer-assisted discriminator to eliminate cardiac motion artifacts. There could also exist perturbations in the following: (1) modifications of the pattern of blood flow in accordance with Poiseuille's Law, (2) flow changes with a change in the Reynolds number, (3) an increase in the pulsatility index, and/or (4) diminished diastolic flow or 'runoff.' Doppler ultrasound devices have been constructed with a three-transducer array and a pulsed frequency generator.

Relativistic corrections for screening effects on the energies of hydrogen-like atoms embedded in plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poszwa, A., E-mail: poszwa@matman.uwm.edu.p; Bahar, M. K., E-mail: mussiv58@gmail.com

2015-01-15

The influence of relativistic and plasma screening effects on energies of hydrogen-like atoms embedded in plasmas has been studied. The Dirac equation with a more general exponential cosine screened potential has been solved numerically and perturbatively, by employing the direct perturbation theory. Properties of spectra corresponding to bound states and to different sets of the potential parameters have been studied both in nonrelativistic and relativistic approximations. Binding energies, fine-structure splittings, and relativistic energy shifts have been determined as functions of parameters of the potential. The results have been compared with the ones known from the literature.

Experimental studies of high-confinement mode plasma response to non-axisymmetric magnetic perturbations in ASDEX Upgrade

DOE PAGES

Suttrop, Wolfgang; Kirk, A.; Nazikian, R.; ...

2016-11-22

Here, the interaction of externally applied small non-axisymmetric magnetic perturbations (MP) with tokamak high-confinement mode (H-mode) plasmas is reviewed and illustrated by recent experiments in ASDEX Upgrade. The plasma response to the vacuum MP field is amplified by stable ideal kink modes with low toroidal mode number n driven by the H-mode edge pressure gradient (and associated bootstrap current) which is experimentally evidenced by an observable shift of the poloidal mode number m away from field alignment (m = qn, with q being the safety factor) at the response maximum. A torque scan experiment demonstrates the importance of the perpendicular electron flow for shielding of the resonant magnetic perturbation, as expected from a two-fluid MHD picture. Two significant effects of MP occur in H-mode plasmas at low pedestal collisionality,more » $$\

The Stark Effect on the Wave Function of Tritium in Relativistic Condition

NASA Astrophysics Data System (ADS)

Supriadi, B.; Prastowo, S. H. B.; Bahri, S.; Ridlo, Z. R.; Prihandono, T.

2018-03-01

Tritium Atom is one of the isotopes of Hydrogen that has two Neutrons in the nucleus and an electron that surrounds the nucleus. The Stark Effect is an effect of a shift or polarization of the atomic spectrum caused by the external electrostatic field. The interaction between the electrons and the external electric field can be reviewed using an approximation method of perturbation theory. The perturbation theory used is a time Independent non-degenerate perturbation and reviewed to second order to obtain correction of Tritium Atomic wave function. The condition that used in the system is a relativistic condition by reviewing the movement of electrons within the Atom. The effects of relativity also affect the correction of the wave function of Atom Tritium in the ground state. Tritium is radioactive material that is still relatively safe, and one of the applications of Tritium Atom is on the battery of betavoltaics (Nano Tritium Battery).

Meditations on birth weight: is it better to reduce the variance or increase the mean?

PubMed

Haig, David

2003-07-01

A conceptual model is presented here in which the birth weight distribution is decomposed into a distribution of target weights and a distribution of perturbations from the target. The target weight is the adaptive goal of fetal development. In the simplest model, perinatal mortality is independent of variation in target weight and determined solely by the magnitude of the perturbation of birth weight from the target. In this model, mortality risk is concentrated in the tails of the birth weight distribution. A difference between populations in their distributions of target weights will be associated with a corresponding shift in their curves of weight-specific risk, without any difference between the populations in overall risk. In this model, risk would be reduced by decreasing the variance of the distribution of perturbations. The model is discussed in the context of the so-called "paradoxes of low birth weight."

Simulation of Rate-Related (Dead-Time) Losses In Passive Neutron Multiplicity Counting Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, L.G.; Norman, P.I.; Leadbeater, T.W.

Passive Neutron Multiplicity Counting (PNMC) based on Multiplicity Shift Register (MSR) electronics (a form of time correlation analysis) is a widely used non-destructive assay technique for quantifying spontaneously fissile materials such as Pu. At high event rates, dead-time losses perturb the count rates with the Singles, Doubles and Triples being increasingly affected. Without correction these perturbations are a major source of inaccuracy in the measured count rates and assay values derived from them. This paper presents the simulation of dead-time losses and investigates the effect of applying different dead-time models on the observed MSR data. Monte Carlo methods have beenmore » used to simulate neutron pulse trains for a variety of source intensities and with ideal detection geometry, providing an event by event record of the time distribution of neutron captures within the detection system. The action of the MSR electronics was modelled in software to analyse these pulse trains. Stored pulse trains were perturbed in software to apply the effects of dead-time according to the chosen physical process; for example, the ideal paralysable (extending) and non-paralysable models with an arbitrary dead-time parameter. Results of the simulations demonstrate the change in the observed MSR data when the system dead-time parameter is varied. In addition, the paralysable and non-paralysable models of deadtime are compared. These results form part of a larger study to evaluate existing dead-time corrections and to extend their application to correlated sources. (authors)« less

Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network

PubMed Central

2011-01-01

Background Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. Results We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism’s metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. Conclusions After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis. PMID:22784571

Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network.

PubMed

Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

2011-01-01

Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism's metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.

Stress and subsidy effects of seagrass wrack duration, frequency, and magnitude on salt marsh community structure.

PubMed

Hanley, Torrance C; Kimbro, David L; Hughes, Anne Randall

2017-07-01

Environmental perturbations can strongly affect community processes and ecosystem functions by acting primarily as a subsidy that increases productivity, a stress that decreases productivity, or both, with the predominant effect potentially shifting from subsidy to stress as the overall intensity of the perturbation increases. While perturbations are often considered along a single axis of intensity, they consist of multiple components (e.g., magnitude, frequency, and duration) that may not have equivalent stress and/or subsidy effects. Thus, different combinations of perturbation components may elicit community and ecosystem responses that differ in strength and/or direction (i.e., stress or subsidy) even if they reflect a similar overall perturbation intensity. To assess the independent and interactive effects of perturbation components, we experimentally manipulated the magnitude, frequency, and duration of wrack deposition, a common stress-subsidy in a variety of coastal systems. The effects of wrack perturbation on salt marsh community and ecosystem properties were assessed both in the short-term (at the end of a 12-week experimental manipulation) and long-term (6 months after the end of the experiment). In the short-term, plants and associated benthic invertebrates exhibited primarily stress-based responses to wrack perturbation. The extent of these stress effects on density of the dominant plant Spartina alterniflora, total plant percent cover, invertebrate abundance, and sediment oxygen availability were largely determined by perturbation duration. Yet, higher nitrogen content of Spartina, which indicates a subsidy effect of wrack, was influenced primarily by perturbation magnitude in the short-term. In the longer term, perturbation magnitude determined the extent of both stress and subsidy effects of wrack perturbation, with lower subordinate plant percent cover and snail density, and higher Spartina nitrogen content in high wrack biomass treatments. However, stress effects on the marsh community were generally less pronounced 6 months after the wrack perturbation, indicating capacity for recovery. Our results demonstrate that individual perturbation components can determine the degree to which its effects on the community elicit primarily stress- and/or subsidy-based responses. Further, the nature and extent of stress-subsidy effects can change over time, depending on species' relative ability to tolerate and/or recover from perturbation. © 2017 by the Ecological Society of America.

Boundary formulations for sensitivity analysis without matrix derivatives

NASA Technical Reports Server (NTRS)

Kane, J. H.; Guru Prasad, K.

1993-01-01

A new hybrid approach to continuum structural shape sensitivity analysis employing boundary element analysis (BEA) is presented. The approach uses iterative reanalysis to obviate the need to factor perturbed matrices in the determination of surface displacement and traction sensitivities via a univariate perturbation/finite difference (UPFD) step. The UPFD approach makes it possible to immediately reuse existing subroutines for computation of BEA matrix coefficients in the design sensitivity analysis process. The reanalysis technique computes economical response of univariately perturbed models without factoring perturbed matrices. The approach provides substantial computational economy without the burden of a large-scale reprogramming effort.

Dispersion relations for η '→ η π π

NASA Astrophysics Data System (ADS)

Isken, Tobias; Kubis, Bastian; Schneider, Sebastian P.; Stoffer, Peter

2017-07-01

We present a dispersive analysis of the decay amplitude for η '→ η π π that is based on the fundamental principles of analyticity and unitarity. In this framework, final-state interactions are fully taken into account. Our dispersive representation relies only on input for the {π π } and {π }η scattering phase shifts. Isospin symmetry allows us to describe both the charged and neutral decay channel in terms of the same function. The dispersion relation contains subtraction constants that cannot be fixed by unitarity. We determine these parameters by a fit to Dalitz-plot data from the VES and BES-III experiments. We study the prediction of a low-energy theorem and compare the dispersive fit to variants of chiral perturbation theory.

Ground-state energies of simple metals

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1974-01-01

A structural expansion for the static ground-state energy of a simple metal is derived. Two methods are presented, one an approach based on single-particle band structure which treats the electron gas as a nonlinear dielectric, the other a more general many-particle analysis using finite-temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi-surface distortions, and chemical-potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron-ion interaction and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero-temperature thermodynamic functions of atomic hydrogen are reported.

Structural expansions for the ground state energy of a simple metal

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1973-01-01

A structural expansion for the static ground state energy of a simple metal is derived. An approach based on single particle band structure which treats the electron gas as a non-linear dielectric is presented, along with a more general many particle analysis using finite temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi surface distortions, and chemical potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron ion interaction, and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero temperature thermodynamic functions of atomic hydrogen are reported.

Inducing the Einstein action in QCD-like theories

NASA Astrophysics Data System (ADS)

Donoghue, John F.; Menezes, Gabriel

2018-03-01

We evaluate the induced value of Newton's constant which would arise in QCD. The ingredients are modern lattice results, perturbation theory and the operator product expansion. The resulting shift in the Planck mass is positive. A scaled-up version of such a theory may be part of a quantum field theory treatment of gravity.

Responses to Intensity-Shifted Auditory Feedback during Running Speech

ERIC Educational Resources Information Center

Patel, Rupal; Reilly, Kevin J.; Archibald, Erin; Cai, Shanqing; Guenther, Frank H.

2015-01-01

Purpose: Responses to intensity perturbation during running speech were measured to understand whether prosodic features are controlled in an independent or integrated manner. Method: Nineteen English-speaking healthy adults (age range = 21-41 years) produced 480 sentences in which emphatic stress was placed on either the 1st or 2nd word. One…

Cosmological perturbation theory in 1+1 dimensions

NASA Astrophysics Data System (ADS)

McQuinn, Matthew; White, Martin

2016-01-01

Many recent studies have highlighted certain failures of the standard Eulerian-space cosmological perturbation theory (SPT). Its problems include (1) not capturing large-scale bulk flows [leading to an Script O( 1) error in the 1-loop SPT prediction for the baryon acoustic peak in the correlation function], (2) assuming that the Universe behaves as a pressureless, inviscid fluid, and (3) treating fluctuations on scales that are non-perturbative as if they were. Recent studies have highlighted the successes of perturbation theory in Lagrangian space or theories that solve equations for the effective dynamics of smoothed fields. Both approaches mitigate some or all of the aforementioned issues with SPT. We discuss these physical developments by specializing to the simplified 1D case of gravitationally interacting sheets, which allows us to substantially reduces the analytic overhead and still (as we show) maintain many of the same behaviors as in 3D. In 1D, linear-order Lagrangian perturbation theory ("the Zeldovich approximation") is exact up to shell crossing, and we prove that nth-order Eulerian perturbation theory converges to the Zeldovich approximation as narrow ∞. In no 1D cosmology that we consider (including a CDM-like case and power-law models) do these theories describe accurately the matter power spectrum on any mildly nonlinear scale. We find that theories based on effective equations are much more successful at describing the dynamics. Finally, we discuss many topics that have recently appeared in the perturbation theory literature such as beat coupling, the shift and smearing of the baryon acoustic oscillation feature, and the advantages of Fourier versus configuration space. Our simplified 1D case serves as an intuitive review of these perturbation theory results.

Characterization of the Head Stabilization Response to a Lateral Perturbation During Walking in Older Adults

NASA Technical Reports Server (NTRS)

Buccello-Stout, Regina R.; Cromwell, Ronita L.; Bloomberg, Jacob J.

2009-01-01

A main contributor of fractures in older adults is from a lateral fall. The decline in sensory systems results in difficulty maintaining balance stability. Head stabilization contributes to postural control by serving as a stable platform for the sensory systems. The purpose of this study was to characterize the head stabilization response to a lateral perturbation while walking. A total of 16 healthy older adults, aged 66-81 years, walked across a foam pathway 6 times. One piece of the foam pathway covered a movable platform that translated to the left when the subject stepped on the foam. Three trials were randomized in which the platform shifted. Angular rate sensors placed on the center of mass of the head and trunk collected head and trunk movement in all three planes of motion. The roll plane was analyzed to examine motion in the plane of the perturbation. Subjects stepped onto the platform with the right foot. Recovery step time and distance were recorded. The first trial was analyzed to capture the novelty of the perturbation. Results indicate a significant difference in footfall distance t=0.004, p<0.05, as well as the speed of foot recovery t=0.001, p<0.05, between natural and perturbed walking. Results indicate that the head t=0.005, p<0.05, and trunk t=0.0001, p<0.05, velocities increase during perturbed compared to natural walking. Older adults place their recovery foot down faster when perturbed to re-establish their base of support. Head and trunk segments are less stable and move with greater velocities to reestablish stability when perturbed.

How does non-linear dynamics affect the baryon acoustic oscillation?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugiyama, Naonori S.; Spergel, David N., E-mail: nao.s.sugiyama@gmail.com, E-mail: dns@astro.princeton.edu

2014-02-01

We study the non-linear behavior of the baryon acoustic oscillation in the power spectrum and the correlation function by decomposing the dark matter perturbations into the short- and long-wavelength modes. The evolution of the dark matter fluctuations can be described as a global coordinate transformation caused by the long-wavelength displacement vector acting on short-wavelength matter perturbation undergoing non-linear growth. Using this feature, we investigate the well known cancellation of the high-k solutions in the standard perturbation theory. While the standard perturbation theory naturally satisfies the cancellation of the high-k solutions, some of the recently proposed improved perturbation theories do notmore » guarantee the cancellation. We show that this cancellation clarifies the success of the standard perturbation theory at the 2-loop order in describing the amplitude of the non-linear power spectrum even at high-k regions. We propose an extension of the standard 2-loop level perturbation theory model of the non-linear power spectrum that more accurately models the non-linear evolution of the baryon acoustic oscillation than the standard perturbation theory. The model consists of simple and intuitive parts: the non-linear evolution of the smoothed power spectrum without the baryon acoustic oscillations and the non-linear evolution of the baryon acoustic oscillations due to the large-scale velocity of dark matter and due to the gravitational attraction between dark matter particles. Our extended model predicts the smoothing parameter of the baryon acoustic oscillation peak at z = 0.35 as ∼ 7.7Mpc/h and describes the small non-linear shift in the peak position due to the galaxy random motions.« less

The Kaon B-parameter in mixed action chiral perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aubin, C.; /Columbia U.; Laiho, Jack

2006-09-01

We calculate the kaon B-parameter, B{sub K}, in chiral perturbation theory for a partially quenched, mixed action theory with Ginsparg-Wilson valence quarks and staggered sea quarks. We find that the resulting expression is similar to that in the continuum, and in fact has only two additional unknown parameters. At one-loop order, taste-symmetry violations in the staggered sea sector only contribute to flavor-disconnected diagrams by generating an {Omicron}(a{sup 2}) shift to the masses of taste-singlet sea-sea mesons. Lattice discretization errors also give rise to an analytic term which shifts the tree-level value of B{sub K} by an amount of {Omicron}(a{sup 2}).more » This term, however, is not strictly due to taste-breaking, and is therefore also present in the expression for B{sub K} for pure G-W lattice fermions. We also present a numerical study of the mixed B{sub K} expression in order to demonstrate that both discretization errors and finite volume effects are small and under control on the MILC improved staggered lattices.« less

Kaon B-parameter in mixed action chiral perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aubin, C.; Laiho, Jack; Water, Ruth S. van de

2007-02-01

We calculate the kaon B-parameter, B{sub K}, in chiral perturbation theory for a partially quenched, mixed-action theory with Ginsparg-Wilson valence quarks and staggered sea quarks. We find that the resulting expression is similar to that in the continuum, and in fact has only two additional unknown parameters. At 1-loop order, taste-symmetry violations in the staggered sea sector only contribute to flavor-disconnected diagrams by generating an O(a{sup 2}) shift to the masses of taste-singlet sea-sea mesons. Lattice discretization errors also give rise to an analytic term which shifts the tree-level value of B{sub K} by an amount of O(a{sup 2}). Thismore » term, however, is not strictly due to taste breaking, and is therefore also present in the expression for B{sub K} for pure Ginsparg-Wilson lattice fermions. We also present a numerical study of the mixed B{sub K} expression in order to demonstrate that both discretization errors and finite volume effects are small and under control on the MILC improved staggered lattices.« less

Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2007-08-07

Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

Model with two periods of inflation

NASA Astrophysics Data System (ADS)

Schettler, Simon; Schaffner-Bielich, Jürgen

2016-01-01

A scenario with two subsequent periods of inflationary expansion in the very early Universe is examined. The model is based on a potential motivated by symmetries being found in field theory at high energy. For various parameter sets of the potential, the spectra of scalar and tensor perturbations that are expected to originate from this scenario are calculated. Also the beginning of the reheating epoch connecting the second inflation with thermal equilibrium is studied. Perturbations with wavelengths leaving the horizon around the transition between the two inflations are special: It is demonstrated that the power spectrum at such scales deviates significantly from expectations based on measurements of the cosmic microwave background. This supports the conclusion that parameters for which this part of the spectrum leaves observable traces in the cosmic microwave background must be excluded. Parameters entailing a very efficient second inflation correspond to standard small-field inflation and can meet observational constraints. Particular attention is paid to the case where the second inflation leads solely to a shift of the observable spectrum from the first inflation. A viable scenario requires this shift to be small.

Femtosecond time-resolved vibrational SFG spectroscopy of CO/Ru( 0 0 1 )

NASA Astrophysics Data System (ADS)

Hess, Ch.; Wolf, M.; Roke, S.; Bonn, M.

2002-04-01

Vibrational sum-frequency generation (SFG) employing femtosecond infrared (IR) laser pulses is used to study the dynamics of the C-O stretch vibration on Ru(0 0 1). Time-resolved measurements of the free induction decay (FID) of the IR-polarization for 0.33 ML CO/Ru(0 0 1) exhibit single exponential decays over three decades corresponding to dephasing times of T2=1.94 ps at 95 K and T2=1.16 ps at 340 K. This is consistent with pure homogeneous broadening due to anharmonic coupling with the thermally activated low-frequency dephasing mode together with a contribution from saturation of the IR transition. In pump-probe SFG experiments using a strong visible (VIS) pump pulse the perturbation of the FID leads to transient line shifts even at negative delay times, i.e. when the IR-VIS SFG probe pair precedes the pump pulse. Based on an analysis of the time-dependent polarization we discuss the influence of the perturbed FID on time-resolved SFG spectra. We investigate how coherent effects affect the SFG spectra and we examine the time resolution in these experiments, in particular in dependence of the dephasing time.

Preheating after multifield inflation with nonminimal couplings. III. Dynamical spacetime results

NASA Astrophysics Data System (ADS)

DeCross, Matthew P.; Kaiser, David I.; Prabhu, Anirudh; Prescod-Weinstein, Chanda; Sfakianakis, Evangelos I.

2018-01-01

This paper concludes our semianalytic study of preheating in inflationary models comprised of multiple scalar fields coupled nonminimally to gravity. Using the covariant framework of paper I in this series, we extend the rigid-spacetime results of paper II by considering both the expansion of the Universe during preheating, as well as the effect of the coupled metric perturbations on particle production. The adiabatic and isocurvature perturbations are governed by different effective masses that scale differently with the nonminimal couplings and evolve differently in time. The effective mass for the adiabatic modes is dominated by contributions from the coupled metric perturbations immediately after inflation. The metric perturbations contribute an oscillating tachyonic term that enhances an early period of significant particle production for the adiabatic modes, which ceases on a time scale governed by the nonminimal couplings ξI . The effective mass of the isocurvature perturbations, on the other hand, is dominated by contributions from the fields' potential and from the curvature of the field-space manifold (in the Einstein frame), the balance between which shifts on a time scale governed by ξI. As in papers I and II, we identify distinct behavior depending on whether the nonminimal couplings are small [ξI≲O (1 ) ], intermediate [ξI˜O (1 -10 ) ], or large (ξI≥100 ).

Sensitivity of shock boundary-layer interactions to weak geometric perturbations

NASA Astrophysics Data System (ADS)

Kim, Ji Hoon; Eaton, John K.

2016-11-01

Shock-boundary layer interactions can be sensitive to small changes in the inlet flow and boundary conditions. Robust computational models must capture this sensitivity, and validation of such models requires a suitable experimental database with well-defined inlet and boundary conditions. To that end, the purpose of this experiment is to systematically document the effects of small geometric perturbations on a SBLI flow to investigate the flow physics and establish an experimental dataset tailored for CFD validation. The facility used is a Mach 2.1, continuous operation wind tunnel. The SBLI is generated using a compression wedge; the region of interest is the resulting reflected shock SBLI. The geometric perturbations, which are small spanwise rectangular prisms, are introduced ahead of the compression ramp on the opposite wall. PIV is used to study the SBLI for 40 different perturbation geometries. Results show that the dominant effect of the perturbations is a global shift of the SBLI itself. In addition, the bumps introduce weaker shocks of varying strength and angles, depending on the bump height and location. Various scalar validation metrics, including a measure of shock unsteadiness, and their uncertainties are also computed to better facilitate CFD validation. Ji Hoon Kim is supported by an OTR Stanford Graduate Fellowship.

Vocalization-Induced Enhancement of the Auditory Cortex Responsiveness during Voice F0 Feedback Perturbation

PubMed Central

Behroozmand, Roozbeh; Karvelis, Laura; Liu, Hanjun; Larson, Charles R.

2009-01-01

Objective The present study investigated whether self-vocalization enhances auditory neural responsiveness to voice pitch feedback perturbation and how this vocalization-induced neural modulation can be affected by the extent of the feedback deviation. Method Event related potentials (ERPs) were recorded in 15 subjects in response to +100, +200 and +500 cents pitch-shifted voice auditory feedback during active vocalization and passive listening to the playback of the self-produced vocalizations. Result The amplitude of the evoked P1 (latency: 73.51 ms) and P2 (latency: 199.55 ms) ERP components in response to feedback perturbation were significantly larger during vocalization than listening. The difference between P2 peak amplitudes during vocalization vs. listening was shown to be significantly larger for +100 than +500 cents stimulus. Conclusion Results indicate that the human auditory cortex is more responsive to voice F0 feedback perturbations during vocalization than passive listening. Greater vocalization-induced enhancement of the auditory responsiveness to smaller feedback perturbations may imply that the audio-vocal system detects and corrects for errors in vocal production that closely match the expected vocal output. Significance Findings of this study support previous suggestions regarding the enhanced auditory sensitivity to feedback alterations during self-vocalization, which may serve the purpose of feedback-based monitoring of one’s voice. PMID:19520602

Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories

PubMed Central

Kubicek, Andreas; Muhando, Christopher; Reuter, Hauke

2012-01-01

Tropical coral reefs feature extraordinary biodiversity and high productivity rates in oligotrophic waters. Due to increasing frequencies of perturbations – anthropogenic and natural – many reefs are under threat. Such perturbations often have devastating effects on these unique ecosystems and especially if they occur simultaneously and amplify each other's impact, they might trigger a phase shift and create irreversible conditions. We developed a generic, spatially explicit, individual-based model in which competition drives the dynamics of a virtual benthic reef community – comprised of scleractinian corals and algae – under different environmental settings. Higher system properties, like population dynamics or community composition arise through self-organization as emergent properties. The model was parameterized for a typical coral reef site at Zanzibar, Tanzania and features coral bleaching and physical disturbance regimes as major sources of perturbations. Our results show that various types and modes (intensities and frequencies) of perturbations create diverse outcomes and that the switch from high diversity to single species dominance can be evoked by small changes in a key parameter. Here we extend the understanding of coral reef resilience and the identification of key processes, drivers and respective thresholds, responsible for changes in local situations. One future goal is to provide a tool which may aid decision making processes in management of coral reefs. PMID:23209397

Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling

NASA Astrophysics Data System (ADS)

Núñez, M.; Robie, T.; Vlachos, D. G.

2017-10-01

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

High Resolution Infrared Studies of the v2, v4 Bands of 34S16O3, Including Both Intensity and Wavenumber Perturbations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barber, Jeffrey B.; Masiello, Tony; Chrysostom, Engelene

2003-06-15

The infrared spectrum of the v2, v4 bending mode region of 34S-substituted sulfur trioxide, 34S16O3, has been recorded at a resolution of 0.0025 cm-1. The v2 and v4 levels are coupled by a Coriolis interaction, yielding significant spectral shifts that have been successfully analyzed to obtain rovibrational constants for the ground state and both fundamentals. Comparisons are made with 32S16O3 parameters and the Bo rotational constant is found to be 0.348 556 04(28) cm-1, only very slightly larger than the corresponding value of 0.348 543 33(5) cm-1 for 32S16O3. Coriolis and l-type resonance interactions between the v2 and v4 levelsmore » produce frequency shifts and strong intensity perturbations in the spectra that are considered for both 34S16O3 and 32S16O3. The resulting analysis yields an average value of+0.62(8) for the dipole derivative ratio (?x/?Q4x) (?z/?Q2) and a positive sign for the product of this ratio with the?y2,4 Coriolis constant, for which experiment gives+0.5940(15) . Ab initio calculations indicate that the signs of?x/?Q4x and?z/?Q2 are both positive and hence?y2,4 is also positive, in agreement with earlier calculations. These signs indicate that the effective charge movement in the xz plane has the same sense of rotation as Q2, Q4x atom motion in this plane that produces a py vibrational angular momentum component, correlated motion that is confirmed by ab initio calculations.« less

Phase correction, phase resetting, and phase shifts after subliminal timing perturbations in sensorimotor synchronization.

PubMed

Repp, B H

2001-06-01

Recent studies of synchronized finger tapping have shown that perceptually subliminal phase shifts in an auditory sequence are rapidly compensated for in the motor activity (B. H. Repp, 2000a). Experiment 1 used a continuation-tapping task to confirm that this compensation is indeed a phase correction, not an adjustment of the central timekeeper period. Experiments 2-5 revealed that this phase correction occurs even when there is no ordinary sensorimotor asynchrony--when the finger taps are in antiphase or arbitrary phase relative to the auditory sequence (Experiments 2 and 3) or when the tap coinciding with the sequence phase shift is withheld (Experiments 4 and 5). The phase correction observed in the latter conditions was instantaneous, which suggests that phase resetting occurs when the motor activity is discontinuous. A prolonged phase shift suggestive of overcompensation was observed in some conditions, which poses a challenge to pure phase correction models.

Helioseismology of a Realistic Magnetoconvective Sunspot Simulation

NASA Technical Reports Server (NTRS)

Braun, D. C.; Birch, A. C.; Rempel, M.; Duvall, T. L., Jr.

2012-01-01

We compare helioseismic travel-time shifts measured from a realistic magnetoconvective sunspot simulation using both helioseismic holography and time-distance helioseismology, and measured from real sunspots observed with the Helioseismic and Magnetic Imager instrument on board the Solar Dynamics Observatory and the Michelson Doppler Imager instrument on board the Solar and Heliospheric Observatory. We find remarkable similarities in the travel-time shifts measured between the methodologies applied and between the simulated and real sunspots. Forward modeling of the travel-time shifts using either Born or ray approximation kernels and the sound-speed perturbations present in the simulation indicates major disagreements with the measured travel-time shifts. These findings do not substantially change with the application of a correction for the reduction of wave amplitudes in the simulated and real sunspots. Overall, our findings demonstrate the need for new methods for inferring the subsurface structure of sunspots through helioseismic inversions.

Southern ocean winds during past (and future) warm periods and their affect on Agulhas Leakage and the Atlantic Merdional Overturning Circulation

NASA Astrophysics Data System (ADS)

Patel, N. P.; Deconto, R. M.; Condron, A.

2013-12-01

The leakage of Agulhas Current water into the South Atlantic is now thought to be a major player in global climate change. The volume of Agulhas Leakage is linked to the strength and position of southern westerlies. Past changes in the westerly winds over the southern ocean have been noted on glacial-interglacial timescales, in response to both Northern Hemispheric conditions and more proximal changes in Antarctic ice volume. Over recent decades, a southward shift in the southern ocean westerlies has been observed and is expected to continue with projected climate warming. The resulting increase in Agulhas Leakage is thought to allow more warm, salty water from the Indian Ocean into the Atlantic, with the potential to impact the Atlantic Meridional Overturning circulation (AMOC). Some climate models have predicted global warming will result in a slowdown and weakening of the AMOC. A strengthening of the Agulhas Leakage therefore has the potential to counteract that slowdown. Much of the Agulhas leakage is carried in small eddies rotating off the main flow south of Cape Horn. High ocean model resolution (< 1/2°) is therefore required to simulate their response to the overlying wind field. However the majority of previous model studies have been too coarse in resolution to quantify the link between the Agulhas Leakage the AMOC. Here we run a series of global high-resolution ocean model (1/6°) experiments using the MITgcm to test the effect of a shift in the southern hemisphere westerlies on the Agulhas Leakage. A prescribed perturbation of the winds near South Africa shows a significant increase in Agulhas eddies into the Atlantic. Following this, we have conducted longer simulations with the winds over the Southern Ocean perturbed to reflect both past and possible future shifts in the wind field to quantify changes in North Atlantic Deep Water formation and the overall response of the AMOC to this perturbation.

Long adaptation reveals mostly attractive shifts of orientation tuning in cat primary visual cortex.

PubMed

Ghisovan, N; Nemri, A; Shumikhina, S; Molotchnikoff, S

2009-12-15

In the adult brain, sensory cortical neurons undergo transient changes of their response properties following prolonged exposure to an appropriate stimulus (adaptation). In cat V1, orientation-selective cells shift their preferred orientation after being adapted to a non-preferred orientation. There are conflicting reports as to the direction of those shifts, towards (attractive) or away (repulsive) from the adapter. Moreover, the mechanisms underlying attractive shifts remain unexplained. In the present investigation we show that attractive shifts are the most frequent outcome of a 12 min adaptation. Overall, cells displaying selectivity for oblique orientations exhibit significantly larger shifts than cells tuned to cardinal orientations. In addition, cells selective to cardinal orientations had larger shift amplitudes when the absolute difference between the original preferred orientation and the adapting orientation increased. Conversely, cells tuned to oblique orientations exhibited larger shift amplitudes when this absolute orientation difference was narrower. Hence, neurons tuned to oblique contours appear to show more plasticity in response to small perturbations. Two different mechanisms appear to produce attractive and repulsive orientation shifts. Attractive shifts result from concurrent response depression on the non-adapted flank and selective response facilitation on the adapted flank of the orientation tuning curve. In contrast, repulsive shifts are caused solely by response depression on the adapted flank. We suggest that an early mechanism leads to repulsive shifts while attractive shifts engage a subsequent late facilitation. A potential role for attractive shifts may be improved stimulus discrimination around the adapting orientation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Junkel, G. C.; Gunderson, M. A.; Hooper, C. F.

Recently, there has been growing experimental evidence for redshifts in line spectra from highly ionized, high-Z radiators immersed in hot, dense plasmas [O. Renner , J. Quant. Spectrosc. Radiat. Transf. 58, 851 (1997); C. F. Hooper , in Strongly Coupled Coulomb Systems (Plenum, New York, 1998); N. C. Woolsey , J. Quant. Spectrosc. Radiat. Transf. 65, 573 (2000); A. Saemann , Phys. Rev. Lett. 82, 4843 (1999)]. A full Coulomb, multielectron formalism of line broadening due to perturbation by plasma electrons will be presented. A red line shift and asymmetries arise naturally from employing a full Coulomb expression for themore » perturber-radiator interaction, rather than applying the dipole approximation. This formalism can now be applied to arbitrary multielectron radiating ions.« less

Resilience and tipping points of an exploited fish population over six decades.

PubMed

Vasilakopoulos, Paraskevas; Marshall, C Tara

2015-05-01

Complex natural systems with eroded resilience, such as populations, ecosystems and socio-ecological systems, respond to small perturbations with abrupt, discontinuous state shifts, or critical transitions. Theory of critical transitions suggests that such systems exhibit fold bifurcations featuring folded response curves, tipping points and alternate attractors. However, there is little empirical evidence of fold bifurcations occurring in actual complex natural systems impacted by multiple stressors. Moreover, resilience of complex systems to change currently lacks clear operational measures with generic application. Here, we provide empirical evidence for the occurrence of a fold bifurcation in an exploited fish population and introduce a generic measure of ecological resilience based on the observed fold bifurcation attributes. We analyse the multivariate development of Barents Sea cod (Gadus morhua), which is currently the world's largest cod stock, over six decades (1949-2009), and identify a population state shift in 1981. By plotting a multivariate population index against a multivariate stressor index, the shift mechanism was revealed suggesting that the observed population shift was a nonlinear response to the combined effects of overfishing and climate change. Annual resilience values were estimated based on the position of each year in relation to the fitted attractors and assumed tipping points of the fold bifurcation. By interpolating the annual resilience values, a folded stability landscape was fit, which was shaped as predicted by theory. The resilience assessment suggested that the population may be close to another tipping point. This study illustrates how a multivariate analysis, supported by theory of critical transitions and accompanied by a quantitative resilience assessment, can clarify shift mechanisms in data-rich complex natural systems. © 2014 John Wiley & Sons Ltd.

Perturbative studies of toroidal momentum transport in KSTAR H-mode and the effect of ion temperature perturbation

NASA Astrophysics Data System (ADS)

Yang, S. M.; Na, Yong-Su; Na, D. H.; Park, J.-K.; Shi, Y. J.; Ko, W. H.; Lee, S. G.; Hahm, T. S.

2018-06-01

Perturbative experiments have been carried out using tangential neutral beam injection (NBI) and non-resonant magnetic perturbation (NRMP) to analyze the momentum transport properties in KSTAR H-modes. Diffusive and non-diffusive terms of momentum transport are evaluated from the transient analysis. Although the operating conditions and methodologies applied in the two cases are similar, the momentum transport properties obtained show clear differences. The estimated momentum diffusivity and pinch obtained in the NBI modulation experiments is larger than that in the NRMP modulation experiments. We found that this discrepancy could be a result of uncertainties in the assumption for the analysis. By introducing time varying momentum transport coefficients depending on the temperature gradient, the linearized equation shows that if the temperature perturbation exists, the evolution of toroidal rotation perturbation could be faster than the transport rate of mean quantity, since the evolution of toroidal rotation perturbation is related to , a momentum diffusivity from perturbative analysis. This could explain the estimated higher momentum diffusivity using time independent transport coefficients in NBI experiments with higher ion temperature perturbation compared to that in NRMP modulation experiments. The differences in the momentum transport coefficient with NRMP and NBI are much reduced by considering time varying momentum transport coefficients in the time dependent transport simulation.

Definition of Shifts of Optical Transitions Frequencies due to Pulse Perturbation Action by the Photon Echo Signal Form

NASA Astrophysics Data System (ADS)

Lisin, V. N.; Shegeda, A. M.; Samartsev, V. V.

2015-09-01

A relative phase shift between the different groups of excited dipoles, which appears as result of its frequency splitting due to action of a pulse of electric or magnetic fields, depends on a time, if the pulse overlaps in time with echo-pulse. As а consequence, the echo waveform is changed. The echo time form is modulated. The inverse modulation period well enough approximates Zeeman and pseudo-Stark splitting in the cases of magnetic and, therefore, electrical fields. Thus the g-factors of ground 4I15/2 and excited 4F9/2 optical states of Er3+ ion in LuLiF4 and YLiF4 have been measured and pseudo-Stark shift of R1 line in ruby has been determined.

Singularity perturbed zero dynamics of nonlinear systems

NASA Technical Reports Server (NTRS)

Isidori, A.; Sastry, S. S.; Kokotovic, P. V.; Byrnes, C. I.

1992-01-01

Stability properties of zero dynamics are among the crucial input-output properties of both linear and nonlinear systems. Unstable, or 'nonminimum phase', zero dynamics are a major obstacle to input-output linearization and high-gain designs. An analysis of the effects of regular perturbations in system equations on zero dynamics shows that whenever a perturbation decreases the system's relative degree, it manifests itself as a singular perturbation of zero dynamics. Conditions are given under which the zero dynamics evolve in two timescales characteristic of a standard singular perturbation form that allows a separate analysis of slow and fast parts of the zero dynamics.

Process for computing geometric perturbations for probabilistic analysis

DOEpatents

Fitch, Simeon H. K. [Charlottesville, VA; Riha, David S [San Antonio, TX; Thacker, Ben H [San Antonio, TX

2012-04-10

A method for computing geometric perturbations for probabilistic analysis. The probabilistic analysis is based on finite element modeling, in which uncertainties in the modeled system are represented by changes in the nominal geometry of the model, referred to as "perturbations". These changes are accomplished using displacement vectors, which are computed for each node of a region of interest and are based on mean-value coordinate calculations.

Sensory-motor interactions for vocal pitch monitoring in non-primary human auditory cortex.

PubMed

Greenlee, Jeremy D W; Behroozmand, Roozbeh; Larson, Charles R; Jackson, Adam W; Chen, Fangxiang; Hansen, Daniel R; Oya, Hiroyuki; Kawasaki, Hiroto; Howard, Matthew A

2013-01-01

The neural mechanisms underlying processing of auditory feedback during self-vocalization are poorly understood. One technique used to study the role of auditory feedback involves shifting the pitch of the feedback that a speaker receives, known as pitch-shifted feedback. We utilized a pitch shift self-vocalization and playback paradigm to investigate the underlying neural mechanisms of audio-vocal interaction. High-resolution electrocorticography (ECoG) signals were recorded directly from auditory cortex of 10 human subjects while they vocalized and received brief downward (-100 cents) pitch perturbations in their voice auditory feedback (speaking task). ECoG was also recorded when subjects passively listened to playback of their own pitch-shifted vocalizations. Feedback pitch perturbations elicited average evoked potential (AEP) and event-related band power (ERBP) responses, primarily in the high gamma (70-150 Hz) range, in focal areas of non-primary auditory cortex on superior temporal gyrus (STG). The AEPs and high gamma responses were both modulated by speaking compared with playback in a subset of STG contacts. From these contacts, a majority showed significant enhancement of high gamma power and AEP responses during speaking while the remaining contacts showed attenuated response amplitudes. The speaking-induced enhancement effect suggests that engaging the vocal motor system can modulate auditory cortical processing of self-produced sounds in such a way as to increase neural sensitivity for feedback pitch error detection. It is likely that mechanisms such as efference copies may be involved in this process, and modulation of AEP and high gamma responses imply that such modulatory effects may affect different cortical generators within distinctive functional networks that drive voice production and control.

Sensory-Motor Interactions for Vocal Pitch Monitoring in Non-Primary Human Auditory Cortex

PubMed Central

Larson, Charles R.; Jackson, Adam W.; Chen, Fangxiang; Hansen, Daniel R.; Oya, Hiroyuki; Kawasaki, Hiroto; Howard, Matthew A.

2013-01-01

The neural mechanisms underlying processing of auditory feedback during self-vocalization are poorly understood. One technique used to study the role of auditory feedback involves shifting the pitch of the feedback that a speaker receives, known as pitch-shifted feedback. We utilized a pitch shift self-vocalization and playback paradigm to investigate the underlying neural mechanisms of audio-vocal interaction. High-resolution electrocorticography (ECoG) signals were recorded directly from auditory cortex of 10 human subjects while they vocalized and received brief downward (−100 cents) pitch perturbations in their voice auditory feedback (speaking task). ECoG was also recorded when subjects passively listened to playback of their own pitch-shifted vocalizations. Feedback pitch perturbations elicited average evoked potential (AEP) and event-related band power (ERBP) responses, primarily in the high gamma (70–150 Hz) range, in focal areas of non-primary auditory cortex on superior temporal gyrus (STG). The AEPs and high gamma responses were both modulated by speaking compared with playback in a subset of STG contacts. From these contacts, a majority showed significant enhancement of high gamma power and AEP responses during speaking while the remaining contacts showed attenuated response amplitudes. The speaking-induced enhancement effect suggests that engaging the vocal motor system can modulate auditory cortical processing of self-produced sounds in such a way as to increase neural sensitivity for feedback pitch error detection. It is likely that mechanisms such as efference copies may be involved in this process, and modulation of AEP and high gamma responses imply that such modulatory effects may affect different cortical generators within distinctive functional networks that drive voice production and control. PMID:23577157

An analysis of the expected eccentricity perturbations for the second Radio Astronomy Explorer (RAE B)

NASA Technical Reports Server (NTRS)

Murphy, J. P.

1972-01-01

Analytical prediction of expected eccentricity perturbations for the RAE 2 lunar orbit shows that the eccentricity will grow linearly in time. Parametric inclination studies and analysis of perturbation equations establish a critical retrograde inclination of 116.565 at which the positive perturbation slope vanishes for a circular orbit about 1100 m above the lunar surface with an eccentricity constraint of less than 0.005 during a period of about one year.

Theory of injection locking and rapid start-up of magnetrons, and effects of manufacturing errors in terahertz traveling wave tubes

NASA Astrophysics Data System (ADS)

Pengvanich, Phongphaeth

In this thesis, several contemporary issues on coherent radiation sources are examined. They include the fast startup and the injection locking of microwave magnetrons, and the effects of random manufacturing errors on phase and small signal gain of terahertz traveling wave amplifiers. In response to the rapid startup and low noise magnetron experiments performed at the University of Michigan that employed periodic azimuthal perturbations in the axial magnetic field, a systematic study of single particle orbits is performed for a crossed electric and periodic magnetic field. A parametric instability in the orbits, which brings a fraction of the electrons from the cathode toward the anode, is discovered. This offers an explanation of the rapid startup observed in the experiments. A phase-locking model has been constructed from circuit theory to qualitatively explain various regimes observed in kilowatt magnetron injection-locking experiments, which were performed at the University of Michigan. These experiments utilize two continuous-wave magnetrons; one functions as an oscillator and the other as a driver. Time and frequency domain solutions are developed from the model, allowing investigations into growth, saturation, and frequency response of the output. The model qualitatively recovers many of the phase-locking frequency characteristics observed in the experiments. Effects of frequency chirp and frequency perturbation on the phase and lockability have also been quantified. Development of traveling wave amplifier operating at terahertz is a subject of current interest. The small circuit size has prompted a statistical analysis of the effects of random fabrication errors on phase and small signal gain of these amplifiers. The small signal theory is treated with a continuum model in which the electron beam is monoenergetic. Circuit perturbations that vary randomly along the beam axis are introduced through the dimensionless Pierce parameters describing the beam-wave velocity mismatch (b), the gain parameter (C), and the cold tube circuit loss ( d). Our study shows that perturbation in b dominates the other two in terms of power gain and phase shift. Extensive data show that standard deviation of the output phase is linearly proportional to standard deviation of the individual perturbations in b, C and d.

Invisible Electronic States and Their Dynamics Revealed by Perturbations

NASA Astrophysics Data System (ADS)

Merer, Anthony J.

2011-06-01

Sooner or later everyone working in the field of spectroscopy encounters perturbations. These can range in size from a small shift of a single rotational level to total destruction of the vibrational and rotational patterns of an electronic state. To some workers perturbations are a source of terror, but to others they are the most fascinating features of molecular spectra, because they give information about molecular dynamics, and about states that would otherwise be invisible as a result of unfavorable selection rules. An example of the latter is the essentially complete characterization of the tilde{b}^3A_2 state of SO_2 from the vibronic perturbations it causes in the tilde{a}^3B_1 state. The S_1-trans state of acetylene is a beautiful example of dynamics in action. The level patterns of the three bending vibrations change dramatically with increasing vibrational excitation as a result of the vibrational angular momentum and the approach to the isomerization barrier. Several vibrational levels of the S_1-cis isomer, previously thought to be unobservable, can now be assigned. They obtain their intensity through interactions with nearby levels of the trans isomer.

Retrospective qualitative analysis of ecological networks under environmental perturbation: a copper-polluted intertidal community as a case study.

