Identification of limit cycles in multi-nonlinearity, multiple path systems

NASA Technical Reports Server (NTRS)

Mitchell, J. R.; Barron, O. L.

1979-01-01

A method of analysis which identifies limit cycles in autonomous systems with multiple nonlinearities and multiple forward paths is presented. The FORTRAN code for implementing the Harmonic Balance