PubMed

Ramos-Jiliberto, Rodrigo; Garay-Narváez, Leslie; Medina, Matías H

2012-01-01

The coast of Chañaral Bay in northern Chile has been affected by copper mine wastes for decades. This sustained perturbation has disrupted the intertidal community in several ways, but the mechanisms behind the observed shifts in local biodiversity remain poorly understood. Our main goal was to identify the species (lumped into trophic groups) belonging to the Chañaral intertidal community that, being directly affected by copper pollution, contributed primarily to the generation of the observed changes in community structure. These groups of species were called initiators. We applied a qualitative modelling approach based only on the sign and direction of effects among species, and present a formula for predicting changes in equilibrium abundances considering stress on multiple variables simultaneously. We then applied this technique retrospectively to identify the most likely set of initiators. Our analyses allowed identification of a unique set of four initiators in the studied intertidal system (a group of algae, sessile invertebrates, a group of herbivores and starfish), which were hypothesized to be the primary drivers of the observed changes in community structure. In addition, a hypothesis was derived about how the perturbation affected these initiators. The hypothesis is that pollution affected negatively the population growth rate of both algae and sessile invertebrates and suppressed the interaction between herbivores and starfish. Our analytic approach, focused on identifying initiators, constitutes an advance towards understanding the mechanisms underlying human-driven ecosystem disruption and permits identifying species that may serve as a focal point for community management and restoration.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Staten, Paul; Reichler, Thomas; Lu, Jian

Tropospheric circulation shifts have strong potential to impact surface climate. But the magnitude of these shifts in a changing climate, and the attending regional hydrological changes, are difficult to project. Part of this difficulty arises from our lack of understanding of the physical mechanisms behind the circulation shifts themselves. In order to better delineate circulation shifts and their respective causes, we decompose the circulation response into (1) the "direct" response to radiative forcings themselves, and (2) the "indirect" response to changing sea surface temperatures. Using ensembles of 90-day climate model simulations with immediate switch-on forcings, including perturbed greenhouse gas concentrations,more » stratospheric ozone concentrations, and sea surface temperatures, we document the direct and indirect transient responses of the zonal mean general circulation, and investigate the roles of previously proposed mechanisms in shifting the midlatitude jet. We find that both the direct and indirect wind responses often begin in the lower stratosphere. Changes in midlatitude eddies are ubiquitous and synchronous with the midlatitude zonal wind response. Shifts in the critical latitude of wave absorption on either flank of the jet are not indicted as primary factors for the poleward shifting jet, although we see some evidence for increasing equatorward wave reflection over the southern hemisphere in response to sea surface warming. Mechanisms for the northern hemisphere jet shift are less clear.« less

Excitability in chemical and biochemical pH-autocatalytic systems.

PubMed

Zagora, J; Voslar, M; Schreiberová, L; Schreiber, I

2001-01-01

Using two different kinds of pH systems--the papain catalyzed hydrolysis of N-benzoyl-L-arginine ethyl ester in a membrane reactor and the bromate-sulfite-ferrocyanide (BSF) reaction in the CSTR--we study the relation among excitability, oscillations and bistability, and the ability of the system to respond to external periodic perturbations. Excitable properties of dynamical systems are examined in terms of a threshold set which is used to characterise dynamics in the reactor subject to external periodic stimuli. A precise definition and a method of calculating the threshold set are formulated. Two kinds of excitability distinguished by either direct or indirect initiation of the activatory process are found in both pH systems. Periodic pulsed perturbations of the BSF system display a nontrivial dependence of an excitation number on the forcing period. We examined this system also in oscillatory mode by looking at the phase shifts caused by single-pulse perturbations and constructing the phase transition curves (PTCs).

Ideal plasma response to vacuum magnetic fields with resonant magnetic perturbations in non-axisymmetric tokamaks

DOE PAGES

Kim, Kimin; Ahn, J. -W.; Scotti, F.; ...

2015-09-03

Ideal plasma shielding and amplification of resonant magnetic perturbations in non-axisymmetric tokamak is presented by field line tracing simulation with full ideal plasma response, compared to measurements of divertor lobe structures. Magnetic field line tracing simulations in NSTX with toroidal non-axisymmetry indicate the ideal plasma response can significantly shield/amplify and phase shift the vacuum resonant magnetic perturbations. Ideal plasma shielding for n = 3 mode is found to prevent magnetic islands from opening as consistently shown in the field line connection length profile and magnetic footprints on the divertor target. It is also found that the ideal plasma shielding modifiesmore » the degree of stochasticity but does not change the overall helical lobe structures of the vacuum field for n = 3. Furthermore, amplification of vacuum fields by the ideal plasma response is predicted for low toroidal mode n = 1, better reproducing measurements of strong striation of the field lines on the divertor plate in NSTX.« less

Dispersion relations for $$\\eta '\\rightarrow \\eta \\pi \\pi $$

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isken, Tobias; Kubis, Bastian; Schneider, Sebastian P.

Here, we present a dispersive analysis of the decay amplitude for η' → ηππ that is based on the fundamental principles of analyticity and unitarity. In this framework, final-state interactions are fully taken into account. Our dispersive representation relies only on input for the ππ and πη scattering phase shifts. Isospin symmetry allows us to describe both the charged and neutral decay channel in terms of the same function. The dispersion relation contains subtraction constants that cannot be fixed by unitarity.We determine these parameters by a fit to Dalitz-plot data from the VES and BES-III experiments. We study the predictionmore » of a low-energy theorem and compare the dispersive fit to variants of chiral perturbation theory.« less

NMR backbone assignments of the tyrosine kinase domain of human fibroblast growth factor receptor 3 in apo state and in complex with inhibitor PD173074.

PubMed

Sanfelice, Domenico; Koss, Hans; Bunney, Tom D; Thompson, Gary S; Farrell, Brendan; Katan, Matilda; Breeze, Alexander L

2018-03-26

Fibroblast growth factors receptors (FGFR) are transmembrane protein tyrosine kinases involved in many cellular process, including growth, differentiation and angiogenesis. Dysregulation of FGFR enzymatic activity is associated with developmental disorders and cancers; therefore FGFRs have become attractive targets for drug discovery, with a number of agents in late-stage clinical trials. Here, we present the backbone resonance assignments of FGFR3 tyrosine kinase domain in the ligand-free form and in complex with the canonical FGFR kinase inhibitor PD173074. Analysis of chemical shift changes upon inhibitor binding highlights a characteristic pattern of allosteric network perturbations that is of relevance for future drug discovery activities aimed at development of conformationally-selective FGFR inhibitors.

Dispersion relations for $$\\eta '\\rightarrow \\eta \\pi \\pi $$

DOE PAGES

Isken, Tobias; Kubis, Bastian; Schneider, Sebastian P.; ...

2017-07-21

Here, we present a dispersive analysis of the decay amplitude for η' → ηππ that is based on the fundamental principles of analyticity and unitarity. In this framework, final-state interactions are fully taken into account. Our dispersive representation relies only on input for the ππ and πη scattering phase shifts. Isospin symmetry allows us to describe both the charged and neutral decay channel in terms of the same function. The dispersion relation contains subtraction constants that cannot be fixed by unitarity.We determine these parameters by a fit to Dalitz-plot data from the VES and BES-III experiments. We study the predictionmore » of a low-energy theorem and compare the dispersive fit to variants of chiral perturbation theory.« less

Detecting and correcting the bias of unmeasured factors using perturbation analysis: a data-mining approach.

PubMed

Lee, Wen-Chung

2014-02-05

The randomized controlled study is the gold-standard research method in biomedicine. In contrast, the validity of a (nonrandomized) observational study is often questioned because of unknown/unmeasured factors, which may have confounding and/or effect-modifying potential. In this paper, the author proposes a perturbation test to detect the bias of unmeasured factors and a perturbation adjustment to correct for such bias. The proposed method circumvents the problem of measuring unknowns by collecting the perturbations of unmeasured factors instead. Specifically, a perturbation is a variable that is readily available (or can be measured easily) and is potentially associated, though perhaps only very weakly, with unmeasured factors. The author conducted extensive computer simulations to provide a proof of concept. Computer simulations show that, as the number of perturbation variables increases from data mining, the power of the perturbation test increased progressively, up to nearly 100%. In addition, after the perturbation adjustment, the bias decreased progressively, down to nearly 0%. The data-mining perturbation analysis described here is recommended for use in detecting and correcting the bias of unmeasured factors in observational studies.

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

DOE PAGES

Vigneron, Adrien; Alsop, Eric B.; Lomans, Bartholomeus P.; ...

2017-05-19

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of themore » entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.« less

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vigneron, Adrien; Alsop, Eric B.; Lomans, Bartholomeus P.

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of themore » entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.« less

Fluctuating Asymmetry and Environmental Stress: Understanding the Role of Trait History

PubMed Central

De Coster, Greet; Van Dongen, Stefan; Malaki, Phillista; Muchane, Muchai; Alcántara-Exposito, Angelica; Matheve, Hans; Lens, Luc

2013-01-01

While fluctuating asymmetry (FA; small, random deviations from perfect symmetry in bilaterally symmetrical traits) is widely regarded as a proxy for environmental and genetic stress effects, empirical associations between FA and stress are often weak or heterogeneous among traits. A conceptually important source of heterogeneity in relationships with FA is variation in the selection history of the trait(s) under study, i.e. traits that experienced a (recent) history of directional change are predicted to be developmentally less stable, potentially through the loss of canalizing modifiers. Here we applied X-ray photography on museum specimens and live captures to test to what extent the magnitude of FA and FA-stress relationships covary with directional shifts in traits related to the flight apparatus of four East-African rainforest birds that underwent recent shifts in habitat quality and landscape connectivity. Both the magnitude and direction of phenotypic change varied among species, with some traits increasing in size while others decreased or maintained their original size. In three of the four species, traits that underwent larger directional changes were less strongly buffered against random perturbations during their development, and traits that increased in size over time developed more asymmetrically than those that decreased. As we believe that spurious relationships due to biased comparisons of historic (museum specimens) and current (field captures) samples can be ruled out, these results support the largely untested hypothesis that directional shifts may increase the sensitivity of developing traits to random perturbations of environmental or genetic origin. PMID:23472123

Least Squares Moving-Window Spectral Analysis.

PubMed

Lee, Young Jong

2017-08-01

Least squares regression is proposed as a moving-windows method for analysis of a series of spectra acquired as a function of external perturbation. The least squares moving-window (LSMW) method can be considered an extended form of the Savitzky-Golay differentiation for nonuniform perturbation spacing. LSMW is characterized in terms of moving-window size, perturbation spacing type, and intensity noise. Simulation results from LSMW are compared with results from other numerical differentiation methods, such as single-interval differentiation, autocorrelation moving-window, and perturbation correlation moving-window methods. It is demonstrated that this simple LSMW method can be useful for quantitative analysis of nonuniformly spaced spectral data with high frequency noise.

Perturbation Selection and Local Influence Analysis for Nonlinear Structural Equation Model

ERIC Educational Resources Information Center

Chen, Fei; Zhu, Hong-Tu; Lee, Sik-Yum

2009-01-01

Local influence analysis is an important statistical method for studying the sensitivity of a proposed model to model inputs. One of its important issues is related to the appropriate choice of a perturbation vector. In this paper, we develop a general method to select an appropriate perturbation vector and a second-order local influence measure…

Correction factors for ionization chamber measurements with the ‘Valencia’ and ‘large field Valencia’ brachytherapy applicators

NASA Astrophysics Data System (ADS)

Gimenez-Alventosa, V.; Gimenez, V.; Ballester, F.; Vijande, J.; Andreo, P.

2018-06-01

Treatment of small skin lesions using HDR brachytherapy applicators is a widely used technique. The shielded applicators currently available in clinical practice are based on a tungsten-alloy cup that collimates the source-emitted radiation into a small region, hence protecting nearby tissues. The goal of this manuscript is to evaluate the correction factors required for dose measurements with a plane-parallel ionization chamber typically used in clinical brachytherapy for the ‘Valencia’ and ‘large field Valencia’ shielded applicators. Monte Carlo simulations have been performed using the PENELOPE-2014 system to determine the absorbed dose deposited in a water phantom and in the chamber active volume with a Type A uncertainty of the order of 0.1%. The average energies of the photon spectra arriving at the surface of the water phantom differ by approximately 10%, being 384 keV for the ‘Valencia’ and 343 keV for the ‘large field Valencia’. The ionization chamber correction factors have been obtained for both applicators using three methods, their values depending on the applicator being considered. Using a depth-independent global chamber perturbation correction factor and no shift of the effective point of measurement yields depth-dose differences of up to 1% for the ‘Valencia’ applicator. Calculations using a depth-dependent global perturbation factor, or a shift of the effective point of measurement combined with a constant partial perturbation factor, result in differences of about 0.1% for both applicators. The results emphasize the relevance of carrying out detailed Monte Carlo studies for each shielded brachytherapy applicator and ionization chamber.

The screening Horndeski cosmologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starobinsky, Alexei A.; Department of General Relativity and Gravitation, Institute of Physics,Kazan Federal University,Kremlevskaya street 18, 420008 Kazan; Sushkov, Sergey V.

2016-06-06

We present a systematic analysis of homogeneous and isotropic cosmologies in a particular Horndeski model with Galileon shift symmetry, containing also a Λ-term and a matter. The model, sometimes called Fab Five, admits a rich spectrum of solutions. Some of them describe the standard late time cosmological dynamic dominated by the Λ-term and matter, while at the early times the universe expands with a constant Hubble rate determined by the value of the scalar kinetic coupling. For other solutions the Λ-term and matter are screened at all times but there are nevertheless the early and late accelerating phases. The modelmore » also admits bounces, as well as peculiar solutions describing “the emergence of time”. Most of these solutions contain ghosts in the scalar and tensor sectors. However, a careful analysis reveals three different branches of ghost-free solutions, all showing a late time acceleration phase. We analyse the dynamical stability of these solutions and find that all of them are stable in the future, since all their perturbations stay bounded at late times. However, they all turn out to be unstable in the past, as their perturbations grow violently when one approaches the initial spacetime singularity. We therefore conclude that the model has no viable solutions describing the whole of the cosmological history, although it may describe the current acceleration phase. We also check that the flat space solution is ghost-free in the model, but it may acquire ghost in more general versions of the Horndeski theory.« less

The screening Horndeski cosmologies

NASA Astrophysics Data System (ADS)

Starobinsky, Alexei A.; Sushkov, Sergey V.; Volkov, Mikhail S.

2016-06-01

We present a systematic analysis of homogeneous and isotropic cosmologies in a particular Horndeski model with Galileon shift symmetry, containing also a Λ-term and a matter. The model, sometimes called Fab Five, admits a rich spectrum of solutions. Some of them describe the standard late time cosmological dynamic dominated by the Λ-term and matter, while at the early times the universe expands with a constant Hubble rate determined by the value of the scalar kinetic coupling. For other solutions the Λ-term and matter are screened at all times but there are nevertheless the early and late accelerating phases. The model also admits bounces, as well as peculiar solutions describing ``the emergence of time''. Most of these solutions contain ghosts in the scalar and tensor sectors. However, a careful analysis reveals three different branches of ghost-free solutions, all showing a late time acceleration phase. We analyse the dynamical stability of these solutions and find that all of them are stable in the future, since all their perturbations stay bounded at late times. However, they all turn out to be unstable in the past, as their perturbations grow violently when one approaches the initial spacetime singularity. We therefore conclude that the model has no viable solutions describing the whole of the cosmological history, although it may describe the current acceleration phase. We also check that the flat space solution is ghost-free in the model, but it may acquire ghost in more general versions of the Horndeski theory.

Accumulation of peptidyl tRNA is lethal to Escherichia coli.

PubMed Central

Menninger, J R

1979-01-01

A mutant strain of Escherichia coli with temperature-sensitive peptidyl-tRNA hydrolase grows at 30 degrees C but, when shifted to 40 degrees C, dies at rates affected by physiological, pharmacological, and genetical perturbations. The rate of killing correlates with the relative accumulation of peptidyl-tRNA, suggesting that it is responsible for the death of the cells. PMID:368041

Shark tooth weapons from the 19th Century reflect shifting baselines in Central Pacific predator assemblies.

PubMed

Drew, Joshua; Philipp, Christopher; Westneat, Mark W

2013-01-01

The reefs surrounding the Gilbert Islands (Republic of Kiribati, Central Pacific), like many throughout the world, have undergone a period of rapid and intensive environmental perturbation over the past 100 years. A byproduct of this perturbation has been a reduction of the number of shark species present in their waters, even though sharks play an important in the economy and culture of the Gilbertese. Here we examine how shark communities changed over time periods that predate the written record in order to understand the magnitude of ecosystem changes in the Central Pacific. Using a novel data source, the shark tooth weapons of the Gilbertese Islanders housed in natural history museums, we show that two species of shark, the Spot-tail (Carcharhinus sorrah) and the Dusky (C. obscurus), were present in the islands during the last half of the 19(th) century but not reported in any historical literature or contemporary ichthyological surveys of the region. Given the importance of these species to the ecology of the Gilbert Island reefs and to the culture of the Gilbertese people, documenting these shifts in baseline fauna represents an important step toward restoring the vivid splendor of both ecological and cultural diversity.

Light propagation in Swiss-cheese models of random close-packed Szekeres structures: Effects of anisotropy and comparisons with perturbative results

NASA Astrophysics Data System (ADS)

Koksbang, S. M.

2017-03-01

Light propagation in two Swiss-cheese models based on anisotropic Szekeres structures is studied and compared with light propagation in Swiss-cheese models based on the Szekeres models' underlying Lemaitre-Tolman-Bondi models. The study shows that the anisotropy of the Szekeres models has only a small effect on quantities such as redshift-distance relations, projected shear and expansion rate along individual light rays. The average angular diameter distance to the last scattering surface is computed for each model. Contrary to earlier studies, the results obtained here are (mostly) in agreement with perturbative results. In particular, a small negative shift, δ DA≔D/A-DA ,b g DA ,b g , in the angular diameter distance is obtained upon line-of-sight averaging in three of the four models. The results are, however, not statistically significant. In the fourth model, there is a small positive shift which has an especially small statistical significance. The line-of-sight averaged inverse magnification at z =1100 is consistent with 1 to a high level of confidence for all models, indicating that the area of the surface corresponding to z =1100 is close to that of the background.

The use of subionospheric VLF/LF propagation for the study of lower ionospheric perturbations associated with earthquakes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayakawa, M.

It is recently recognized that the ionosphere is very sensitive to seismic effects, and the detection of ionospheric perturbations associated with earthquakes (EQs), attracts a lot of attention as a very promising candidate for short-term EQ prediction. In this review we propose a possible use of VLF/LF (very low frequency (3-30 kHz)/low frequency (30-300 kHz)) radio sounding of seismo-ionospheric perturbations. We first present the first convincing evidence on the presence of ionospheric perturbations for the disastrous Kobe EQ in 1995. The significant shift in terminator times in the VLF/LF diurnal variation, is successfully interpreted in terms of lowering of themore » lower ionosphere prior to the EQ, which is the confirmation of seismo-ionospheric perturbations. In order to avoid the overlapping with my own previous reviews [1, 2], we try to present the latest results including the statistical evidence on the correlation between the VLF/LF propagation anomalies (ionospheric perturbations) and EQs (especially with large magnitude and with shallow depth), a case study on the Indonesia Sumatra EQ (wavelike structures in the VLF/LF data), medium-distance (6{approx}8 Mm) propagation anomalies, the fluctuation spectra of subionospheric VLF/LF data (atmospheric gravity waves effect, the effect of Earth's tides etc.), and the mechanism of lithosphere - atmosphere - ionosphere coupling. Finally, we indicate the present situation of this kind of VLF/LF activities going on in different parts of the globe and we suggest the importance of international collaboration in this seismo-electromagnetics study.« less

Changes in Purkinje cell simple spike encoding of reach kinematics during adaption to a mechanical perturbation.

PubMed

Hewitt, Angela L; Popa, Laurentiu S; Ebner, Timothy J

2015-01-21

The cerebellum is essential in motor learning. At the cellular level, changes occur in both the simple spike and complex spike firing of Purkinje cells. Because simple spike discharge reflects the main output of the cerebellar cortex, changes in simple spike firing likely reflect the contribution of the cerebellum to the adapted behavior. Therefore, we investigated in Rhesus monkeys how the representation of arm kinematics in Purkinje cell simple spike discharge changed during adaptation to mechanical perturbations of reach movements. Monkeys rapidly adapted to a novel assistive or resistive perturbation along the direction of the reach. Adaptation consisted of matching the amplitude and timing of the perturbation to minimize its effect on the reach. In a majority of Purkinje cells, simple spike firing recorded before and during adaptation demonstrated significant changes in position, velocity, and acceleration sensitivity. The timing of the simple spike representations change within individual cells, including shifts in predictive versus feedback signals. At the population level, feedback-based encoding of position increases early in learning and velocity decreases. Both timing changes reverse later in learning. The complex spike discharge was only weakly modulated by the perturbations, demonstrating that the changes in simple spike firing can be independent of climbing fiber input. In summary, we observed extensive alterations in individual Purkinje cell encoding of reach kinematics, although the movements were nearly identical in the baseline and adapted states. Therefore, adaption to mechanical perturbation of a reaching movement is accompanied by widespread modifications in the simple spike encoding. Copyright © 2015 the authors 0270-6474/15/351106-19$15.00/0.

Changes in Purkinje Cell Simple Spike Encoding of Reach Kinematics during Adaption to a Mechanical Perturbation

PubMed Central

Hewitt, Angela L.; Popa, Laurentiu S.

2015-01-01

The cerebellum is essential in motor learning. At the cellular level, changes occur in both the simple spike and complex spike firing of Purkinje cells. Because simple spike discharge reflects the main output of the cerebellar cortex, changes in simple spike firing likely reflect the contribution of the cerebellum to the adapted behavior. Therefore, we investigated in Rhesus monkeys how the representation of arm kinematics in Purkinje cell simple spike discharge changed during adaptation to mechanical perturbations of reach movements. Monkeys rapidly adapted to a novel assistive or resistive perturbation along the direction of the reach. Adaptation consisted of matching the amplitude and timing of the perturbation to minimize its effect on the reach. In a majority of Purkinje cells, simple spike firing recorded before and during adaptation demonstrated significant changes in position, velocity, and acceleration sensitivity. The timing of the simple spike representations change within individual cells, including shifts in predictive versus feedback signals. At the population level, feedback-based encoding of position increases early in learning and velocity decreases. Both timing changes reverse later in learning. The complex spike discharge was only weakly modulated by the perturbations, demonstrating that the changes in simple spike firing can be independent of climbing fiber input. In summary, we observed extensive alterations in individual Purkinje cell encoding of reach kinematics, although the movements were nearly identical in the baseline and adapted states. Therefore, adaption to mechanical perturbation of a reaching movement is accompanied by widespread modifications in the simple spike encoding. PMID:25609626

Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2009-04-14

Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.

Do recreational activities affect coastal biodiversity?

NASA Astrophysics Data System (ADS)

Riera, Rodrigo; Menci, Cristiano; Sanabria-Fernández, José Antonio; Becerro, Mikel A.

2016-09-01

Human activities are largely affecting coastal communities worldwide. Recreational perturbations have been overlooked in comparison to other perturbations, yet they are potential threats to marine biodiversity. They affect coastal communities in different ways, underpinning consistent shifts in fish and invertebrates assemblages. Several sites were sampled subjected to varying effects by recreational fishermen (low and high pressure) and scuba divers (low and high) in an overpopulated Atlantic island. Non-consistent differences in ecological, trophic and functional diversity were found in coastal communities, considering both factors (;diving; and ;fishing;). Multivariate analyses only showed significant differences in benthic invertebrates between intensively-dived and non-dived sites. The lack of clear trends may be explained by the depletion of coastal resources in the study area, an extensively-affected island by overfishing.

Collisional phase shifts of ring dark solitons in inhomogeneous Bose Einstein condensates

NASA Astrophysics Data System (ADS)

Peng, Ping; Li, Guan-Qiang; Xue, Ju-Kui

2007-06-01

The head-on collisions of two ring dark solitons in inhomogeneous Bose Einstein condensates (BECs) with thin disk-shaped potential are studied by the extended Poincaré Lighthill Kuo (PLK) perturbation method. The result shows that the system admits a solution with two concentric ring solitons, one moving inwards and the other moving outwards, which in small-amplitude limit, are described by two modified cylindrical KdV equations in the respective reference frames. In particular, the analytical phase shifts induced by the head-on collisions between two ring dark solitary waves are derived, and the result shows that the phase shifts change with the radial coordinate r according to the (1+σr)r law (where σ˜ωr2/ωz2), which are quite different with the homogeneous case.

Lattice-Induced Frequency Shifts in Sr Optical Lattice Clocks at the 10{sup -17} Level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Westergaard, P. G.; Lodewyck, J.; Lecallier, A.

2011-05-27

We present a comprehensive study of the frequency shifts associated with the lattice potential in a Sr lattice clock by comparing two such clocks with a frequency stability reaching 5x10{sup -17} after a 1 h integration time. We put the first experimental upper bound on the multipolar M1 and E2 interactions, significantly smaller than the recently predicted theoretical upper limit, and give a 30-fold improved upper limit on the effect of hyperpolarizability. Finally, we report on the first observation of the vector and tensor shifts in a Sr lattice clock. Combining these measurements, we show that all known lattice relatedmore » perturbations will not affect the clock accuracy down to the 10{sup -17} level, even for lattices as deep as 150 recoil energies.« less

More-frequent extreme northward shifts of eastern Indian Ocean tropical convergence under greenhouse warming

PubMed Central

Weller, Evan; Cai, Wenju; Min, Seung-Ki; Wu, Lixin; Ashok, Karumuri; Yamagata, Toshio

2014-01-01

The Intertropical Convergence Zone (ITCZ) in the tropical eastern Indian Ocean exhibits strong interannual variability, often co-occurring with positive Indian Ocean Dipole (pIOD) events. During what we identify as an extreme ITCZ event, a drastic northward shift of atmospheric convection coincides with an anomalously strong north-minus-south sea surface temperature (SST) gradient over the eastern equatorial Indian Ocean. Such shifts lead to severe droughts over the maritime continent and surrounding islands but also devastating floods in southern parts of the Indian subcontinent. Understanding future changes of the ITCZ is therefore of major scientific and socioeconomic interest. Here we find a more-than-doubling in the frequency of extreme ITCZ events under greenhouse warming, estimated from climate models participating in the Coupled Model Intercomparison Project phase 5 that are able to simulate such events. The increase is due to a mean state change with an enhanced north-minus-south SST gradient and a weakened Walker Circulation, facilitating smaller perturbations to shift the ITCZ northwards. PMID:25124737

First demonstration of the fast-to-slow corrector current shift in the NSLS-II storage ring

NASA Astrophysics Data System (ADS)

Yang, Xi; Tian, Yuke; Yu, Li Hua; Smaluk, Victor

2018-04-01

To realize the full benefits of the high brightness and ultra-small beam sizes of NSLS-II, it is essential that the photon beams are exceedingly stable. In the circumstances of implementing local bumps, changing ID gaps, and long term drifting, the fast orbit feedback (FOFB) requires shifting the fast corrector strengths to the slow correctors to prevent the fast corrector saturation and to make the beam orbit stable in the sub-micron level. As the result, a reliable and precise technique of fast-to-slow corrector strength shift has been developed and tested at NSLS-II. This technique is based on the fast corrector response to the slow corrector change when the FOFB is on. In this article, the shift technique is described and the result of proof-of-principle experiment carried out at NSLS-II is presented. The maximum fast corrector current was reduced from greater than 0.45 A to less than 0.04 A with the orbit perturbation within ±1 μm.

Resonance Shift of Single-Axis Acoustic Levitation

NASA Astrophysics Data System (ADS)

Xie, Wen-Jun; Wei, Bing-Bo

2007-01-01

The resonance shift due to the presence and movement of a rigid spherical sample in a single-axis acoustic levitator is studied with the boundary element method on the basis of a two-cylinder model of the levitator. The introduction of a sample into the sound pressure nodes, where it is usually levitated, reduces the resonant interval Hn (n is the mode number) between the reflector and emitter. The larger the sample radius, the greater the resonance shift. When the sample moves along the symmetric axis, the resonance interval Hn varies in an approximately periodical manner, which reaches the minima near the pressure nodes and the maxima near the pressure antinodes. This suggests a resonance interval oscillation around its minimum if the stably levitated sample is slightly perturbed. The dependence of the resonance shift on the sample radius R and position h for the single-axis acoustic levitator is compared with Leung's theory for a closed rectangular chamber, which shows a good agreement.

Bayesian Sensitivity Analysis of Statistical Models with Missing Data

PubMed Central

ZHU, HONGTU; IBRAHIM, JOSEPH G.; TANG, NIANSHENG

2013-01-01

Methods for handling missing data depend strongly on the mechanism that generated the missing values, such as missing completely at random (MCAR) or missing at random (MAR), as well as other distributional and modeling assumptions at various stages. It is well known that the resulting estimates and tests may be sensitive to these assumptions as well as to outlying observations. In this paper, we introduce various perturbations to modeling assumptions and individual observations, and then develop a formal sensitivity analysis to assess these perturbations in the Bayesian analysis of statistical models with missing data. We develop a geometric framework, called the Bayesian perturbation manifold, to characterize the intrinsic structure of these perturbations. We propose several intrinsic influence measures to perform sensitivity analysis and quantify the effect of various perturbations to statistical models. We use the proposed sensitivity analysis procedure to systematically investigate the tenability of the non-ignorable missing at random (NMAR) assumption. Simulation studies are conducted to evaluate our methods, and a dataset is analyzed to illustrate the use of our diagnostic measures. PMID:24753718

Hydrazine and hydroxylamine as probes for O2-reduction site of mitochondrial cytochrome c oxidase.

PubMed Central

Kubota, T; Yoshikawa, S

1993-01-01

Reactions of hydrazine and hydroxylamine with bovine heart cytochrome c oxidase in the fully reduced state were investigated under anaerobic conditions following the visible-Soret spectral change. Hydrazine gave a sharp band at 575 nm with 20% decrease in the alpha band at 603 nm, and hydroxylamine induced a 2 nm blue-shift for the alpha band without any clear splitting. The Soret band at 443 nm was decreased significantly in intensity, with the concomitant appearance of a shoulder with hydrazine or a peak with hydroxylamine, both near 430 nm. The dependence on pH of the affinity of these reagents for the enzyme indicates that only the deprotonated forms of these reagents bind to the enzyme, suggesting a highly hydrophobic environment of the haem ligand-biding site. These spectral changes were largely removed by addition of cyanide or CO. However, detailed analysis of these spectral changes indicates that hydrazine perturbs the shape of the spectral change induced by cyanide and hydroxylamine perturbs that induced by CO. These results suggest that these aldehyde reagents bind to haem a3 iron as well as to a second site which is most likely to be the formyl group on the haem periphery, and that these two sites bind these reagents anti-cooperatively with each other. PMID:8389138

Scanless nonlinear optical microscope for image reconstruction and space-time correlation analysis

NASA Astrophysics Data System (ADS)

Ceffa, N. G.; Radaelli, F.; Pozzi, P.; Collini, M.; Sironi, L.; D'alfonso, L.; Chirico, G.

2017-06-01

Optical Microscopy has been applied to life science from its birth and reached widespread application due to its major advantages: limited perturbation of the biological tissue and the easy accessibility of the light sources. However, as the spatial and time resolution requirements and the time stability of the microscopes increase, researchers are struggling against some of its limitations: limited transparency and the refractivity of the living tissue to light and the field perturbations induced by the path in the tissue. We have developed a compact stand-alone, completely scan-less, optical setup that allows to acquire non-linear excitation images and to measure the sample dynamics simultaneously on an ensemble of arbitrary chosen regions of interests. The image is obtained by shining a square array of spots on the sample obtained by a spatial light modulator and by shifting it (10 ms refresh time) on the sample. The final image is computed from the superposition of (100-1000) images. Filtering procedures can be applied to the raw images of the excitation array before building the image. We discuss results that show how this setup can be used for the correction of wave front aberrations induced by turbid samples (such as living tissues) and for the computation of space-time cross-correlations in complex networks.

Synaptic efficacy shapes resource limitations in working memory.

PubMed

Krishnan, Nikhil; Poll, Daniel B; Kilpatrick, Zachary P

2018-06-01

Working memory (WM) is limited in its temporal length and capacity. Classic conceptions of WM capacity assume the system possesses a finite number of slots, but recent evidence suggests WM may be a continuous resource. Resource models typically assume there is no hard upper bound on the number of items that can be stored, but WM fidelity decreases with the number of items. We analyze a neural field model of multi-item WM that associates each item with the location of a bump in a finite spatial domain, considering items that span a one-dimensional continuous feature space. Our analysis relates the neural architecture of the network to accumulated errors and capacity limitations arising during the delay period of a multi-item WM task. Networks with stronger synapses support wider bumps that interact more, whereas networks with weaker synapses support narrower bumps that are more susceptible to noise perturbations. There is an optimal synaptic strength that both limits bump interaction events and the effects of noise perturbations. This optimum shifts to weaker synapses as the number of items stored in the network is increased. Our model not only provides a circuit-based explanation for WM capacity, but also speaks to how capacity relates to the arrangement of stored items in a feature space.

A large aberrant stem ichthyosauriform indicating early rise and demise of ichthyosauromorphs in the wake of the end-Permian extinction

PubMed Central

Jiang, Da-Yong; Motani, Ryosuke; Huang, Jian-Dong; Tintori, Andrea; Hu, Yuan-Chao; Rieppel, Olivier; Fraser, Nicholas C.; Ji, Cheng; Kelley, Neil P.; Fu, Wan-Lu; Zhang, Rong

2016-01-01

Contrary to the fast radiation of most metazoans after the end-Permian mass extinction, it is believed that early marine reptiles evolved slowly during the same time interval. However, emerging discoveries of Early Triassic marine reptiles are questioning this traditional view. Here we present an aberrant basal ichthyosauriform with a hitherto unknown body design that suggests a fast radiation of early marine reptiles. The new species is larger than coeval marine reptiles and has an extremely small head and a long tail without a fluke. Its heavily-built body bears flattened and overlapping gastral elements reminiscent of hupehsuchians. A phylogenetic analysis places the new species at the base of ichthyosauriforms, as the sister taxon of Cartorhynchus with which it shares a short snout with rostrally extended nasals. It now appears that ichthyosauriforms evolved rapidly within the first one million years of their evolution, in the Spathian (Early Triassic), and their true diversity has yet to be fully uncovered. Early ichthyosauromorphs quickly became extinct near the Early-Middle Triassic boundary, during the last large environmental perturbation after the end-Permian extinction involving redox fluctuations, sea level changes and volcanism. Marine reptile faunas shifted from ichthyosauromorph-dominated to sauropterygian-dominated composition after the perturbation. PMID:27211319

The electron affinity of Al13H cluster: high level ab initio study

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the respective CCSD(T)/CBS thermodynamic EA values are 2.79 and 2.80 eV.

Influence diagnostics in meta-regression model.

PubMed

Shi, Lei; Zuo, ShanShan; Yu, Dalei; Zhou, Xiaohua

2017-09-01

This paper studies the influence diagnostics in meta-regression model including case deletion diagnostic and local influence analysis. We derive the subset deletion formulae for the estimation of regression coefficient and heterogeneity variance and obtain the corresponding influence measures. The DerSimonian and Laird estimation and maximum likelihood estimation methods in meta-regression are considered, respectively, to derive the results. Internal and external residual and leverage measure are defined. The local influence analysis based on case-weights perturbation scheme, responses perturbation scheme, covariate perturbation scheme, and within-variance perturbation scheme are explored. We introduce a method by simultaneous perturbing responses, covariate, and within-variance to obtain the local influence measure, which has an advantage of capable to compare the influence magnitude of influential studies from different perturbations. An example is used to illustrate the proposed methodology. Copyright © 2017 John Wiley & Sons, Ltd.

The impact of 3D volume of interest definition on accuracy and precision of activity estimation in quantitative SPECT and planar processing methods

NASA Astrophysics Data System (ADS)

He, Bin; Frey, Eric C.

2010-06-01

Accurate and precise estimation of organ activities is essential for treatment planning in targeted radionuclide therapy. We have previously evaluated the impact of processing methodology, statistical noise and variability in activity distribution and anatomy on the accuracy and precision of organ activity estimates obtained with quantitative SPECT (QSPECT) and planar (QPlanar) processing. Another important factor impacting the accuracy and precision of organ activity estimates is accuracy of and variability in the definition of organ regions of interest (ROI) or volumes of interest (VOI). The goal of this work was thus to systematically study the effects of VOI definition on the reliability of activity estimates. To this end, we performed Monte Carlo simulation studies using randomly perturbed and shifted VOIs to assess the impact on organ activity estimates. The 3D NCAT phantom was used with activities that modeled clinically observed 111In ibritumomab tiuxetan distributions. In order to study the errors resulting from misdefinitions due to manual segmentation errors, VOIs of the liver and left kidney were first manually defined. Each control point was then randomly perturbed to one of the nearest or next-nearest voxels in three ways: with no, inward or outward directional bias, resulting in random perturbation, erosion or dilation, respectively, of the VOIs. In order to study the errors resulting from the misregistration of VOIs, as would happen, e.g. in the case where the VOIs were defined using a misregistered anatomical image, the reconstructed SPECT images or projections were shifted by amounts ranging from -1 to 1 voxels in increments of with 0.1 voxels in both the transaxial and axial directions. The activity estimates from the shifted reconstructions or projections were compared to those from the originals, and average errors were computed for the QSPECT and QPlanar methods, respectively. For misregistration, errors in organ activity estimations were linear in the shift for both the QSPECT and QPlanar methods. QPlanar was less sensitive to object definition perturbations than QSPECT, especially for dilation and erosion cases. Up to 1 voxel misregistration or misdefinition resulted in up to 8% error in organ activity estimates, with the largest errors for small or low uptake organs. Both types of VOI definition errors produced larger errors in activity estimates for a small and low uptake organs (i.e. -7.5% to 5.3% for the left kidney) than for a large and high uptake organ (i.e. -2.9% to 2.1% for the liver). We observed that misregistration generally had larger effects than misdefinition, with errors ranging from -7.2% to 8.4%. The different imaging methods evaluated responded differently to the errors from misregistration and misdefinition. We found that QSPECT was more sensitive to misdefinition errors, but less sensitive to misregistration errors, as compared to the QPlanar method. Thus, sensitivity to VOI definition errors should be an important criterion in evaluating quantitative imaging methods.

Frequency domain analysis of noise in simple gene circuits

NASA Astrophysics Data System (ADS)

Cox, Chris D.; McCollum, James M.; Austin, Derek W.; Allen, Michael S.; Dar, Roy D.; Simpson, Michael L.

2006-06-01

Recent advances in single cell methods have spurred progress in quantifying and analyzing stochastic fluctuations, or noise, in genetic networks. Many of these studies have focused on identifying the sources of noise and quantifying its magnitude, and at the same time, paying less attention to the frequency content of the noise. We have developed a frequency domain approach to extract the information contained in the frequency content of the noise. In this article we review our work in this area and extend it to explicitly consider sources of extrinsic and intrinsic noise. First we review applications of the frequency domain approach to several simple circuits, including a constitutively expressed gene, a gene regulated by transitions in its operator state, and a negatively autoregulated gene. We then review our recent experimental study, in which time-lapse microscopy was used to measure noise in the expression of green fluorescent protein in individual cells. The results demonstrate how changes in rate constants within the gene circuit are reflected in the spectral content of the noise in a manner consistent with the predictions derived through frequency domain analysis. The experimental results confirm our earlier theoretical prediction that negative autoregulation not only reduces the magnitude of the noise but shifts its content out to higher frequency. Finally, we develop a frequency domain model of gene expression that explicitly accounts for extrinsic noise at the transcriptional and translational levels. We apply the model to interpret a shift in the autocorrelation function of green fluorescent protein induced by perturbations of the translational process as a shift in the frequency spectrum of extrinsic noise and a decrease in its weighting relative to intrinsic noise.

Herpetofaunal Community Change in Multiple Habitats after Fifteen Years in a Southwest Florida Preserve, USA

PubMed Central

Cassani, John R.; Croshaw, Dean A.; Bozzo, Joseph; Brooks, Brenda; Everham, Edwin M.; Ceilley, David W.; Hanson, Deborah

2015-01-01

Herpetofaunal declines have been documented globally, and southern Florida, USA, is an especially vulnerable region because of high impacts from hydrological perturbations and nonindigenous species. To assess the extent of recent change in herpetofauna community composition, we established a baseline inventory during 1995-97 at a managed preserve in a habitat rich area of southwest Florida, and repeated our sampling methods fifteen years later (2010-11). Nine drift fence arrays were placed in four habitat types: mesic flatwood, mesic hammock, depression marsh, and wet prairie. Trapping occurred daily for one week during 7-8 sampling runs in each period (57 and 49 total sampling days, respectively). Species richness was maintained in mesic hammock habitats but varied in the others. Catch rates of several native species (Anaxyrus terrestris, Lithobates grylio, Anolis carolinensis, Nerodia fasciata) declined significantly. Other native species (Lithobates sphenocephalus, Siren lacertian, and Notophthalmus viridescens piaropicola) that were abundant in 1995-97 declined by greater than 50%. Catch rate of only two species (the nonindigenous Anolis sagrei and the native Diadophis punctatus) increased significantly. Hierarchical cluster analysis indicated similarity within habitat types but significant dissimilarity between sampling periods, confirming shifts in community composition. Analysis of individual species’ contributions to overall similarity across habitats shows a shift from dominance of native species in the 1990s to increased importance of nonindigenous species in 2010-11. Although natural population fluctuations may have influenced differences between the two sampling periods, our results suggest considerable recent change in the structure and composition of this southwest Florida herpetofaunal community. The causes are unknown, but hydrological shifts and ecological impacts of nonindigenous species may have contributed. PMID:26016475

Automatic alignment of individual peaks in large high-resolution spectral data sets

NASA Astrophysics Data System (ADS)

Stoyanova, Radka; Nicholls, Andrew W.; Nicholson, Jeremy K.; Lindon, John C.; Brown, Truman R.

2004-10-01

Pattern recognition techniques are effective tools for reducing the information contained in large spectral data sets to a much smaller number of significant features which can then be used to make interpretations about the chemical or biochemical system under study. Often the effectiveness of such approaches is impeded by experimental and instrument induced variations in the position, phase, and line width of the spectral peaks. Although characterizing the cause and magnitude of these fluctuations could be important in its own right (pH-induced NMR chemical shift changes, for example) in general they obscure the process of pattern discovery. One major area of application is the use of large databases of 1H NMR spectra of biofluids such as urine for investigating perturbations in metabolic profiles caused by drugs or disease, a process now termed metabonomics. Frequency shifts of individual peaks are the dominant source of such unwanted variations in this type of data. In this paper, an automatic procedure for aligning the individual peaks in the data set is described and evaluated. The proposed method will be vital for the efficient and automatic analysis of large metabonomic data sets and should also be applicable to other types of data.

CCR5 RNA Pseudoknots: Residue and Site-Specific Labeling correlate Internal Motions with microRNA Binding.

PubMed

Chen, Bin; Longhini, Andrew P; Nußbaumer, Felix; Kreutz, Christoph; Dinman, Jonathan D; Dayie, T Kwaku

2018-04-11

Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNA dynamic behavior sheds important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution-state NMR are difficult for large RNA molecules (>70 nt; nt=nucleotides) owing to severe spectral overlap, homonuclear 13 C scalar couplings, and line broadening. Herein, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites, and enzymatic ligation is introduced. This approach allowed the position-specific insertion of isotopic probes into a 96 nt CCR5 RNA fragment. Accurate measurements of functional dynamics using the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments enabled extraction of the exchange rates and populations of this RNA. NMR chemical shift perturbation analysis of the RNA/microRNA-1224 complex indicated that A90-C1' of the pseudoknot exhibits similar changes in chemical shift observed in the excited state. This work demonstrates the general applicability of a NMR-labeling strategy to probe functional RNA structural dynamics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of encapsulation damping on the excitation threshold for subharmonic generation from contrast microbubbles.

PubMed

Katiyar, Amit; Sarkar, Kausik

2012-11-01

A recent study [Katiyar and Sarkar (2011). J. Acoust. Soc. Am. 130, 3137-3147] showed that in contrast to the analytical result for free bubbles, the minimum threshold for subharmonic generation for contrast microbubbles does not necessarily occur at twice the resonance frequency. Here increased damping-either due to the small radius or the encapsulation-is shown to shift the minimum threshold away from twice the resonance frequency. Free bubbles as well as four models of the contrast agent encapsulation are investigated varying the surface dilatational viscosity. Encapsulation properties are determined using measured attenuation data for a commercial contrast agent. For sufficiently small damping, models predict two minima for the threshold curve-one at twice the resonance frequency being lower than the other at resonance frequency-in accord with the classical analytical result. However, increased damping damps the bubble response more at twice the resonance than at resonance, leading to a flattening of the threshold curve and a gradual shift of the absolute minimum from twice the resonance frequency toward the resonance frequency. The deviation from the classical result stems from the fact that the perturbation analysis employed to obtain it assumes small damping, not always applicable for contrast microbubbles.

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

PubMed Central

Jo, Kyuri; Jung, Inuk; Moon, Ji Hwan; Kim, Sun

2016-01-01

Motivation: To understand the dynamic nature of the biological process, it is crucial to identify perturbed pathways in an altered environment and also to infer regulators that trigger the response. Current time-series analysis methods, however, are not powerful enough to identify perturbed pathways and regulators simultaneously. Widely used methods include methods to determine gene sets such as differentially expressed genes or gene clusters and these genes sets need to be further interpreted in terms of biological pathways using other tools. Most pathway analysis methods are not designed for time series data and they do not consider gene-gene influence on the time dimension. Results: In this article, we propose a novel time-series analysis method TimeTP for determining transcription factors (TFs) regulating pathway perturbation, which narrows the focus to perturbed sub-pathways and utilizes the gene regulatory network and protein–protein interaction network to locate TFs triggering the perturbation. TimeTP first identifies perturbed sub-pathways that propagate the expression changes along the time. Starting points of the perturbed sub-pathways are mapped into the network and the most influential TFs are determined by influence maximization technique. The analysis result is visually summarized in TF-Pathway map in time clock. TimeTP was applied to PIK3CA knock-in dataset and found significant sub-pathways and their regulators relevant to the PIP3 signaling pathway. Availability and Implementation: TimeTP is implemented in Python and available at http://biohealth.snu.ac.kr/software/TimeTP/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: sunkim.bioinfo@snu.ac.kr PMID:27307609

Anticipating regime shifts in gene expression: The case of an autoactivating positive feedback loop

NASA Astrophysics Data System (ADS)

Sharma, Yogita; Dutta, Partha Sharathi; Gupta, A. K.

2016-03-01

Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task; examples include ecosystems, financial markets, and complex diseases. In this paper, we investigate the effects of additive, multiplicative, and cross-correlated stochastic perturbations on determining the regime shifts in a bistable gene regulatory system, which gives rise to two distinct states of low and high concentrations of protein. We obtain the stationary probability density and mean first-passage time of the system. We show that increasing the additive (multiplicative) noise intensity induces a regime shift from a low (high) to a high (low) protein concentration state. However, an increase in the cross-correlation intensity always induces regime shifts from a high to a low protein concentration state. For both bifurcation-induced (often called the tipping point) and noise-induced (called stochastic switching) regime shifts, we further explore the robustness of recently developed critical-down-based early warning signal (EWS) indicators (e.g., rising variance and lag-1 autocorrelation) on our simulated time-series data. We identify that using EWS indicators, prediction of an impending bifurcation-induced regime shift is relatively easier than that of a noise-induced regime shift in the considered system. Moreover, the success of EWS indicators also strongly depends upon the nature of the noise.

Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics

PubMed Central

Puniya, Bhanwar Lal; Allen, Laura; Hochfelder, Colleen; Majumder, Mahbubul; Helikar, Tomáš

2016-01-01

Dysregulation in signal transduction pathways can lead to a variety of complex disorders, including cancer. Computational approaches such as network analysis are important tools to understand system dynamics as well as to identify critical components that could be further explored as therapeutic targets. Here, we performed perturbation analysis of a large-scale signal transduction model in extracellular environments that stimulate cell death, growth, motility, and quiescence. Each of the model’s components was perturbed under both loss-of-function and gain-of-function mutations. Using 1,300 simulations under both types of perturbations across various extracellular conditions, we identified the most and least influential components based on the magnitude of their influence on the rest of the system. Based on the premise that the most influential components might serve as better drug targets, we characterized them for biological functions, housekeeping genes, essential genes, and druggable proteins. The most influential components under all environmental conditions were enriched with several biological processes. The inositol pathway was found as most influential under inactivating perturbations, whereas the kinase and small lung cancer pathways were identified as the most influential under activating perturbations. The most influential components were enriched with essential genes and druggable proteins. Moreover, known cancer drug targets were also classified in influential components based on the affected components in the network. Additionally, the systemic perturbation analysis of the model revealed a network motif of most influential components which affect each other. Furthermore, our analysis predicted novel combinations of cancer drug targets with various effects on other most influential components. We found that the combinatorial perturbation consisting of PI3K inactivation and overactivation of IP3R1 can lead to increased activity levels of apoptosis-related components and tumor-suppressor genes, suggesting that this combinatorial perturbation may lead to a better target for decreasing cell proliferation and inducing apoptosis. Finally, our approach shows a potential to identify and prioritize therapeutic targets through systemic perturbation analysis of large-scale computational models of signal transduction. Although some components of the presented computational results have been validated against independent gene expression data sets, more laboratory experiments are warranted to more comprehensively validate the presented results. PMID:26904540

Practical scheme for optimal measurement in quantum interferometric devices

NASA Astrophysics Data System (ADS)

Takeoka, Masahiro; Ban, Masashi; Sasaki, Masahide

2003-06-01

We apply a Kennedy-type detection scheme, which was originally proposed for a binary communications system, to interferometric sensing devices. We show that the minimum detectable perturbation of the proposed system reaches the ultimate precision bound which is predicted by quantum Neyman-Pearson hypothesis testing. To provide concrete examples, we apply our interferometric scheme to phase shift detection by using coherent and squeezed probe fields.

Changes in the referent body location and configuration may underlie human gait, as confirmed by findings of multi-muscle activity minimizations and phase resetting.

PubMed

Feldman, Anatol G; Krasovsky, Tal; Baniña, Melanie C; Lamontagne, Anouk; Levin, Mindy F

2011-04-01

Locomotion is presumably guided by feed-forward shifts in the referent body location in the desired direction in the environment. We propose that the difference between the actual and the referent body locations is transmitted to neurons that virtually diminish this difference by appropriately changing the referent body configuration, i.e. the body posture at which muscles reach their recruitment thresholds. Muscles are activated depending on the gap between the actual and the referent body configurations resulting in a step being made to minimize this gap. This hypothesis implies that the actual and the referent leg configurations can match each other at certain phases of the gait cycle, resulting in minimization of leg muscle activity. We found several leg configurations at which EMG minima occurred, both during forward and backward gait. It was also found that the set of limb configurations associated with EMG minima can be changed by modifying the pattern of forward and backward gait. Our hypothesis predicts that, in response to perturbations of gait, the rate of shifts in the referent body location can temporarily be changed to avoid falling. The rate influences the phase of rhythmic limb movements during gait. Therefore, following the change in the rate of the referent body location, the whole gait pattern, for all four limbs, will irreversibly be shifted in time (long-lasting and global phase resetting) with only transient changes in the gait speed, swing and stance timing and cycle duration. Aside from transient changes in the duration of the swing and/or stance phase in response to perturbation, few previous studies have documented long-lasting and global phase resetting of human gait in response to perturbation. Such resetting was a robust finding in our study. By confirming the notion that feed-forward changes in the referent body location and configuration underlie human locomotion, this study solves the classical problem in the relationship between stability of posture and gait and advances the understanding of how human locomotion involves the whole body and is accomplished in a spatial frame of reference associated with the environment.

Using Local Perturbations To Manipulate and Control Pointer States in Quantum Dot Systems

NASA Astrophysics Data System (ADS)

Akis, Richard; Speyer, Gil; Ferry, David; Brunner, Roland

2012-02-01

Recently, scanning gate microscopy (SGM) was used to image scarred wave functions in an open InAs quantum dot[1]. The SGM tip provides a local potential perturbation and imaging is performed by measuring changes in conductance. Scarred wave functions, long associated with quantum chaos, have been shown in open dots to correspond to pointer states[2], eigenstates that survive the decoherence process that occurs via coupling to the environment. Pointer states modulate the conductance, yielding periodic fluctuations and the scars, normally thought unstable, are stabilized by quantum Darwinism [3]. We shall show that, beyond probing, pointer states can be manipulated by local perturbations. Particularly interesting effects occur in coupled quantum dot arrays, where a pointer state localized in one dot can be shifted over into another with a perturbation in a completely different part of the system. These nonlocal effects may perhaps be exploited to give such systems an exotic functionality. [1] A. M. Burke, R. Akis, T. E. Day, Gil Speyer, D. K. Ferry, and B. R. Bennett, Phys. Rev. Lett. 104, 176801 (2010). [2] D. K. Ferry, R. Akis, and J. P. Bird, Phys. Rev. Lett. 104, 176801 (2004). [3] R. Brunner, R. Akis,D. K. Ferry, F. Kuchar,and R. Meisels, Phys. Rev. Lett. 101, 024102 (2008).

Using Solar Radiation Pressure to Control L2 Orbits

NASA Technical Reports Server (NTRS)

Tene, Noam; Richon, Karen; Folta, David

1998-01-01

The main perturbations at the Sun-Earth Lagrange points L1 and L2 are from solar radiation pressure (SRP), the Moon and the planets. Traditional approaches to trajectory design for Lagrange-point orbits use maneuvers every few months to correct for these perturbations. The gravitational effects of the Moon and the planets are small and periodic. However, they cannot be neglected because small perturbations in the direction of the unstable eigenvector are enough to cause exponential growth within a few months. The main effect of a constant SRP is to shift the center of the orbit by a small distance. For spacecraft with large sun-shields like the Microwave Anisotropy Probe (MAP) and the Next Generation Space Telescope (NGST), the SRP effect is larger than all other perturbations and depends mostly on spacecraft attitude. Small variations in the spacecraft attitude are large enough to excite or control the exponential eigenvector. A closed-loop linear controller based on the SRP variations would eliminate one of the largest errors to the orbit and provide a continuous acceleration for use in controlling other disturbances. It is possible to design reference trajectories that account for the periodic lunar and planetary perturbations and still satisfy mission requirements. When such trajectories are used the acceleration required to control the unstable eigenvector is well within the capabilities of a continuous linear controller. Initial estimates show that by using attitude control it should be possible to minimize and even eliminate thruster maneuvers for station keeping.

Statistics of Smoothed Cosmic Fields in Perturbation Theory. I. Formulation and Useful Formulae in Second-Order Perturbation Theory

NASA Astrophysics Data System (ADS)

Matsubara, Takahiko

2003-02-01

We formulate a general method for perturbative evaluations of statistics of smoothed cosmic fields and provide useful formulae for application of the perturbation theory to various statistics. This formalism is an extensive generalization of the method used by Matsubara, who derived a weakly nonlinear formula of the genus statistic in a three-dimensional density field. After describing the general method, we apply the formalism to a series of statistics, including genus statistics, level-crossing statistics, Minkowski functionals, and a density extrema statistic, regardless of the dimensions in which each statistic is defined. The relation between the Minkowski functionals and other geometrical statistics is clarified. These statistics can be applied to several cosmic fields, including three-dimensional density field, three-dimensional velocity field, two-dimensional projected density field, and so forth. The results are detailed for second-order theory of the formalism. The effect of the bias is discussed. The statistics of smoothed cosmic fields as functions of rescaled threshold by volume fraction are discussed in the framework of second-order perturbation theory. In CDM-like models, their functional deviations from linear predictions plotted against the rescaled threshold are generally much smaller than that plotted against the direct threshold. There is still a slight meatball shift against rescaled threshold, which is characterized by asymmetry in depths of troughs in the genus curve. A theory-motivated asymmetry factor in the genus curve is proposed.

Analysis of the control structures for an integrated ethanol processor for proton exchange membrane fuel cell systems

NASA Astrophysics Data System (ADS)

Biset, S.; Nieto Deglioumini, L.; Basualdo, M.; Garcia, V. M.; Serra, M.

The aim of this work is to investigate which would be a good preliminary plantwide control structure for the process of Hydrogen production from bioethanol to be used in a proton exchange membrane (PEM) accounting only steady-state information. The objective is to keep the process under optimal operation point, that is doing energy integration to achieve the maximum efficiency. Ethanol, produced from renewable feedstocks, feeds a fuel processor investigated for steam reforming, followed by high- and low-temperature shift reactors and preferential oxidation, which are coupled to a polymeric fuel cell. Applying steady-state simulation techniques and using thermodynamic models the performance of the complete system with two different control structures have been evaluated for the most typical perturbations. A sensitivity analysis for the key process variables together with the rigorous operability requirements for the fuel cell are taking into account for defining acceptable plantwide control structure. This is the first work showing an alternative control structure applied to this kind of process.

Stability analysis of ultrasound thick-shell contrast agents

PubMed Central

Lu, Xiaozhen; Chahine, Georges L.; Hsiao, Chao-Tsung

2012-01-01

The stability of thick shell encapsulated bubbles is studied analytically. 3-D small perturbations are introduced to the spherical oscillations of a contrast agent bubble in response to a sinusoidal acoustic field with different amplitudes of excitation. The equations of the perturbation amplitudes are derived using asymptotic expansions and linear stability analysis is then applied to the resulting differential equations. The stability of the encapsulated microbubbles to nonspherical small perturbations is examined by solving an eigenvalue problem. The approach then identifies the fastest growing perturbations which could lead to the breakup of the encapsulated microbubble or contrast agent. PMID:22280568

Dynamics of Social Group Competition: Modeling the Decline of Religious Affiliation

NASA Astrophysics Data System (ADS)

Abrams, Daniel M.; Yaple, Haley A.; Wiener, Richard J.

2011-08-01

When social groups compete for members, the resulting dynamics may be understandable with mathematical models. We demonstrate that a simple ordinary differential equation (ODE) model is a good fit for religious shift by comparing it to a new international data set tracking religious nonaffiliation. We then generalize the model to include the possibility of nontrivial social interaction networks and examine the limiting case of a continuous system. Analytical and numerical predictions of this generalized system, which is robust to polarizing perturbations, match those of the original ODE model and justify its agreement with real-world data. The resulting predictions highlight possible causes of social shift and suggest future lines of research in both physics and sociology.

Trial-by-trial analysis of intermanual transfer during visuomotor adaptation

PubMed Central

Wojaczynski, Greg J.; Ivry, Richard B.

2011-01-01

Studies of intermanual transfer have been used to probe representations formed during skill acquisition. We employ a new method that provides a continuous assay of intermanual transfer, intermixing right- and left-hand trials while limiting visual feedback to right-hand movements. We manipulated the degree of awareness of the visuomotor rotation, introducing a 22.5° perturbation in either an abrupt single step or gradually in ∼1° increments every 10 trials. Intermanual transfer was observed with the direction of left-hand movements shifting in the opposite direction of the rotation over the course of training. The transfer on left-hand trials was less than that observed in the right hand. Moreover, the magnitude of transfer was larger in our mixed-limb design compared with the standard blocked design in which transfer is only probed at the end of training. Transfer was similar in the abrupt and gradual groups, suggesting that awareness of the perturbation has little effect on intermanual transfer. In a final experiment, participants were provided with a strategy to offset an abrupt rotation, a method that has been shown to increase error over the course of training due to the operation of sensorimotor adaptation. This deterioration was also observed on left-hand probe trials, providing further support that awareness has little effect on intermanual transfer. These results indicate that intermanual transfer is not dependent on the implementation of cognitively assisted strategies that participants might adopt when they become aware that the visuomotor mapping has been perturbed. Rather, the results indicate that the information available to processes involved in adaptation entails some degree of effector independence. PMID:21917998

Lamb Shift in the Near Field of Hyperbolic Metamaterial Half Space

NASA Astrophysics Data System (ADS)

Deng, Nai Jing; Yu, Kin Wah

2013-03-01

Hyperbolic metamaterials give a large magnification of the density of states in a specific frequency ranges, and has motivated various applications in emission lifetime reduction, strong absorption, and extraordinary black body radiation, etc. The boost of vacuum energy, which is proportional to the density of states, is expected in hyperbolic metamaterial. We have studied the Lamb shift in vacuum-hyperbolic-metamterial half spaces and shown the non-trivial role of vacuum energy. In our calculation, the easy-fabricated multilayer structure is employed to generate a hyperbolic dispersion relation. The spectrum of hydrogen atoms is calculated with a perturbation method after quantizing the half spaces with a complete mode expansion. It appears that the shift of spectrum is mainly contributed by the terahertz response of materials, which has been well described and predicted in both theories and experiments. Work supported by the General Research Fund of the Hong Kong SAR Government

An ab initio study of some binary complexes containing methyl fluoride and difluoromethane: red-shifting and blue-shifting hydrogen bonds

NASA Astrophysics Data System (ADS)

Ramasami, Ponnadurai; Ford, Thomas A.

2018-07-01

The properties of a number of hydrogen-bonded complexes of methyl fluoride and difluoromethane with a range of hydrides of the first two rows of the periodic table have been computed using ab initio molecular orbital theory. The aim of this work was to identify possible examples of blue-shifting hydrogen-bonded species analogous to those formed between fluoroform and ammonia, water, phosphine and hydrogen sulphide, reported earlier. The calculations were carried out using the Gaussian-09 program, at the second-order level of Møller-Plesset perturbation theory, and with the aug-cc-pVTZ basis sets of Dunning. The properties studied include the molecular structures, the hydrogen bond energies and the vibrational spectra. The results have been interpreted with the aid of natural bond orbital theory and the quantum theory of atoms in molecules.

Alternative stable states and phase shifts in coral reefs under anthropogenic stress.

PubMed

Fung, Tak; Seymour, Robert M; Johnson, Craig R

2011-04-01

Ecosystems with alternative stable states (ASS) may shift discontinuously from one stable state to another as environmental parameters cross a threshold. Reversal can then be difficult due to hysteresis effects. This contrasts with continuous state changes in response to changing environmental parameters, which are less difficult to reverse. Worldwide degradation of coral reefs, involving "phase shifts" from coral to algal dominance, highlights the pressing need to determine the likelihood of discontinuous phase shifts in coral reefs, in contrast to continuous shifts with no ASS. However, there is little evidence either for or against the existence of ASS for coral reefs. We use dynamic models to investigate the likelihood of continuous and discontinuous phase shifts in coral reefs subject to sustained environmental perturbation by fishing, nutrification, and sedimentation. Our modeling results suggest that coral reefs with or without anthropogenic stress can exhibit ASS, such that discontinuous phase shifts can occur. We also find evidence to support the view that high macroalgal growth rates and low grazing rates on macroalgae favor ASS in coral reefs. Further, our results suggest that the three stressors studied, either alone or in combination, can increase the likelihood of both continuous and discontinuous phase shifts by altering the competitive balance between corals and algae. However, in contrast to continuous phase shifts, we find that discontinuous shifts occur only in model coral reefs with parameter values near the extremes of their empirically determined ranges. This suggests that continuous shifts are more likely than discontinuous shifts in coral reefs. Our results also suggest that, for ecosystems in general, tackling multiple human stressors simultaneously maximizes resilience to phase shifts, ASS, and hysteresis, leading to improvements in ecosystem health and functioning.

Vision can recalibrate the vestibular reafference signal used to re-establish postural equilibrium following a platform perturbation.

PubMed

Toth, Adam J; Harris, Laurence R; Zettel, John; Bent, Leah R

2017-02-01

Visuo-vestibular recalibration, in which visual information is used to alter the interpretation of vestibular signals, has been shown to influence both oculomotor control and navigation. Here we investigate whether vision can recalibrate the vestibular feedback used during the re-establishment of equilibrium following a perturbation. The perturbation recovery responses of nine participants were examined following exposure to a period of 11 s of galvanic vestibular stimulation (GVS). During GVS in VISION trials, occlusion spectacles provided 4 s of visual information that enabled participants to correct for the GVS-induced tilt and associate this asymmetric vestibular signal with a visually provided 'upright'. NoVISION trials had no such visual experience. Participants used the visual information to assist in realigning their posture compared to when visual information was not provided (p < 0.01). The initial recovery response to a platform perturbation was not impacted by whether vision had been provided during the preceding GVS, as determined by peak centre of mass and pressure deviations (p = 0.09). However, after using vision to reinterpret the vestibular signal during GVS, final centre of mass and pressure equilibrium positions were significantly shifted compared to trials in which vision was not available (p < 0.01). These findings support previous work identifying a prominent role of vestibular input for re-establishing postural equilibrium following a perturbation. Our work is the first to highlight the capacity for visual feedback to recalibrate the vertical interpretation of vestibular reafference for re-establishing equilibrium following a perturbation. This demonstrates the rapid adaptability of the vestibular reafference signal for postural control.

Numerical modeling of possible lower ionospheric anomalies associated with Nepal earthquake in May, 2015

NASA Astrophysics Data System (ADS)

Chakraborty, Suman; Sasmal, Sudipta; Basak, Tamal; Ghosh, Soujan; Palit, Sourav; Chakrabarti, Sandip K.; Ray, Suman

2017-10-01

We present perturbations due to seismo-ionospheric coupling processes in propagation characteristics of sub-ionospheric Very Low Frequency (VLF) signals received at Ionospheric & Earthquake Research Centre (IERC) (Lat. 22.50°N, Long. 87.48°E), India. The study is done during and prior to an earthquake of Richter scale magnitude M = 7.3 occurring at a depth of 18 km at southeast of Kodari, Nepal on 12 May 2015 at 12:35:19 IST (07:05:19 UT). The recorded VLF signal of Japanese transmitter JJI at frequency 22.2 kHz (Lat. 32.08°N, Long. 130.83°E) suffers from strong shifts in sunrise and sunset terminator times towards nighttime starting from three to four days prior to the earthquake. The signal shows a similar variation in terminator times during a major aftershock of magnitude M = 6.7 on 16 May, 2015 at 17:04:10 IST (11:34:10 UT). These shifts in terminator times is numerically modeled using Long Wavelength Propagation Capability (LWPC) Programme. The unperturbed VLF signal is simulated by using the day and night variation of reflection height (h‧) and steepness parameter (β) fed in LWPC for the entire path. The perturbed signal is obtained by additional variation of these parameters inside the earthquake preparation zone. It is found that the shift of the terminator time towards nighttime happens only when the reflection height is increased. We also calculate electron density profile by using the Wait's exponential formula for specified location over the propagation path.

Self-monitoring in the cerebral cortex: Neural responses to small pitch shifts in auditory feedback during speech production.

PubMed

Franken, Matthias K; Eisner, Frank; Acheson, Daniel J; McQueen, James M; Hagoort, Peter; Schoffelen, Jan-Mathijs

2018-06-21

Speaking is a complex motor skill which requires near instantaneous integration of sensory and motor-related information. Current theory hypothesizes a complex interplay between motor and auditory processes during speech production, involving the online comparison of the speech output with an internally generated forward model. To examine the neural correlates of this intricate interplay between sensory and motor processes, the current study uses altered auditory feedback (AAF) in combination with magnetoencephalography (MEG). Participants vocalized the vowel/e/and heard auditory feedback that was temporarily pitch-shifted by only 25 cents, while neural activity was recorded with MEG. As a control condition, participants also heard the recordings of the same auditory feedback that they heard in the first half of the experiment, now without vocalizing. The participants were not aware of any perturbation of the auditory feedback. We found auditory cortical areas responded more strongly to the pitch shifts during vocalization. In addition, auditory feedback perturbation resulted in spectral power increases in the θ and lower β bands, predominantly in sensorimotor areas. These results are in line with current models of speech production, suggesting auditory cortical areas are involved in an active comparison between a forward model's prediction and the actual sensory input. Subsequently, these areas interact with motor areas to generate a motor response. Furthermore, the results suggest that θ and β power increases support auditory-motor interaction, motor error detection and/or sensory prediction processing. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Symmetry-adapted perturbation theory interaction energy decomposition for some noble gas complexes

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Sadlej, Joanna

2008-06-01

This Letter contains a study of the interaction energy in HArF⋯N 2 and HArF⋯P 2 complexes. Symmetry-adapted perturbation theory (SAPT) has been applied to analyze the electrostatic, induction, dispersion and exchange contributions to the total interaction energy. The interaction energy has also been obtained by supermolecular method at the MP2, MP4, CCSD, CCSD(T) levels. The interaction energy for the studied complexes results from a partial cancelation of large attractive electrostatic, induction, dispersion terms by a strong repulsive exchange contribution. The induction and dispersion effects proved to be crucial in establishing the preference for the colinear HArF⋯N 2 and HArF⋯P 2 structures and shift direction of νHAr stretching vibrations.

Impact of inward turbulence spreading on energy loss of edge-localized modes

DOE PAGES

Ma, C. H.; Xu, X. Q.; Xi, P. W.; ...

2015-05-18

Nonlinear two-fluid and gyrofluid simulations show that an edge localized modes(ELM) crash has two phases: fast initial crash of ion temperature perturbation on the Alfvén time scale and slow turbulence spreading. The turbulencetransport phase is a slow encroachment of electron temperature perturbation due to the ELM event into pedestal region. Because of the inward turbulence spreading effect, the energy loss of an ELM decreases when density pedestal height increases. The Landau resonance yields the different cross phase-shift of ions and electrons. A 3 + 1 gyro-Landau-fluid model is implemented in BOUT++ framework. As a result, the gyrofluid simulations show thatmore » the kinetic effects have stabilizing effects on the ideal ballooning mode and the energy loss increases with the pedestal height.« less

Generalized Autobalanced Ramsey Spectroscopy of Clock Transitions

NASA Astrophysics Data System (ADS)

Yudin, V. I.; Taichenachev, A. V.; Basalaev, M. Yu.; Zanon-Willette, T.; Pollock, J. W.; Shuker, M.; Donley, E. A.; Kitching, J.

2018-05-01

When performing precision measurements, the quantity being measured is often perturbed by the measurement process itself. Such measurements include precision frequency measurements for atomic clock applications carried out with Ramsey spectroscopy. With the aim of eliminating probe-induced perturbations, a method of generalized autobalanced Ramsey spectroscopy (GABRS) is presented and rigorously substantiated. The usual local-oscillator frequency control loop is augmented with a second control loop derived from secondary Ramsey sequences interspersed with the primary sequences and with a different Ramsey period. This second loop feeds back to a secondary clock variable and ultimately compensates for the perturbation of the clock frequency caused by the measurements in the first loop. We show that such a two-loop scheme can lead to perfect compensation for measurement-induced light shifts and does not suffer from the effects of relaxation, time-dependent pulse fluctuations and phase-jump modulation errors that are typical of other hyper-Ramsey schemes. Several variants of GABRS are explored based on different secondary variables including added relative phase shifts between Ramsey pulses, external frequency-step compensation, and variable second-pulse duration. We demonstrate that a universal antisymmetric error signal, and hence perfect compensation at a finite modulation amplitude, is generated only if an additional frequency step applied during both Ramsey pulses is used as the concomitant variable parameter. This universal technique can be applied to the fields of atomic clocks, high-resolution molecular spectroscopy, magnetically induced and two-photon probing schemes, Ramsey-type mass spectrometry, and the field of precision measurements. Some variants of GABRS can also be applied for rf atomic clocks using coherent-population-trapping-based Ramsey spectroscopy of the two-photon dark resonance.

Modeling of sub-ionospheric VLF signal anomalies associated with precursory effects of the latest earthquakes in Nepal

NASA Astrophysics Data System (ADS)

Sasmal, Sudipta; Chakrabarti, Sandip Kumar; Palit, Sourav; Chakraborty, Suman; Ghosh, Soujan; Ray, Suman

2016-07-01

We present the nature of perturbations in the propagation characteristics of Very Low Frequency (VLF) signals received at Ionospheric & Earthquake Research Centre (IERC) (Lat. 22.50 ^{o}N, Long. 87.48 ^{o}E) during and prior to the latest strong earthquakes in Nepal on 12 May 2015 at 12:50 pm local time (07:05 UTC) with a magnitude of 7.3 and depth 18 km at southeast of Kodari. The VLF signal emitted from JJI transmitter (22.2kHz) in Japan (Lat. 32.08 ^{o}N, Long. 130.83 ^{o}E) shows strong shifts in sunrise and sunset terminator times towards nighttime beginning three to four days prior to the earthquake. The shift in terminator times is numerically simulated using Long Wavelength Propagation Capability (LWPC) code. Electron density variation as a function of height is calculated for seismically quiet days using the Wait's exponential profile and it matches with the IRI model. The perturbed electron density is calculated using the effective reflection height (h') and sharpness parameter (β) and the rate of ionization due to earthquake is being obtained by the equation of continuity for ionospheric D-layer. We compute the ion production and recombination profiles during seismic and non-seismic conditions incorporating D-region ion chemistry processes and calculate the unperturbed and perturbed electron density profile and ionization rate at different heights which matches with the exponential profile. During the seismic condition, for both the cases, the rate of ionization and the electron density profile differ significantly from the normal values. We interpret this to be due to the seismo-ionospheric coupling processes.

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein–DNA Complex

PubMed Central

2016-01-01

Metal ion cofactors can alter the energetics and specificity of sequence specific protein–DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein–DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H–15N amide resonances, for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex. PMID:27786446

Enhancing vibration measurements by Mössbauer effect

NASA Astrophysics Data System (ADS)

Pasquevich, G. A.; Veiga, A.; Zélis, P. Mendoza; Martínez, N.; van Raap, M. Fernández; Sánchez, F. H.

2014-01-01

The measurement of the Mössbauer effect in a system excited with a periodic perturbation can provide information about it. For that purpose, the Mössbauer absorption of a source-absorber set which hyperfine parameters are well known, is measured at a constant relative velocity (i.e. at a defined spectral energy). The resulting Mössbauer absorption periodic signal provides information of the sample ac perturbation response. This approach has been used time ago to measure small tympanic vibrations (mechanical perturbations). In this work we present an extension of the vibration experiments, by measuring them at various absorber-source relative velocities within a constant-velocity strategy. As a demonstration test, the frequency response of a piezoelectric diaphragm in the 100 Hz-5 kHz range is obtained with a custom electronic counter. The experiments are performed using a 57Co( Rh) source and a 25-m-thick stainless-steel absorber fixed to a piezoelectric diaphragm. Phase shifts and amplitude vibrations with velocities in the range from 1.5 m/s to 20 mm/s are well characterized, extending the linearity limit well beyond the earlier suggested one of 1 mm/s.

Comprehensive analysis of the simplest curvaton model

NASA Astrophysics Data System (ADS)

Byrnes, Christian T.; Cortês, Marina; Liddle, Andrew R.

2014-07-01

We carry out a comprehensive analysis of the simplest curvaton model, which is based on two noninteracting massive fields. Our analysis encompasses cases where the inflaton and curvaton both contribute to observable perturbations, and where the curvaton itself drives a second period of inflation. We consider both power spectrum and non-Gaussianity observables, and focus on presenting constraints in model parameter space. The fully curvaton-dominated regime is in some tension with observational data, while an admixture of inflaton-generated perturbations improves the fit. The inflating curvaton regime mimics the predictions of Nflation. Some parts of parameter space permitted by power spectrum data are excluded by non-Gaussianity constraints. The recent BICEP2 results [P. A. R. Ade et al. (BICEP2 Collaboration), Phys. Rev. Lett. 112, 241101 (2014)], if confirmed as of predominantly primordial origin, require that the inflaton perturbations provide a significant fraction of the total perturbation, ruling out the usual curvaton scenario in which the inflaton perturbations are negligible, though not the admixture regime where both inflaton and curvaton contribute to the spectrum.

Anomalous, extreme weather disrupts obligate seed dispersal mutualism: snow in a subtropical forest ecosystem.

PubMed

Zhou, Youbing; Newman, Chris; Chen, Jin; Xie, Zongqiang; Macdonald, David W

2013-09-01

Ongoing global climate change is predicted to increase the frequency and magnitude of extreme weather events, impacting population dynamics and community structure. There is, however, a critical lack of case studies considering how climatic perturbations affect biotic interactions. Here, we document how an obligate seed dispersal mutualism was disrupted by a temporally anomalous and meteorologically extreme interlude of unseasonably frigid weather, with accompanying snowstorms, in subtropical China, during January-February 2008. Based on the analysis of 5892 fecal samples (representing six mammalian seed dispersers), this event caused a substantial disruption to the relative seed dispersal function for the raisin tree Hovenia dulcis from prestorm 6.29 (2006) and 11.47 (2007), down to 0.35 during the storm (2008). Crucially, this was due to impacts on mammalian seed dispersers and not due to a paucity of fruit, where 4.63 fruit per branch were available in January 2008, vs. 3.73 in 2006 and 3.58 in 2007. An induced dietary shift occurred among omnivorous carnivores during this event, from the consumption fruit to small mammals and birds, reducing their role in seed dispersal substantially. Induced range shift extinguished the functionality of herbivorous mammals completely, however, seed dispersal function was compensated in part by three omnivorous carnivores during poststorm years, and thus while the mutualism remained intact it was enacted by a narrower assemblage of species, rendering the system more vulnerable to extrinsic perturbations. The storm's extended effects also had anthropogenic corollaries - migrating ungulates becoming exposed to heightened levels of illegal hunting - causing long-term modification to the seed dispersal community and mutualism dynamics. Furthermore, degraded forests proved especially vulnerable to the storm's effects. Considering increasing climate variability and anthropogenic disturbance, the impacts of such massive, aberrant events warrant conservation concern, while affording unique insights into the stability of mutualisms and the processes that structure biodiversity and mediate ecosystem dynamics. © 2013 John Wiley & Sons Ltd.

Hard sphere perturbation theory of dense fluids with singular perturbation

NASA Astrophysics Data System (ADS)

Mon, K. K.

2000-02-01

Hard sphere perturbation theories (HSPT) played a significant role in the fundamental understanding of fluids and continues to be a popular method in a wide range of applications. The possibility of difficulty with singular perturbation for some classical soft core model fluids appears to have been overlooked or ignored in the literature. We address this issue in this short note and show by analysis that a region of phase space has been neglected in the standard application of HSPT involving singular perturbation.

Ab Initio Theory of Nuclear Magnetic Resonance Shifts in Metals

NASA Astrophysics Data System (ADS)

D'Avezac, Mayeul; Marzari, Nicola; Mauri, Francesco

2005-03-01

A comprehensive approach for the first-principles determination of all-electron NMR shifts in metallic systems is presented. Our formulation is based on a combination of density-functional perturbation theory and all-electron wavefunction reconstruction, starting from periodic-boundary calculations in the pseudopotential approximation. The orbital contribution to the NMR shift (the chemical shift) is obtained by combining the gauge-including projector augmented-wave approach (GIPAW), originally developed for the case of insulatorsootnotetextC. J. Pickard, Francesco Mauri, Phys. Rev. B, 63, 245101(2001), with the extension of linear-response theory to the case of metallic systemsootnotetextS. de Gironcoli, Phys. Rev. B, 51, 6773(1995). The spin contribution (the Knight shift) is obtained as a response to a finite uniform magnetic field, and through reconstructing the hyperfine interaction between the electron-spin density and the nuclear spins with the projector augmented-wave method (PAWootnotetextC. G. Van de Walle, P. E. Blöchl, Phys. Rev. B, 47, 4244(1993)). Our method is validated with applications to the case of the homogeneous electron gas and of simple metals. (Work supported by MURI grant DAAD 19-03-1-0169 and MIT-France)

Perturbations of the Richardson number field by gravity waves

NASA Technical Reports Server (NTRS)

Wurtele, M. G.; Sharman, R. D.

1985-01-01

An analytic solution is presented for a stratified fluid of arbitrary constant Richardson number. By computer aided analysis the perturbation fields, including that of the Richardson number can be calculated. The results of the linear analytic model were compared with nonlinear simulations, leading to the following conclusions: (1) the perturbations in the Richardson number field, when small, are produced primarily by the perturbations of the shear; (2) perturbations of in the Richardson number field, even when small, are not symmetric, the increase being significantly larger than the decrease (the linear analytic solution and the nonlinear simulations both confirm this result); (3) as the perturbations grow, this asymmetry increases, but more so in the nonlinear simulations than in the linear analysis; (4) for large perturbations of the shear flow, the static stability, as represented by N2, is the dominating mechanism, becoming zero or negative, and producing convective overturning; and (5) the convectional measure of linearity in lee wave theory, NH/U, is no longer the critical parameter (it is suggested that (H/u sub 0) (du sub 0/dz) takes on this role in a shearing flow).

Relationship between gait initiation and disability in individuals affected by multiple sclerosis.

PubMed

Galli, Manuela; Coghe, Giancarlo; Sanna, Paola; Cocco, Eleonora; Marrosu, Maria Giovanna; Pau, Massimiliano

2015-11-01

This study analyzes how multiple sclerosis (MS) does affect one of the most common voluntary activities in life: the gait initiation (GI). The main aim of the work is to characterize the execution of this task by measuring and comparing relevant parameters based on center of pressure (COP) patterns and to study the relationship between these and the level of expanded disability status scale (EDSS). To this aim, 95 MS subjects with an average EDSS score of 2.4 and 35 healthy subjects were tested using a force platform during the transition from standing posture to gait. COP time-series were acquired and processed to extract a number of parameters related to the trajectory followed by the COP. The statistical analysis revealed that only a few measurements were statistically different between the two groups and only these were subsequently correlated with EDSS score. The correlation analysis underlined that a progressive alteration of the task execution can be directly related with the increase of EDSS score. These finding suggest that most of the impairment found in people with MS comes from the first part of the COP pattern, the anticipatory postural adjustments (APAs). The central nervous system performs APAs before every voluntary movement to minimize balance perturbation due to the movement itself. Gait Initiation's APAs consist in some ankle muscles contractions that induce a backward COP shift to the swing limb. The analysis here performed highlighted that MS affected patients have a reduced posterior COP shift that reveals that the anticipatory mechanism is impaired. Copyright © 2015 Elsevier B.V. All rights reserved.

Stability analysis of ultrasound thick-shell contrast agents.

PubMed

Lu, Xiaozhen; Chahine, Georges L; Hsiao, Chao-Tsung

2012-01-01

The stability of thick shell encapsulated bubbles is studied analytically. 3-D small perturbations are introduced to the spherical oscillations of a contrast agent bubble in response to a sinusoidal acoustic field with different amplitudes of excitation. The equations of the perturbation amplitudes are derived using asymptotic expansions and linear stability analysis is then applied to the resulting differential equations. The stability of the encapsulated microbubbles to nonspherical small perturbations is examined by solving an eigenvalue problem. The approach then identifies the fastest growing perturbations which could lead to the breakup of the encapsulated microbubble or contrast agent. © 2012 Acoustical Society of America.

Remarks on Chern-Simons Invariants

NASA Astrophysics Data System (ADS)

Cattaneo, Alberto S.; Mnëv, Pavel

2010-02-01

The perturbative Chern-Simons theory is studied in a finite-dimensional version or assuming that the propagator satisfies certain properties (as is the case, e.g., with the propagator defined by Axelrod and Singer). It turns out that the effective BV action is a function on cohomology (with shifted degrees) that solves the quantum master equation and is defined modulo certain canonical transformations that can be characterized completely. Out of it one obtains invariants.

On the problem of meteor shower's radiants displacement

NASA Astrophysics Data System (ADS)

Tikhomirova, E. N.

2011-06-01

In the context of the perturbed two-body problem a method to evaluate radiant shift for a meteor shower is suggested. We consider the evolution of a meteoroid particle which after every complete revolution "migrates" from one elliptic orbit to another with slightly changed orbital parameters. The obtained analytical solutions of the equations of particle's motion take into account radiation pressure, Poynting-Robertson effect and its corpuscular part.

Ultrasensitive Laser Spectroscopy in Solids: Statistical Fine Structure and Single-Molecule Detection

DTIC Science & Technology

1990-03-28

observation, detection of the optical absorption of a single pentacene molecule in a p-terphenyl crystal, opens the door to new studies of single local ...produce appreciable quadratic Stark shifting. Such effects would greatly perturb the local field around the pentacene molecule, making detection of the...of the local surroundings of pentacene molecules with single injected charge carriers nearby may become an interesting field; however, for the

SU‐C‐105‐05: Reference Dosimetry of High‐Energy Electron Beams with a Farmer‐Type Ionization Chamber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muir, B; Rogers, D

2013-06-15

Purpose: To investigate gradient effects and provide Monte Carlo calculated beam quality conversion factors to characterize the Farmer‐type NE2571 ion chamber for high‐energy reference dosimetry of clinical electron beams. Methods: The EGSnrc code system is used to calculate the absorbed dose to water and to the gas in a fully modeled NE2571 chamber as a function of depth in a water phantom. Electron beams incident on the surface of the phantom are modeled using realistic BEAMnrc accelerator simulations and electron beam spectra. Beam quality conversion factors are determined using calculated doses to water and to air in the chamber inmore » high‐energy electron beams and in a cobalt‐60 reference field. Calculated water‐to‐air stopping power ratios are employed for investigation of the overall ion chamber perturbation factor. Results: An upstream shift of 0.3–0.4 multiplied by the chamber radius, r-cav, both minimizes the variation of the overall ion chamber perturbation factor with depth and reduces the difference between the beam quality specifier (R{sub 5} {sub 0}) calculated using ion chamber simulations and that obtained with simulations of dose‐to‐water in the phantom. Beam quality conversion factors are obtained at the reference depth and gradient effects are optimized using a shift of 0.2r-cav. The photon‐electron conversion factor, k-ecal, amounts to 0.906 when gradient effects are minimized using the shift established here and 0.903 if no shift of the data is used. Systematic uncertainties in beam quality conversion factors are investigated and amount to between 0.4 to 1.1% depending on assumptions used. Conclusion: The calculations obtained in this work characterize the use of an NE2571 ion chamber for reference dosimetry of high‐energy electron beams. These results will be useful as the AAPM continues to review their reference dosimetry protocols.« less

Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments.

PubMed

Dubinets, Nikita; Slipchenko, Lyudmila V

2017-07-20

Accuracy of the effective fragment potential (EFP) method was explored for describing intermolecular interaction energies in three dimers with strong H-bonded interactions, formic acid, formamide, and formamidine dimers, which are a part of HBC6 database of noncovalent interactions. Monomer geometries in these dimers change significantly as a function of intermonomer separation. Several EFP schemes were considered, in which fragment parameters were prepared for a fragment in its gas-phase geometry or recomputed for each unique fragment geometry. Additionally, a scheme in which gas-phase fragment parameters are shifted according to relaxed fragment geometries is introduced and tested. EFP data are compared against the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in a complete basis set (CBS) and the symmetry adapted perturbation theory (SAPT). All considered EFP schemes provide a good agreement with CCSD(T)/CBS for binding energies at equilibrium separations, with discrepancies not exceeding 2 kcal/mol. However, only the schemes that utilize relaxed fragment geometries remain qualitatively correct at shorter than equilibrium intermolecular distances. The EFP scheme with shifted parameters behaves quantitatively similar to the scheme in which parameters are recomputed for each monomer geometry and thus is recommended as a computationally efficient approach for large-scale EFP simulations of flexible systems.

Shark Tooth Weapons from the 19th Century Reflect Shifting Baselines in Central Pacific Predator Assemblies

PubMed Central

Drew, Joshua; Philipp, Christopher; Westneat, Mark W.

2013-01-01

The reefs surrounding the Gilbert Islands (Republic of Kiribati, Central Pacific), like many throughout the world, have undergone a period of rapid and intensive environmental perturbation over the past 100 years. A byproduct of this perturbation has been a reduction of the number of shark species present in their waters, even though sharks play an important in the economy and culture of the Gilbertese. Here we examine how shark communities changed over time periods that predate the written record in order to understand the magnitude of ecosystem changes in the Central Pacific. Using a novel data source, the shark tooth weapons of the Gilbertese Islanders housed in natural history museums, we show that two species of shark, the Spot-tail (Carcharhinus sorrah) and the Dusky (C. obscurus), were present in the islands during the last half of the 19th century but not reported in any historical literature or contemporary ichthyological surveys of the region. Given the importance of these species to the ecology of the Gilbert Island reefs and to the culture of the Gilbertese people, documenting these shifts in baseline fauna represents an important step toward restoring the vivid splendor of both ecological and cultural diversity. PMID:23573214

Solution structure of leptospiral LigA4 Big domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Song; Zhang, Jiahai; Zhang, Xuecheng

Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Bigmore » domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca{sup 2+} binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca{sup 2+}-binding site was identified by strains-all and NMR chemical shift perturbation.« less

Interactions between Human Liver Fatty Acid Binding Protein and Peroxisome Proliferator Activated Receptor Selective Drugs

PubMed Central

Velkov, Tony

2013-01-01

Fatty acid binding proteins (FABPs) act as intracellular shuttles for fatty acids as well as lipophilic xenobiotics to the nucleus, where these ligands are released to a group of nuclear receptors called the peroxisome proliferator activated receptors (PPARs). PPAR mediated gene activation is ultimately involved in maintenance of cellular homeostasis through the transcriptional regulation of metabolic enzymes and transporters that target the activating ligand. Here we show that liver- (L-) FABP displays a high binding affinity for PPAR subtype selective drugs. NMR chemical shift perturbation mapping and proteolytic protection experiments show that the binding of the PPAR subtype selective drugs produces conformational changes that stabilize the portal region of L-FABP. NMR chemical shift perturbation studies also revealed that L-FABP can form a complex with the PPAR ligand binding domain (LBD) of PPARα. This protein-protein interaction may represent a mechanism for facilitating the activation of PPAR transcriptional activity via the direct channeling of ligands between the binding pocket of L-FABP and the PPARαLBD. The role of L-FABP in the delivery of ligands directly to PPARα via this channeling mechanism has important implications for regulatory pathways that mediate xenobiotic responses and host protection in tissues such as the small intestine and the liver where L-FABP is highly expressed. PMID:23476633

A computational study of hydrogen-bonded X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) complexes

NASA Astrophysics Data System (ADS)

McDowell, Sean A. C.

2018-03-01

An MP2/6-311++G(3df,3pd) computational study of a series of hydrogen-bonded complexes X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) was undertaken to assess the trends in the relative stability and other molecular properties with variation of both the X group and the chemical hardness of the Y atom of YZ. The red- and blue-shifting propensities of the proton donor X3CH were investigated by considering the Csbnd H bond length change and its associated vibrational frequency shift. The proton donor Cl3CH, which has a positive dipole moment derivative with respect to Csbnd H bond extension, tends to form red-shifted complexes, this tendency being modified by the hardness (and dipole moment) associated with the proton acceptor. On the other hand, F3CH has a negative dipole moment derivative and tends to form blue-shifted complexes, suggesting that as X becomes more electron-withdrawing, the proton donor should have a negative dipole moment derivative and form blue-shifted complexes. Surprisingly, the most polar proton donor (NC)3CH was found to have a positive dipole moment derivative and produces red-shifted complexes. A perturbative model was found useful in rationalizing the trends for the Csbnd H bond length change and associated frequency shift.

Critical Layers and Protoplanetary Disk Turbulence

NASA Astrophysics Data System (ADS)

Umurhan, Orkan M.; Shariff, Karim; Cuzzi, Jeffrey N.

2016-10-01

A linear analysis of the zombie vortex instability (ZVI) is performed in a stratified shearing sheet setting for three model barotropic shear flows. The linear analysis is done by utilizing a Green’s function formulation to resolve the critical layers of the associated normal-mode problem. The instability is the result of a resonant interaction between a Rossby wave and a gravity wave that we refer to as Z-modes. The associated critical layer is the location where the Doppler-shifted frequency of a distant Rossby wave equals the local Brunt-Väisälä frequency. The minimum required Rossby number for instability, {\\mathtt{Ro}}=0.2, is confirmed for parameter values reported in the literature. It is also found that the shear layer supports the instability in the limit where stratification vanishes. The ZVI is examined in a jet model, finding that the instability can occur for {\\mathtt{Ro}}=0.05. Nonlinear vorticity forcing due to unstable Z-modes is shown to result in the creation of a jet flow at the critical layer emerging as the result of the competition between the vertical lifting of perturbation radial vorticity and the radial transport of perturbation vertical vorticity. We find that the picture of this instability leading to a form of nonlinearly driven self-replicating pattern of creation and destruction is warranted: a parent jet spawns a growing child jet at associated critical layers. A mature child jet creates a next generation of child jets at associated critical layers of the former while simultaneously contributing to its own destruction via the Rossby wave instability.

Aeroelasticity Analysis of AN Industrial Gas Turbine Combustor Using a Simplified Combustion Model

NASA Astrophysics Data System (ADS)

Bréard, C.; Sayma, A. I.; Vahdati, M.; Imregun, M.

2002-12-01

Lean premixed industrial gas turbine combustors are susceptible to flame instabilities, resulting in large unsteady pressure waves that may cause the discharge nozzle to experience excessive vibration levels. A detailed aeroelasticity analysis, aimed at investigating possible structural failure mechanisms, was undertaken using a time-accurate unsteady flow representation, a simplified combustion disturbance and a structural model of the discharge nozzle. The computational domain included the lower part of the combustor geometry as well as the nozzle guide vanes (NGVs) at the HP turbine inlet. A pressure perturbation, representing the unsteadiness due to the combustion process, was applied below the tertiary fuel inlet and its frequency was set to each structural natural frequency in turn. The propagation of the pressure perturbation through the combustor nozzle, its reflection from the NGVs and further reflections were monitored using two different models. The first one, the so-called ``open'' system, ignored the reflections from the upper part of the combustion chamber while the second one, the ``closed'' system, assumed full reflection with an appropriate time shift. The calculations have shown that the imposed excitation could generate unsteady pressure shapes that were correlated with the ``flap'' modes of the discharge nozzle. In addition, an acoustic resonance condition was observed when the forcing pressure wave had a frequency close to 550 Hz, the experimentally observed failure frequency of the nozzle. The co-existence of these two factors, i.e., excitation/structural-mode match and the possibility of acoustic resonance, was thought to have the potential of producing very high vibration response.

SU-E-P-34: Dose Perturbation Caused by Sun Nuclear QED Diode When Used for Very Small Electron Fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klash, S; Steinman, J; Stanley, T

2015-06-15

Purpose: Diodes are utilized by radiotherapy departments to help verify that treatment fields are being delivered correctly to the patient. Some treatment fields utilize electron beams along with a cerrobend cutout to shape the beam to the area to be treated. Cerrobend cutouts can sometimes be very small < 2×2-cm2. Some published work has addressed diode perturbation for cutout sizes down to 1.5-cm, this work addresses the diode perturbation of the Sun Nuclear QEDTM diode for cutouts as small as 0.5-cm in diameter. Methods: Measurements were taken with an A16 Exradin micro-chamber in Solid Water to 100-cm SSD. Dmax wasmore » determined for each cutout using various amounts of Solid Water in 1–2 mm increments to account for the dmax shifting in small fields. The diode was placed on top of the solid water to 100-cm SSD in the center of the cutout. Measurements were taken with no diode for comparison. The cutouts ranged in diameter from 0.5-cm to 5.0-cm and included the open 6×6 insert. Measurements were made for energies 6, 9, 12, 15,&18 MeV. Results: For 6 MeV, the percent dose reduction from the diode in the cutout field compared to the field without the diode ranged from 35% to 25% as a function of cutout size. For higher energies, this percentage decreased and generally was 25% to 15%. It was observed that dmax shifts significantly upstream for very small cutouts (<2-cm diameter) to less than 1 cm for all energies. Conclusion: The presence of diodes in small electron fields is enough to cause significant dose perturbation to the target volume. It is recommended that diodes for very small electron fields be used sparingly or possibly with a dose correction per treatment fraction(s), if the total projected delivered dose is going to be significantly different from that prescribed by the physician.« less

Noise Reduction in High-Throughput Gene Perturbation Screens

USDA-ARS?s Scientific Manuscript database

Motivation: Accurate interpretation of perturbation screens is essential for a successful functional investigation. However, the screened phenotypes are often distorted by noise, and their analysis requires specialized statistical analysis tools. The number and scope of statistical methods available...

Perturbations from strings don't look like strings!

NASA Technical Reports Server (NTRS)

Albrecht, Andreas; Stebbins, Albert

1991-01-01

A systematic analysis is challenging popular ideas about perturbation from cosmic strings. One way in which the picture has changed is reviewed. It is concluded that, while the scaling properties of cosmic strings figure significantly in the analysis, care must be taken when thinking in terms of single time snapshots. The process of seeding density perturbations is not fundamentally localized in time, and this fact can wash out many of the details which appear in a single snapshot.

A search for thermospheric composition perturbations due to vertical winds

NASA Astrophysics Data System (ADS)

Krynicki, Matthew P.

The thermosphere is generally in hydrostatic equilibrium, with winds blowing horizontally along stratified constant-pressure surfaces, driven by the dayside-to-nightside pressure gradient. A marked change in this paradigm resulted after Spencer et al. [1976] reported vertical wind measurements of 80 m·s-1 from analyses of AE-C satellite data. It is now established that the thermosphere routinely supports large-magnitude (˜30-150 m·s-1) vertical winds at auroral latitudes. These vertical winds represent significant departure from hydrostatic and diffusive equilibrium, altering locally---and potentially globally---the thermosphere's and ionosphere's composition, chemistry, thermodynamics and energy budget. Because of their localized nature, large-magnitude vertical wind effects are not entirely known. This thesis presents ground-based Fabry-Perot Spectrometer OI(630.0)-nm observations of upper-thermospheric vertical winds obtained at Inuvik, NT, Canada and Poker Flat, AK. The wind measurements are compared with vertical displacement estimates at ˜104 km2 horizontal spatial scales determined from a new modification to the electron transport code of Lummerzheim and Lilensten [1994] as applied to FUV-wavelength observations by POLAR spacecraft's Ultraviolet Imager [Torr et al. , 1995]. The modification, referred to as the column shift, simulates vertical wind effects such as neutral transport and disruption of diffusive equilibrium by vertically displacing the Hedin [1991] MSIS-90 [O2]/[N2] and [O]/([N2]+[O2]) mixing ratios and subsequently redistributing the O, O2, and N 2 densities used in the transport code. Column shift estimates are inferred from comparisons of UVI OI(135.6)-nm auroral observations to their corresponding modeled emission. The modeled OI(135.6)-nm brightness is determined from the modeled thermospheric response to electron precipitation and estimations of the energy flux and characteristic energy of the precipitation, which are inferred from UVI-observed Lyman-Birge-Hopfield N2 emissions in two wavelength ranges. Two-dimensional column shift maps identify the spatial morphology of thermospheric composition perturbations associated with auroral forms relative to the model thermosphere. Case-study examples and statistical analyses of the column shift data sets indicate that column shifts can be attributed to vertical winds. Unanticipated limitations associated with modeling of the OI(135.6)-nm auroral emission make absolute column shift estimates indeterminate. Insufficient knowledge of thermospheric air-parcel time histories hinders interpretations of point-to-point time series comparisons between column shifts and vertical winds.

First demonstration of the fast-to-slow corrector current shift in the NSLS-II storage ring

DOE PAGES

Yang, Xi; Tian, Yuke; Yu, Li Hua; ...

2018-04-01

In order to realize the full benefits of the high brightness and ultra-small beam sizes of NSLS-II, it is essential that the photon beams are exceedingly stable. In the circumstances of implementing local bumps, changing ID gaps, and long term drifting, the fast orbit feedback (FOFB) requires shifting the fast corrector strengths to the slow correctors to prevent the fast corrector saturation and to make the beam orbit stable in the sub-micron level. As the result, a reliable and precise technique of fast-to-slow corrector strength shift has been developed and tested at NSLS-II. This technique is based on the fastmore » corrector response to the slow corrector change when the FOFB is on. In this article, the shift technique is described and the result of proof-of-principle experiment carried out at NSLS-II is presented. The maximum fast corrector current was reduced from greater than 0.45 A to less than 0.04 A with the orbit perturbation within ±1 μm.« less

First demonstration of the fast-to-slow corrector current shift in the NSLS-II storage ring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xi; Tian, Yuke; Yu, Li Hua

In order to realize the full benefits of the high brightness and ultra-small beam sizes of NSLS-II, it is essential that the photon beams are exceedingly stable. In the circumstances of implementing local bumps, changing ID gaps, and long term drifting, the fast orbit feedback (FOFB) requires shifting the fast corrector strengths to the slow correctors to prevent the fast corrector saturation and to make the beam orbit stable in the sub-micron level. As the result, a reliable and precise technique of fast-to-slow corrector strength shift has been developed and tested at NSLS-II. This technique is based on the fastmore » corrector response to the slow corrector change when the FOFB is on. In this article, the shift technique is described and the result of proof-of-principle experiment carried out at NSLS-II is presented. The maximum fast corrector current was reduced from greater than 0.45 A to less than 0.04 A with the orbit perturbation within ±1 μm.« less

Exceptional points enhance sensing in an optical microcavity

NASA Astrophysics Data System (ADS)

Chen, Weijian; Kaya Özdemir, Şahin; Zhao, Guangming; Wiersig, Jan; Yang, Lan

2017-08-01

Sensors play an important part in many aspects of daily life such as infrared sensors in home security systems, particle sensors for environmental monitoring and motion sensors in mobile phones. High-quality optical microcavities are prime candidates for sensing applications because of their ability to enhance light-matter interactions in a very confined volume. Examples of such devices include mechanical transducers, magnetometers, single-particle absorption spectrometers, and microcavity sensors for sizing single particles and detecting nanometre-scale objects such as single nanoparticles and atomic ions. Traditionally, a very small perturbation near an optical microcavity introduces either a change in the linewidth or a frequency shift or splitting of a resonance that is proportional to the strength of the perturbation. Here we demonstrate an alternative sensing scheme, by which the sensitivity of microcavities can be enhanced when operated at non-Hermitian spectral degeneracies known as exceptional points. In our experiments, we use two nanoscale scatterers to tune a whispering-gallery-mode micro-toroid cavity, in which light propagates along a concave surface by continuous total internal reflection, in a precise and controlled manner to exceptional points. A target nanoscale object that subsequently enters the evanescent field of the cavity perturbs the system from its exceptional point, leading to frequency splitting. Owing to the complex-square-root topology near an exceptional point, this frequency splitting scales as the square root of the perturbation strength and is therefore larger (for sufficiently small perturbations) than the splitting observed in traditional non-exceptional-point sensing schemes. Our demonstration of exceptional-point-enhanced sensitivity paves the way for sensors with unprecedented sensitivity.

Using variance structure to quantify responses to perturbation in fish catches

USGS Publications Warehouse

Vidal, Tiffany E.; Irwin, Brian J.; Wagner, Tyler; Rudstam, Lars G.; Jackson, James R.; Bence, James R.

2017-01-01

We present a case study evaluation of gill-net catches of Walleye Sander vitreus to assess potential effects of large-scale changes in Oneida Lake, New York, including the disruption of trophic interactions by double-crested cormorants Phalacrocorax auritus and invasive dreissenid mussels. We used the empirical long-term gill-net time series and a negative binomial linear mixed model to partition the variability in catches into spatial and coherent temporal variance components, hypothesizing that variance partitioning can help quantify spatiotemporal variability and determine whether variance structure differs before and after large-scale perturbations. We found that the mean catch and the total variability of catches decreased following perturbation but that not all sampling locations responded in a consistent manner. There was also evidence of some spatial homogenization concurrent with a restructuring of the relative productivity of individual sites. Specifically, offshore sites generally became more productive following the estimated break point in the gill-net time series. These results provide support for the idea that variance structure is responsive to large-scale perturbations; therefore, variance components have potential utility as statistical indicators of response to a changing environment more broadly. The modeling approach described herein is flexible and would be transferable to other systems and metrics. For example, variance partitioning could be used to examine responses to alternative management regimes, to compare variability across physiographic regions, and to describe differences among climate zones. Understanding how individual variance components respond to perturbation may yield finer-scale insights into ecological shifts than focusing on patterns in the mean responses or total variability alone.

Science & Technology Review May 2006

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aufderheide III, M B

2006-04-03

This month's issue has the following articles: (1) Science and Technology Help the Nation Counter Terrorism--Commentary by Raymond J. Juzaitis; (2) Imagers Provide Eyes to See Gamma Rays--Gamma-ray imagers provide increased radiation detection capabilities and enhance the nation's arsenal for homeland security; (3) Protecting the Nation's Livestock--Foot-and-mouth disease could devastate America's livestock; a new assay provides a rapid means to detect it; (4) Measures for Measures--Laboratory physicists combine emissivity and reflectivity to achieve highly accurate temperature measurements of metal foils; and (5) Looping through the Lamb Shift--Livermore scientists measured a small perturbation in the spectra of highly ionized uranium--the firstmore » measurement of the two-loop Lamb shift in a bound state.« less

Head-on collision of ring dark solitons in Bose Einstein condensates

NASA Astrophysics Data System (ADS)

Xue, Ju-Kui; Peng, Ping

2006-06-01

The ring dark solitons and their head-on collisions in a Bose-Einstein condensates with thin disc-shaped potential are studied. It is shown that the system admits a solution with two concentric ring solitons, one moving inwards and the other moving outwards, which in small-amplitude limit, are described by the two cylindrical KdV equations in the respective reference frames. By using the extended Poincaré-Lighthill-Kuo perturbation method, the analytical phase shifts following the head-on collisions between two ring dark solitary waves are derived. It is shown that the phase shifts decrease with the radial coordinate r according to the r-1/3 law and depend on the initial soliton amplitude and radius.

Composite pulsed field gradients with refocused chemical shifts and short recovery time.

PubMed

Hu, H; Shaka, A J

1999-01-01

An improved self-compensating pulsed field gradient (PFG) technique that combines antiphase gradient pairs with broadband frequency-modulated 180 degrees pulses is proposed. The antiphase gradient pairs lead to superb system recovery. In addition, evolution under chemical shift and heteronuclear J coupling are refocused during the PFG, making it appear effectively instantaneous. This new approach makes it possible to obtain high-resolution phase-sensitive 2D spectra for the PFG version of many experiments such as COSY, DQF-COSY, and HSQC without adding extra compensating delays or pulses. While reasonable suppression of unwanted magnetization is achieved, this method also gives satisfactory retention of desired signals. As a bonus, the field-frequency lock is not perturbed during the experiments. Copyright 1999 Academic Press.

5-HT in the enteric nervous system: gut function and neuropharmacology.

PubMed

McLean, Peter G; Borman, Richard A; Lee, Kevin

2007-01-01

In recent times, the perception of functional gastrointestinal disorders such as irritable bowel syndrome (IBS) has shifted fundamentally. Such disorders are now thought of as serious diseases characterized by perturbations in the neuronal regulation of gastrointestinal function. The concept of visceral hypersensitivity, the characterization of neuronal networks in the 'brain-gut axis' and the identification of several novel 5-HT-mediated mechanisms have contributed to this shift. Here, we review how some of the more promising of these new mechanisms (e.g. those involving 5-HT transporters and the 5-HT(2B), 5-HT(7) and putative 5-HT(1p) receptors) might lead to a range of second-generation therapies that could revolutionize the treatment of functional gastrointestinal disorders, particularly IBS.

Modal control of an unstable periodic orbit

NASA Astrophysics Data System (ADS)

Wiesel, W.; Shelton, W.

1983-03-01

Floquet theory is applied to the problem of designing a control system for a satellite in an unstable periodic orbit. Expansion about a periodic orbit produces a time-periodic linear system, which is augmented by a time-periodic control term. It is shown that this can be done such that (1) the application of control produces only inertial accelerations, (2) positive real Poincareexponents are shifted into the left half-plane, and (3) the shift of the exponent is linear with control gain. These developments are applied to an unstable orbit near the earth-moon L(3) point pertubed by the sun. Finally, it is shown that the control theory can be extended to include first order perturbations about the periodic orbit without increase in control cost.

Modal control of an unstable periodic orbit

NASA Technical Reports Server (NTRS)

Wiesel, W.; Shelton, W.

1983-01-01

Floquet theory is applied to the problem of designing a control system for a satellite in an unstable periodic orbit. Expansion about a periodic orbit produces a time-periodic linear system, which is augmented by a time-periodic control term. It is shown that this can be done such that (1) the application of control produces only inertial accelerations, (2) positive real Poincareexponents are shifted into the left half-plane, and (3) the shift of the exponent is linear with control gain. These developments are applied to an unstable orbit near the earth-moon L(3) point pertubed by the sun. Finally, it is shown that the control theory can be extended to include first order perturbations about the periodic orbit without increase in control cost.

How different is the borazine-acetylene dimer from the benzene-acetylene dimer? A matrix isolation infrared and ab initio quantum chemical study

NASA Astrophysics Data System (ADS)

Verma, Kanupriya; Viswanathan, K. S.; Majumder, Moumita; Sathyamurthy, N.

2017-11-01

The 1:1 dimer of borazine-acetylene has been studied for the first time, both experimentally and computationally. The borazine-acetylene dimer was trapped in Ar and N2 matrices, and studied using infrared spectroscopy. Our experiments clearly revealed two isomers of the borazine-acetylene complex, one in which the N-H of borazine interacted with the carbon of acetylene, and another in which the C-H of acetylene formed a hydrogen bond with a nitrogen atom of borazine. The formation of both isomers in the matrix was evidenced by shifts in the vibrational frequencies of the appropriate modes. Reassuringly, the experimental observations were corroborated by our computations using the second-order Møller-Plesset perturbation theoretic method and coupled-cluster singles, doubles and perturbative triples method in conjunction with different Dunning basis sets, which indicated both these isomers to be stable minima, with the N-HṡṡṡC complex being the global minimum. Atoms-in-molecules and energy decomposition analysis were also carried out for the different isomers of the dimer. These studies reveal that replacing the three C-C linkages in benzene with three B-N linkages in borazine modifies the interaction in the dimer sufficiently, to result in a different potential energy landscape for the borazine-acetylene system when compared with the benzene-acetylene system.

Adaptive control of center of mass (global) motion and its joint (local) origin in gait.

PubMed

Yang, Feng; Pai, Yi-Chung

2014-08-22

Dynamic gait stability can be quantified by the relationship of the motion state (i.e. the position and velocity) between the body center of mass (COM) and its base of support (BOS). Humans learn how to adaptively control stability by regulating the absolute COM motion state (i.e. its position and velocity) and/or by controlling the BOS (through stepping) in a predictable manner, or by doing both simultaneously following an external perturbation that disrupts their regular relationship. Post repeated-slip perturbation training, for instance, older adults learned to forward shift their COM position while walking with a reduced step length, hence reduced their likelihood of slip-induced falls. How and to what extent each individual joint influences such adaptive alterations is mostly unknown. A three-dimensional individualized human kinematic model was established. Based on the human model, sensitivity analysis was used to systematically quantify the influence of each lower limb joint on the COM position relative to the BOS and the step length during gait. It was found that the leading foot had the greatest effect on regulating the COM position relative to the BOS; and both hips bear the most influence on the step length. These findings could guide cost-effective but efficient fall-reduction training paradigm among older population. Copyright © 2014 Elsevier Ltd. All rights reserved.

Experimental studies of high-confinement mode plasma response to non-axisymmetric magnetic perturbations in ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Suttrop, W.; Kirk, A.; Nazikian, R.; Leuthold, N.; Strumberger, E.; Willensdorfer, M.; Cavedon, M.; Dunne, M.; Fischer, R.; Fietz, S.; Fuchs, J. C.; Liu, Y. Q.; McDermott, R. M.; Orain, F.; Ryan, D. A.; Viezzer, E.; The ASDEX Upgrade Team; The DIII-D Team; The Eurofusion MST1 Team

2017-01-01

The interaction of externally applied small non-axisymmetric magnetic perturbations (MP) with tokamak high-confinement mode (H-mode) plasmas is reviewed and illustrated by recent experiments in ASDEX Upgrade. The plasma response to the vacuum MP field is amplified by stable ideal kink modes with low toroidal mode number n driven by the H-mode edge pressure gradient (and associated bootstrap current) which is experimentally evidenced by an observable shift of the poloidal mode number m away from field alignment (m  =  qn, with q being the safety factor) at the response maximum. A torque scan experiment demonstrates the importance of the perpendicular electron flow for shielding of the resonant magnetic perturbation, as expected from a two-fluid MHD picture. Two significant effects of MP occur in H-mode plasmas at low pedestal collisionality, ν \\text{ped}\\ast≤slant 0.4 : (a) a reduction of the global plasma density by up to 61 % and (b) a reduction of the energy loss associated with edge localised modes (ELMs) by a factor of up to 9. A comprehensive database of ELM mitigation pulses at low {ν\\ast} in ASDEX Upgrade shows that the degree of ELM mitigation correlates with the reduction of pedestal pressure which in turn is limited and defined by the onset of ELMs, i. e. a modification of the ELM stability limit by the magnetic perturbation.

A Systems Approach to Stress, Stressors and Resilience in Humans

PubMed Central

Oken, Barry S.; Chamine, Irina; Wakeland, Wayne

2014-01-01

The paper focuses on the biology of stress and resilience and their biomarkers in humans from the system science perspective. A stressor pushes the physiological system away from its baseline state towards a lower utility state. The physiological system may return towards the original state in one attractor basin but may be shifted to a state in another, lower utility attractor basin. While some physiological changes induced by stressors may benefit health, there is often a chronic wear and tear cost due to implementing changes to enable the return of the system to its baseline state and maintain itself in the high utility baseline attractor basin following repeated perturbations. This cost, also called allostatic load, is the utility reduction associated with both a change in state and with alterations in the attractor basin that affect system responses following future perturbations. This added cost can increase the time course of the return to baseline or the likelihood of moving into a different attractor basin following a perturbation. Opposite to this is the system’s resilience which influences its ability to return to the high utility attractor basin following a perturbation by increasing the likelihood and/or speed of returning to the baseline state following a stressor. This review paper is a qualitative systematic review; it covers areas most relevant for moving the stress and resilience field forward from a more quantitative and neuroscientific perspective. PMID:25549855

Two color laser driven THz generation in clustered plasma

NASA Astrophysics Data System (ADS)

Malik, Rakhee; Uma, R.; Kumar, Pawan

2017-07-01

A scheme of terahertz (THz) generation, using nonlinear mixing of two color laser (fundamental ω1 and slightly frequency shifted second harmonic ω2 ) in clustered plasma, is investigated. The lasers exert ponderomotive force on cluster electrons and drive density perturbations at 2 ω1 and ω2-ω1 . The density perturbations beat with the oscillatory velocities to produce nonlinear current at ω2-2 ω1 , generating THz radiation. The radiation is enhanced due to cluster plasmon resonance and by phase matching introduced through a density ripple. The generation involves third order nonlinearity and does not require a magnetic field or inhomogeneity to sustain it. We report THz power conversion efficiency ˜ 10-4 at 1 μm and 0.5 μm wavelengths with intensity ˜ 3 ×1014W/cm 2 .

Pressure-enabled phonon engineering in metals

PubMed Central

Lanzillo, Nicholas A.; Thomas, Jay B.; Watson, Bruce; Washington, Morris; Nayak, Saroj K.

2014-01-01

We present a combined first-principles and experimental study of the electrical resistivity in aluminum and copper samples under pressures up to 2 GPa. The calculations are based on first-principles density functional perturbation theory, whereas the experimental setup uses a solid media piston–cylinder apparatus at room temperature. We find that upon pressurizing each metal, the phonon spectra are blue-shifted and the net electron–phonon interaction is suppressed relative to the unstrained crystal. This reduction in electron–phonon scattering results in a decrease in the electrical resistivity under pressure, which is more pronounced for aluminum than for copper. We show that density functional perturbation theory can be used to accurately predict the pressure response of the electrical resistivity in these metals. This work demonstrates how the phonon spectra in metals can be engineered through pressure to achieve more attractive electrical properties. PMID:24889627

Microwave measurement of the mass of frozen hydrogen pellets

DOEpatents

Talanker, Vera; Greenwald, Martin

1990-01-01

A nondestructive apparatus and method for measuring the mass of a moving object, based on the perturbation of the dielectric character of a resonant microwave cavity caused by the object passing through the cavity. An oscillator circuit is formed with a resonant cavity in a positive feedback loop of a microwave power amplifier. The moving object perturbs the resonant characteristics of the cavity causing a shift in the operating frequency of the oscillator proportional to the ratio of the pellet volume to the volume of the cavity. Signals from the cavity oscillation are mixed with a local oscillator. Then the IF frequency from the mixer is measured thereby providing a direct measurement of pellet mass based upon known physical properties and relationships. This apparatus and method is particularly adapted for the measurement of frozen hydrogen pellets.

Defining the interaction of human soluble lectin ZG16p and mycobacterial phosphatidylinositol mannosides

PubMed Central

Ikeda, Akemi; Kojima-Aikawa, Kyoko; Taniguchi, Naoyuki; Varón Silva, Daniel; Feizi, Ten; Seeberger, Peter H.; Yamaguchi, Yoshiki

2018-01-01

ZG16p is a soluble mammalian lectin that interacts with mannose and heparan sulfate. Here we describe detailed analyses of the interactions of human ZG16p with mycobacterial phosphatidylinositol mannosides (PIMs), using glycan microarray and NMR. Pathogen-related glycan microarray analysis identified phosphatidylinositol mono- and di-mannosides (PIM1 and PIM2) as novel ligand candidates of ZG16p. Saturation Transfer Difference (STD) NMR and transferred NOE experiments with chemically synthesized PIM glycans indicate that PIMs preferentially interacts with ZG16p using the mannose residues. Binding site of PIMs is identified by chemical shift perturbation experiments using uniformly 15N-labeled ZG16p. NMR results with docking simulations suggest a binding mode of ZG16p and PIM glycan, which would help to consider the physiological role of ZG16p. PMID:25919894

Kinetic Alfvén waves and particle response associated with a shock-induced, global ULF perturbation of the terrestrial magnetosphere

DOE PAGES

Malaspina, David M.; Claudepierre, Seth G.; Takahashi, Kazue; ...

2015-11-14

On 2 October 2013, the arrival of an interplanetary shock compressed the Earth's magnetosphere and triggered a global ULF (ultra low frequency) oscillation. Furthermore, the Van Allen Probe B spacecraft observed this large-amplitude ULF wave in situ with both magnetic and electric field data. Broadband waves up to approximately 100 Hz were observed in conjunction with, and modulated by, this ULF wave. Detailed analysis of fields and particle data reveals that these broadband waves are Doppler-shifted kinetic Alfvén waves. This event then suggests that magnetospheric compression by interplanetary shocks can induce abrupt generation of kinetic Alfvén waves over large portionsmore » of the inner magnetosphere, potentially driving previously unconsidered wave-particle interactions throughout the inner magnetosphere during the initial response of the magnetosphere to shock impacts.« less

Perturbation Effects on a Supercritical C7H16/N2 Mixing Layer

NASA Technical Reports Server (NTRS)

Okongo'o, Nora; Bellan, Josette

2008-01-01

A computational-simulation study has been presented of effects of perturbation wavelengths and initial Reynolds numbers on the transition to turbulence of a heptane/nitrogen mixing layer at supercritical pressure. The governing equations for the simulations were the same as those of related prior studies reported in NASA Tech Briefs. Two-dimensional (2D) simulations were performed with initially im posed span wise perturbations whereas three-dimensional (3D) simulations had both streamwise and spanwise initial perturbations. The 2D simulations were undertaken to ascertain whether perturbations having the shortest unstable wavelength obtained from a linear stability analysis for inviscid flow are unstable in viscous nonlinear flows. The goal of the 3D simulations was to ascertain whether perturbing the mixing layer at different wavelengths affects the transition to turbulence. It was found that transitions to turbulence can be obtained at different perturbation wavelengths, provided that they are longer than the shortest unstable wavelength as determined by 2D linear stability analysis for the inviscid case and that the initial Reynolds number is proportionally increased as the wavelength is decreased. The transitional states thus obtained display different dynamic and mixture characteristics, departing strongly from the behaviors of perfect gases and ideal mixtures.

Agents Within our Midst

DTIC Science & Technology

2012-03-14

agents; and the development of bio -monitoring protocols for civilian and service personnel during a chemical attack. These efforts have resulted in greater...produced by staphylococcal bacteria that is and is classified as a CDC select agent which has the potential to be used as a biological weapon .1...NMR chemical shift perturbation titrations with Fab (fragment, antigen binding regions) domains of 20B1, 14G8, and 6D3 using deuterated (2H) SEB

Comparative evaluation of differential laser-induced perturbation spectroscopy as a technique to discriminate emerging skin pathology

NASA Astrophysics Data System (ADS)

Kozikowski, Raymond T.; Smith, Sarah E.; Lee, Jennifer A.; Castleman, William L.; Sorg, Brian S.; Hahn, David W.

2012-06-01

Fluorescence spectroscopy has been widely investigated as a technique for identifying pathological tissue; however, unrelated subject-to-subject variations in spectra complicate data analysis and interpretation. We describe and evaluate a new biosensing technique, differential laser-induced perturbation spectroscopy (DLIPS), based on deep ultraviolet (UV) photochemical perturbation in combination with difference spectroscopy. This technique combines sequential fluorescence probing (pre- and post-perturbation) with sub-ablative UV perturbation and difference spectroscopy to provide a new spectral dimension, facilitating two improvements over fluorescence spectroscopy. First, the differential technique eliminates significant variations in absolute fluorescence response within subject populations. Second, UV perturbations alter the extracellular matrix (ECM), directly coupling the DLIPS response to the biological structure. Improved biosensing with DLIPS is demonstrated in vivo in a murine model of chemically induced skin lesion development. Component loading analysis of the data indicates that the DLIPS technique couples to structural proteins in the ECM. Analysis of variance shows that DLIPS has a significant response to emerging pathology as opposed to other population differences. An optimal likelihood ratio classifier for the DLIPS dataset shows that this technique holds promise for improved diagnosis of epithelial pathology. Results further indicate that DLIPS may improve diagnosis of tissue by augmenting fluorescence spectra (i.e. orthogonal sensing).

SHORT-WAVELENGTH MAGNETIC BUOYANCY INSTABILITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mizerski, K. A.; Davies, C. R.; Hughes, D. W., E-mail: kamiz@igf.edu.pl, E-mail: tina@maths.leeds.ac.uk, E-mail: d.w.hughes@leeds.ac.uk

2013-04-01

Magnetic buoyancy instability plays an important role in the evolution of astrophysical magnetic fields. Here we revisit the problem introduced by Gilman of the short-wavelength linear stability of a plane layer of compressible isothermal fluid permeated by a horizontal magnetic field of strength decreasing with height. Dissipation of momentum and magnetic field is neglected. By the use of a Rayleigh-Schroedinger perturbation analysis, we explain in detail the limit in which the transverse horizontal wavenumber of the perturbation, denoted by k, is large (i.e., short horizontal wavelength) and show that the fastest growing perturbations become localized in the vertical direction asmore » k is increased. The growth rates are determined by a function of the vertical coordinate z since, in the large k limit, the eigenmodes are strongly localized in the vertical direction. We consider in detail the case of two-dimensional perturbations varying in the directions perpendicular to the magnetic field, which, for sufficiently strong field gradients, are the most unstable. The results of our analysis are backed up by comparison with a series of initial value problems. Finally, we extend the analysis to three-dimensional perturbations.« less

Flap-lag-torsional dynamics of helicopter rotor blades in forward flight

NASA Technical Reports Server (NTRS)

Crespodasilva, M. R. M.

1986-01-01

A perturbation/numerical methodology to analyze the flap-lead/lag motion of a centrally hinged spring restrained rotor blade that is valid for both hover and for forward flight was developed. The derivation of the nonlinear differential equations of motion and the analysis of the stability of the steady state response of the blade were conducted entirely in a Symbolics 3670 Machine using MACSYMA to perform all the lengthy symbolic manipulations. It also includes generation of the fortran codes and plots of the results. The Floquet theory was also applied to the differential equations of motion in order to compare results with those obtained from the perturbation analysis. The results obtained from the perturbation methodology and from Floquet theory were found to be very close to each other, which demonstrates the usefullness of the perturbation methodology. Another problem under study consisted in the analysis of the influence of higher order terms in the response and stability of a flexible rotor blade in forward flight using Computerized Symbolic Manipulation and a perturbation technique to bypass the Floquet theory. The derivation of the partial differential equations of motion is presented.

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

PubMed Central

Luo, Chengwei; Rodriguez-R, Luis M.; Johnston, Eric R.; Wu, Liyou; Cheng, Lei; Xue, Kai; Tu, Qichao; Deng, Ye; He, Zhili; Shi, Jason Zhou; Yuan, Mengting Maggie; Sherry, Rebecca A.; Li, Dejun; Luo, Yiqi; Schuur, Edward A. G.; Chain, Patrick; Tiedje, James M.

2014-01-01

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO2 production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations. PMID:24375144

Substructure Versus Property-Level Dispersed Modes Calculation

NASA Technical Reports Server (NTRS)

Stewart, Eric C.; Peck, Jeff A.; Bush, T. Jason; Fulcher, Clay W.

2016-01-01

This paper calculates the effect of perturbed finite element mass and stiffness values on the eigenvectors and eigenvalues of the finite element model. The structure is perturbed in two ways: at the "subelement" level and at the material property level. In the subelement eigenvalue uncertainty analysis the mass and stiffness of each subelement is perturbed by a factor before being assembled into the global matrices. In the property-level eigenvalue uncertainty analysis all material density and stiffness parameters of the structure are perturbed modified prior to the eigenvalue analysis. The eigenvalue and eigenvector dispersions of each analysis (subelement and property-level) are also calculated using an analytical sensitivity approximation. Two structural models are used to compare these methods: a cantilevered beam model, and a model of the Space Launch System. For each structural model it is shown how well the analytical sensitivity modes approximate the exact modes when the uncertainties are applied at the subelement level and at the property level.

Optical microphone with fiber Bragg grating and signal processing techniques

NASA Astrophysics Data System (ADS)

Tosi, Daniele; Olivero, Massimo; Perrone, Guido

2008-06-01

In this paper, we discuss the realization of an optical microphone array using fiber Bragg gratings as sensing elements. The wavelength shift induced by acoustic waves perturbing the sensing Bragg grating is transduced into an intensity modulation. The interrogation unit is based on a fixed-wavelength laser source and - as receiver - a photodetector with proper amplification; the system has been implemented using devices for standard optical communications, achieving a low-cost interrogator. One of the advantages of the proposed approach is that no voltage-to-strain calibration is required for tracking dynamic shifts. The optical sensor is complemented by signal processing tools, including a data-dependent frequency estimator and adaptive filters, in order to improve the frequency-domain analysis and mitigate the effects of disturbances. Feasibility and performances of the optical system have been tested measuring the output of a loudspeaker. With this configuration, the sensor is capable of correctly detecting sounds up to 3 kHz, with a frequency response that exhibits a top sensitivity within the range 200-500 Hz; single-frequency input sounds inducing an axial strain higher than ~10nɛ are correctly detected. The repeatability range is ~0.1%. The sensor has also been applied for the detection of pulsed stimuli generated from a metronome.

On the use of the exact exchange optimized effective potential method for static response properties

NASA Astrophysics Data System (ADS)

Krykunov, Mykhaylo; Ziegler, Tom

In the present work, we question the notion that the modified Kohn-Sham orbital energies and smaller HOMO-LUMO gaps, produced from the exact exchange optimized effective potential (EXX-OEP) method, might significantly improve the paramagnetic contribution to the NMR chemical shifts compared with the regular Hartree-Fock (HF) scheme. First of all, it is shown analytically that if there is such a local potential that produces the HF energy, and the Kohn-Sham orbitals are obtained as a result of separate rotations of the occupied and virtual HF orbitals, any static magnetic property obtained from the coupled perturbed HF method will be identical to that obtained from the EXX-OEP approach. In fact the EXX-OEP method is equivalent to the improved virtual orbitals (IVO) scheme in which the energies of the virtual orbitals are modified by an effective potential. It is shown that the IVO procedure leaves static response properties unchanged. To test our analysis numerically we have employed several variants of the EXX-OEP method, based on the expansion of the local exchange potential into a linear combination of fit functions. The different EXX-OEP schemes have been used to calculate the NMR chemical shifts for a set of small molecules containing C, H, N, O, and F atoms. Comparison of the deviation between experimental and calculated chemical shifts from the HF, the EXX-OEP, and the common energy denominator approximation (CEDA) approximation to the EXX-OEP methods has shown that for carbon, hydrogen, and fluorine the EXX-OEP methods do not yield any improvement over the HF method. For nitrogen and oxygen we have found that the EXX-OEP performs better than the HF method. However, in the limit of infinite fit basis set and, as a consequence of it, a perfect fit of the HF potential the EXX-OEP and the HF methods would afford the same chemical shifts according to our theoretical analysis. Unfortunately, without a perfect fit the chemical shifts from the EXX-OEP method strongly depend on the fit convergence. In our opinion, the EXX-OEP method should not be used for response properties as it is numerically unstable. Thus, any apparent improvement of the EXX-OEP method over the HF scheme for a finite fit basis set must be considered spurious.

Complete Hamiltonian analysis of cosmological perturbations at all orders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nandi, Debottam; Shankaranarayanan, S., E-mail: debottam@iisertvm.ac.in, E-mail: shanki@iisertvm.ac.in

2016-06-01

In this work, we present a consistent Hamiltonian analysis of cosmological perturbations at all orders. To make the procedure transparent, we consider a simple model and resolve the 'gauge-fixing' issues and extend the analysis to scalar field models and show that our approach can be applied to any order of perturbation for any first order derivative fields. In the case of Galilean scalar fields, our procedure can extract constrained relations at all orders in perturbations leading to the fact that there is no extra degrees of freedom due to the presence of higher time derivatives of the field in themore » Lagrangian. We compare and contrast our approach to the Lagrangian approach (Chen et al. [2006]) for extracting higher order correlations and show that our approach is efficient and robust and can be applied to any model of gravity and matter fields without invoking slow-roll approximation.« less

Hemiparetic stepping to the beat: asymmetric response to metronome phase shift during treadmill gait.

PubMed

Pelton, Trudy A; Johannsen, Leif; Huiya Chen; Wing, Alan M

2010-06-01

Walking in time with a metronome is associated with improved spatiotemporal parameters in hemiparetic gait; however, the mechanism linking auditory and motor systems is poorly understood. Hemiparetic cadence control with metronome synchronization was examined to determine specific influences of metronome timing on treadmill walking. A within-participant experiment examined correction processes used to maintain heel strike synchrony with the beat by applying perturbations to the timing of a metronome. Eight chronic hemiparetic participants (mean age = 70 years; standard deviation = 12) were required to synchronize heel strikes with metronome pulses set according to each individual's comfortable speed (mean 0.4 m/s). During five 100-pulse trials, a fixed-phase baseline was followed by 4 unpredictable metronome phase shifts (20% of the interpulse interval), which amounted to 10 phase shifts on each foot. Infrared cameras recorded the motion of bilateral heel markers at 120 Hz. Relative asynchrony between heel strike responses and metronome pulses was used to index compensation for metronome phase shifts. Participants demonstrated compensation for phase shifts with convergence back to pre-phase shift asynchrony. This was significantly slower when the error occurred on the nonparetic side (requiring initial correction with the paretic limb) compared with when the error occurred on the paretic side (requiring initial nonparetic correction). Although phase correction of gait is slowed when the phase shift is delivered to the nonparetic side compared with the paretic side, phase correction is still present. This may underlie the utility of rhythmic auditory cueing in hemiparetic gait rehabilitation.

Further conventions for NMR shielding and chemical shifts IUPAC recommendations 2008.

PubMed

Harris, Robin K; Becker, Edwin D; Cabral De Menezes, Sonia M; Granger, Pierre; Hoffman, Roy E; Zilm, Kurt W

2008-03-01

IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the (1)H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3-(trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating (13)C NMR chemical shifts in solids to the scales used for high-resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice.

Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008).

PubMed

Harris, Robin K; Becker, Edwin D; De Menezes, Sonia M Cabral; Granger, Pierre; Hoffman, Roy E; Zilm, Kurt W

2008-06-01

IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the (1)H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3-(trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating (13)C NMR chemical shifts in solids to the scales used for high-resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. Copyright (c) 2008 John Wiley & Sons, Ltd

General theory for multiple input-output perturbations in complex molecular systems. 1. Linear QSPR electronegativity models in physical, organic, and medicinal chemistry.

PubMed

González-Díaz, Humberto; Arrasate, Sonia; Gómez-SanJuan, Asier; Sotomayor, Nuria; Lete, Esther; Besada-Porto, Lina; Ruso, Juan M

2013-01-01

In general perturbation methods starts with a known exact solution of a problem and add "small" variation terms in order to approach to a solution for a related problem without known exact solution. Perturbation theory has been widely used in almost all areas of science. Bhor's quantum model, Heisenberg's matrix mechanincs, Feyman diagrams, and Poincare's chaos model or "butterfly effect" in complex systems are examples of perturbation theories. On the other hand, the study of Quantitative Structure-Property Relationships (QSPR) in molecular complex systems is an ideal area for the application of perturbation theory. There are several problems with exact experimental solutions (new chemical reactions, physicochemical properties, drug activity and distribution, metabolic networks, etc.) in public databases like CHEMBL. However, in all these cases, we have an even larger list of related problems without known solutions. We need to know the change in all these properties after a perturbation of initial boundary conditions. It means, when we test large sets of similar, but different, compounds and/or chemical reactions under the slightly different conditions (temperature, time, solvents, enzymes, assays, protein targets, tissues, partition systems, organisms, etc.). However, to the best of our knowledge, there is no QSPR general-purpose perturbation theory to solve this problem. In this work, firstly we review general aspects and applications of both perturbation theory and QSPR models. Secondly, we formulate a general-purpose perturbation theory for multiple-boundary QSPR problems. Last, we develop three new QSPR-Perturbation theory models. The first model classify correctly >100,000 pairs of intra-molecular carbolithiations with 75-95% of Accuracy (Ac), Sensitivity (Sn), and Specificity (Sp). The model predicts probabilities of variations in the yield and enantiomeric excess of reactions due to at least one perturbation in boundary conditions (solvent, temperature, temperature of addition, or time of reaction). The model also account for changes in chemical structure (connectivity structure and/or chirality paterns in substrate, product, electrophile agent, organolithium, and ligand of the asymmetric catalyst). The second model classifies more than 150,000 cases with 85-100% of Ac, Sn, and Sp. The data contains experimental shifts in up to 18 different pharmacological parameters determined in >3000 assays of ADMET (Absorption, Distribution, Metabolism, Elimination, and Toxicity) properties and/or interactions between 31723 drugs and 100 targets (metabolizing enzymes, drug transporters, or organisms). The third model classifies more than 260,000 cases of perturbations in the self-aggregation of drugs and surfactants to form micelles with Ac, Sn, and Sp of 94-95%. The model predicts changes in 8 physicochemical and/or thermodynamics output parameters (critic micelle concentration, aggregation number, degree of ionization, surface area, enthalpy, free energy, entropy, heat capacity) of self-aggregation due to perturbations. The perturbations refers to changes in initial temperature, solvent, salt, salt concentration, solvent, and/or structure of the anion or cation of more than 150 different drugs and surfactants. QSPR-Perturbation Theory models may be useful for multi-objective optimization of organic synthesis, physicochemical properties, biological activity, metabolism, and distribution profiles towards the design of new drugs, surfactants, asymmetric ligands for catalysts, and other materials.

Changes in the convective population and thermodynamic environments in convection-permitting regional climate simulations over the United States

NASA Astrophysics Data System (ADS)

Rasmussen, K. L.; Prein, A. F.; Rasmussen, R. M.; Ikeda, K.; Liu, C.

2017-11-01

Novel high-resolution convection-permitting regional climate simulations over the US employing the pseudo-global warming approach are used to investigate changes in the convective population and thermodynamic environments in a future climate. Two continuous 13-year simulations were conducted using (1) ERA-Interim reanalysis and (2) ERA-Interim reanalysis plus a climate perturbation for the RCP8.5 scenario. The simulations adequately reproduce the observed precipitation diurnal cycle, indicating that they capture organized and propagating convection that most climate models cannot adequately represent. This study shows that weak to moderate convection will decrease and strong convection will increase in frequency in a future climate. Analysis of the thermodynamic environments supporting convection shows that both convective available potential energy (CAPE) and convective inhibition (CIN) increase downstream of the Rockies in a future climate. Previous studies suggest that CAPE will increase in a warming climate, however a corresponding increase in CIN acts as a balancing force to shift the convective population by suppressing weak to moderate convection and provides an environment where CAPE can build to extreme levels that may result in more frequent severe convection. An idealized investigation of fundamental changes in the thermodynamic environment was conducted by shifting a standard atmospheric profile by ± 5 °C. When temperature is increased, both CAPE and CIN increase in magnitude, while the opposite is true for decreased temperatures. Thus, even in the absence of synoptic and mesoscale variations, a warmer climate will provide more CAPE and CIN that will shift the convective population, likely impacting water and energy budgets on Earth.

Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plugge, Caroline M.; Scholten, Johannes C.; Culley, David E.

2010-09-01

Abstract Desulfovibrio vulgaris is a metabolically flexible microorganism. It can use sulfate as electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with hydrogen scavenging partner to relieve inhibition by hydrogen. These alternativemetabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntroph in a lactate-oxidizing dual-culture with Methanosarcina barkeri tomore » a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 hours after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Up-regulation was observed for genes encoding ATPase and the membrane-integrated energy conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipo- and membrane-bound proteins was down-regulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologs found only in another syntrophic bacterium Syntrophobacter fumaroxidans and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome encoding genes which may be involved in the sulfidogenic metabolism.« less

Impact of Mono-Fluorination on the Photophysics of the Flavin Chromophore.

PubMed

Reiffers, Anna; Torres Ziegenbein, Christian; Engelhardt, Alyn; Kühnemuth, Ralf; Gilch, Peter; Czekelius, Constantin

2018-03-31

Three mono-fluorinated derivatives of the flavin core system 10-methyl-isoalloxazine (MIA) were synthesized. Aqueous solutions of these compounds were characterized by steady-state and time-resolved spectroscopy. The positions for the fluorination (6, 7 and 8) were motivated by the nodal structure of the frontier orbitals of MIA. In comparison with MIA, the fluorination results in bathochromic (6F- and 7F-MIA) and hypsochromic (8F-MIA) shifts of the adiabatic excitation energy of the lowest allowed transition. Shifts of up to ~500 cm -1 were observed. These spectroscopic shifts go along with changes in fluorescence quantum yields and lifetimes. In addition, triplet yields are affected. For 7F-MIA, a 50% increase in the fluorescence quantum yield as well as a 50% decrease in triplet yield is observed rendering the compound interesting for fluorescence applications. The measured effects are discussed in terms of qualitative perturbation theory. © 2018 The American Society of Photobiology.

Arginine Interactions with Anatase TiO2 (100) Surface and the Perturbation of 49Ti NMR Chemical Shifts - A DFT Investigation: Relevance to Renu-Seeram Bio Solar Cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koch, Rainer; Lipton, Andrew S.; Filipek, S.

2011-06-01

Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7more » ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.« less

Estimation of Venus wind velocities from high-resolution infrared spectra. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Smith, M. A. H.

1978-01-01

Zonal velocity profiles in the Venus atmosphere above the clouds were estimated from measured asymmetries of HCl and HF infrared absorption lines in high-resolution Fourier interferometer spectra of the planet. These asymmetries are caused by both pressure-induced shifts in the positions of the hydrogen-halide lines perturbed by CO2 and Doppler shifts due to atmospheric motions. Particularly in the case of the HCl 2-0 band, the effects of the two types of line shifts can be easily isolated, making it possible to estimate a profile of average Venus equatorial zonal velocity as a function of pressure in the region roughly 60 to 70 km above the surface of the planet. The mean profiles obtained show strong vertical shear in the Venus zonal winds near the cloud-top level, and both the magnitude and direction of winds at all levels in this region appear to vary greatly with longitude relative to the sub-solar point.

Cosmology with a light ghost

NASA Astrophysics Data System (ADS)

Ivanov, Mikhail M.; Tokareva, Anna A.

2016-12-01

We study the creation and evolution of cosmological perturbations in renormalizable quadratic gravity with a Weyl term. We adopt a prescription that implies the stability of the vacuum at the price of introducing a massive spin-two ghost state, leading to the loss of unitarity. The theory may still be predictive regardless the interpretation of non-unitary processes provided that their rate is negligible compared to the Universe expansion rate. This implies that the ghost is effectively stable. In such a setup, there are two scalar degrees of freedom excited during inflation. The first one is the usual curvature perturbation whose power spectrum appears to coincide with that of single-field inflation. The second one is a scalar component of the ghost encoded in the shift vector of the metric in the uniform inflaton gauge. The amplitudes of primordial tensor and vector perturbations are strongly suppressed. After inflation the ghost field starts to oscillate and its energy density shortly becomes dominant in the Universe. For all ghost masses allowed by laboratory constraints ghosts should have ``overclosed'' the Universe at temperatures higher than that of primordial nucleosynthesis. Thus, the model with the light Weyl ghost is ruled out.

The time course of phase correction: A kinematic investigation of motor adjustment to timing perturbations during sensorimotor synchronization

PubMed Central

Hove, Michael J.; Balasubramaniam, Ramesh; Keller, Peter E.

2014-01-01

Synchronizing movements with a beat requires rapid compensation for timing errors. The phase-correction response (PCR) has been studied extensively in finger tapping by shifting a metronome onset and measuring the adjustment of the following tap time. How the response unfolds during the subsequent tap cycle remains unknown. Using motion capture, we examined finger kinematics during the PCR. Participants tapped with a metronome containing phase perturbations. They tapped in ‘legato’ and ‘staccato’ style at various tempi, which altered the timing of the constituent movement stages (dwell at the surface, extension, flexion). After a phase perturbation, tapping kinematics changed compared to baseline, and the PCR was distributed differently across movement stages. In staccato tapping, the PCR trajectory changed primarily during finger extension across tempi. In legato tapping, at fast tempi the PCR occurred primarily during extension, whereas at slow tempi most phase correction was already completed during dwell. Across conditions, timing adjustments occurred primarily 100-250 ms into the following tap cycle. The change in movement around 100 ms represents the time to integrate information into an already planned movement and the rapidity suggests a subcortical route. PMID:25151103

Spreading out of perturbations in reversible reaction networks

NASA Astrophysics Data System (ADS)

Maslov, Sergei; Sneppen, Kim; Ispolatov, I.

2007-08-01

Using an example of physical interactions between proteins, we study how a perturbation propagates in the equilibrium of a network of reversible reactions governed by the law of mass action. We introduce a matrix formalism to describe the linear response of all equilibrium concentrations to shifts in total abundances of individual reactants, and reveal its heuristic analogy to the flow of electric current in a network of resistors. Our main conclusion is that, on average, the induced changes in equilibrium concentrations decay exponentially as a function of network distance from the source of perturbation. We analyze how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. We find that the minimal branching of the network, small values of dissociation constants, and low equilibrium free (unbound) concentrations of reacting substances all decrease the decay constant and thus increase the range of propagation. Exact analytic expressions for the decay constant are obtained for the case of equally strong interactions and uniform as well as oscillating concentrations on the Bethe lattice. Our general findings are illustrated using a real network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations.

Formation of rogue waves from a locally perturbed condensate.

PubMed

Gelash, A A

2018-02-01

The one-dimensional focusing nonlinear Schrödinger equation (NLSE) on an unstable condensate background is the fundamental physical model that can be applied to study the development of modulation instability (MI) and formation of rogue waves. The complete integrability of the NLSE via inverse scattering transform enables the decomposition of the initial conditions into elementary nonlinear modes: breathers and continuous spectrum waves. The small localized condensate perturbations (SLCP) that grow as a result of MI have been of fundamental interest in nonlinear physics for many years. Here, we demonstrate that Kuznetsov-Ma and superregular NLSE breathers play the key role in the dynamics of a wide class of SLCP. During the nonlinear stage of MI development, collisions of these breathers lead to the formation of rogue waves. We present new scenarios of rogue wave formation for randomly distributed breathers as well as for artificially prepared initial conditions. For the latter case, we present an analytical description based on the exact expressions found for the space-phase shifts that breathers acquire after collisions with each other. Finally, the presence of Kuznetsov-Ma and superregular breathers in arbitrary-type condensate perturbations is demonstrated by solving the Zakharov-Shabat eigenvalue problem with high numerical accuracy.

Formation of rogue waves from a locally perturbed condensate

NASA Astrophysics Data System (ADS)

Gelash, A. Â. A.

2018-02-01

The one-dimensional focusing nonlinear Schrödinger equation (NLSE) on an unstable condensate background is the fundamental physical model that can be applied to study the development of modulation instability (MI) and formation of rogue waves. The complete integrability of the NLSE via inverse scattering transform enables the decomposition of the initial conditions into elementary nonlinear modes: breathers and continuous spectrum waves. The small localized condensate perturbations (SLCP) that grow as a result of MI have been of fundamental interest in nonlinear physics for many years. Here, we demonstrate that Kuznetsov-Ma and superregular NLSE breathers play the key role in the dynamics of a wide class of SLCP. During the nonlinear stage of MI development, collisions of these breathers lead to the formation of rogue waves. We present new scenarios of rogue wave formation for randomly distributed breathers as well as for artificially prepared initial conditions. For the latter case, we present an analytical description based on the exact expressions found for the space-phase shifts that breathers acquire after collisions with each other. Finally, the presence of Kuznetsov-Ma and superregular breathers in arbitrary-type condensate perturbations is demonstrated by solving the Zakharov-Shabat eigenvalue problem with high numerical accuracy.

Cosmology with a light ghost

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ivanov, Mikhail M.; Tokareva, Anna A., E-mail: mikhail.ivanov@cern.ch, E-mail: anna.tokareva@epfl.ch

2016-12-01

We study the creation and evolution of cosmological perturbations in renormalizable quadratic gravity with a Weyl term. We adopt a prescription that implies the stability of the vacuum at the price of introducing a massive spin-two ghost state, leading to the loss of unitarity. The theory may still be predictive regardless the interpretation of non-unitary processes provided that their rate is negligible compared to the Universe expansion rate. This implies that the ghost is effectively stable. In such a setup, there are two scalar degrees of freedom excited during inflation. The first one is the usual curvature perturbation whose powermore » spectrum appears to coincide with that of single-field inflation. The second one is a scalar component of the ghost encoded in the shift vector of the metric in the uniform inflaton gauge. The amplitudes of primordial tensor and vector perturbations are strongly suppressed. After inflation the ghost field starts to oscillate and its energy density shortly becomes dominant in the Universe. For all ghost masses allowed by laboratory constraints ghosts should have ''overclosed'' the Universe at temperatures higher than that of primordial nucleosynthesis. Thus, the model with the light Weyl ghost is ruled out.« less

An inverse approach to perturb historical rainfall data for scenario-neutral climate impact studies

NASA Astrophysics Data System (ADS)

Guo, Danlu; Westra, Seth; Maier, Holger R.

2018-01-01

Scenario-neutral approaches are being used increasingly for climate impact assessments, as they allow water resource system performance to be evaluated independently of climate change projections. An important element of these approaches is the generation of perturbed series of hydrometeorological variables that form the inputs to hydrologic and water resource assessment models, with most scenario-neutral studies to-date considering only shifts in the average and a limited number of other statistics of each climate variable. In this study, a stochastic generation approach is used to perturb not only the average of the relevant hydrometeorological variables, but also attributes such as the intermittency and extremes. An optimization-based inverse approach is developed to obtain hydrometeorological time series with uniform coverage across the possible ranges of rainfall attributes (referred to as the 'exposure space'). The approach is demonstrated on a widely used rainfall generator, WGEN, for a case study at Adelaide, Australia, and is shown to be capable of producing evenly-distributed samples over the exposure space. The inverse approach expands the applicability of the scenario-neutral approach in evaluating a water resource system's sensitivity to a wider range of plausible climate change scenarios.

Mitral leaflet geometry perturbations with papillary muscle displacement and annular dilatation: an in-vitro study of ischemic mitral regurgitation.

PubMed

He, Shengqiu; Jimenez, Jorge; He, Zhaoming; Yoganathan, Ajit P

2003-05-01

Perturbations of leaflet geometry are the final end point through which left ventricular (LV) ischemia causes incomplete mitral leaflet closure and resultant mitral regurgitation (MR). Geometric inconsistencies observed with valvular or subvalvular structural alterations raise several questions. A new in-vitro LV flexible bag model was developed in order to visualize and analyze leaflet geometric changes under simulated pathological ischemic MR conditions. Papillary muscle (PM) displacement and annular dilatation decreased leaflet coaptation length, leading to significant MR. Symmetrical PM displacement shifted the coaptation line towards the leaflet edges and created central gaps along this line. Asymmetric PM displacement generated diametrically uneven coaptation with a tent-shaped leaflet at the tethered PM side, while the leaflet bulged at the opposite side towards the left atrium. Leaflet geometry during systole is affected by subvalvular structures. Asymmetric PM displacement, which may occur in regional or acute myocardial infarction, induces irregular deformation of the leaflet's coaptation line and, as a result, MR at the tethered side. Direct visualization of leaflet perturbation under these simulated pathological conditions may promote understanding of mechanisms present in ischemic MR.

PRESSURE SHIFT AND GRAVITATIONAL REDSHIFT OF BALMER LINES IN WHITE DWARFS: REDISCUSSION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halenka, Jacek; Olchawa, Wieslaw; Madej, Jerzy

2015-08-01

The Stark-induced shift and asymmetry, the so-called pressure shift (PS) of H{sub α} and H{sub β} Balmer lines in spectra of DA white dwarfs (WDs), have been examined in detail as masking effects in measurements of the gravitational redshift in WDs. The results are compared with our earlier ones from a quarter of a century ago. In these earlier papers, the standard, symmetrical Stark line profiles, as a dominant constituent of the Balmer line profiles but shifted as a whole by the PS effect, were applied to all spectrally active layers of the WD atmosphere. At present, in each ofmore » the WD layers, the Stark line profiles (especially of H{sub β}) are inherently asymmetrical and shifted due to the effects of strong inhomogeneity of the perturbing fields in plasma. To calculate the Stark line profiles in successive layers of the WD atmosphere we used the modified Full Computer Simulation Method, able to take adequately into account the complexity of local elementary quantum processes in plasma. In the case of the H{sub α} line, the present value of Stark-induced shift of the synthetic H{sub α} line profile is about half the previous one and it is negligible in comparison with the gravitational redshift. In the case of the H{sub β} line, the present value of Stark-induced shift of the synthetic H{sub β} line profile is about twice the previous one. The source of this extra shift is the asymmetry of H{sub β} peaks.« less

SU-E-T-115: Dose Perturbation Study of Self-Expandable Metal and Polyester Esophageal Stents in Proton Therapy Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, S; Li, Z; Jalaj, S

2014-06-01

Purpose: This work investigates dose perturbations due to Self-expandable metal and polyester esophageal stents undergoing proton radiotherapy for esophageal cancer. Methods: Five commercially available esophageal stents made of nitinol (Evolution, Wallflex and Ultraflex), stainless steel (Z-Stent) and polyester (Polyflex) were tested. Radiochromic film (GafChromic EBT3 film, Ashland, Covington, KY) wrapped around a stent and a 12cc syringe was irradiated with 2CGE (Cobalt Gray Equivalent) of proton beam in a custom fabricated acrylic phantom. An air-hollow syringe simulates the esophagus. Results: The Z-stent created the largest dose perturbations ranges from -14.5% to 6.1% due to the steel composition. The WallFlex, Evolutionmore » and Ultraflex stents produced the dose perturbation ranges of (−9.2%∼8.6%), (−6.8%∼5.7%) and (−6.2%∼6.2%), respectively. The PolyFlex stent contains the radiopaque tungsten markers located top, middle and bottom portions. When the focal cold spots induced by the markers were excluded in the analysis, the dose perturbation range was changed from (−11.6%∼6.4%) to (−0.6%∼5.0%). Conclusion: The magnitude of dose perturbation is related to material of a metallic stent. The non-metallic stent such as PolyFlex shows relatively lower dose perturbation than metallic stents except a radiopaque marker region. Overall Evolution and Ultraflex stent appear to be less dose perturbations. The largest dose perturbations (cold spots) were located at both edges of stents in distal area for the single proton beam irradiation study. The analysis of more than two proton beam which is more typical clinical beam arrangement would be necessary to minimize the doe perturbation effect in proton ratiotherapy.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gubser, Steven S.; van der Schee, Wilke

At strong coupling holographic studies have shown that heavy ion collisions do not obey normal boost invariance. Here we study a modified boost invariance through a complex shift in time, and show that this leads to surprisingly good agreement with numerical holographic computations. When including perturbations the agreement becomes even better, both in the hydrodynamic and the far-from-equilibrium regime. Finally, one of the main advantages is an analytic formulation of the stress-energy tensor of the longitudinal dynamics of holographic heavy ion collisions.

Time-Distance Helioseismology Data-Analysis Pipeline for Helioseismic and Magnetic Imager Onboard Solar Dynamics Observatory (SDO-HMI) and Its Initial Results

NASA Technical Reports Server (NTRS)

Zhao, J.; Couvidat, S.; Bogart, R. S.; Parchevsky, K. V.; Birch, A. C.; Duvall, Thomas L., Jr.; Beck, J. G.; Kosovichev, A. G.; Scherrer, P. H.

2011-01-01

The Helioseismic and Magnetic Imager onboard the Solar Dynamics Observatory (SDO/HMI) provides continuous full-disk observations of solar oscillations. We develop a data-analysis pipeline based on the time-distance helioseismology method to measure acoustic travel times using HMI Doppler-shift observations, and infer solar interior properties by inverting these measurements. The pipeline is used for routine production of near-real-time full-disk maps of subsurface wave-speed perturbations and horizontal flow velocities for depths ranging from 0 to 20 Mm, every eight hours. In addition, Carrington synoptic maps for the subsurface properties are made from these full-disk maps. The pipeline can also be used for selected target areas and time periods. We explain details of the pipeline organization and procedures, including processing of the HMI Doppler observations, measurements of the travel times, inversions, and constructions of the full-disk and synoptic maps. Some initial results from the pipeline, including full-disk flow maps, sunspot subsurface flow fields, and the interior rotation and meridional flow speeds, are presented.

Helical variation of density profiles and fluctuations in the tokamak pedestal with applied 3D fields and implications for confinement

DOE PAGES

Wilcox, R. S.; Rhodes, T. L.; Shafer, M. W.; ...

2018-04-19

Smore » mall 3D perturbations to the magnetic field in DIII-D ( δ B / B ~ 2 × 10 - 4 ) result in large modulations of density fluctuation amplitudes in the pedestal, which are shown using Doppler backscattering measurements to vary by a factor of 2. Helical perturbations of equilibrium density within flux surfaces have previously been observed in the pedestal of DIII-D plasmas when 3D fields are applied and were correlated with density fluctuation asymmetries in the pedestal. These intra-surface density and pressure variations are shown through two fluid MHD modeling studies using the M3D-C1 code to be due to the misalignment of the density and temperature equilibrium iso-surfaces in the pedestal region. This modeling demonstrates that the phase shift between the two iso-surfaces corresponds to the diamagnetic direction of the two species, with the mass density surfaces shifted in the ion diamagnetic direction relative to the temperature and magnetic flux iso-surfaces. Finally, the resulting pedestal density, potential, and turbulence asymmetries within flux surfaces near the separatrix may be at least partially responsible for several poorly understood phenomena that occur with the application of 3D fields in tokamaks, including density pump out and the increase in power required to transition from L- to H-mode.« less

Spherically symmetric vacuum in covariant F (T )=T +α/2 T2+O (Tγ) gravity theory

NASA Astrophysics Data System (ADS)

DeBenedictis, Andrew; Ilijić, Saša

2016-12-01

Recently, a fully covariant version of the theory of F (T ) torsion gravity has been introduced by M. Kršśák and E. Saridakis [Classical Quantum Gravity 33, 115009 (2016)]. In covariant F (T ) gravity, the Schwarzschild solution is not a vacuum solution for F (T )≠T , and therefore determining the spherically symmetric vacuum is an important open problem. Within the covariant framework, we perturbatively solve the spherically symmetric vacuum gravitational equations around the Schwarzschild solution for the scenario with F (T )=T +(α /2 )T2 , representing the dominant terms in theories governed by Lagrangians analytic in the torsion scalar. From this, we compute the perihelion shift correction to solar system planetary orbits as well as perturbative gravitational effects near neutron stars. This allows us to set an upper bound on the magnitude of the coupling constant, α , which governs deviations from general relativity. We find the bound on this nonlinear torsion coupling constant by specifically considering the uncertainty in the perihelion shift of Mercury. We also analyze a bound from a similar comparison with the periastron orbit of the binary pulsar PSR J0045-7319 as an independent check for consistency. Setting bounds on the dominant nonlinear coupling is important in determining if other effects in the Solar System or greater universe could be attributable to nonlinear torsion.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lavinto, Mikko; Räsänen, Syksy, E-mail: mikko.lavinto@helsinki.fi, E-mail: syksy.rasanen@iki.fi

We consider a Swiss Cheese model with a random arrangement of Lemaȋtre-Tolman-Bondi holes in ΛCDM cheese. We study two kinds of holes with radius r{sub b}=50 h{sup −1} Mpc, with either an underdense or an overdense centre, called the open and closed case, respectively. We calculate the effect of the holes on the temperature, angular diameter distance and, for the first time in Swiss Cheese models, shear of the CMB . We quantify the systematic shift of the mean and the statistical scatter, and calculate the power spectra. In the open case, the temperature power spectrum is three orders of magnitude belowmore » the linear ISW spectrum. It is sensitive to the details of the hole, in the closed case the amplitude is two orders of magnitude smaller. In contrast, the power spectra of the distance and shear are more robust, and agree with perturbation theory and previous Swiss Cheese results. We do not find a statistically significant mean shift in the sky average of the angular diameter distance, and obtain the 95% limit |Δ D{sub A}/ D-bar {sub A}|∼< 10{sup −4}. We consider the argument that areas of spherical surfaces are nearly unaffected by perturbations, which is often invoked in light propagation calculations. The closed case is consistent with this at 1σ, whereas in the open case the probability is only 1.4%.« less

CMB seen through random Swiss Cheese

NASA Astrophysics Data System (ADS)

Lavinto, Mikko; Räsänen, Syksy

2015-10-01

We consider a Swiss Cheese model with a random arrangement of Lemaȋtre-Tolman-Bondi holes in ΛCDM cheese. We study two kinds of holes with radius rb=50 h-1 Mpc, with either an underdense or an overdense centre, called the open and closed case, respectively. We calculate the effect of the holes on the temperature, angular diameter distance and, for the first time in Swiss Cheese models, shear of the CMB . We quantify the systematic shift of the mean and the statistical scatter, and calculate the power spectra. In the open case, the temperature power spectrum is three orders of magnitude below the linear ISW spectrum. It is sensitive to the details of the hole, in the closed case the amplitude is two orders of magnitude smaller. In contrast, the power spectra of the distance and shear are more robust, and agree with perturbation theory and previous Swiss Cheese results. We do not find a statistically significant mean shift in the sky average of the angular diameter distance, and obtain the 95% limit |Δ DA/bar DA|lesssim 10-4. We consider the argument that areas of spherical surfaces are nearly unaffected by perturbations, which is often invoked in light propagation calculations. The closed case is consistent with this at 1σ, whereas in the open case the probability is only 1.4%.

Nonperturbative evaluation of the physical classical velocity in the lattice heavy quark effective theory

NASA Astrophysics Data System (ADS)

Mandula, Jeffrey E.; Ogilvie, Michael C.

1998-02-01

In the lattice formulation of heavy quark effective theory, the value of the ``classical velocity'' v, as defined through the separation of the four-momentum of a heavy quark into a part proportional to the heavy quark mass and a residual part that remains finite in the heavy quark limit (P=Mv+p), is different from its value as it appears in the bare heavy quark propagator [S-1(p)=v.p]. The origin of the difference, which is effectively a lattice-induced renormalization, is the reduction of Lorentz [or O(4)] invariance to (hyper)cubic invariance. The renormalization is finite and depends specifically on the form of the discretization of the reduced heavy quark Dirac equation. For the forward time, centered space discretization, we compute this renormalization nonperturbatively, using an ensemble of lattices at β=6.1 provided by the Fermilab ACP-MAPS Collaboration. The calculation makes crucial use of a variationally optimized smeared operator for creating composite heavy-light mesons. It has the property that its propagator achieves an asymptotic plateau in just a few Euclidean time steps. For comparison, we also compute the shift perturbatively, to one loop in lattice perturbation theory. The nonperturbative calculation of the leading multiplicative shift in the classical velocity is considerably different from the one-loop estimate and indicates that for the above parameters v--> is reduced by about 10-13 %.

Helical variation of density profiles and fluctuations in the tokamak pedestal with applied 3D fields and implications for confinement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilcox, R. S.; Rhodes, T. L.; Shafer, M. W.

Smore » mall 3D perturbations to the magnetic field in DIII-D ( δ B / B ~ 2 × 10 - 4 ) result in large modulations of density fluctuation amplitudes in the pedestal, which are shown using Doppler backscattering measurements to vary by a factor of 2. Helical perturbations of equilibrium density within flux surfaces have previously been observed in the pedestal of DIII-D plasmas when 3D fields are applied and were correlated with density fluctuation asymmetries in the pedestal. These intra-surface density and pressure variations are shown through two fluid MHD modeling studies using the M3D-C1 code to be due to the misalignment of the density and temperature equilibrium iso-surfaces in the pedestal region. This modeling demonstrates that the phase shift between the two iso-surfaces corresponds to the diamagnetic direction of the two species, with the mass density surfaces shifted in the ion diamagnetic direction relative to the temperature and magnetic flux iso-surfaces. Finally, the resulting pedestal density, potential, and turbulence asymmetries within flux surfaces near the separatrix may be at least partially responsible for several poorly understood phenomena that occur with the application of 3D fields in tokamaks, including density pump out and the increase in power required to transition from L- to H-mode.« less

Helical variation of density profiles and fluctuations in the tokamak pedestal with applied 3D fields and implications for confinement

NASA Astrophysics Data System (ADS)

Wilcox, R. S.; Rhodes, T. L.; Shafer, M. W.; Sugiyama, L. E.; Ferraro, N. M.; Lyons, B. C.; McKee, G. R.; Paz-Soldan, C.; Wingen, A.; Zeng, L.

2018-05-01

Small 3D perturbations to the magnetic field in DIII-D ( δB /B ˜2 ×10-4 ) result in large modulations of density fluctuation amplitudes in the pedestal, which are shown using Doppler backscattering measurements to vary by a factor of 2. Helical perturbations of equilibrium density within flux surfaces have previously been observed in the pedestal of DIII-D plasmas when 3D fields are applied and were correlated with density fluctuation asymmetries in the pedestal. These intra-surface density and pressure variations are shown through two fluid MHD modeling studies using the M3D-C1 code to be due to the misalignment of the density and temperature equilibrium iso-surfaces in the pedestal region. This modeling demonstrates that the phase shift between the two iso-surfaces corresponds to the diamagnetic direction of the two species, with the mass density surfaces shifted in the ion diamagnetic direction relative to the temperature and magnetic flux iso-surfaces. The resulting pedestal density, potential, and turbulence asymmetries within flux surfaces near the separatrix may be at least partially responsible for several poorly understood phenomena that occur with the application of 3D fields in tokamaks, including density pump out and the increase in power required to transition from L- to H-mode.

Persistent landfalling atmospheric rivers over the west coast of North America

NASA Astrophysics Data System (ADS)

Payne, Ashley E.; Magnusdottir, Gudrun

2016-11-01

Landfalling atmospheric rivers (ARs) are linked to heavy precipitation and extreme flooding, and are well known along the western coast of North America. The hydrological impacts of ARs upon landfall are correlated with their duration and magnitude. In order to improve the forecast of these hydrologically significant landfalling events, a better understanding of how they differ from other landfalling events must be established through an investigation of the mechanisms leading to their development prior to landfall. A subset of persistent landfalling AR events between 30°N and 50°N is identified in 3-hourly Modern-Era Retrospective Analysis for Research and Applications reanalysis and validated against existing data sets. These events are identified as features in the low troposphere with high moisture transport and extended geometry that persist over a limited region of the coastline for longer than 63 h (85th percentile of AR duration). A composite analysis shows that persistent events have distinct thermodynamical and dynamical characteristics compared to all AR events. They are characterized by greater moisture content, suggestive of Pineapple Express-type events, a perturbed upper level jet and anticyclonic overturning of potential vorticity contours associated with anticyclonic Rossby wave breaking. Moreover, the location of the Rossby wave breaking is shifted inland compared to all AR events. Analogue analysis of the 500 hPa geopotential height anomalies is used to find nonpersistent events with similar dynamical characteristics to persistent events. Despite their similarity to persistent events, nonpersistent analogues show very little shift toward longer duration. A comparison of the development of persistent and nonpersistent analogues shows that persistent events have much greater moisture content.

PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

PubMed

Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

2016-03-10

Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and signalling systems. It allows for simulation and analysis of models under a variety of environmental conditions and for experimental optimisation of complex combined experiments. With its unique set of tools it makes a valuable addition to the current library of sensitivity analysis toolboxes. We believe that this software will be of great use to the wider biological, systems biology and modelling communities.

Ghost-Free APT Analysis of Perturbative QCD Observables

NASA Astrophysics Data System (ADS)

Shirkov, Dmitry V.

The review of the essence and of application of recently devised ghost-free Analytic Perturbation Theory (APT) is presented. First, we discuss the main intrinsic problem of perturbative QCD - ghost singularities and with the resume of its resolving within the APT. By examples for diverse energy and momentum transfer values we show the property of better convergence for the APT modified QCD expansion. It is shown that in the APT analysis the three-loop contribution (sim alpha_s^3) is numerically inessential. This gives raise a hope for practical solution of the well-known problem of non-satisfactory convergence of QFT perturbation series due to its asymptotic nature. Our next result is that a usual perturbative analysis of time-like events is not adequate at sleq 2 GeV2. In particular, this relates to tau decay. Then, for the "high" (f=5) region it is shown that the common NLO, NLLA perturbation approximation widely used there (at 10 GeV lesssimsqrt{s}lesssim 170 GeV) yields a systematic theoretic negative error of a couple per cent level for the bar {alpha}_s^2 values. This results in a conclusion that the bar α_s(M^2_Z) value averaged over the f=5 data appreciably differs < bar {alpha}_s(M^2_Z)rangle_{f=5} simeq 0.124 from the currently popular "world average" (=0.118 ).

ELM suppression in helium plasmas with 3D magnetic fields

DOE PAGES

Evans, T. E.; Loarte, A.; Orlov, D. M.; ...

2017-06-21

Experiments in DIII-D, using non-axisymmetric magnetic perturbation fields in high-purity low toroidal rotation, 4He plasmas have resulted in Type-I edge localized mode (ELM) suppression and mitigation. Suppression is obtained in plasmas with zero net input torque near the L–H power threshold using either electron cyclotron resonant heating (ECRH) or balanced co- and counter-I p neutral beam injection (NBI) resulting in conditions equivalent to those expected in ITER's non-active operating phase. In low-power ECRH H-modes, periods with uncontrolled density and impurity radiation excursions are prevented by applying n = 3 non-axisymmetric magnetic perturbation fields. ELM suppression results from a reduction andmore » an outward shift of the electron pressure gradient peak compared to that in the high-power ELMing phase. Here, the change in the electron pressure gradient peak is primarily due to a drop in the pedestal temperature rather than the pedestal density.« less

Fourth generation CP violation effects on B-->Kpi, phiK, and rhoK in next-to-leading-order perturbative QCD.

PubMed

Hou, Wei-Shu; Li, Hsiang-nan; Mishima, Satoshi; Nagashima, Makiko

2007-03-30

We study the effect from a sequential fourth generation quark on penguin-dominated two-body nonleptonic B meson decays in the next-to-leading order perturbative QCD formalism. With an enhancement of the color-suppressed tree amplitude and possibility of a new CP phase in the electroweak penguin amplitude, we can account better for A(CP)(B(0)-->K+ pi-)-A(CP)(B+-->K+ pi0). Taking |V(t's)V(t'b)| approximately 0.02 with a phase just below 90 degrees, which is consistent with the b-->sl+ l- rate and the B(s) mixing parameter Deltam(B)(s), we find a downward shift in the mixing-induced CP asymmetries of B(0)-->K(S)(pi 0) and phi(K)(S). The predicted behavior for B(0)-->rho(0)(K)(S) is opposite.

A Consistent Definition of Phase Resetting Using Hilbert Transform.

PubMed

Oprisan, Sorinel A

2017-01-01

A phase resetting curve (PRC) measures the transient change in the phase of a neural oscillator subject to an external perturbation. The PRC encapsulates the dynamical response of a neural oscillator and, as a result, it is often used for predicting phase-locked modes in neural networks. While phase is a fundamental concept, it has multiple definitions that may lead to contradictory results. We used the Hilbert Transform (HT) to define the phase of the membrane potential oscillations and HT amplitude to estimate the PRC of a single neural oscillator. We found that HT's amplitude and its corresponding instantaneous frequency are very sensitive to membrane potential perturbations. We also found that the phase shift of HT amplitude between the pre- and poststimulus cycles gives an accurate estimate of the PRC. Moreover, HT phase does not suffer from the shortcomings of voltage threshold or isochrone methods and, as a result, gives accurate and reliable estimations of phase resetting.

ELM suppression in helium plasmas with 3D magnetic fields

NASA Astrophysics Data System (ADS)

Evans, T. E.; Loarte, A.; Orlov, D. M.; Grierson, B. A.; Knölker, M. M.; Lyons, B. C.; Cui, L.; Gohil, P.; Groebner, R. J.; Moyer, R. A.; Nazikian, R.; Osborne, T. H.; Unterberg, E. A.

2017-08-01

Experiments in DIII-D, using non-axisymmetric magnetic perturbation fields in high-purity low toroidal rotation, 4He plasmas have resulted in Type-I edge localized mode (ELM) suppression and mitigation. Suppression is obtained in plasmas with zero net input torque near the L-H power threshold using either electron cyclotron resonant heating (ECRH) or balanced co- and counter-I p neutral beam injection (NBI) resulting in conditions equivalent to those expected in ITER’s non-active operating phase. In low-power ECRH H-modes, periods with uncontrolled density and impurity radiation excursions are prevented by applying n  =  3 non-axisymmetric magnetic perturbation fields. ELM suppression results from a reduction and an outward shift of the electron pressure gradient peak compared to that in the high-power ELMing phase. The change in the electron pressure gradient peak is primarily due to a drop in the pedestal temperature rather than the pedestal density.

Effective field theory of broken spatial diffeomorphisms

DOE PAGES

Lin, Chunshan; Labun, Lance Z.

2016-03-17

We study the low energy effective theory describing gravity with broken spatial diffeomorphism invariance. In the unitary gauge, the Goldstone bosons associated with broken diffeomorphisms are eaten and the graviton becomes a massive spin-2 particle with 5 well-behaved degrees of freedom. In this gauge, the most general theory is built with the lowest dimension operators invariant under only temporal diffeomorphisms. Imposing the additional shift and SO(3) internal symmetries, we analyze the perturbations on a FRW background. At linear perturbation level, the observables of this theory are characterized by five parameters, including the usual cosmological parameters and one additional coupling constantmore » for the symmetry-breaking scalars. In the de Sitter and Minkowski limit, the three Goldstone bosons are supermassive and can be integrated out, leaving two massive tensor modes as the only propagating degrees of freedom. In conclusion, we discuss several examples relevant to theories of massive gravity.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bukh, Boris; Lund, Steven M.

We present an analysis of envelope perturbations evolving in the limit of a fully space-charge depressed (zero emittance) beam in periodic, thin-lens focusing channels. Both periodic solenoidal and FODO quadrupole focusing channels are analyzed. The phase advance and growth rate of normal mode perturbations are analytically calculated as a function of the undepressed particle phase advance to characterize the evolution of envelope perturbations.

Topology of large-scale structure in seeded hot dark matter models

NASA Technical Reports Server (NTRS)

Beaky, Matthew M.; Scherrer, Robert J.; Villumsen, Jens V.

1992-01-01

The topology of the isodensity surfaces in seeded hot dark matter models, in which static seed masses provide the density perturbations in a universe dominated by massive neutrinos is examined. When smoothed with a Gaussian window, the linear initial conditions in these models show no trace of non-Gaussian behavior for r0 equal to or greater than 5 Mpc (h = 1/2), except for very low seed densities, which show a shift toward isolated peaks. An approximate analytic expression is given for the genus curve expected in linear density fields from randomly distributed seed masses. The evolved models have a Gaussian topology for r0 = 10 Mpc, but show a shift toward a cellular topology with r0 = 5 Mpc; Gaussian models with an identical power spectrum show the same behavior.

Adaptive optics in multiphoton microscopy: comparison of two, three and four photon fluorescence

PubMed Central

Sinefeld, David; Paudel, Hari P.; Ouzounov, Dimitre G.; Bifano, Thomas G.; Xu, Chris

2015-01-01

We demonstrate adaptive optics system based on nonlinear feedback from 3- and 4-photon fluorescence. The system is based on femtosecond pulses created by soliton self-frequency shift of a 1550-nm fiber-based femtosecond laser together with micro-electro-mechanical system (MEMS) phase spatial light modulator (SLM). We perturb the 1020-segment SLM using an orthogonal Walsh sequence basis set with a modified version of three-point phase shifting interferometry. We show the improvement after aberrations correction in 3-photon signal from fluorescent beads. In addition, we compare the improvement obtained in the same adaptive optical system for 2-, 3- and 4-photon fluorescence using dye pool. We show that signal improvement resulting from aberration correction grows exponentially as a function of the order of nonlinearity. PMID:26698772

Hamiltonian mean-field model: effect of temporal perturbation in coupling matrix

NASA Astrophysics Data System (ADS)

Bhadra, Nivedita; Patra, Soumen K.

2018-05-01

The Hamiltonian mean-field (HMF) model is a system of fully coupled rotators which exhibits a second-order phase transition at some critical energy in its canonical ensemble. We investigate the case where the interaction between the rotors is governed by a time-dependent coupling matrix. Our numerical study reveals a shift in the critical point due to the temporal modulation. The shift in the critical point is shown to be independent of the modulation frequency above some threshold value, whereas the impact of the amplitude of modulation is dominant. In the microcanonical ensemble, the system with constant coupling reaches a quasi-stationary state (QSS) at an energy near the critical point. Our result indicates that the QSS subsists in presence of such temporal modulation of the coupling parameter.

Fourth-order self-energy contribution to the Lamb shift

NASA Astrophysics Data System (ADS)

Mallampalli, S.; Sapirstein, J.

1998-03-01

Two-loop self-energy contributions to the fourth-order Lamb shift of ground-state hydrogenic ions are treated to all orders in Zα by using exact Dirac-Coulomb propagators. A rearrangement of the calculation into four ultraviolet finite parts, the M, P, F, and perturbed orbital (PO) terms, is made. Reference-state singularities present in the M and P terms are shown to cancel. The most computationally intensive part of the calculation, the M term, is evaluated for hydrogenlike uranium and bismuth, the F term is evaluated for a range of Z values, but the P term is left for a future calculation. For hydrogenlike uranium, previous calculations of the PO term give -0.971 eV: the contributions from the M and F terms calculated here sum to -0.325 eV.

From data towards knowledge: revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data.

PubMed

Lu, Songjian; Jin, Bo; Cowart, L Ashley; Lu, Xinghua

2013-01-01

Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically derive knowledge of a cellular signaling system at a conceptual level from systematic perturbation-response data. In this study, we explored a framework that unifies knowledge mining and data mining towards the goal. The framework consists of the following automated processes: 1) applying an ontology-driven knowledge mining approach to identify functional modules among the genes responding to a perturbation in order to reveal potential signals affected by the perturbation; 2) applying a graph-based data mining approach to search for perturbations that affect a common signal; and 3) revealing the architecture of a signaling system by organizing signaling units into a hierarchy based on their relationships. Applying this framework to a compendium of yeast perturbation-response data, we have successfully recovered many well-known signal transduction pathways; in addition, our analysis has led to many new hypotheses regarding the yeast signal transduction system; finally, our analysis automatically organized perturbed genes as a graph reflecting the architecture of the yeast signaling system. Importantly, this framework transformed molecular findings from a gene level to a conceptual level, which can be readily translated into computable knowledge in the form of rules regarding the yeast signaling system, such as "if genes involved in the MAPK signaling are perturbed, genes involved in pheromone responses will be differentially expressed."

Linear analysis of the Richtmyer-Meshkov instability in shock-flame interactions

NASA Astrophysics Data System (ADS)

Massa, L.; Jha, P.

2012-05-01

Shock-flame interactions enhance supersonic mixing and detonation formation. Therefore, their analysis is important to explosion safety, internal combustion engine performance, and supersonic combustor design. The fundamental process at the basis of the interaction is the Richtmyer-Meshkov instability supported by the density difference between burnt and fresh mixtures. In the present study we analyze the effect of reactivity on the Richtmyer-Meshkov instability with particular emphasis on combustion lengths that typify the scaling between perturbation growth and induction. The results of the present linear analysis study show that reactivity changes the perturbation growth rate by developing a pressure gradient at the flame surface. The baroclinic torque based on the density gradient across the flame acts to slow down the instability growth of high wave-number perturbations. A gasdynamic flame representation leads to the definition of a Peclet number representing the scaling between perturbation and thermal diffusion lengths within the flame. Peclet number effects on perturbation growth are observed to be marginal. The gasdynamic model also considers a finite flame Mach number that supports a separation between flame and contact discontinuity. Such a separation destabilizes the interface growth by augmenting the tangential shear.

Perturbational formulation of principal component analysis in molecular dynamics simulation.

PubMed

Koyama, Yohei M; Kobayashi, Tetsuya J; Tomoda, Shuji; Ueda, Hiroki R

2008-10-01

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate. Other PCAs with general applicability, such as the PCA using pairwise atomic distances, do not represent the physical meaning clearly. Therefore, a formulation that provides general applicability and clearly represents the physical meaning is yet to be developed. For developing such a formulation, we consider the conformational distribution change by the perturbation with arbitrary linearly independent perturbation functions. Within the second order approximation of the Kullback-Leibler divergence by the perturbation, the PCA can be naturally interpreted as a method for (1) decomposing a given perturbation into perturbations that independently contribute to the conformational distribution change or (2) successively finding the perturbation that induces the largest conformational distribution change. In this perturbational formulation of PCA, (i) the eigenvalue measures the Kullback-Leibler divergence from the unperturbed to perturbed distributions, (ii) the eigenvector identifies the combination of the perturbation functions, and (iii) the principal component determines the probability change induced by the perturbation. Based on this formulation, we propose a PCA using potential energy terms, and we designate it as potential energy PCA (PEPCA). The PEPCA provides both general applicability and clear physical meaning. For demonstrating its power, we apply the PEPCA to an alanine dipeptide molecule in vacuum as a minimal model of a nonsingle dominant conformational biomolecule. The first and second principal components clearly characterize two stable states and the transition state between them. Positive and negative components with larger absolute values of the first and second eigenvectors identify the electrostatic interactions, which stabilize or destabilize each stable state and the transition state. Our result therefore indicates that PCA can be applied, by carefully selecting the perturbation functions, not only to identify the molecular conformational fluctuation but also to predict the conformational distribution change by the perturbation beyond the limitation of the previous methods.

Perturbational formulation of principal component analysis in molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Tomoda, Shuji; Ueda, Hiroki R.

2008-10-01

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate. Other PCAs with general applicability, such as the PCA using pairwise atomic distances, do not represent the physical meaning clearly. Therefore, a formulation that provides general applicability and clearly represents the physical meaning is yet to be developed. For developing such a formulation, we consider the conformational distribution change by the perturbation with arbitrary linearly independent perturbation functions. Within the second order approximation of the Kullback-Leibler divergence by the perturbation, the PCA can be naturally interpreted as a method for (1) decomposing a given perturbation into perturbations that independently contribute to the conformational distribution change or (2) successively finding the perturbation that induces the largest conformational distribution change. In this perturbational formulation of PCA, (i) the eigenvalue measures the Kullback-Leibler divergence from the unperturbed to perturbed distributions, (ii) the eigenvector identifies the combination of the perturbation functions, and (iii) the principal component determines the probability change induced by the perturbation. Based on this formulation, we propose a PCA using potential energy terms, and we designate it as potential energy PCA (PEPCA). The PEPCA provides both general applicability and clear physical meaning. For demonstrating its power, we apply the PEPCA to an alanine dipeptide molecule in vacuum as a minimal model of a nonsingle dominant conformational biomolecule. The first and second principal components clearly characterize two stable states and the transition state between them. Positive and negative components with larger absolute values of the first and second eigenvectors identify the electrostatic interactions, which stabilize or destabilize each stable state and the transition state. Our result therefore indicates that PCA can be applied, by carefully selecting the perturbation functions, not only to identify the molecular conformational fluctuation but also to predict the conformational distribution change by the perturbation beyond the limitation of the previous methods.

An Examination of Environment Perturbation Effects on Single Event Upset Rates

NASA Technical Reports Server (NTRS)

Gates, Michele M.; Leidecker, Henning W.; Lewis, Mark J.

1997-01-01

This paper presents an analysis of the sensitivity of single event upset (SEU) rate predictions to changes in the direct ionization-inducing environment. An examination based on the nature of the SEU rate equation is presented for the case in which the perturbation is constant across varying particle linear energy transfer (LET). It is shown that the relative variation in SEU rate is equal to the relative perturbation in flux. Results are also presented for the case in which the environment perturbations exist in small LET bins. Through this analysis it is shown that the relative variation in expected SEU rate is equal to that in flux only for the LET regime in which the product of the cross section and differential flux is maximum.

Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides.

PubMed

Keiderling, Timothy A

2017-12-01

Isotope labeling has a long history in chemistry as a tool for probing structure, offering enhanced sensitivity, or enabling site selection with a wide range of spectroscopic tools. Chirality sensitive methods such as electronic circular dichroism are global structural tools and have intrinsically low resolution. Consequently, they are generally insensitive to modifications to enhance site selectivity. The use of isotope labeling to modify vibrational spectra with unique resolvable frequency shifts can provide useful site-specific sensitivity, and these methods have been recently more widely expanded in biopolymer studies. While the spectral shifts resulting from changes in isotopic mass can provide resolution of modes from specific parts of the molecule and can allow detection of local change in structure with perturbation, these shifts alone do not directly indicate structure or chirality. With vibrational circular dichroism (VCD), the shifted bands and their resultant sign patterns can be used to indicate local conformations in labeled biopolymers, particularly if multiple labels are used and if their coupling is theoretically modeled. This mini-review discusses selected examples of the use of labeling specific amides in peptides to develop local structural insight with VCD spectra. © 2017 Wiley Periodicals, Inc.

Metal Nanoparticle Aerogel Composites

NASA Technical Reports Server (NTRS)

Smith, David D.; Sibille, Laurent; Ignont, Erica; Snow, Lanee; Rose, M. Franklin (Technical Monitor)

2000-01-01

We have fabricated sol-gels containing gold and silver nanoparticles. Formation of an aerogel produces a blue shift in the surface plasmon resonance as a result of the decrease in the dielectric constant of the matrix upon supercritical extraction of the solvent. However, as a result of chemical interface damping this blue shift does not obey effective medium theories. Annealing the samples in a reducing atmosphere at 400 C eliminates this discrepancy and results in narrowing and further blue shifting of the plasmon resonance. Metal particle aggregation also results in a deviation from the predictions of effective medium theories, but can be controlled through careful handling and by avoiding the use of alcohol. By applying effective medium theories to the heterogeneous interlayer surrounding each metal particle, we extend the technique of immersion spectroscopy to inhomogeneous materials characterized by spatially dependent dielectric constants, such as aerogels. We demonstrate that the shift in the surface plasmon wavelength provides the average fractional composition of each component (air and silica) in this inhomogeneous layer, i.e. the porosity of the aerogel or equivalently, for these materials, the catalytic dispersion. Additionally, the kinetics suggest that collective particle interactions in coagulated metal clusters are perturbed during silica gelation resulting in a change in the aggregate geometry.

A perturbation approach for assessing trends in precipitation extremes across Iran

NASA Astrophysics Data System (ADS)

Tabari, Hossein; AghaKouchak, Amir; Willems, Patrick

2014-11-01

Extreme precipitation events have attracted a great deal of attention among the scientific community because of their devastating consequences on human livelihood and socio-economic development. To assess changes in precipitation extremes in a given region, it is essential to analyze decadal oscillations in precipitation extremes. This study examines temporal oscillations in precipitation data in several sub-regions of Iran using a novel quantile perturbation method during 1980-2010. Precipitation data from NASA's Modern-Era Retrospective Analysis for Research and Applications-Land (MERRA-Land) are used in this study. The results indicate significant anomalies in precipitation extremes in the northwest and southeast regions of Iran. Analysis of extreme precipitation perturbations reveals that perturbations for the monthly aggregation level are generally lower than the annual perturbations. Furthermore, high-oscillation and low-oscillation periods are found in extreme precipitation quantiles across different seasons. In all selected regions, a significant anomaly (i.e., extreme wet/dry conditions) in precipitation extremes is observed during spring.

Notes on hyperscaling violating Lifshitz and shear diffusion

NASA Astrophysics Data System (ADS)

Kolekar, Kedar S.; Mukherjee, Debangshu; Narayan, K.

2017-07-01

We explore in greater detail our investigations of shear diffusion in hyperscaling violating Lifshitz theories in Phys. Lett. B 760, 86 (2016), 10.1016/j.physletb.2016.06.046. This adapts and generalizes the membrane-paradigm-like analysis of Kovtun, Son, and Starinets for shear gravitational perturbations in the near horizon region given certain self-consistent approximations, leading to the shear diffusion constant on an appropriately defined stretched horizon. In theories containing a gauge field, some of the metric perturbations mix with some of the gauge field perturbations and the above analysis is somewhat more complicated. We find a similar near-horizon analysis can be obtained in terms of new field variables involving a linear combination of the metric and the gauge field perturbation resulting in a corresponding diffusion equation. Thereby as before, for theories with Lifshitz and hyperscaling violating exponents z , θ satisfying z <4 -θ in four bulk dimensions, our analysis here results in a similar expression for the shear diffusion constant with power-law scaling with temperature suggesting universal behavior in relation to the viscosity bound. For z =4 -θ , we find logarithmic behavior.

QCD PHASE TRANSITIONS-VOLUME 15.

DOE Office of Scientific and Technical Information (OSTI.GOV)

SCHAFER,T.

1998-11-04

The title of the workshop, ''The QCD Phase Transitions'', in fact happened to be too narrow for its real contents. It would be more accurate to say that it was devoted to different phases of QCD and QCD-related gauge theories, with strong emphasis on discussion of the underlying non-perturbative mechanisms which manifest themselves as all those phases. Before we go to specifics, let us emphasize one important aspect of the present status of non-perturbative Quantum Field Theory in general. It remains true that its studies do not get attention proportional to the intellectual challenge they deserve, and that the theoristsmore » working on it remain very fragmented. The efforts to create Theory of Everything including Quantum Gravity have attracted the lion share of attention and young talent. Nevertheless, in the last few years there was also a tremendous progress and even some shift of attention toward emphasis on the unity of non-perturbative phenomena. For example, we have seen some. efforts to connect the lessons from recent progress in Supersymmetric theories with that in QCD, as derived from phenomenology and lattice. Another example is Maldacena conjecture and related development, which connect three things together, string theory, super-gravity and the (N=4) supersymmetric gauge theory. Although the progress mentioned is remarkable by itself, if we would listen to each other more we may have chance to strengthen the field and reach better understanding of the spectacular non-perturbative physics.« less

QCD Phase Transitions, Volume 15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaefer, T.; Shuryak, E.

1999-03-20

The title of the workshop, ''The QCD Phase Transitions'', in fact happened to be too narrow for its real contents. It would be more accurate to say that it was devoted to different phases of QCD and QCD-related gauge theories, with strong emphasis on discussion of the underlying non-perturbative mechanisms which manifest themselves as all those phases. Before we go to specifics, let us emphasize one important aspect of the present status of non-perturbative Quantum Field Theory in general. It remains true that its studies do not get attention proportional to the intellectual challenge they deserve, and that the theoristsmore » working on it remain very fragmented. The efforts to create Theory of Everything including Quantum Gravity have attracted the lion share of attention and young talent. Nevertheless, in the last few years there was also a tremendous progress and even some shift of attention toward emphasis on the unity of non-perturbative phenomena. For example, we have seen some efforts to connect the lessons from recent progress in Supersymmetric theories with that in QCD, as derived from phenomenology and lattice. Another example is Maldacena conjecture and related development, which connect three things together, string theory, super-gravity and the (N=4) supersymmetric gauge theory. Although the progress mentioned is remarkable by itself, if we would listen to each other more we may have chance to strengthen the field and reach better understanding of the spectacular non-perturbative physics.« less

Carbon Flux Signal Detection for the ASCENDS mission

NASA Astrophysics Data System (ADS)

Hammerling, D.; Michalak, A. M.; Kawa, S. R.; Doney, S. C.; Schaefer, K. M.

2012-12-01

Emerging satellite observations of carbon dioxide (CO2) offer novel and distinctive opportunities for quantifying the carbon cycle, which is an important scientific and societal challenge with anthropogenic CO2 emissions and accumulation rates in the atmosphere still on the rise. One mission in the planning stage is the Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) mission, which is a laser CO2 sensing mission with an anticipated launch date around 2022. Notable features of this mission include the ability to sample at night and at high latitudes, which passive missions cannot do because of their reliance on reflected sunlight. In this work we present findings from signal detection studies, i.e. experiments that investigate if perturbations in carbon fluxes can be detected in the ASCENDS observations of atmospheric CO2 concentrations. The experiments employ a realistic synthetic-data setup using the PCTM/GEOS-5/CASA GFED CO2 flux and transport model in combination with CALIPSO and MODIS measurements. The signal detection approach applied uses a geostatistical mapping methodology that can leverage the information content of nearby observations, thereby potentially facilitating enhanced signal detection. The specific perturbation scenarios investigated are: carbon release from the melting of permafrost in the high Northern latitudes, the shifting of fossil fuel emissions from Europe to P.R. China, and natural variability in the CO2 fluxes in the Southern Ocean. Results indicate that the permafrost carbon release is comparatively easy to detect, while the Southern Ocean change is more challenging. The ability to detect a shift in fossil fuel emissions strongly depends on its magnitude: a 50% decrease in Europe is easily detectible, while a 20% decrease is only marginally so. A key conclusion is that the optimal signal detection strategy is intrinsically linked to how the carbon flux perturbations translate into atmospheric CO2 concentrations, which varies significantly among the investigated scenarios.

Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer.

PubMed

Hanni, Matti; Lantto, Perttu; Ilias, Miroslav; Jensen, Hans Jorgen Aagaard; Vaara, Juha

2007-10-28

Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For chi( parallel), the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the (129)Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe(2), are in excellent agreement with the experiment for the first time.

Non-perturbative String Theory from Water Waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iyer, Ramakrishnan; Johnson, Clifford V.; /Southern California U.

2012-06-14

We use a combination of a 't Hooft limit and numerical methods to find non-perturbative solutions of exactly solvable string theories, showing that perturbative solutions in different asymptotic regimes are connected by smooth interpolating functions. Our earlier perturbative work showed that a large class of minimal string theories arise as special limits of a Painleve IV hierarchy of string equations that can be derived by a similarity reduction of the dispersive water wave hierarchy of differential equations. The hierarchy of string equations contains new perturbative solutions, some of which were conjectured to be the type IIA and IIB string theoriesmore » coupled to (4, 4k ? 2) superconformal minimal models of type (A, D). Our present paper shows that these new theories have smooth non-perturbative extensions. We also find evidence for putative new string theories that were not apparent in the perturbative analysis.« less

Strength and viscosity effects on perturbed shock front stability in metals

DOE PAGES

Opie, Saul; Loomis, Eric Nicholas; Peralta, Pedro; ...

2017-05-09

Here, computational modeling and experimental measurements on metal samples subject to a laser-driven, ablative Richtmyer-Meshkov instability showed differences between viscosity and strength effects. In particular, numerical and analytical solutions, coupled with measurements of fed-through perturbations, generated by perturbed shock fronts onto initially flat surfaces, show promise as a validation method for models of deviatoric response in the post shocked material. Analysis shows that measurements of shock perturbation amplitudes at low sample thickness-to-wavelength ratios are not enough to differentiate between strength and viscosity effects, but that surface displacement data of the fed-through fed-thru perturbations appears to resolve the ambiguity. Additionally, analyticalmore » and numerical results show shock front perturbation evolution dependence on initial perturbation amplitude and wavelength is significantly different in viscous and materials with strength, suggesting simple experimental geometry changes should provide data supporting one model or the other.« less

Numerical Analysis of Orbital Perturbation Effects on Inclined Geosynchronous SAR

PubMed Central

Dong, Xichao; Hu, Cheng; Long, Teng; Li, Yuanhao

2016-01-01

The geosynchronous synthetic aperture radar (GEO SAR) is susceptible to orbit perturbations, leading to orbit drifts and variations. The influences behave very differently from those in low Earth orbit (LEO) SAR. In this paper, the impacts of perturbations on GEO SAR orbital elements are modelled based on the perturbed dynamic equations, and then, the focusing is analyzed theoretically and numerically by using the Systems Tool Kit (STK) software. The accurate GEO SAR slant range histories can be calculated according to the perturbed orbit positions in STK. The perturbed slant range errors are mainly the first and second derivatives, leading to image drifts and defocusing. Simulations of the point target imaging are performed to validate the aforementioned analysis. In the GEO SAR with an inclination of 53° and an argument of perigee of 90°, the Doppler parameters and the integration time are different and dependent on the geometry configurations. Thus, the influences are varying at different orbit positions: at the equator, the first-order phase errors should be mainly considered; at the perigee and apogee, the second-order phase errors should be mainly considered; at other positions, first-order and second-order exist simultaneously. PMID:27598168

Perturbation and Nonlinear Dynamic Analysis of Different Singing Styles

PubMed Central

Butte, Caitlin J.; Zhang, Yu; Song, Huangqiang; Jiang, Jack J.

2012-01-01

Summary Previous research has used perturbation analysis methods to study the singing voice. Using perturbation and nonlinear dynamic analysis (NDA) methods in conjunction may provide more accurate information on the singing voice and may distinguish vocal usage in different styles. Acoustic samples from different styles of singing were compared using nonlinear dynamic and perturbation measures. Twenty-six songs from different musical styles were obtained from an online music database (Rhapsody, RealNetworks, Inc., Seattle, WA). One-second samples were selected from each song for analysis. Perturbation analyses of jitter, shimmer, and signal-to-noise ratio and NDA of correlation dimension (D2) were performed on samples from each singing style. Percent jitter and shimmer median values were low normal for country (0.32% and 3.82%), musical theater (MT) (0.280% and 2.80%), jazz (0.440% and 2.34%), and soul (0.430% and 6.42%). The popular style had slightly higher median jitter and shimmer values (1.13% and 6.78%) than other singing styles, although this was not statistically significant. The opera singing style had median jitter of 0.520%, and yielded significantly high shimmer (P = 0.001) of 7.72%. All six singing styles were measured reliably using NDA, indicating that operatic singing is notably more chaotic than other singing styles. Median correlation dimension values were low to normal, compared to healthy voices, in country (median D2 = 2.14), jazz (median D2 = 2.24), pop (median D2 = 2.60), MT (median D2 = 2.73), and soul (mean D2 = 3.26). Correlation dimension was significantly higher in opera (P < 0.001) with median D2 = 6.19. In this study, acoustic analysis in opera singing gave significantly high values for shimmer and D2, suggesting that it is more irregular than other singing styles; a previously unknown quality of opera singing. Perturbation analysis also suggested significant differences in vocal output in different singing styles. This preliminary study using acoustic analysis with nonlinear dynamic measures and perturbation measures may represent a valuable procedure in quantitatively describing the properties of the singing voice. Further research with human test subjects may allow us to characterize singing styles and diagnose vocal dysfunction in the singing voice. PMID:18504114

Frontiers of Two-Dimensional Correlation Spectroscopy. Part 1. New concepts and noteworthy developments

NASA Astrophysics Data System (ADS)

Noda, Isao

2014-07-01

A comprehensive survey review of new and noteworthy developments, which are advancing forward the frontiers in the field of 2D correlation spectroscopy during the last four years, is compiled. This review covers books, proceedings, and review articles published on 2D correlation spectroscopy, a number of significant conceptual developments in the field, data pretreatment methods and other pertinent topics, as well as patent and publication trends and citation activities. Developments discussed include projection 2D correlation analysis, concatenated 2D correlation, and correlation under multiple perturbation effects, as well as orthogonal sample design, predicting 2D correlation spectra, manipulating and comparing 2D spectra, correlation strategy based on segmented data blocks, such as moving-window analysis, features like determination of sequential order and enhanced spectral resolution, statistical 2D spectroscopy using covariance and other statistical metrics, hetero-correlation analysis, and sample-sample correlation technique. Data pretreatment operations prior to 2D correlation analysis are discussed, including the correction for physical effects, background and baseline subtraction, selection of reference spectrum, normalization and scaling of data, derivatives spectra and deconvolution technique, and smoothing and noise reduction. Other pertinent topics include chemometrics and statistical considerations, peak position shift phenomena, variable sampling increments, computation and software, display schemes, such as color coded format, slice and power spectra, tabulation, and other schemes.

Triphenylamine Derived 3-Acetyl and 3-Benzothiazolyl Bis and Tris Coumarins: Synthesis, Photophysical and DFT Assisted Hyperpolarizability Study

NASA Astrophysics Data System (ADS)

Erande, Yogesh; Kothavale, Shantaram; Sreenath, Mavila C.; Chitrambalam, Subramaniyan; Joe, Isaac H.; Sekar, Nagaiyan

2018-02-01

Triphenylamine derived bis- and tris-branched donor-pi-acceptor coumarins with acetyl and benzothiazolyl acceptors are studied for their linear and nonlinear optical properties that originate from their photophysical and molecular structure. Plots of solvent polarities versus the Stokes shift, frontier molecular orbital analysis and Generalised Mulliken Hush analysis have established their strong charge transfer character supported by the strong emission solvatochromism of these chromophores. On the basis of excited state intramolecular charge transfer, the first-, second- and third-order polarizability of these dyes are determined by a solvatochromic method and supported by density functional theory calculations using CAM-B3LYP/6-31g(d). Compared to the acetyl group, the benzothiazolyl group is a strong acceptor, and its corresponding derivatives show enhanced absorption, emission maxima and non-linear optical response. Bond length alternation and bond order alternation analysis reveals that these chromophores approach the cyanine-like framework which is responsible for maximum perturbation to produce high nonlinear optical response. Third order nonlinear susceptibility for dyes 1 and 2 is determined by Z-scan measurement. All of these methods are used to determine the nonlinear optical properties, and thermogravimetric analysis suggests that these chromophores are thermally robust and efficient nonlinear optical materials.

Phosphorus-31, sup 15 N, and sup 13 C NMR of glyphosate: Comparison of pH titrations to the herbicidal dead-end complex with 5-enolpyruvoylshikimate-3-phosphate synthase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castellino, S.; Leo, G.C.; Sammons, R.D.

1989-05-02

The herbicidal dead-end ternary complex (E{sup S3P}{sub Glyph}) of glyphosate (N-(phosphonomethyl)glycine) with 5-enolpyruvoylshikimate-3-phosphate synthase (EPSPS) and the substrate shikimate 3-phosphate (S3P) has been characterized by {sup 31}P, {sup 15}N, and {sup 13}C NMR. The NMR spectra of EPSPS-bound glyphosate show unique chemical shifts ({delta}) for each of the three nuclei. By {sup 31}P NMR, glyphosate in the dead-end complex is a distinct species 3.5 ppm downfield from free glyphosate. The {sup 13}C signal of glyphosate in the dead-end complex is shifted 4 ppm downfield from that of free glyphosate. The {sup 15}N signal for glyphosate (99%) in the dead-end complexmore » is 5 ppm further downfield than that of any free zwitterionic species and 10 ppm downfield from that of the average free species at pH 10.1. The structures of each ionic state of glyphosate are modeled with force field calculations by using MacroModel. A correlation is made for the {sup 31}P {delta} and the C-P-O bond angle, and the {sup 13}C and {sup 15}N {delta} values are postulated to be related to C-C-O and C-N-C bond angles, respectively. The downfield {sup 31}P chemical shift perturbation for S3P in the EPSPS binary complex is consistent with ionization of the 3-phosphate of S3P upon binding. Comparison with the S3P {sup 31}P {delta} vs pH titration curve specifies predominantly the dianion of the 3-phosphate in the E{sup S3P} binary complex, while the E{sup S3P}{sub Glyph} complex indicates net protonation at the 3-phosphate. Chemical shift perturbations of this latter type may be explained by changes in the O-P-O bond angle.« less

Red and blue shift of liquid water's excited states: A many body perturbation study

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2016-08-01

In the present paper, accurate optical absorption spectrum of liquid H2O is calculated in the energy range of 5-20 eV to probe the nature of water's excited states by means of many body perturbation approach. Main features of recent inelastic X-ray measurements are well reproduced, such as a bound excitonic peak at 7.9 eV with a shoulder at 9.4 eV as well as the absorption maximum at 13.9 eV, followed by a broad shoulder at 18.4 eV. The spectrum is dominated by excitonic effects impacting the structures of the spectrum at low and higher energy regimes mixed by single particle effects at high energies. The exciton distribution of the low-energy states, in particular of S1, is highly anisotropic and localized mostly on one water molecule. The S1 state is essentially a HOCO-LUCO (highest occupied crystal orbital - lowest unoccupied crystal orbital) transition and of intra-molecular type, showing a localized valence character. Once the excitation energy is increased, a significant change in the character of the electronically excited states occurs, characterized through emergence of multiple quasi-particle peaks at 7.9 eV in the quasi-particle (QP) transition profile and in the occurring delocalized exciton density distribution, spread over many more water molecules. The exciton delocalization following a change of the character of excited states at around 7.9 eV causes the blue shift of the first absorption band with respect to water monomer S1. However, due to reduction of the electronic band gap from gas to liquid phase, following enhanced screening upon condensation, the localized S1 state of liquid water is red-shifted with respect to S1 state of water monomer. For higher excitations, near vertical ionization energy (11 eV), quasi-free electrons emerge, in agreement with the conduction band electron picture. Furthermore, the occurring red and blue shift of the excited states are independent of the coupling of resonant and anti-resonant contributions to the spectrum.

Red and blue shift of liquid water’s excited states: A many body perturbation study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ziaei, Vafa, E-mail: ziaei@thch.uni-bonn.de; Bredow, Thomas, E-mail: bredow@thch.uni-bonn.de

In the present paper, accurate optical absorption spectrum of liquid H{sub 2}O is calculated in the energy range of 5–20 eV to probe the nature of water’s excited states by means of many body perturbation approach. Main features of recent inelastic X-ray measurements are well reproduced, such as a bound excitonic peak at 7.9 eV with a shoulder at 9.4 eV as well as the absorption maximum at 13.9 eV, followed by a broad shoulder at 18.4 eV. The spectrum is dominated by excitonic effects impacting the structures of the spectrum at low and higher energy regimes mixed by singlemore » particle effects at high energies. The exciton distribution of the low-energy states, in particular of S{sub 1}, is highly anisotropic and localized mostly on one water molecule. The S{sub 1} state is essentially a HOCO-LUCO (highest occupied crystal orbital - lowest unoccupied crystal orbital) transition and of intra-molecular type, showing a localized valence character. Once the excitation energy is increased, a significant change in the character of the electronically excited states occurs, characterized through emergence of multiple quasi-particle peaks at 7.9 eV in the quasi-particle (QP) transition profile and in the occurring delocalized exciton density distribution, spread over many more water molecules. The exciton delocalization following a change of the character of excited states at around 7.9 eV causes the blue shift of the first absorption band with respect to water monomer S{sub 1}. However, due to reduction of the electronic band gap from gas to liquid phase, following enhanced screening upon condensation, the localized S{sub 1} state of liquid water is red-shifted with respect to S{sub 1} state of water monomer. For higher excitations, near vertical ionization energy (11 eV), quasi-free electrons emerge, in agreement with the conduction band electron picture. Furthermore, the occurring red and blue shift of the excited states are independent of the coupling of resonant and anti-resonant contributions to the spectrum.« less

Improvements to the ion Doppler spectrometer diagnostic on the HIT-SI experiments.

PubMed

Hossack, Aaron; Chandra, Rian; Everson, Chris; Jarboe, Tom

2018-03-01

An ion Doppler spectrometer diagnostic system measuring impurity ion temperature and velocity on the HIT-SI and HIT-SI3 spheromak devices has been improved with higher spatiotemporal resolution and lower error than previously described devices. Hardware and software improvements to the established technique have resulted in a record of 6.9 μs temporal and ≤2.8 cm spatial resolution in the midplane of each device. These allow Ciii and Oii flow, displacement, and temperature profiles to be observed simultaneously. With 72 fused-silica fiber channels in two independent bundles, and an f/8.5 Czerny-Turner spectrometer coupled to a video camera, frame rates of up to ten times the imposed magnetic perturbation frequency of 14.5 kHz were achieved in HIT-SI, viewing the upper half of the midplane. In HIT-SI3, frame rates of up to eight times the perturbation frequency were achieved viewing both halves of the midplane. Biorthogonal decomposition is used as a novel filtering tool, reducing uncertainty in ion temperature from ≲13 to ≲5 eV (with an instrument temperature of 8-16 eV) and uncertainty in velocity from ≲2 to ≲1 km/s. Doppler shift and broadening are calculated via the Levenberg-Marquardt algorithm, after which the errors in velocity and temperature are uniquely specified. Axisymmetric temperature profiles on HIT-SI3 for Ciii peaked near the inboard current separatrix at ≈40 eV are observed. Axisymmetric plasma displacement profiles have been measured on HIT-SI3, peaking at ≈6 cm at the outboard separatrix. Both profiles agree with the upper half of the midplane observable by HIT-SI. With its complete midplane view, HIT-SI3 has unambiguously extracted axisymmetric, toroidal current dependent rotation of up to 3 km/s. Analysis of the temporal phase of the displacement uncovers a coherent structure, locked to the applied perturbation. Previously described diagnostic systems could not achieve such results.

Improvements to the ion Doppler spectrometer diagnostic on the HIT-SI experiments

NASA Astrophysics Data System (ADS)

Hossack, Aaron; Chandra, Rian; Everson, Chris; Jarboe, Tom

2018-03-01

An ion Doppler spectrometer diagnostic system measuring impurity ion temperature and velocity on the HIT-SI and HIT-SI3 spheromak devices has been improved with higher spatiotemporal resolution and lower error than previously described devices. Hardware and software improvements to the established technique have resulted in a record of 6.9 μs temporal and ≤2.8 cm spatial resolution in the midplane of each device. These allow Ciii and Oii flow, displacement, and temperature profiles to be observed simultaneously. With 72 fused-silica fiber channels in two independent bundles, and an f/8.5 Czerny-Turner spectrometer coupled to a video camera, frame rates of up to ten times the imposed magnetic perturbation frequency of 14.5 kHz were achieved in HIT-SI, viewing the upper half of the midplane. In HIT-SI3, frame rates of up to eight times the perturbation frequency were achieved viewing both halves of the midplane. Biorthogonal decomposition is used as a novel filtering tool, reducing uncertainty in ion temperature from ≲13 to ≲5 eV (with an instrument temperature of 8-16 eV) and uncertainty in velocity from ≲2 to ≲1 km/s. Doppler shift and broadening are calculated via the Levenberg-Marquardt algorithm, after which the errors in velocity and temperature are uniquely specified. Axisymmetric temperature profiles on HIT-SI3 for Ciii peaked near the inboard current separatrix at ≈40 eV are observed. Axisymmetric plasma displacement profiles have been measured on HIT-SI3, peaking at ≈6 cm at the outboard separatrix. Both profiles agree with the upper half of the midplane observable by HIT-SI. With its complete midplane view, HIT-SI3 has unambiguously extracted axisymmetric, toroidal current dependent rotation of up to 3 km/s. Analysis of the temporal phase of the displacement uncovers a coherent structure, locked to the applied perturbation. Previously described diagnostic systems could not achieve such results.

Improvements to the Ion Doppler Spectrometer Diagnostic on the HIT-SI Experiments

DOE PAGES

Hossack, Aaron; Chandra, Rian; Everson, Christopher; ...

2018-03-09

An Ion Doppler Spectrometer diagnostic system measuring impurity ion temperature and velocity on the HIT-SI and HIT-SI3 spheromak devices has been improved with higher spatiotemporal resolution and lower error than previously described devices. Hardware and software improvements to the established technique have resulted in a record 6.9 µs temporal and <=2.8 cm spatial resolution in the midplane of each device. These allow C III and O II flow, displacement, and temperature profiles to be simultaneously observed. With 72 fused-silica fiber channels in two independent bundles, and an f/8.5 Czerny-Turner spectrometer coupled to video camera, frame-rates of up to ten timesmore » the imposed magnetic perturbation frequency of 14.5 kHz were achieved in HIT-SI, viewing the upper 1/2 of the midplane. In HIT-SI3 frame-rates of up to eight times the perturbation frequency were achieved viewing both halves of the midplane. Biorthogonal Decomposition is used as a novel filtering tool, reducing uncertainty in ion temperature from <=13 to <=5 eV (with an instrument temperature of 8-16 eV), and uncertainty in velocity from <=2 to <=1 km/s. Doppler shift and broadening is calculated via the Levenberg-Marquart algorithm, after which errors in velocity and temperature are uniquely specified. Axisymmetric temperature profiles on HIT-SI3 for C III peaked near the inboard current separatrix at approximately 40 eV are observed. Axisymmetric plasma displacement profiles have been measured on HIT-SI3, peaking at approximately 6 cm at the outboard separatrix. Both profiles agree with the upper half of the midplane observable by HIT-SI. With its complete midplane view, HIT-SI3 has unambiguously extracted axisymmetric, toroidal current dependent rotation of up to 3 km/s. Analysis of the temporal phase of the displacement uncovers a coherent structure, locked to the applied perturbation. Previously described diagnostic systems could not achieve such results.« less

Improvements to the Ion Doppler Spectrometer Diagnostic on the HIT-SI Experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hossack, Aaron; Chandra, Rian; Everson, Christopher

An Ion Doppler Spectrometer diagnostic system measuring impurity ion temperature and velocity on the HIT-SI and HIT-SI3 spheromak devices has been improved with higher spatiotemporal resolution and lower error than previously described devices. Hardware and software improvements to the established technique have resulted in a record 6.9 µs temporal and <=2.8 cm spatial resolution in the midplane of each device. These allow C III and O II flow, displacement, and temperature profiles to be simultaneously observed. With 72 fused-silica fiber channels in two independent bundles, and an f/8.5 Czerny-Turner spectrometer coupled to video camera, frame-rates of up to ten timesmore » the imposed magnetic perturbation frequency of 14.5 kHz were achieved in HIT-SI, viewing the upper 1/2 of the midplane. In HIT-SI3 frame-rates of up to eight times the perturbation frequency were achieved viewing both halves of the midplane. Biorthogonal Decomposition is used as a novel filtering tool, reducing uncertainty in ion temperature from <=13 to <=5 eV (with an instrument temperature of 8-16 eV), and uncertainty in velocity from <=2 to <=1 km/s. Doppler shift and broadening is calculated via the Levenberg-Marquart algorithm, after which errors in velocity and temperature are uniquely specified. Axisymmetric temperature profiles on HIT-SI3 for C III peaked near the inboard current separatrix at approximately 40 eV are observed. Axisymmetric plasma displacement profiles have been measured on HIT-SI3, peaking at approximately 6 cm at the outboard separatrix. Both profiles agree with the upper half of the midplane observable by HIT-SI. With its complete midplane view, HIT-SI3 has unambiguously extracted axisymmetric, toroidal current dependent rotation of up to 3 km/s. Analysis of the temporal phase of the displacement uncovers a coherent structure, locked to the applied perturbation. Previously described diagnostic systems could not achieve such results.« less

Calculation of the physicochemical properties of thienopyridines by the Pariser-Parr-Pople (PPP) method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vysotskii, Yu.B.; Zemskaya, E.A.; Zemskii, B.P.

1987-10-01

The dipole moments, diamagnetic susceptibilities, chemical shifts of the /sup 1/H, /sup 13/C, and /sup 14/N nuclei, and the energies of the lowest singlet-singlet transitions of aza-substituted thiophenes and benzo(b)thiophenes were calculated within the framework of the bonded variant of perturbation theory by the Pariser-Parr-Pople (PPP) method. A scale of aromatic character of the investigated class of compounds is given on the basis of the current distributions found.

Bidirectional solitons on water.

PubMed

Zhang, Jin E; Li, Yishen

2003-01-01

A theory of bidirectional solitons on water is developed by using an integrable Boussinesq surface-variable equation. We present an explicit transformation between the system and a member of the Ablowitz-Kaup-Newell-Segur system, and derive an exact multisoliton solution by using a Darboux transformation. The phase shifts and the maximum wave heights during the interaction are studied for two-soliton overtaking and head-on collisions. They agree with the Korteweg-de Vries solution for overtaking collision and the perturbation solution for head-on collision.

Asymptotic coefficients for one-interacting-level Voigt profiles

NASA Astrophysics Data System (ADS)

Cope, D.; Lovett, R. J.

1988-02-01

The asymptotic behavior of general Voigt profiles with general width and shift functions has been determined by Cope and Lovett (1987). The resulting asymptotic coefficients are functions of the perturber/radiator mass ratio; also, the coefficients for the one-interacting-level (OIL) profiles proposed by Ward et al. (1974) were studied. In this paper, the behavior of the OIL asymptotic coefficients for large mass ratio values is determined, thereby providing a complete picture of OIL asymptotics for all mass ratios.

Complexified boost invariance and holographic heavy ion collisions

DOE PAGES

Gubser, Steven S.; van der Schee, Wilke

2015-01-08

At strong coupling holographic studies have shown that heavy ion collisions do not obey normal boost invariance. Here we study a modified boost invariance through a complex shift in time, and show that this leads to surprisingly good agreement with numerical holographic computations. When including perturbations the agreement becomes even better, both in the hydrodynamic and the far-from-equilibrium regime. Finally, one of the main advantages is an analytic formulation of the stress-energy tensor of the longitudinal dynamics of holographic heavy ion collisions.

Perturbations to the Spatial and Temporal Characteristics of the Diurnally-Varying Atmospheric Boundary Layer Due to an Extensive Wind Farm

NASA Astrophysics Data System (ADS)

Sharma, V.; Parlange, M. B.; Calaf, M.

2017-02-01

The effect of extensive terrestrial wind farms on the spatio-temporal structure of the diurnally-evolving atmospheric boundary layer is explored. High-resolution large-eddy simulations of a realistic diurnal cycle with an embedded wind farm are performed. Simulations are forced by a constant geostrophic velocity with time-varying surface boundary conditions derived from a selected period of the CASES-99 field campaign. Through analysis of the bulk statistics of the flow as a function of height and time, it is shown that extensive wind farms shift the inertial oscillations and the associated nocturnal low-level jet vertically upwards by approximately 200 m; cause a three times stronger stratification between the surface and the rotor-disk region, and as a consequence, delay the formation and growth of the convective boundary layer (CBL) by approximately 2 h. These perturbations are shown to have a direct impact on the potential power output of an extensive wind farm with the displacement of the low-level jet causing lower power output during the night as compared to the day. The low-power regime at night is shown to persist for almost 2 h beyond the morning transition due to the reduced growth of the CBL. It is shown that the wind farm induces a deeper entrainment region with greater entrainment fluxes. Finally, it is found that the diurnally-averaged effective roughness length for wind farms is much lower than the reference value computed theoretically for neutral conditions.

Common and Specific Protein Accumulation Patterns in Different Albino/Pale-Green Mutants Reveals Regulon Organization at the Proteome Level1[W

PubMed Central

Motohashi, Reiko; Rödiger, Anja; Agne, Birgit; Baerenfaller, Katja; Baginsky, Sacha

2012-01-01

Research interest in proteomics is increasingly shifting toward the reverse genetic characterization of gene function at the proteome level. In plants, several distinct gene defects perturb photosynthetic capacity, resulting in the loss of chlorophyll and an albino or pale-green phenotype. Because photosynthesis is interconnected with the entire plant metabolism and its regulation, all albino plants share common characteristics that are determined by the switch from autotrophic to heterotrophic growth. Reverse genetic characterizations of such plants often cannot distinguish between specific consequences of a gene defect from generic effects in response to perturbations in photosynthetic capacity. Here, we set out to define common and specific features of protein accumulation in three different albino/pale-green plant lines. Using quantitative proteomics, we report a common molecular phenotype that connects the loss of photosynthetic capacity with other chloroplast and cellular functions, such as protein folding and stability, plastid protein import, and the expression of stress-related genes. Surprisingly, we do not find significant differences in the expression of key transcriptional regulators, suggesting that substantial regulation occurs at the posttranscriptional level. We examine the influence of different normalization schemes on the quantitative proteomics data and report all identified proteins along with their fold changes and P values in albino plants in comparison with the wild type. Our analysis provides initial guidance for the distinction between general and specific adaptations of the proteome in photosynthesis-impaired plants. PMID:23027667

Interhemispheric gradient of atmospheric radiocarbon reveals natural variability of Southern Ocean winds

NASA Astrophysics Data System (ADS)

Rodgers, K. B.; Fletcher, S. E. M.; Bianchi, D.; Beaulieu, C.; Galbraith, E. D.; Gnanadesikan, A.; Hogg, A. G.; Iudicone, D.; Lintner, B.; Naegler, T.; Reimer, P. J.; Sarmiento, J. L.; Slater, R. D.

2011-01-01

Tree ring Δ14C data (Reimer et al., 2004; McCormac et al., 2004) indicate that atmospheric Δ14C varied on multi-decadal to centennial timescales, in both hemispheres, over the pre-industrial period AD 950-1830. Although the Northern and Southern Hemispheric Δ14C records display similar variability, it is difficult from these data alone to distinguish between variations driven by 14CO2 production in the upper atmosphere (Stuiver, 1980) and exchanges between carbon reservoirs (Siegenthaler, 1980). Here we consider rather the Interhemispheric Gradient in atmospheric Δ14C as revealing of the background pre-bomb air-sea Disequilbrium Flux between 14CO2 and CO2. As the global maximum of the Disequilibrium Flux is squarely centered in the open ocean regions of the Southern Ocean, relatively modest perturbations to the winds over this region drive significant perturbations to the Interhemispheric Gradient. The analysis presented here implies that changes to Southern Ocean windspeeds are likely a main driver of the observed variability in the Interhemispheric Gradient over 950-1830, and further, that this variability may be larger than the Southern Ocean wind trends that have been reported for recent decades (notably 1980-2004). This interpretation also implies a significant weakening of the winds over the Southern Ocean within a few decades of AD 1375, associated with the transition between the Medieval Climate Anomaly and the Little Ice Age. The driving forces that could have produced such a shift in the winds remain unkown.

A quasilinear operator retaining magnetic drift effects in tokamak geometry

NASA Astrophysics Data System (ADS)

Catto, Peter J.; Lee, Jungpyo; Ram, Abhay K.

2017-12-01

The interaction of radio frequency waves with charged particles in a magnetized plasma is usually described by the quasilinear operator that was originally formulated by Kennel & Engelmann (Phys. Fluids, vol. 9, 1966, pp. 2377-2388). In their formulation the plasma is assumed to be homogenous and embedded in a uniform magnetic field. In tokamak plasmas the Kennel-Engelmann operator does not capture the magnetic drifts of the particles that are inherent to the non-uniform magnetic field. To overcome this deficiency a combined drift and gyrokinetic derivation is employed to derive the quasilinear operator for radio frequency heating and current drive in a tokamak with magnetic drifts retained. The derivation requires retaining the magnetic moment to higher order in both the unperturbed and perturbed kinetic equations. The formal prescription for determining the perturbed distribution function then follows a novel procedure in which two non-resonant terms must be evaluated explicitly. The systematic analysis leads to a diffusion equation that is compact and completely expressed in terms of the drift kinetic variables. The equation is not transit averaged, and satisfies the entropy principle, while retaining the full poloidal angle variation without resorting to Fourier decomposition. As the diffusion equation is in physical variables, it can be implemented in any computational code. In the Kennel-Engelmann formalism, the wave-particle resonant delta function is either for the Landau resonance or the Doppler shifted cyclotron resonance. In the combined gyro and drift kinetic approach, a term related to the magnetic drift modifies the resonance condition.

Phosphoenolpyruvate Transporter Enables Targeted Perturbation During Metabolic Analysis of L-Phenylalanine Production With Escherichia coli.

PubMed

Tröndle, Julia; Albermann, Christoph; Weiner, Michael; Sprenger, Georg A; Weuster-Botz, Dirk

2018-05-01

Usually perturbation of the metabolism of cells by addition of substrates is applied for metabolic analysis of production organisms, but perturbation studies are restricted to the endogenous substrates of the cells under study. The goal of this study is to overcome this limitation by making phosphoenolpyruvate (PEP) available for perturbation studies with Escherichia coli producing L-phenylalanine. A production strain overexpressing a PEP-transporter variant (UhpT-D388C) is applied in a standardized fed-batch production-process on a 42 L-scale. Four parallel short-term perturbation experiments of 20 min are performed with glucose and glycerol as fed-batch carbon sources after rapid media transition of cells from the production-process. PEP is added after 9 min and is immediately consumed by the cells with up to 1.5 mmol g CDW -1  h -1 . L-phenylalanine production rates increased by up to 200% after addition of PEP. This clearly indicates an intracellular PEP-limitation in the L-phenylalanine production strain under study. Thus, it is shown that overexpressing specific transporters for analytical reasons makes exogenous substrates available as perturbation substrates for metabolic analyses of cells sampled from production-processes and thereby allows a very targeted perturbation of whole-cell metabolism. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Constrained Perturbation Regularization Approach for Signal Estimation Using Random Matrix Theory

NASA Astrophysics Data System (ADS)

Suliman, Mohamed; Ballal, Tarig; Kammoun, Abla; Al-Naffouri, Tareq Y.

2016-12-01

In this supplementary appendix we provide proofs and additional extensive simulations that complement the analysis of the main paper (constrained perturbation regularization approach for signal estimation using random matrix theory).

Rapid distortion analysis of high speed homogeneous turbulence subject to periodic shear

DOE PAGES

Bertsch, Rebecca L.; Girimaji, Sharath S.

2015-12-30

The effect of unsteady shear forcing on small perturbation growth in compressible flow is investigated. In particular, flow-thermodynamic field interaction and the resulting effect on the phase-lag between applied shear and Reynolds stress are examined. Simplified linear analysis of the perturbation pressure equation reveals crucial differences between steady and unsteady shear effects. The analytical findings are validated with numerical simulations of inviscid rapid distortion theory (RDT) equations. In contrast to steadily sheared compressible flows, perturbations in the unsteady (periodic) forcing case do not experience an asymptotic growth phase. Further, the resonance growth phenomenon found in incompressible unsteady shear turbulence ismore » absent in the compressible case. Overall, the stabilizing influence of both unsteadiness and compressibility is compounded leading to suppression of all small perturbations. As a result, the underlying mechanisms are explained.« less

Rapid distortion analysis of high speed homogeneous turbulence subject to periodic shear

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertsch, Rebecca L., E-mail: rlb@lanl.gov; Girimaji, Sharath S., E-mail: girimaji@aero.tamu.edu

2015-12-15

The effect of unsteady shear forcing on small perturbation growth in compressible flow is investigated. In particular, flow-thermodynamic field interaction and the resulting effect on the phase-lag between applied shear and Reynolds stress are examined. Simplified linear analysis of the perturbation pressure equation reveals crucial differences between steady and unsteady shear effects. The analytical findings are validated with numerical simulations of inviscid rapid distortion theory (RDT) equations. In contrast to steadily sheared compressible flows, perturbations in the unsteady (periodic) forcing case do not experience an asymptotic growth phase. Further, the resonance growth phenomenon found in incompressible unsteady shear turbulence ismore » absent in the compressible case. Overall, the stabilizing influence of both unsteadiness and compressibility is compounded leading to suppression of all small perturbations. The underlying mechanisms are explained.« less

Perturbing Hele-Shaw flow with a small gap gradient

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, H.; Casademunt, J.; Yeung, C.

1992-02-15

A controlled perturbation is introduced into the Saffman-Taylor flow problem by adding a gradient to the gap of a Hele-Shaw cell. The stability of the single-finger steady state was found to be strongly affected by such a perturbation. Compared with patterns in a standard Hele-Shaw cell, the single Saffman-Taylor finger was stabilized or destabilized according to the sign of the gap gradient. While a linear stability analysis shows that this perturbation should have a negligible effect on the early-stage pattern formation, the experimental data indicate that the characteristic length for the initial breakup of a flat interface has been changedmore » by the perturbation.« less

Perturbations from cosmic strings in cold dark matter

NASA Technical Reports Server (NTRS)

Albrecht, Andreas; Stebbins, Albert

1992-01-01

A systematic linear analysis of the perturbations induced by cosmic strings in cold dark matter is presented. The power spectrum is calculated and it is found that the strings produce a great deal of power on small scales. It is shown that the perturbations on interesting scales are the result of many uncorrelated string motions, which indicates a much more Gaussian distribution than was previously supposed.

Perturbations from cosmic strings in cold dark matter

NASA Technical Reports Server (NTRS)

Albrecht, Andreas; Stebbins, Albert

1991-01-01

A systematic linear analysis of the perturbations induced by cosmic strings in cold dark matter is presented. The power spectrum is calculated and it is found that the strings produce a great deal of power on small scales. It is shown that the perturbations on interesting scales are the result of many uncorrelated string motions, which indicates a much more Gaussian distribution than was previously supposed.

Simulated shift work in rats perturbs multiscale regulation of locomotor activity

PubMed Central

Hsieh, Wan-Hsin; Escobar, Carolina; Yugay, Tatiana; Lo, Men-Tzung; Pittman-Polletta, Benjamin; Salgado-Delgado, Roberto; Scheer, Frank A. J. L.; Shea, Steven A.; Buijs, Ruud M.; Hu, Kun

2014-01-01

Motor activity possesses a multiscale regulation that is characterized by fractal activity fluctuations with similar structure across a wide range of timescales spanning minutes to hours. Fractal activity patterns are disturbed in animals after ablating the master circadian pacemaker (suprachiasmatic nucleus, SCN) and in humans with SCN dysfunction as occurs with aging and in dementia, suggesting the crucial role of the circadian system in the multiscale activity regulation. We hypothesized that the normal synchronization between behavioural cycles and the SCN-generated circadian rhythms is required for multiscale activity regulation. To test the hypothesis, we studied activity fluctuations of rats in a simulated shift work protocol that was designed to force animals to be active during the habitual resting phase of the circadian/daily cycle. We found that these animals had gradually decreased mean activity level and reduced 24-h activity rhythm amplitude, indicating disturbed circadian and behavioural cycles. Moreover, these animals had disrupted fractal activity patterns as characterized by more random activity fluctuations at multiple timescales from 4 to 12 h. Intriguingly, these activity disturbances exacerbated when the shift work schedule lasted longer and persisted even in the normal days (without forced activity) following the shift work. The disrupted circadian and fractal patterns resemble those of SCN-lesioned animals and of human patients with dementia, suggesting a detrimental impact of shift work on multiscale activity regulation. PMID:24829282

A Solution NMR Investigation into the Murine Amelogenin Splice-Variant LRAP (Leucine-Rich Amelogenin Protein).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Tarasevich, Barbara J.; Roberts, Jacky

2010-09-01

Amelogenins are the dominant proteins present in ameloblasts during the early stages of enamel biomineralization, making up >90% of the matrix protein. Along with the full-length protein there are several splice-variant isoforms of amelogenin present including LRAP (Leucine-Rich Amelogenin Protein), a protein that consists of the first 33 and the last 26 residues of full-length amelogenin. Using solution-state NMR spectroscopy we have assigned the 1H-15N HSQC spectrum of murine LRAP (rp(H)LRAP) in 2% acetic acid at pH 3.0 by making extensive use of previous chemical shift assignments for full-length murine amelogenin (rp(H)M180). This correlation was possible because LRAP, like themore » full-length protein, is intrinsically disordered under these solution conditions. The major difference between the 1H-15N HSQC spectra of rp(H)M180 and rp(H)LRAP was an additional set of amide resonances for each of the seven non-proline residues between S12* and Y12 at the N-terminus of rp(H)LRAP indicating that the N-terminal region of LRAP exists in two different conformations. Analysis of the proline carbon chemical shifts suggest that the molecular basis for the two states is not a cis-trans isomerization of one or more of the proline residues in the N-terminal region and is likely due to a slow exchange process. As observed with rp(H)M180, residue specific changes in molecular dynamics, manifested by the reduction in intensity and disappearance of 1H-15N HSQC cross peaks, were observed with the addition of NaCl to rp(H)LRAP. These perturbations may signal early events governing supramolecular self-assembly of rp(H)LRAP into nanospheres. However, the different pattern of 1H-15N HSQC cross peak perturbation between rp(H)LRAP and rp(H)M180 in high salt suggest that the termini may behave differently in their respective nanospheres, and perhaps, these differences account for the cell signaling properties attributable to LRAP but not the full-length protein.« less

The Effect of Extratropical Warming Amplification on the Future Tropical Precipitation

NASA Astrophysics Data System (ADS)

Yoshimori, M.; Hamano, Y.; Abe-Ouchi, A.

2016-12-01

The Arctic warms much more than the rest of the world under relatively uniform radiative forcing. Recent observations verify this characteristics of global warming. On the other hand, previous studies based on paleo-proxy data and paleo- and idealized numerical experiments have indicated that asymmetric warming between the two hemispheres can impact on the distribution of tropical precipitation. It was suggested diagnostically that the Arctic warming amplification may become responsible for a part of the future precipitation change in the tropics. In the current study, we have conducted several sensitivity experiments that isolate the effect of remote warming on the tropical precipitation using an atmospheric general circulation model with a mixture of prescribed and predicted mixed-layer sea surface conditions, depending of the region. Additional experiments including ocean dynamics will also be presented. In a standard equilibrium experiment of doubling of atmospheric CO2 concentration (2xCO2), the Northern Hemisphere mid-high latitude (40-90ºN) warms by about 7ºC and precipitation change occurs mostly in the tropical Pacific (20ºS-20ºN). In the zonal average, the increase in precipitation is larger in the North than the South by about 0.5 mm/day and the peak latitude of precipitation shifted northward by about 1º. Sensitivity experiments were designed to amplify or suppress the Northern Hemisphere mid-high latitude warming to different levels and to allow for the tropics to respond freely to those perturbations. The perturbations of the mid-high latitude warming range from -5ºC to +7ºC from the standard 2xCO2 experiment, and precipitation change range from -160% to +160% relative to the difference between 2xCO2 and control experiments. The peak latitude of precipitation shifted northward from -1.5º to +2.5º, and it was verified that most of the change is contributed by the change in the Hadley circulation, rather than the change in the moisture amount in the atmosphere. The response is understood through the energy budget analysis.

Fourth-order self-energy contribution to the two loop Lamb shift

NASA Astrophysics Data System (ADS)

Palur Mallampalli, Subrahmanyam

1998-11-01

The calculation of the two loop Lamb shift in hydrogenic ions involves the numerical evaluation of ten Feynman diagrams. In this thesis, four fourth-order Feynman diagrams including the pure self-energy contributions are evaluated using exact Dirac-Coulomb propagators, so that higher order binding corrections can be extracted by comparing with the known terms in the Z/alpha expansion. The entire calculation is performed in Feynman gauge. One of the vacuum polarization diagrams is evaluated in the Uehling approximation. At low Z, it is seen to be perturbative in Z/alpha, while new predictions for high Z are made. The calculation of the three self-energy diagrams is reorganized into four terms, which we call the PO, M, F and P terms. The PO term is separately gauge invariant while the latter three form a gauge invariant set. The PO term is shown to exhibit the most non-perturbative behavior yet encountered in QED at low Z, so much so that even at Z = 1, the complete result is of the opposite sign as that of the leading term in its Z/alpha expansion. At high Z, we agree with an earlier calculation. The analysis of ultraviolet divergences in the two loop self-energy is complicated by the presence of sub- divergences. All divergences except the self-mass are shown to cancel. The self-mass is then removed by a self- mass counterterm. Parts of the calculation are shown to contain reference state singularities, that finally cancel. A numerical regulator to handle these singularities is described. The M term, an ultraviolet finite quantity, is defined through a subtraction scheme in coordinate space. Being computationally intensive, it is evaluated only at high Z, specifically Z = 83 and 92. The F term involves the evaluation of several Feynman diagrams with free electron propagators. These are computed for a range of values of Z. The P term, also ultraviolet finite, involves Dirac- Coulomb propagators that are best defined in coordinate space, as well as functions associated with the one loop self-energy that are best defined in momentum space. Possible methods of evaluating the P term are discussed.

Kinematid Parameters of Corrective Postural Responses Differ between Upper and Lower Body Perturbations

NASA Technical Reports Server (NTRS)

Sayenko, G.

2004-01-01

Balance control is disrupted following prolonged microgravity exposure, and to better understand this, both upper and lower body perturbations have been used to study postural control in space flight crewmembers. However, differences between several postural response indicators observed using the two techniques suggest that different sensory systems may be involved in organizing responses to these different perturbation approaches. The present study sought to compare differences in parameters of corrective postural responses between upper body perturbations (pushes to the chest) and forward translations of the support surface. Nine subjects participated in this study. Forward translations were performed using a NeuroCom EquiTest(TM) CDP system, which was synchronized with a Northern Digital OptoTrak motion tracking system (3 subjects). Chest pushes were applied using a hand-held force transducer device and were performed using a stabilometric system (6 subjects). Analysis of EMG has shown that: i) the earliest response of the leg muscles was registered significantly later during forward translation of the support surface than during chest pushes, and ii) there was a tendency for the different order of leg muscles activation during the translation tests. Analysis of the kinematic data showed a significant difference in the subject's body segments inclinations during corrective postural responses to upper and lower body perturbations. It appears that upper body perturbations likely engage the vestibular system more rapidly, while lower body perturbations likely engage somatosensory systems more rapidly. These differences must be taken into account when choosing the type of perturbation for testing postural function.

Local influence for generalized linear models with missing covariates.

PubMed

Shi, Xiaoyan; Zhu, Hongtu; Ibrahim, Joseph G

2009-12-01

In the analysis of missing data, sensitivity analyses are commonly used to check the sensitivity of the parameters of interest with respect to the missing data mechanism and other distributional and modeling assumptions. In this article, we formally develop a general local influence method to carry out sensitivity analyses of minor perturbations to generalized linear models in the presence of missing covariate data. We examine two types of perturbation schemes (the single-case and global perturbation schemes) for perturbing various assumptions in this setting. We show that the metric tensor of a perturbation manifold provides useful information for selecting an appropriate perturbation. We also develop several local influence measures to identify influential points and test model misspecification. Simulation studies are conducted to evaluate our methods, and real datasets are analyzed to illustrate the use of our local influence measures.

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Increased Ocean Heat Convergence Into the High Latitudes With CO2 Doubling Enhances Polar-Amplified Warming

NASA Astrophysics Data System (ADS)

Singh, H. A.; Rasch, P. J.; Rose, B. E. J.

2017-10-01

We isolate the role of the ocean in polar climate change by directly evaluating how changes in ocean dynamics with quasi-equilibrium CO2 doubling impact high-latitude climate. With CO2 doubling, the ocean heat flux convergence (OHFC) shifts poleward in winter in both hemispheres. Imposing this pattern of perturbed OHFC in a global climate model results in a poleward shift in ocean-to-atmosphere turbulent heat fluxes (both sensible and latent) and sea ice retreat; the high latitudes warm, while the midlatitudes cool, thereby amplifying polar warming. Furthermore, midlatitude cooling is propagated to the polar midtroposphere on isentropic surfaces, augmenting the (positive) lapse rate feedback at high latitudes. These results highlight the key role played by the partitioning of meridional energy transport changes between the atmosphere and ocean in high-latitude climate change.

Aging does not affect the intralimb coordination elicited by slip-like perturbation of different intensities.

PubMed

Aprigliano, Federica; Martelli, Dario; Tropea, Peppino; Pasquini, Guido; Micera, Silvestro; Monaco, Vito

2017-09-01

This study was aimed at verifying whether aging modifies intralimb coordination strategy during corrective responses elicited by unexpected slip-like perturbations delivered during steady walking on a treadmill. To this end, 10 young and 10 elderly subjects were asked to manage unexpected slippages of different intensities. We analyzed the planar covariation law of the lower limb segments, using the principal component analysis, to verify whether elevation angles of older subjects covaried along a plan before and after the perturbation. Results showed that segments related to the perturbed limbs of both younger and older people do not covary after all perturbations. Conversely, the planar covariation law of the unperturbed limb was systematically held for younger and older subjects. These results occurred despite differences in spatio-temporal and kinematic parameters being observed among groups and perturbation intensities. Overall, our analysis revealed that aging does not affect intralimb coordination during corrective responses induced by slip-like perturbation, suggesting that both younger and older subjects adopt this control strategy while managing sudden and unexpected postural transitions of increasing intensities. Accordingly, results corroborate the hypothesis that balance control emerges from a governing set of biomechanical invariants, that is, suitable control schemes (e.g., planar covariation law) shared across voluntary and corrective motor behaviors, and across different sensory contexts due to different perturbation intensities, in both younger and older subjects. In this respect, our findings provide further support to investigate the effects of specific task training programs to counteract the risk of fall. NEW & NOTEWORTHY This study was aimed at investigating how aging affects the intralimb coordination of lower limb segments, described by the planar covariation law, during unexpected slip-like perturbations of increasing intensity. Results revealed that neither the aging nor the perturbation intensity affects this coordination strategy. Accordingly, we proposed that the balance control emerges from an invariant set of control schemes shared across different sensory motor contexts and despite age-related neuromuscular adaptations. Copyright © 2017 the American Physiological Society.

Analysis of vibration frequencies of uranyl ion in complexes with neutral bases (in Russian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobets, L.V.; Umreiko, D.S.

1986-12-01

It has been shown that any estimate of the changes in vibration frequencies of UO/sub 2//sup 2 +/ applies only to the series of isostructural compounds with similar stoichiometry. Either the same values of stretching vibration frequencies of uranyl correspond to complexes with ligands that have different donor abilities, or changes in these frequencies are not great and do not reflect the real increase in the donor ability of the bases with respect to proton-containing acceptors. When the acido ligands are replaced or the stoichiometry of the complexes is changed, no correlations can be carried out, since, besides the basicitiesmore » of donors, other parameters such as the dentateness of the ligand, and hence the symmetry and the structure of the compound, are also varied. In this paper, the authors evaluate the contributions of the ligands to the shift of the vibration frequencies of uranyl that have been made and do not take into account the characteristic features of the compounds which therefore led to very different values of the contributions for one and the same ligand in different compounds. To evaluate the shifts produced by the ligands, the value of 1065 cm/sup -1/ was taken as the vibration frequency of a hypothetical fee uranyl ion, not perturbed by bonds with equatorial ligands. The authors also evaluate the contributions of ions able to form polymer structures.« less

The AdS/CFT Correspondence: Classical, Quantum, and Thermodynamical Aspects

NASA Astrophysics Data System (ADS)

Young, Donovan

2007-06-01

Certain aspects of the AdS/CFT correspondence are studied in detail. We investigate the one-loop mass shift to certain two-impurity string states in light-cone string field theory on a plane wave background. We find that there exist logarithmic divergences in the sums over intermediate mode numbers which cancel between the cubic Hamiltonian and quartic "contact term". We argue that generically, every order in intermediate state impurities contributes to the mass shift at leading perturbative order. The same mass shift is also computed using an improved 3-string vertex proposed by Dobashi and Yoneya. The result is found to agree with gauge theory at leading order and is close but not quite in agreement at subleading order. We extend the analysis to include discrete light-cone quantization, considering states with up to three units of p+. We study the (apparently) first-order phase transition in the weakly coupled plane-wave matrix model at finite temperature. We analyze the effect of interactions by computing the relevant parts of the effective potential for the Polyakov loop operator to three loop order. We show that the phase transition is indeed of first order. We also compute the 2-loop correction to the Hagedorn temperature. Finally, correlation functions of 1/4 BPS Wilson loops with the infinite family of 1/2 BPS chiral primary operators are computed in N=4 super Yang-Mills theory by summing planar ladder diagrams. The correlation functions are also computed in the strong-coupling limit using string theory; the result is found to agree with the extrapolation of the planar ladders. The result is related to similar correlators of 1/2 BPS loops by a simple re-scaling of the coupling constant, discovered by Drukker for the case of the 1/4 BPS loop VEV.

Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance

PubMed Central

Preisner, Eva C.; Fichot, Erin B.; Norman, Robert S.

2016-01-01

The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011–2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models. PMID:27799927

Shuttle derived atmospheric density model. Part 2: STS atmospheric implications for AOTV trajectory analysis, a proposed GRAM perturbation density model

NASA Technical Reports Server (NTRS)

Findlay, J. T.; Kelly, G. M.; Troutman, P. A.

1984-01-01

A perturbation model to the Marshall Space Flight Center (MSFC) Global Reference Atmosphere Model (GRAM) was developed for use in the Aeroassist Orbital Transfer Vehicle (AOTV) trajectory and analysis. The model reflects NASA Space Shuttle experience over the first twelve entry flights. The GRAM was selected over the Air Force 1978 Reference Model because of its more general formulation and wider use throughout NASA. The add-on model, a simple scaling with altitude to reflect density structure encountered by the Shuttle Orbiter was selected principally to simplify implementation. Perturbations, by season, can be utilized to minimize the number of required simulations, however, exact Shuttle flight history can be exercised using the same model if desired. Such a perturbation model, though not meteorologically motivated, enables inclusion of High Resolution Accelerometer Package (HiRAP) results in the thermosphere. Provision is made to incorporate differing perturbations during the AOTV entry and exit phases of the aero-asist maneuver to account for trajectory displacement (geographic) along the ground track.

Approaches to the Treatment of Equilibrium Perturbations

NASA Astrophysics Data System (ADS)

Canagaratna, Sebastian G.

2003-10-01

Perturbations from equilibrium are treated in the textbooks by a combination of Le Châtelier's principle, the comparison of the equilibrium constant K with the reaction quotient Q,and the kinetic approach. Each of these methods is briefly reviewed. This is followed by derivations of the variation of the equilibrium value of the extent of reaction, ξeq, with various parameters on which it depends. Near equilibrium this relationship can be represented by a straight line. The equilibrium system can be regarded as moving on this line as the parameter is varied. The slope of the line depends on quantities like enthalpy of reaction, volume of reaction and so forth. The derivation shows that these quantities pertain to the equilibrium system, not the standard state. Also, the derivation makes clear what kind of assumptions underlie our conclusions. The derivation of these relations involves knowledge of thermodynamics that is well within the grasp of junior level physical chemistry students. The conclusions that follow from the derived relations are given as subsidiary rules in the form of the slope of ξeq, with T, p, et cetera. The rules are used to develop a visual way of predicting the direction of shift of a perturbed system. This method can be used to supplement one of the other methods even at the introductory level.

Exact renormalization group in Batalin-Vilkovisky theory

NASA Astrophysics Data System (ADS)

Zucchini, Roberto

2018-03-01

In this paper, inspired by the Costello's seminal work [11], we present a general formulation of exact renormalization group (RG) within the Batalin-Vilkovisky (BV) quantization scheme. In the spirit of effective field theory, the BV bracket and Laplacian structure as well as the BV effective action (EA) depend on an effective energy scale. The BV EA at a certain scale satisfies the BV quantum master equation at that scale. The RG flow of the EA is implemented by BV canonical maps intertwining the BV structures at different scales. Infinitesimally, this generates the BV exact renormalization group equation (RGE). We show that BV RG theory can be extended by augmenting the scale parameter space R to its shifted tangent bundle T [1]ℝ. The extra odd direction in scale space allows for a BV RG supersymmetry that constrains the structure of the BV RGE bringing it to Polchinski's form [6]. We investigate the implications of BV RG supersymmetry in perturbation theory. Finally, we illustrate our findings by constructing free models of BV RG flow and EA exhibiting RG supersymmetry in the degree -1 symplectic framework and studying the perturbation theory thereof. We find in particular that the odd partner of effective action describes perturbatively the deviation of the interacting RG flow from its free counterpart.

Non linear processes modulated by low doses of radiation exposure

NASA Astrophysics Data System (ADS)

Mariotti, Luca; Ottolenghi, Andrea; Alloni, Daniele; Babini, Gabriele; Morini, Jacopo; Baiocco, Giorgio

The perturbation induced by radiation impinging on biological targets can stimulate the activation of several different pathways, spanning from the DNA damage processing to intra/extra -cellular signalling. In the mechanistic investigation of radiobiological damage this complex “system” response (e.g. omics, signalling networks, micro-environmental modifications, etc.) has to be taken into account, shifting from a focus on the DNA molecule solely to a systemic/collective view. An additional complication comes from the finding that the individual response of each of the involved processes is often not linear as a function of the dose. In this context, a systems biology approach to investigate the effects of low dose irradiations on intra/extra-cellular signalling will be presented, where low doses of radiation act as a mild perturbation of a robustly interconnected network. Results obtained through a multi-level investigation of both DNA damage repair processes (e.g. gamma-H2AX response) and of the activation kinetics for intra/extra cellular signalling pathways (e.g. NFkB activation) show that the overall cell response is dominated by non-linear processes - such as negative feedbacks - leading to possible non equilibrium steady states and to a poor signal-to-noise ratio. Together with experimental data of radiation perturbed pathways, different modelling approaches will be also discussed.

DYNAMICAL INSTABILITIES IN HIGH-OBLIQUITY SYSTEMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamayo, D.; Nicholson, P. D.; Burns, J. A.

2013-03-01

High-inclination circumplanetary orbits that are gravitationally perturbed by the central star can undergo Kozai oscillations-large-amplitude, coupled variations in the orbital eccentricity and inclination. We first study how this effect is modified by incorporating perturbations from the planetary oblateness. Tremaine et al. found that, for planets with obliquities >68. Degree-Sign 875, orbits in the equilibrium local Laplace plane are unstable to eccentricity perturbations over a finite radial range and execute large-amplitude chaotic oscillations in eccentricity and inclination. In the hope of making that treatment more easily understandable, we analyze the problem using orbital elements, confirming this threshold obliquity. Furthermore, we findmore » that orbits inclined to the Laplace plane will be unstable over a broader radial range, and that such orbits can go unstable for obliquities less than 68. Degree-Sign 875. Finally, we analyze the added effects of radiation pressure, which are important for dust grains and provide a natural mechanism for particle semimajor axes to sweep via Poynting-Robertson drag through any unstable range. For low-eccentricity orbits in the equilibrium Laplace plane, we find that generally the effect persists; however, the unstable radial range is shifted and small retrograde particles can avoid the instability altogether. We argue that this occurs because radiation pressure modifies the equilibrium Laplace plane.« less

Statistical analysis of effective singular values in matrix rank determination

NASA Technical Reports Server (NTRS)

Konstantinides, Konstantinos; Yao, Kung

1988-01-01

A major problem in using SVD (singular-value decomposition) as a tool in determining the effective rank of a perturbed matrix is that of distinguishing between significantly small and significantly large singular values to the end, conference regions are derived for the perturbed singular values of matrices with noisy observation data. The analysis is based on the theories of perturbations of singular values and statistical significance test. Threshold bounds for perturbation due to finite-precision and i.i.d. random models are evaluated. In random models, the threshold bounds depend on the dimension of the matrix, the noisy variance, and predefined statistical level of significance. Results applied to the problem of determining the effective order of a linear autoregressive system from the approximate rank of a sample autocorrelation matrix are considered. Various numerical examples illustrating the usefulness of these bounds and comparisons to other previously known approaches are given.

Perturbative stability of SFT-based cosmological models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galli, Federico; Koshelev, Alexey S., E-mail: fgalli@tena4.vub.ac.be, E-mail: alexey.koshelev@vub.ac.be

2011-05-01

We review the appearance of multiple scalar fields in linearized SFT based cosmological models with a single non-local scalar field. Some of these local fields are canonical real scalar fields and some are complex fields with unusual coupling. These systems only admit numerical or approximate analysis. We introduce a modified potential for multiple scalar fields that makes the system exactly solvable in the cosmological context of Friedmann equations and at the same time preserves the asymptotic behavior expected from SFT. The main part of the paper consists of the analysis of inhomogeneous cosmological perturbations in this system. We show numericallymore » that perturbations corresponding to the new type of complex fields always vanish. As an example of application of this model we consider an explicit construction of the phantom divide crossing and prove the perturbative stability of this process at the linear order. The issue of ghosts and ways to resolve it are briefly discussed.« less

Instability of black strings in the third-order Lovelock theory

NASA Astrophysics Data System (ADS)

Giacomini, Alex; Henríquez-Báez, Carla; Lagos, Marcela; Oliva, Julio; Vera, Aldo

2016-05-01

We show that homogeneous black strings of third-order Lovelock theory are unstable under s-wave perturbations. This analysis is done in dimension D =9 , which is the lowest dimension that allows the existence of homogeneous black strings in a theory that contains only the third-order Lovelock term in the Lagrangian. As is the case in general relativity, the instability is produced by long wavelength perturbations and it stands for the perturbative counterpart of a thermal instability. We also provide a comparative analysis of the instabilities of black strings at a fixed radius in general relativity, Gauss-Bonnet, and third-order Lovelock theories. We show that the minimum critical wavelength that triggers the instability grows with the power of the curvature defined in the Lagrangian. The maximum exponential growth during the time of the perturbation is the largest in general relativity and it decreases with the number of curvatures involved in the Lagrangian.

Tapping in synchrony with a perturbed metronome: the phase correction response to small and large phase shifts as a function of tempo.

PubMed

Repp, Bruno H

2011-01-01

When tapping is paced by an auditory sequence containing small phase shift (PS) perturbations, the phase correction response (PCR) of the tap following a PS increases with the baseline interonset interval (IOI), leading eventually to overcorrection (B. H. Repp, 2008). Experiment 1 shows that this holds even for fixed-size PSs that become imperceptible as the IOI increases (here, from 400 to 1200 ms). Earlier research has also shown (but only for IOI=500 ms) that the PCR is proportionally smaller for large than for small PSs (B. H. Repp, 2002a, 2002b). Experiment 2 introduced large PSs and found smaller PCRs than in Experiment 1, at all of the same IOIs. In Experiments 3A and 3B, the author investigated whether the change in slope of the sigmoid function relating PCR and PS magnitudes occurs at a fixed absolute or relative PS magnitude across different IOIs (600, 1000, 1400 ms). The results suggest no clear answer; the exact shape of the function may depend on the range of PSs used in an experiment. Experiment 4 examined the PCR in the IOI range from 1000 to 2000 ms and found overcorrection throughout, but with the PCR increasing much more gradually than in Experiment 1. These results provide important new information about the phase correction process and pose challenges for models of sensorimotor synchronization, which presently cannot explain nonlinear PCR functions and overcorrection. Copyright © Taylor & Francis Group, LLC

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

PubMed Central

Erickson, David W; Schink, Severin J.; Patsalo, Vadim; Williamson, James R.; Gerland, Ulrich; Hwa, Terence

2018-01-01

A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms1–3 and they remain a topic of active investigation4–11. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations12–17, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models15,18–20 from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions. PMID:29072300

Cancer-Associated Mutants of RNA Helicase DDX3X Are Defective in RNA-Stimulated ATP Hydrolysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Epling, Leslie B.; Grace, Christy R.; Lowe, Brandon R.

The DEAD-box RNA helicase DDX3X is frequently mutated in pediatric medulloblastoma. We dissect how these mutants affect DDX3X function with structural, biochemical, and genetic experiments. We identify an N-terminal extension (“ATP-binding loop”, ABL) that is critical for the stimulation of ATP hydrolysis by RNA. We present crystal structures suggesting that the ABL interacts dynamically with ATP and confirming that the interaction occurs in solution by NMR chemical shift perturbation and isothermal titration calorimetry. DEAD-box helicases require interaction between two conserved RecA-like helicase domains, D1 and D2 for function. We use NMR chemical shift perturbation to show that DDX3X interacts specificallymore » with double-stranded RNA through its D1 domain, with contact mediated by residues G302 and G325. Mutants of these residues, G302V and G325E, are associated with pediatric medulloblastoma. These mutants are defective in RNA-stimulated ATP hydrolysis. We show that DDX3X complements the growth defect in a ded1 temperature-sensitive strain of Schizosaccharomyces pombe, but the cancer-associated mutants G302V and G325E do not complement and exhibit protein expression defects. In conclusion, taken together, our results suggest that impaired translation of important mRNA targets by mutant DDX3X represents a key step in the development of medulloblastoma.« less

Influence of non-spatial working memory demands on reach-grasp responses to loss of balance: Effects of age and fall risk.

PubMed

Westlake, Kelly P; Johnson, Brian P; Creath, Robert A; Neff, Rachel M; Rogers, Mark W

2016-03-01

Reactive balance recovery strategies following an unexpected loss of balance are crucial to the prevention of falls, head trauma and other major injuries in older adults. While a longstanding focus has been on understanding lower limb recovery responses, the upper limbs also play a critical role. However, when a fall occurs, little is known about the role of memory and attention shifting on the reach to grasp recovery strategy and what factors determine the speed and precision of this response beyond simple reaction time. The objective of this study was to compare response time and accuracy of a stabilizing grasp following a balance perturbation in older adult fallers compared to non-fallers and younger adults while loading the processing demands of non-spatial, verbal working memory. Working memory was engaged with a progressively challenging verb-generation task that was interrupted by an unexpected sideways platform perturbation and a pre-instructed reach to grasp response. Results revealed that the older adults, particularly those at high fall risk, demonstrated significantly increased movement time to handrail contact and grasping errors during conditions in which non-spatial memory was actively engaged. These findings provide preliminary evidence of the cognitive deficit in attention shifting away from an ongoing working memory task that underlies delayed and inaccurate protective reach to grasp responses in older adult fallers. Copyright © 2016 Elsevier B.V. All rights reserved.

Temporal Information Partitioning Networks (TIPNets): A process network approach to infer ecohydrologic shifts

NASA Astrophysics Data System (ADS)

Goodwell, Allison E.; Kumar, Praveen

2017-07-01

In an ecohydrologic system, components of atmospheric, vegetation, and root-soil subsystems participate in forcing and feedback interactions at varying time scales and intensities. The structure of this network of complex interactions varies in terms of connectivity, strength, and time scale due to perturbations or changing conditions such as rainfall, drought, or land use. However, characterization of these interactions is difficult due to multivariate and weak dependencies in the presence of noise, nonlinearities, and limited data. We introduce a framework for Temporal Information Partitioning Networks (TIPNets), in which time-series variables are viewed as nodes, and lagged multivariate mutual information measures are links. These links are partitioned into synergistic, unique, and redundant information components, where synergy is information provided only jointly, unique information is only provided by a single source, and redundancy is overlapping information. We construct TIPNets from 1 min weather station data over several hour time windows. From a comparison of dry, wet, and rainy conditions, we find that information strengths increase when solar radiation and surface moisture are present, and surface moisture and wind variability are redundant and synergistic influences, respectively. Over a growing season, network trends reveal patterns that vary with vegetation and rainfall patterns. The framework presented here enables us to interpret process connectivity in a multivariate context, which can lead to better inference of behavioral shifts due to perturbations in ecohydrologic systems. This work contributes to more holistic characterizations of system behavior, and can benefit a wide variety of studies of complex systems.

Cancer-Associated Mutants of RNA Helicase DDX3X Are Defective in RNA-Stimulated ATP Hydrolysis

DOE PAGES

Epling, Leslie B.; Grace, Christy R.; Lowe, Brandon R.; ...

2015-02-25

The DEAD-box RNA helicase DDX3X is frequently mutated in pediatric medulloblastoma. We dissect how these mutants affect DDX3X function with structural, biochemical, and genetic experiments. We identify an N-terminal extension (“ATP-binding loop”, ABL) that is critical for the stimulation of ATP hydrolysis by RNA. We present crystal structures suggesting that the ABL interacts dynamically with ATP and confirming that the interaction occurs in solution by NMR chemical shift perturbation and isothermal titration calorimetry. DEAD-box helicases require interaction between two conserved RecA-like helicase domains, D1 and D2 for function. We use NMR chemical shift perturbation to show that DDX3X interacts specificallymore » with double-stranded RNA through its D1 domain, with contact mediated by residues G302 and G325. Mutants of these residues, G302V and G325E, are associated with pediatric medulloblastoma. These mutants are defective in RNA-stimulated ATP hydrolysis. We show that DDX3X complements the growth defect in a ded1 temperature-sensitive strain of Schizosaccharomyces pombe, but the cancer-associated mutants G302V and G325E do not complement and exhibit protein expression defects. In conclusion, taken together, our results suggest that impaired translation of important mRNA targets by mutant DDX3X represents a key step in the development of medulloblastoma.« less

Anticipatory phase correction in sensorimotor synchronization.

PubMed

Repp, Bruno H; Moseley, Gordon P

2012-10-01

Studies of phase correction in sensorimotor synchronization often introduce timing perturbations that are unpredictable with regard to direction, magnitude, and position in the stimulus sequence. If participants knew any or all of these parameters in advance, would they be able to anticipate perturbations and thus regain synchrony more quickly? In Experiment 1, we asked musically trained participants to tap in synchrony with short isochronous tone sequences containing a phase shift (PS) of -100, -40, 40, or 100 ms and provided advance information about its direction, position, or both (but not about its magnitude). The first two conditions had little effect, but in the third condition participants shifted their tap in anticipation of the PS, though only by about ±40 ms on average. The phase correction response to the residual PS was also enhanced. In Experiment 2, we provided complete advance information about PSs of various magnitudes either at the time of the immediately preceding tone ("late") or at the time of the tone one position back ("early") while also varying sequence tempo. Anticipatory phase correction was generally conservative and was impeded by fast tempo in the "late" condition. At fast tempi in both conditions, advancing a tap was more difficult than delaying a tap. The results indicate that temporal constraints on anticipatory phase correction resemble those on reactive phase correction. While the latter is usually automatic, this study shows that phase correction can also be controlled consciously for anticipatory purposes. Copyright © 2011 Elsevier B.V. All rights reserved.

Instabilities in mimetic matter perturbations

NASA Astrophysics Data System (ADS)

Firouzjahi, Hassan; Gorji, Mohammad Ali; Mansoori, Seyed Ali Hosseini

2017-07-01

We study cosmological perturbations in mimetic matter scenario with a general higher derivative function. We calculate the quadratic action and show that both the kinetic term and the gradient term have the wrong sings. We perform the analysis in both comoving and Newtonian gauges and confirm that the Hamiltonians and the associated instabilities are consistent with each other in both gauges. The existence of instabilities is independent of the specific form of higher derivative function which generates gradients for mimetic field perturbations. It is verified that the ghost instability in mimetic perturbations is not associated with the higher derivative instabilities such as the Ostrogradsky ghost.

The mechanism by which nonlinearity sustains turbulence in plane Couette flow

NASA Astrophysics Data System (ADS)

Nikolaidis, M.-A.; Farrell, B. F.; Ioannou, P. J.

2018-04-01

Turbulence in wall-bounded shear flow results from a synergistic interaction between linear non-normality and nonlinearity in which non-normal growth of a subset of perturbations configured to transfer energy from the externally forced component of the turbulent state to the perturbation component maintains the perturbation energy, while the subset of energy-transferring perturbations is replenished by nonlinearity. Although it is accepted that both linear non-normality mediated energy transfer from the forced component of the mean flow and nonlinear interactions among perturbations are required to maintain the turbulent state, the detailed physical mechanism by which these processes interact in maintaining turbulence has not been determined. In this work a statistical state dynamics based analysis is performed on turbulent Couette flow at R = 600 and a comparison to DNS is used to demonstrate that the perturbation component in Couette flow turbulence is replenished by a non-normality mediated parametric growth process in which the fluctuating streamwise mean flow has been adjusted to marginal Lyapunov stability. It is further shown that the alternative mechanism in which the subspace of non-normally growing perturbations is maintained directly by perturbation-perturbation nonlinearity does not contribute to maintaining the turbulent state. This work identifies parametric interaction between the fluctuating streamwise mean flow and the streamwise varying perturbations to be the mechanism of the nonlinear interaction maintaining the perturbation component of the turbulent state, and identifies the associated Lyapunov vectors with positive energetics as the structures of the perturbation subspace supporting the turbulence.

Optimal guidance law development for an advanced launch system

NASA Technical Reports Server (NTRS)

Calise, Anthony J.; Leung, Martin S. K.

1995-01-01

The objective of this research effort was to develop a real-time guidance approach for launch vehicles ascent to orbit injection. Various analytical approaches combined with a variety of model order and model complexity reduction have been investigated. Singular perturbation methods were first attempted and found to be unsatisfactory. The second approach based on regular perturbation analysis was subsequently investigated. It also fails because the aerodynamic effects (ignored in the zero order solution) are too large to be treated as perturbations. Therefore, the study demonstrates that perturbation methods alone (both regular and singular perturbations) are inadequate for use in developing a guidance algorithm for the atmospheric flight phase of a launch vehicle. During a second phase of the research effort, a hybrid analytic/numerical approach was developed and evaluated. The approach combines the numerical methods of collocation and the analytical method of regular perturbations. The concept of choosing intelligent interpolating functions is also introduced. Regular perturbation analysis allows the use of a crude representation for the collocation solution, and intelligent interpolating functions further reduce the number of elements without sacrificing the approximation accuracy. As a result, the combined method forms a powerful tool for solving real-time optimal control problems. Details of the approach are illustrated in a fourth order nonlinear example. The hybrid approach is then applied to the launch vehicle problem. The collocation solution is derived from a bilinear tangent steering law, and results in a guidance solution for the entire flight regime that includes both atmospheric and exoatmospheric flight phases.

GOCE: The first seismometer in orbit around the Earth

NASA Astrophysics Data System (ADS)

Garcia, Raphael F.; Bruinsma, Sean; Lognonné, Philippe; Doornbos, Eelco; Cachoux, Florian

2013-03-01

The first in situ sounding of a post-seismic infrasound wavefront is presented, using data from the GOCE mission. The atmospheric infrasounds following the great Tohoku earthquake (on 11 March 2011) induce variations of air density and vertical acceleration of the GOCE platform. These signals are detected at two positions along the GOCE orbit corresponding to a crossing and a doubling of the infrasonic wavefront created by seismic surface waves. Perturbations up to 11% of air density and 1.35 × 10 - 7 m/s2 of vertical acceleration are observed and modeled with two different solid-atmosphere coupling codes. These perturbations are a due to acoustic waves creating vertical velocities up to 130 m/s. Amplitudes and arrival times of these perturbations are reproduced respectively within a factor 2, and within a 60 s time window. Waveforms present a good agreement with observed data. The vertical acceleration to air density perturbation ratio is higher for these acoustic waves than for gravity waves. Combining these two pieces of information offers a new way to distinguish between these two wave types. This new type of data is a benchmark for the models of solid-atmosphere coupling. Amplitude and frequency content constrain the infrasound attenuation related to atmosphere viscosity and thermal conductivity. Observed time shifts between data and synthetics are ascribed to lateral variations of the seismic and atmospheric sound velocities and to the influence of atmospheric winds. These effects should be included in future modeling. This validation of our modeling tools allows to specify more precisely future observation projects.

Effect of a Jurassic oceanic anoxic event on belemnite ecology and evolution

PubMed Central

Ullmann, Clemens Vinzenz; Thibault, Nicolas; Ruhl, Micha; Hesselbo, Stephen P.; Korte, Christoph

2014-01-01

The Toarcian oceanic anoxic event (T-OAE; ∼183 million y ago) is possibly the most extreme episode of widespread ocean oxygen deficiency in the Phanerozoic, coinciding with rapid atmospheric pCO2 increase and significant loss of biodiversity in marine faunas. The event is a unique past tipping point in the Earth system, where rapid and massive release of isotopically light carbon led to a major perturbation in the global carbon cycle as recorded in organic and inorganic C isotope records. Modern marine ecosystems are projected to experience major loss in biodiversity in response to enhanced ocean anoxia driven by anthropogenic release of greenhouse gases. Potential consequences of this anthropogenic forcing can be approximated by studying analog environmental perturbations in the past such as the T-OAE. Here we present to our knowledge the first organic carbon isotope record derived from the organic matrix in the calcite rostra of early Toarcian belemnites. We combine both organic and calcite carbon isotope analyses of individual specimens of these marine predators to obtain a refined reconstruction of the early Toarcian global exogenic carbon cycle perturbation and belemnite paleoecology. The organic carbon isotope data combined with measurements of oxygen isotope values from the same specimens allow for a more robust interpretation of the interplay between the global carbon cycle perturbation, environmental change, and biotic response during the T-OAE. We infer that belemnites adapted to environmental change by shifting their habitat from cold bottom waters to warm surface waters in response to expanded seafloor anoxia. PMID:24982187

Adaptive strategies of remote systems operators exposed to perturbed camera-viewing conditions

NASA Technical Reports Server (NTRS)

Stuart, Mark A.; Manahan, Meera K.; Bierschwale, John M.; Sampaio, Carlos E.; Legendre, A. J.

1991-01-01

This report describes a preliminary investigation of the use of perturbed visual feedback during the performance of simulated space-based remote manipulation tasks. The primary objective of this NASA evaluation was to determine to what extent operators exhibit adaptive strategies which allow them to perform these specific types of remote manipulation tasks more efficiently while exposed to perturbed visual feedback. A secondary objective of this evaluation was to establish a set of preliminary guidelines for enhancing remote manipulation performance and reducing the adverse effects. These objectives were accomplished by studying the remote manipulator performance of test subjects exposed to various perturbed camera-viewing conditions while performing a simulated space-based remote manipulation task. Statistical analysis of performance and subjective data revealed that remote manipulation performance was adversely affected by the use of perturbed visual feedback and performance tended to improve with successive trials in most perturbed viewing conditions.

Auxiliary principle technique and iterative algorithm for a perturbed system of generalized multi-valued mixed quasi-equilibrium-like problems.

PubMed

Rahaman, Mijanur; Pang, Chin-Tzong; Ishtyak, Mohd; Ahmad, Rais

2017-01-01

In this article, we introduce a perturbed system of generalized mixed quasi-equilibrium-like problems involving multi-valued mappings in Hilbert spaces. To calculate the approximate solutions of the perturbed system of generalized multi-valued mixed quasi-equilibrium-like problems, firstly we develop a perturbed system of auxiliary generalized multi-valued mixed quasi-equilibrium-like problems, and then by using the celebrated Fan-KKM technique, we establish the existence and uniqueness of solutions of the perturbed system of auxiliary generalized multi-valued mixed quasi-equilibrium-like problems. By deploying an auxiliary principle technique and an existence result, we formulate an iterative algorithm for solving the perturbed system of generalized multi-valued mixed quasi-equilibrium-like problems. Lastly, we study the strong convergence analysis of the proposed iterative sequences under monotonicity and some mild conditions. These results are new and generalize some known results in this field.

Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

2016-12-01

In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

Effective potentials for H2O-He and H2O-Ar systems. Isotropic induction-dispersion potentials

NASA Astrophysics Data System (ADS)

Starikov, Vitali I.; Petrova, Tatiana M.; Solodov, Alexander M.; Solodov, Alexander A.; Deichuli, Vladimir M.

2017-05-01

The vibrational and rotational dependence of the effective isotropic interaction potential of H2O-He and H2O-Ar systems, taken in the form of Lennard-Jones 6-12 potential has been analyzed. The analysis is based on the experimental line broadening (γ) and line shift (δ) coefficients obtained for different vibrational bands of H2O molecule perturbed by He and Ar. The first and second derivatives of the function C(1)(q) for the long-range part of the induction-dispersion potential with respect to the dimensionless normal coordinates q were calculated using literature information for the dipole moment and mean polarizability functions μ(q) and α(q), respectively. These derivatives have been used in the calculations of the quantities which determine the vibrational and rotational dependence of the long-range part of the effective isotropic potential. The optimal set of the derivatives for the function C(1)(q) is proposed. The comparison with the experimental data has been performed.

Late Cretaceous restructuring of terrestrial communities facilitated the end-Cretaceous mass extinction in North America.

PubMed

Mitchell, Jonathan S; Roopnarine, Peter D; Angielczyk, Kenneth D

2012-11-13

The sudden environmental catastrophe in the wake of the end-Cretaceous asteroid impact had drastic effects that rippled through animal communities. To explore how these effects may have been exacerbated by prior ecological changes, we used a food-web model to simulate the effects of primary productivity disruptions, such as those predicted to result from an asteroid impact, on ten Campanian and seven Maastrichtian terrestrial localities in North America. Our analysis documents that a shift in trophic structure between Campanian and Maastrichtian communities in North America led Maastrichtian communities to experience more secondary extinction at lower levels of primary production shutdown and possess a lower collapse threshold than Campanian communities. Of particular note is the fact that changes in dinosaur richness had a negative impact on the robustness of Maastrichtian ecosystems against environmental perturbations. Therefore, earlier ecological restructuring may have exacerbated the impact and severity of the end-Cretaceous extinction, at least in North America.

Late Cretaceous restructuring of terrestrial communities facilitated the end-Cretaceous mass extinction in North America

PubMed Central

Roopnarine, Peter D.; Angielczyk, Kenneth D.

2012-01-01

The sudden environmental catastrophe in the wake of the end-Cretaceous asteroid impact had drastic effects that rippled through animal communities. To explore how these effects may have been exacerbated by prior ecological changes, we used a food-web model to simulate the effects of primary productivity disruptions, such as those predicted to result from an asteroid impact, on ten Campanian and seven Maastrichtian terrestrial localities in North America. Our analysis documents that a shift in trophic structure between Campanian and Maastrichtian communities in North America led Maastrichtian communities to experience more secondary extinction at lower levels of primary production shutdown and possess a lower collapse threshold than Campanian communities. Of particular note is the fact that changes in dinosaur richness had a negative impact on the robustness of Maastrichtian ecosystems against environmental perturbations. Therefore, earlier ecological restructuring may have exacerbated the impact and severity of the end-Cretaceous extinction, at least in North America. PMID:23112149

Analysis and modeling of photomask edge effects for 3D geometries and the effect on process window

NASA Astrophysics Data System (ADS)

Miller, Marshal A.; Neureuther, Andrew R.

2009-03-01

Simulation was used to explore boundary layer models for 1D and 2D patterns that would be appropriate for fast CAD modeling of physical effects during design. FDTD simulation was used to compare rigorous thick mask modeling to a thin mask approximation (TMA). When features are large, edges can be viewed as independent and modeled as separate from one another, but for small mask features, edges experience cross-talk. For attenuating phase-shift masks, interaction distances as large as 150nm were observed. Polarization effects are important for accurate EMF models. Due to polarization effects, the edge perturbations in line ends become different compared to a perpendicular edge. For a mask designed to be real, the 90o transmission created at edges produces an asymmetry through focus, which is also polarization dependent. Thick mask fields are calculated using TEMPEST and Panoramic Technologies software. Fields are then analyzed in the near field and on wafer CDs to examine deviations from TMA.

Nonlinear spherical perturbations in quintessence models of dark energy

NASA Astrophysics Data System (ADS)

Pratap Rajvanshi, Manvendra; Bagla, J. S.

2018-06-01

Observations have confirmed the accelerated expansion of the universe. The accelerated expansion can be modelled by invoking a cosmological constant or a dynamical model of dark energy. A key difference between these models is that the equation of state parameter w for dark energy differs from ‑1 in dynamical dark energy (DDE) models. Further, the equation of state parameter is not constant for a general DDE model. Such differences can be probed using the variation of scale factor with time by measuring distances. Another significant difference between the cosmological constant and DDE models is that the latter must cluster. Linear perturbation analysis indicates that perturbations in quintessence models of dark energy do not grow to have a significant amplitude at small length scales. In this paper we study the response of quintessence dark energy to non-linear perturbations in dark matter. We use a fully relativistic model for spherically symmetric perturbations. In this study we focus on thawing models. We find that in response to non-linear perturbations in dark matter, dark energy perturbations grow at a faster rate than expected in linear perturbation theory. We find that dark energy perturbation remains localised and does not diffuse out to larger scales. The dominant drivers of the evolution of dark energy perturbations are the local Hubble flow and a supression of gradients of the scalar field. We also find that the equation of state parameter w changes in response to perturbations in dark matter such that it also becomes a function of position. The variation of w in space is correlated with density contrast for matter. Variation of w and perturbations in dark energy are more pronounced in response to large scale perturbations in matter while the dependence on the amplitude of matter perturbations is much weaker.

Global Links to Local Carbon Cycling Perturbation

NASA Astrophysics Data System (ADS)

Chen, J.; Montanez, I. P.; Wang, X.; Qi, Y.

2016-12-01

Carbon cycle perturbations recorded by stable carbon isotope excursions (CIEs) play an important role in understanding climate, oceanography, and the biosphere through time. Recent studies, however, reveal the influence of regional processes on apparent global CIEs. Deconvolving local/regional from global processes imprinted in the carbon isotopic records of sedimentary successions requires integrated sedimentologic, stratigraphic, and geochemical study. Here we present coupled C and Sr isotopic records of diagenetically screened micrite and brachiopods from late Mississippian shallow-marine, carbonate platform and contemporaneous carbonate slope successions from the east Paleotethys Ocean region (South China). These records reveal distinctly different signatures of the depositional response to the onset of Carboniferous glaciation. C and Sr isotopic compositions of the platform carbonates exhibit systematic fluctuations in step with inferred sea-level changes captured by depositional cycles. CIEs in the platform succession can be correlated to the contemporaneous C isotope record from the Antler carbonate ramp (Idaho, USA). In contrast, slope carbonate and conodont isotopic records exhibit minimal variability interpreted to record the open-ocean seawater composition. The isotopic disparity between successions is interpreted to record the influence of local depositional, but not diagenetic, processes operating on the carbonate platform in response to glacioeustasy. Variability in the nature of coupled isotopic and inferred sea level fluctuations is interpreted to record stepwise onset of the late Paleozoic ice age in the late Mississippian. Initial large magnitude shifts in C and Sr isotopic compositions of late Visean to early Serpukhovian carbonates correspond to 1 to 2 myr-scale cycles driven by the buildup of continental glaciers. Subsequent decreased magnitude of isotopic shifts coincident with a shift to shorter duration and smaller magnitude sea-level fluctuations in the middle to late Serpukhovian interval is interpreted to record temporary retraction of the ice sheets in response to late Serpukhovian warming. Overall, the coupled stratigraphic and isotopic records indicate stepwise ice buildup prior to widespread glaciation across the mid-Carboniferous boundary.

Modal analysis of untransposed bilateral three-phase lines -- a perturbation approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faria, J.A.B.; Mendes, J.H.B.

1997-01-01

Model analysis of three-phase power lines exhibiting bilateral symmetry leads to modal transformation matrices that closely resemble Clarke`s transformation. The authors develop a perturbation theory approach to justify, interpret, and gain understanding of this well known fact. Further, the authors show how to find new frequency dependent correction terms that once added to Clarke`s transformation lead to improved accuracy.

An Extrinsic Fabry-Perot Interferometric Sensor using Intermodal Phase Shifting and Demultiplexing of the Propagating Modes in a Few-Mode Fiber

NASA Astrophysics Data System (ADS)

Chatterjee, Julius

This dissertation demonstrates a fiber-optic phase shifted Fabry-Perot interferometer (PS-FPI) as a sensor using modal demultiplexing. Single wavelength Fabry-Perot interferometers suffer from fringe ambiguity and loss of sensitivity at fringe extremes. These hindrances cause it to be a secondary choice when being selected for a measurement task at hand, and more often than not, white light based sensors are selected in favor of the single wavelength Fabry-Perot sensors. This work aims to introduce a technique involving the demultiplexing of the propagating linearly polarized (LP) modes in few mode fibers to obtain two fringe systems from the same sensing cavity. This results in a few-mode interferometer that effectively has two to three orders of magnitude higher perturbation sensitivity than a conventional few mode interferometer for the same sensing region. In this work, two different modal demultiplexing techniques (MD) are used to demodulate the propagating modes and to obtain two fringe sets. These output fringe sets are shifted in phase with respect to each other by a phase shift due to the propagation of the modes in the fiber-optic layout. A method of controlling this phase shift by straining a length of a two mode fiber located separate from the PS-FPI cavity is demonstrated and corresponding changes in phase shifts are shown. The results show a controllable phase shift for both the MD techniques, which is useful in sensing by permitting quadrature demodulation of interferometric fringes and also results in a novel few-mode sensing system having more than two orders of magnitude sensitivity than conventional few-mode devices.

Low energy peripheral scaling in nucleon-nucleon scattering and uncertainty quantification

NASA Astrophysics Data System (ADS)

Ruiz Simo, I.; Amaro, J. E.; Ruiz Arriola, E.; Navarro Pérez, R.

2018-03-01

We analyze the peripheral structure of the nucleon-nucleon interaction for LAB energies below 350 MeV. To this end we transform the scattering matrix into the impact parameter representation by analyzing the scaled phase shifts (L + 1/2) δ JLS (p) and the scaled mixing parameters (L + 1/2)ɛ JLS (p) in terms of the impact parameter b = (L + 1/2)/p. According to the eikonal approximation, at large angular momentum L these functions should become an universal function of b, independent on L. This allows to discuss in a rather transparent way the role of statistical and systematic uncertainties in the different long range components of the two-body potential. Implications for peripheral waves obtained in chiral perturbation theory interactions to fifth order (N5LO) or from the large body of NN data considered in the SAID partial wave analysis are also drawn from comparing them with other phenomenological high-quality interactions, constructed to fit scattering data as well. We find that both N5LO and SAID peripheral waves disagree more than 5σ with the Granada-2013 statistical analysis, more than 2σ with the 6 statistically equivalent potentials fitting the Granada-2013 database and about 1σ with the historical set of 13 high-quality potentials developed since the 1993 Nijmegen analysis.

Effects of sudden walking perturbations on neuromuscular reflex activity and three-dimensional motion of the trunk in healthy controls and back pain symptomatic subjects.

PubMed

Mueller, Juliane; Engel, Tilman; Mueller, Steffen; Stoll, Josefine; Baur, Heiner; Mayer, Frank

2017-01-01

Back pain patients (BPP) show delayed muscle onset, increased co-contractions, and variability as response to quasi-static sudden trunk loading in comparison to healthy controls (H). However, it is unclear whether these results can validly be transferred to suddenly applied walking perturbations, an automated but more functional and complex movement pattern. There is an evident need to develop research-based strategies for the rehabilitation of back pain. Therefore, the investigation of differences in trunk stability between H and BPP in functional movements is of primary interest in order to define suitable intervention regimes. The purpose of this study was to analyse neuromuscular reflex activity as well as three-dimensional trunk kinematics between H and BPP during walking perturbations. Eighty H (31m/49f;29±9yrs;174±10cm;71±13kg) and 14 BPP (6m/8f;30±8yrs;171±10cm;67±14kg) walked (1m/s) on a split-belt treadmill while 15 right-sided perturbations (belt decelerating, 40m/s2, 50ms duration; 200ms after heel contact) were randomly applied. Trunk muscle activity was assessed using a 12-lead EMG set-up. Trunk kinematics were measured using a 3-segment-model consisting of 12 markers (upper thoracic (UTA), lower thoracic (LTA), lumbar area (LA)). EMG-RMS ([%],0-200ms after perturbation) was calculated and normalized to the RMS of unperturbed gait. Latency (TON;ms) and time to maximum activity (TMAX;ms) were analysed. Total motion amplitude (ROM;[°]) and mean angle (Amean;[°]) for extension-flexion, lateral flexion and rotation were calculated (whole stride cycle; 0-200ms after perturbation) for each of the three segments during unperturbed and perturbed gait. For ROM only, perturbed was normalized to unperturbed step [%] for the whole stride as well as the 200ms after perturbation. Data were analysed descriptively followed by a student´s t-test to account for group differences. Co-contraction was analyzed between ventral and dorsal muscles (V:R) as well as side right:side left ratio (Sright:Sleft). The coefficient of variation (CV;%) was calculated (EMG-RMS;ROM) to evaluate variability between the 15 perturbations for all groups. With respect to unequal distribution of participants to groups, an additional matched-group analysis was conducted. Fourteen healthy controls out of group H were sex-, age- and anthropometrically matched (group Hmatched) to the BPP. No group differences were observed for EMG-RMS or CV analysis (EMG/ROM) (p>0.025). Co-contraction analysis revealed no differences for V:R and Srigth:Sleft between the groups (p>0.025). BPP showed an increased TON and TMAX, being significant for Mm. rectus abdominus (p = 0.019) and erector spinae T9/L3 (p = 0.005/p = 0.015). ROM analysis over the unperturbed stride cycle revealed no differences between groups (p>0.025). Normalization of perturbed to unperturbed step lead to significant differences for the lumbar segment (LA) in lateral flexion with BPP showing higher normalized ROM compared to Hmatched (p = 0.02). BPP showed a significant higher flexed posture (UTA (p = 0.02); LTA (p = 0.004)) during normal walking (Amean). Trunk posture (Amean) during perturbation showed higher trunk extension values in LTA segments for H/Hmatched compared to BPP (p = 0.003). Matched group (BPP vs. Hmatched) analysis did not show any systematic changes of all results between groups. BPP present impaired muscle response times and trunk posture, especially in the sagittal and transversal planes, compared to H. This could indicate reduced trunk stability and higher loading during gait perturbations.

Effects of sudden walking perturbations on neuromuscular reflex activity and three-dimensional motion of the trunk in healthy controls and back pain symptomatic subjects

PubMed Central

Mueller, Juliane; Engel, Tilman; Mueller, Steffen; Stoll, Josefine; Baur, Heiner; Mayer, Frank

2017-01-01

Background Back pain patients (BPP) show delayed muscle onset, increased co-contractions, and variability as response to quasi-static sudden trunk loading in comparison to healthy controls (H). However, it is unclear whether these results can validly be transferred to suddenly applied walking perturbations, an automated but more functional and complex movement pattern. There is an evident need to develop research-based strategies for the rehabilitation of back pain. Therefore, the investigation of differences in trunk stability between H and BPP in functional movements is of primary interest in order to define suitable intervention regimes. The purpose of this study was to analyse neuromuscular reflex activity as well as three-dimensional trunk kinematics between H and BPP during walking perturbations. Methods Eighty H (31m/49f;29±9yrs;174±10cm;71±13kg) and 14 BPP (6m/8f;30±8yrs;171±10cm;67±14kg) walked (1m/s) on a split-belt treadmill while 15 right-sided perturbations (belt decelerating, 40m/s2, 50ms duration; 200ms after heel contact) were randomly applied. Trunk muscle activity was assessed using a 12-lead EMG set-up. Trunk kinematics were measured using a 3-segment-model consisting of 12 markers (upper thoracic (UTA), lower thoracic (LTA), lumbar area (LA)). EMG-RMS ([%],0-200ms after perturbation) was calculated and normalized to the RMS of unperturbed gait. Latency (TON;ms) and time to maximum activity (TMAX;ms) were analysed. Total motion amplitude (ROM;[°]) and mean angle (Amean;[°]) for extension-flexion, lateral flexion and rotation were calculated (whole stride cycle; 0-200ms after perturbation) for each of the three segments during unperturbed and perturbed gait. For ROM only, perturbed was normalized to unperturbed step [%] for the whole stride as well as the 200ms after perturbation. Data were analysed descriptively followed by a student´s t-test to account for group differences. Co-contraction was analyzed between ventral and dorsal muscles (V:R) as well as side right:side left ratio (Sright:Sleft). The coefficient of variation (CV;%) was calculated (EMG-RMS;ROM) to evaluate variability between the 15 perturbations for all groups. With respect to unequal distribution of participants to groups, an additional matched-group analysis was conducted. Fourteen healthy controls out of group H were sex-, age- and anthropometrically matched (group Hmatched) to the BPP. Results No group differences were observed for EMG-RMS or CV analysis (EMG/ROM) (p>0.025). Co-contraction analysis revealed no differences for V:R and Srigth:Sleft between the groups (p>0.025). BPP showed an increased TON and TMAX, being significant for Mm. rectus abdominus (p = 0.019) and erector spinae T9/L3 (p = 0.005/p = 0.015). ROM analysis over the unperturbed stride cycle revealed no differences between groups (p>0.025). Normalization of perturbed to unperturbed step lead to significant differences for the lumbar segment (LA) in lateral flexion with BPP showing higher normalized ROM compared to Hmatched (p = 0.02). BPP showed a significant higher flexed posture (UTA (p = 0.02); LTA (p = 0.004)) during normal walking (Amean). Trunk posture (Amean) during perturbation showed higher trunk extension values in LTA segments for H/Hmatched compared to BPP (p = 0.003). Matched group (BPP vs. Hmatched) analysis did not show any systematic changes of all results between groups. Conclusion BPP present impaired muscle response times and trunk posture, especially in the sagittal and transversal planes, compared to H. This could indicate reduced trunk stability and higher loading during gait perturbations. PMID:28319133

Rubidium D1 collision shift by heavy noble gases

NASA Astrophysics Data System (ADS)

Wells, N. P.; Driskell, T. U.; Camparo, J. C.

2015-10-01

Using an isoclinic-point technique, we measured the D1 collision shift by Xe, ∂ [δ ν ]/∂ P , and the exponent κ of the shift's temperature dependence (i.e., δ ν ˜Tκ ). As demonstrated in our examination of the Rb-Kr system [N. P. Wells et al., Phys. Rev. A 89, 052516 (2014), 10.1103/PhysRevA.89.052516], the isoclinic point provides (arguably) the only means of assessing κ unambiguously: κKr=0.36 ±0.06 and in the present work κXe=0.32 ±0.05 . With our estimate of κ for the Rb-Kr and Rb-Xe systems, we were able to combine our Kr and Xe collision shift measurements with those of Rotondaro and Perram [M. D. Rotondaro and G. P. Perram, J. Quant. Spectrosc. Radiat. Transfer 57, 497 (1997), 10.1016/S0022-4073(96)00147-1] (another set of high quality ∂ [δ ν ]/∂ P measurements) to obtain a highly accurate experimental estimate for the D1 collision shift resulting from Rb's interaction with the heavy noble gases: For the Rb-Kr interaction ∂ [δ ν ] /∂ P |T =323 K=-5.02 ±0.07 MHz /torr and for the Rb-Xe interaction ∂ [δ ν ] /∂ P |T =323 K=-5.46 ±0.09 MHz /torr . These measured values for the collision-shift coefficient are approximately 20 % smaller (in magnitude) than the best theoretical estimates, suggesting that there is room for theoretical improvement regarding our present understanding of how noble-gas collisions perturb the alkali-metal P1 /2 state.

Assessment of the impact of climate shifts on malaria transmission in the Sahel.

PubMed

Bomblies, Arne; Eltahir, Elfatih A B

2009-09-01

Climate affects malaria transmission through a complex network of causative pathways. We seek to evaluate the impact of hypothetical climate change scenarios on malaria transmission in the Sahel by using a novel mechanistic, high spatial- and temporal-resolution coupled hydrology and agent-based entomology model. The hydrology model component resolves individual precipitation events and individual breeding pools. The impact of future potential climate shifts on the representative Sahel village of Banizoumbou, Niger, is estimated by forcing the model of Banizoumbou environment with meteorological data from two locations along the north-south climatological gradient observed in the Sahel--both for warmer, drier scenarios from the north and cooler, wetter scenarios from the south. These shifts in climate represent hypothetical but historically realistic climate change scenarios. For Banizoumbou climatic conditions (latitude 13.54 N), a shift toward cooler, wetter conditions may dramatically increase mosquito abundance; however, our modeling results indicate that the increased malaria transmissibility is not simply proportional to the precipitation increase. The cooler, wetter conditions increase the length of the sporogonic cycle, dampening a large vectorial capacity increase otherwise brought about by increased mosquito survival and greater overall abundance. Furthermore, simulations varying rainfall event frequency demonstrate the importance of precipitation patterns, rather than simply average or time-integrated precipitation, as a controlling factor of these dynamics. Modeling results suggest that in addition to changes in temperature and total precipitation, changes in rainfall patterns are very important to predict changes in disease susceptibility resulting from climate shifts. The combined effect of these climate-shift-induced perturbations can be represented with the aid of a detailed mechanistic model.

Climate-Driven Range Extension of Amphistegina (Protista, Foraminiferida): Models of Current and Predicted Future Ranges

PubMed Central

Langer, Martin R.; Weinmann, Anna E.; Lötters, Stefan; Bernhard, Joan M.; Rödder, Dennis

2013-01-01

Species-range expansions are a predicted and realized consequence of global climate change. Climate warming and the poleward widening of the tropical belt have induced range shifts in a variety of marine and terrestrial species. Range expansions may have broad implications on native biota and ecosystem functioning as shifting species may perturb recipient communities. Larger symbiont-bearing foraminifera constitute ubiquitous and prominent components of shallow water ecosystems, and range shifts of these important protists are likely to trigger changes in ecosystem functioning. We have used historical and newly acquired occurrence records to compute current range shifts of Amphistegina spp., a larger symbiont-bearing foraminifera, along the eastern coastline of Africa and compare them to analogous range shifts currently observed in the Mediterranean Sea. The study provides new evidence that amphisteginid foraminifera are rapidly progressing southwestward, closely approaching Port Edward (South Africa) at 31°S. To project future species distributions, we applied a species distribution model (SDM) based on ecological niche constraints of current distribution ranges. Our model indicates that further warming is likely to cause a continued range extension, and predicts dispersal along nearly the entire southeastern coast of Africa. The average rates of amphisteginid range shift were computed between 8 and 2.7 km year−1, and are projected to lead to a total southward range expansion of 267 km, or 2.4° latitude, in the year 2100. Our results corroborate findings from the fossil record that some larger symbiont-bearing foraminifera cope well with rising water temperatures and are beneficiaries of global climate change. PMID:23405081

Climate-driven range extension of Amphistegina (protista, foraminiferida): models of current and predicted future ranges.

PubMed

Langer, Martin R; Weinmann, Anna E; Lötters, Stefan; Bernhard, Joan M; Rödder, Dennis

2013-01-01

Species-range expansions are a predicted and realized consequence of global climate change. Climate warming and the poleward widening of the tropical belt have induced range shifts in a variety of marine and terrestrial species. Range expansions may have broad implications on native biota and ecosystem functioning as shifting species may perturb recipient communities. Larger symbiont-bearing foraminifera constitute ubiquitous and prominent components of shallow water ecosystems, and range shifts of these important protists are likely to trigger changes in ecosystem functioning. We have used historical and newly acquired occurrence records to compute current range shifts of Amphistegina spp., a larger symbiont-bearing foraminifera, along the eastern coastline of Africa and compare them to analogous range shifts currently observed in the Mediterranean Sea. The study provides new evidence that amphisteginid foraminifera are rapidly progressing southwestward, closely approaching Port Edward (South Africa) at 31°S. To project future species distributions, we applied a species distribution model (SDM) based on ecological niche constraints of current distribution ranges. Our model indicates that further warming is likely to cause a continued range extension, and predicts dispersal along nearly the entire southeastern coast of Africa. The average rates of amphisteginid range shift were computed between 8 and 2.7 km year(-1), and are projected to lead to a total southward range expansion of 267 km, or 2.4° latitude, in the year 2100. Our results corroborate findings from the fossil record that some larger symbiont-bearing foraminifera cope well with rising water temperatures and are beneficiaries of global climate change.

Non-perturbative calculation of orbital and spin effects in molecules subject to non-uniform magnetic fields

NASA Astrophysics Data System (ADS)

Sen, Sangita; Tellgren, Erik I.

2018-05-01

External non-uniform magnetic fields acting on molecules induce non-collinear spin densities and spin-symmetry breaking. This necessitates a general two-component Pauli spinor representation. In this paper, we report the implementation of a general Hartree-Fock method, without any spin constraints, for non-perturbative calculations with finite non-uniform fields. London atomic orbitals are used to ensure faster basis convergence as well as invariance under constant gauge shifts of the magnetic vector potential. The implementation has been applied to investigate the joint orbital and spin response to a field gradient—quantified through the anapole moments—of a set of small molecules. The relative contributions of orbital and spin-Zeeman interaction terms have been studied both theoretically and computationally. Spin effects are stronger and show a general paramagnetic behavior for closed shell molecules while orbital effects can have either direction. Basis set convergence and size effects of anapole susceptibility tensors have been reported. The relation of the mixed anapole susceptibility tensor to chirality is also demonstrated.

N-dimensional hypervolumes to study stability of complex ecosystems

PubMed Central

Barros, Ceres; Thuiller, Wilfried; Georges, Damien; Boulangeat, Isabelle; Münkemüller, Tamara

2016-01-01

Although our knowledge on the stabilising role of biodiversity and on how it is affected by perturbations has greatly improved, we still lack a comprehensive view on ecosystem stability that is transversal to different habitats and perturbations. Hence, we propose a framework that takes advantage of the multiplicity of components of an ecosystem and their contribution to stability. Ecosystem components can range from species or functional groups, to different functional traits, or even the cover of different habitats in a landscape mosaic. We make use of n-dimensional hypervolumes to define ecosystem states and assess how much they shift after environmental changes have occurred. We demonstrate the value of this framework with a study case on the effects of environmental change on Alpine ecosystems. Our results highlight the importance of a multidimensional approach when studying ecosystem stability and show that our framework is flexible enough to be applied to different types of ecosystem components, which can have important implications for the study of ecosystem stability and transient dynamics. PMID:27282314

Decoupling biogeochemical records, extinction, and environmental change during the Cambrian SPICE event

PubMed Central

Schiffbauer, James D.; Huntley, John Warren; Fike, David A.; Jeffrey, Matthew Jarrell; Gregg, Jay M.; Shelton, Kevin L.

2017-01-01

Several positive carbon isotope excursions in Lower Paleozoic rocks, including the prominent Upper Cambrian Steptoean Positive Carbon Isotope Excursion (SPICE), are thought to reflect intermittent perturbations in the hydrosphere-biosphere system. Models explaining these secular changes are abundant, but the synchronicity and regional variation of the isotope signals are not well understood. Examination of cores across a paleodepth gradient in the Upper Cambrian central Missouri intrashelf basin (United States) reveals a time-transgressive, facies-dependent nature of the SPICE. Although the SPICE event may be a global signal, the manner in which it is recorded in rocks should and does vary as a function of facies and carbonate platform geometry. We call for a paradigm shift to better constrain facies, stratigraphic, and biostratigraphic architecture and to apply these observations to the variability in magnitude, stratigraphic extent, and timing of the SPICE signal, as well as other biogeochemical perturbations, to elucidate the complex processes driving the ocean-carbonate system. PMID:28275734

The stark effect on the spectrum energy of tritium in first excited state with relativistic condition

NASA Astrophysics Data System (ADS)

Prastowo, S. H. B.; Supriadi, B.; Bahri, S.; Ridlo, Z. R.

2018-04-01

This research discussed about the correction of Stark Effect on Tritium atoms in the first excited state with relativistic conditions. The approach used to solve this Stark Effect correction was the perturbation theory which was from time independent degenerate perturbation theory to second-order correction. The Stark Effect on the excited state made the spectrum energy polarization of Tritium which was included in the isotope of hydrogen with an electron moving around the nucleus with high velocity. Hence, the relativistic correction affected the spectrum energy shift. Tritium was a radioactive material having half-time 12,3 years and relatively safe. The Tritium application was a material for the manufacture of nuclear battery. The most effective external electric field that should give to Tritium was 108 V/mith the total correction energy that was 0,97398557 × 10-21 Joule. Therefore, its effect reduced the binding energy between electron and nucleus, and increased the power of Tritium Betavoltaics Battery.

First results of a study on turbulent boundary layers in oscillating flow with a mean adverse pressure gradient

NASA Technical Reports Server (NTRS)

Houdeville, R.; Cousteix, J.

1979-01-01

The development of a turbulent unsteady boundary layer with a mean pressure gradient strong enough to induce separation, in order to complete the extend results obtained for the flat plate configuration is presented. The longitudinal component of the velocity is measured using constant temperature hot wire anemometer. The region where negative velocities exist is investigated with a laser Doppler velocimeter system with BRAGG cells. The boundary layer responds by forced pulsation to the perturbation of potential flow. The unsteady effects observed are very important. The average location of the zero skin friction point moves periodically at the perturbation frequency. Average velocity profiles from different instants in the cycle are compared. The existence of a logarithmic region enables a simple calculation of the maximum phase shift of the velocity in the boundary layer. An attempt of calculation by an integral method of boundary layer development is presented, up to the point where reverse flow starts appearing.

Faraday spectroscopy of ultracold atoms guided in hollow core optical fibers

NASA Astrophysics Data System (ADS)

Fatemi, Fredrik; Pechkis, Joseph

2013-05-01

We have performed spatially and temporally resolved magnetometry using Faraday spectroscopy of ultracold rubidium atoms confined in hollow core optical fibers. We first guide 105 Rb atoms into a 3-cm-long, 100-micron-core hollow fiber using blue-detuned hollow waveguide modes. Inside the fiber, the atoms are exposed to an optical pumping pulse, and the Larmor precession is monitored by the polarization rotation of a probe laser beam detuned by 50 GHz. The intense guide beams can perturb the detected Larmor precession frequencies, but we show that by confining the atoms to the intensity null of higher order blue-detuned hollow modes, these perturbations are reduced by over 95% compared to red-detuned guides. By adjusting the guide beam detuning and polarization, the deleterious effects of both photon scattering and frequency shifts can be suppressed such that multiple magnetic field measurements with sensitivity of 30 nT per sampling pulse can be obtained throughout the length of the fiber in a single loading cycle. Work supported by ONR and DARPA.

Bifurcated helical core equilibrium states in tokamaks

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Chapman, I. T.; Schmitz, O.; Turnbull, A. D.; Tobias, B. J.; Lazarus, E. A.; Turco, F.; Lanctot, M. J.; Evans, T. E.; Graves, J. P.; Brunetti, D.; Pfefferlé, D.; Reimerdes, H.; Sauter, O.; Halpern, F. D.; Tran, T. M.; Coda, S.; Duval, B. P.; Labit, B.; Pochelon, A.; Turnyanskiy, M. R.; Lao, L.; Luce, T. C.; Buttery, R.; Ferron, J. R.; Hollmann, E. M.; Petty, C. C.; van Zeeland, M.; Fenstermacher, M. E.; Hanson, J. M.; Lütjens, H.

2013-07-01

Tokamaks with weak to moderate reversed central shear in which the minimum inverse rotational transform (safety factor) qmin is in the neighbourhood of unity can trigger bifurcated magnetohydrodynamic equilibrium states, one of which is similar to a saturated ideal internal kink mode. Peaked prescribed pressure profiles reproduce the ‘snake’ structures observed in many tokamaks which has led to a novel explanation of the snake as a bifurcated equilibrium state. Snake equilibrium structures are computed in simulations of the tokamak à configuration variable (TCV), DIII-D and mega amp spherical torus (MAST) tokamaks. The internal helical deformations only weakly modulate the plasma-vacuum interface which is more sensitive to ripple and resonant magnetic perturbations. On the other hand, the external perturbations do not alter the helical core deformation in a significant manner. The confinement of fast particles in MAST simulations deteriorate with the amplitude of the helical core distortion. These three-dimensional bifurcated solutions constitute a paradigm shift that motivates the applications of tools developed for stellarator research in tokamak physics investigations.

Diet dominates host genotype in shaping the murine gut microbiota

PubMed Central

Carmody, Rachel N.; Gerber, Georg K.; Luevano, Jesus M.; Gatti, Daniel M.; Somes, Lisa; Svenson, Karen L.; Turnbaugh, Peter J.

2014-01-01

SUMMARY Mammals exhibit marked inter-individual variations in their gut microbiota, but it remains unclear if this is primarily driven by host genetics or by extrinsic factors like dietary intake. To address this, we examined the effect of dietary perturbations on the gut microbiota of five inbred mouse strains, mice deficient for genes relevant to host-microbial interactions (MyD88−/−, NOD2−/−, ob/ob, and Rag1−/−), and >200 outbred mice. In each experiment, consumption of a high-fat, high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype. The gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial groups to reach a new steady state. Repeated dietary shifts demonstrated that most changes to the gut microbiota are reversible, while also uncovering bacteria whose abundance depends on prior consumption. These results emphasize the dominant role that diet plays in shaping inter-individual variations in host-associated microbial communities. PMID:25532804

Reduced conservatism in stability robustness bounds by state transformation

NASA Technical Reports Server (NTRS)

Yedavalli, R. K.; Liang, Z.

1986-01-01

This note addresses the issue of 'conservatism' in the time domain stability robustness bounds obtained by the Liapunov approach. A state transformation is employed to improve the upper bounds on the linear time-varying perturbation of an asymptotically stable linear time-invariant system for robust stability. This improvement is due to the variance of the conservatism of the Liapunov approach with respect to the basis of the vector space in which the Liapunov function is constructed. Improved bounds are obtained, using a transformation, on elemental and vector norms of perturbations (i.e., structured perturbations) as well as on a matrix norm of perturbations (i.e., unstructured perturbations). For the case of a diagonal transformation, an algorithm is proposed to find the 'optimal' transformation. Several examples are presented to illustrate the proposed analysis.

Radiotherapy Dose Perturbation of Esophageal Stents Examined in an Experimental Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atwood, Todd F.; Hsu, Annie; Ogara, Maydeen M.

2012-04-01

Purpose: To investigate the radiotherapy dose perturbations caused by esophageal stents in patients undergoing external beam treatments for esophageal cancer. Methods and Materials: Four esophageal stents were examined (three metallic stents: WallFlex, Ultraflex, and Alveolus; one nonmetallic stent with limited radiopaque markers for visualization: Polyflex). All experiments were performed in a liquid water phantom with a custom acrylic stent holder. Radiochromic film was used to measure the dose distributions adjacent to the stents at locations proximal and distal to the radiation source. The stents were placed in an air-filled cavity to simulate the esophagus. Treatment plans were created and deliveredmore » for photon energies of 6 and 15 MV, and data analysis was performed on uniform regions of interest, according to the size and geometric placement of the films, to quantify the dose perturbations. Results: The three metallic stents produced the largest dose perturbations with distinct patterns of 'hot' spots (increased dose) measured proximal to the radiation source (up to 15.4%) and both 'cold' (decreased dose) and hot spots measured distal to the radiation source (range, -6.1%-5.8%). The polymeric Polyflex stent produced similar dose perturbations when the radiopaque markers were examined (range, -7.6%-15.4%). However, when the radiopaque markers were excluded from the analysis, the Polyflex stent produced significantly smaller dose perturbations, with maximum hot spots of 7.3% and cold spots of -3.2%. Conclusions: The dose perturbations caused by esophageal stents during the treatment of esophageal cancer using external beam radiotherapy should be understood. These perturbations will result in hot and cold spots in the esophageal mucosa, with varying magnitudes depending on the stent. The nonmetallic Polyflex stent appears to be the most suitable for patients undergoing radiotherapy, but further studies are necessary to determine the clinical significance of the dose perturbations.« less

Radiotherapy dose perturbation of esophageal stents examined in an experimental model.

PubMed

Atwood, Todd F; Hsu, Annie; Ogara, Maydeen M; Luba, Daniel G; Tamler, Bradley J; Disario, James A; Maxim, Peter G

2012-04-01

To investigate the radiotherapy dose perturbations caused by esophageal stents in patients undergoing external beam treatments for esophageal cancer. Four esophageal stents were examined (three metallic stents: WallFlex, Ultraflex, and Alveolus; one nonmetallic stent with limited radiopaque markers for visualization: Polyflex). All experiments were performed in a liquid water phantom with a custom acrylic stent holder. Radiochromic film was used to measure the dose distributions adjacent to the stents at locations proximal and distal to the radiation source. The stents were placed in an air-filled cavity to simulate the esophagus. Treatment plans were created and delivered for photon energies of 6 and 15 MV, and data analysis was performed on uniform regions of interest, according to the size and geometric placement of the films, to quantify the dose perturbations. The three metallic stents produced the largest dose perturbations with distinct patterns of "hot" spots (increased dose) measured proximal to the radiation source (up to 15.4%) and both "cold" (decreased dose) and hot spots measured distal to the radiation source (range, -6.1%-5.8%). The polymeric Polyflex stent produced similar dose perturbations when the radiopaque markers were examined (range, -7.6%-15.4%). However, when the radiopaque markers were excluded from the analysis, the Polyflex stent produced significantly smaller dose perturbations, with maximum hot spots of 7.3% and cold spots of -3.2%. The dose perturbations caused by esophageal stents during the treatment of esophageal cancer using external beam radiotherapy should be understood. These perturbations will result in hot and cold spots in the esophageal mucosa, with varying magnitudes depending on the stent. The nonmetallic Polyflex stent appears to be the most suitable for patients undergoing radiotherapy, but further studies are necessary to determine the clinical significance of the dose perturbations. Copyright © 2012 Elsevier Inc. All rights reserved.

Analysis of the electrodeposition and surface chemistry of CdTe, CdSe, and CdS thin films through substrate-overlayer surface-enhanced Raman spectroscopy.

PubMed

Gu, Junsi; Fahrenkrug, Eli; Maldonado, Stephen

2014-09-02

The substrate-overlayer approach has been used to acquire surface enhanced Raman spectra (SERS) during and after electrochemical atomic layer deposition (ECALD) of CdSe, CdTe, and CdS thin films. The collected data suggest that SERS measurements performed with off-resonance (i.e. far from the surface plasmonic wavelength of the underlying SERS substrate) laser excitation do not introduce perturbations to the ECALD processes. Spectra acquired in this way afford rapid insight on the quality of the semiconductor film during the course of an ECALD process. For example, SERS data are used to highlight ECALD conditions that yield crystalline CdSe and CdS films. In contrast, SERS measurements with short wavelength laser excitation show evidence of photoelectrochemical effects that were not germane to the intended ECALD process. Using the semiconductor films prepared by ECALD, the substrate-overlayer SERS approach also affords analysis of semiconductor surface adsorbates. Specifically, Raman spectra of benzenethiol adsorbed onto CdSe, CdTe, and CdS films are detailed. Spectral shifts in the vibronic features of adsorbate bonding suggest subtle differences in substrate-adsorbate interactions, highlighting the sensitivity of this methodology.

Inherent flexibility of CLIC6 revealed by crystallographic and solution studies.

PubMed

Ferofontov, Alisa; Strulovich, Roi; Marom, Milit; Giladi, Moshe; Haitin, Yoni

2018-05-02

Chloride intracellular channels (CLICs) are a family of unique proteins, that were suggested to adopt both soluble and membrane-associated forms. Moreover, following this unusual metamorphic change, CLICs were shown to incorporate into membranes and mediate ion conduction in vitro, suggesting multimerization upon membrane insertion. Here, we present a 1.8 Å resolution crystal structure of the CLIC domain of mouse CLIC6 (mCLIC6). The structure reveals a monomeric arrangement and shows a high degree of structural conservation with other CLICs. Small-angle X-ray scattering (SAXS) analysis of mCLIC6 demonstrated that the overall solution structure is similar to the crystallographic conformation. Strikingly, further analysis of the SAXS data using ensemble optimization method unveiled additional elongated conformations, elucidating high structural plasticity as an inherent property of the protein. Moreover, structure-guided perturbation of the inter-domain interface by mutagenesis resulted in a population shift towards elongated conformations of mCLIC6. Additionally, we demonstrate that oxidative conditions induce an increase in mCLIC6 hydrophobicity along with mild oligomerization, which was enhanced by the presence of membrane mimetics. Together, these results provide mechanistic insights into the metamorphic nature of mCLIC6.

Analysis of a Waveguide-Fed Metasurface Antenna

NASA Astrophysics Data System (ADS)

Smith, David R.; Yurduseven, Okan; Mancera, Laura Pulido; Bowen, Patrick; Kundtz, Nathan B.

2017-11-01

The metasurface concept has emerged as an advantageous reconfigurable antenna architecture for beam forming and wave-front shaping, with applications that include satellite and terrestrial communications, radar, imaging, and wireless power transfer. The metasurface antenna consists of an array of metamaterial elements distributed over an electrically large structure, each subwavelength in dimension and with subwavelength separation between elements. In the antenna configuration we consider, the metasurface is excited by the fields from an attached waveguide. Each metamaterial element can be modeled as a polarizable dipole that couples the waveguide mode to radiation modes. Distinct from the phased array and electronically-scanned-antenna architectures, a dynamic metasurface antenna does not require active phase shifters and amplifiers but rather achieves reconfigurability by shifting the resonance frequency of each individual metamaterial element. We derive the basic properties of a one-dimensional waveguide-fed metasurface antenna in the approximation in which the metamaterial elements do not perturb the waveguide mode and are noninteracting. We derive analytical approximations for the array factors of the one-dimensional antenna, including the effective polarizabilities needed for amplitude-only, phase-only, and binary constraints. Using full-wave numerical simulations, we confirm the analysis, modeling waveguides with slots or complementary metamaterial elements patterned into one of the surfaces.

Quantum chemical study, spectroscopic investigations, NBO and HOMO-LUMO analyses of 3-aminoquinoline (3AQ) and [Ag(3AQ)2(TCA)] complex (TCA = Trichloroacetate)

NASA Astrophysics Data System (ADS)

Soliman, Saied M.; Kassem, Taher S.; Badr, Ahmed M. A.; Abu Youssef, Morsy A.; Assem, Rania

2014-09-01

The new [Ag(3AQ)2(TCA)]; (3AQ = 3-aminoquinoline and TCA = Trichloroacetate) complex is synthesized and characterized using elemental analysis, FTIR, NMR and mass spectroscopy. The molecular geometry, vibrational frequencies, gauge-including atomic orbital (GIAO) 1H chemical shift values of the free and coordinated 3AQ in the ground state have been calculated by using DFT/B3LYP method. The TD-DFT results of the [Ag(3AQ)2(TCA)] complex showed a π-π* transition band at 240.3-242.6 nm (f = 0.1334-0.1348) which has longer wavelength and lower absorption intensity than that for the free 3AQ (233.2 nm, f = 0.3958). Dipole moment, polarizability and HOMO-LUMO gap values predicted better nonlinear optical properties (NLO) for the [Ag(3AQ)2(TCA)] than the 3AQ ligand. NBO analysis has been used to predict the most accurate Lewis structure of the studied molecules. The energies of the different intramolecular charge transfer (ICT) interactions within the studied molecules were estimated using second order perturbation theory.

Adaptive Modeling Procedure Selection by Data Perturbation.

PubMed

Zhang, Yongli; Shen, Xiaotong

2015-10-01

Many procedures have been developed to deal with the high-dimensional problem that is emerging in various business and economics areas. To evaluate and compare these procedures, modeling uncertainty caused by model selection and parameter estimation has to be assessed and integrated into a modeling process. To do this, a data perturbation method estimates the modeling uncertainty inherited in a selection process by perturbing the data. Critical to data perturbation is the size of perturbation, as the perturbed data should resemble the original dataset. To account for the modeling uncertainty, we derive the optimal size of perturbation, which adapts to the data, the model space, and other relevant factors in the context of linear regression. On this basis, we develop an adaptive data-perturbation method that, unlike its nonadaptive counterpart, performs well in different situations. This leads to a data-adaptive model selection method. Both theoretical and numerical analysis suggest that the data-adaptive model selection method adapts to distinct situations in that it yields consistent model selection and optimal prediction, without knowing which situation exists a priori. The proposed method is applied to real data from the commodity market and outperforms its competitors in terms of price forecasting accuracy.

Instabilities in mimetic matter perturbations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Firouzjahi, Hassan; Gorji, Mohammad Ali; Mansoori, Seyed Ali Hosseini, E-mail: firouz@ipm.ir, E-mail: gorji@ipm.ir, E-mail: shosseini@shahroodut.ac.ir, E-mail: shossein@ipm.ir

2017-07-01

We study cosmological perturbations in mimetic matter scenario with a general higher derivative function. We calculate the quadratic action and show that both the kinetic term and the gradient term have the wrong sings. We perform the analysis in both comoving and Newtonian gauges and confirm that the Hamiltonians and the associated instabilities are consistent with each other in both gauges. The existence of instabilities is independent of the specific form of higher derivative function which generates gradients for mimetic field perturbations. It is verified that the ghost instability in mimetic perturbations is not associated with the higher derivative instabilitiesmore » such as the Ostrogradsky ghost.« less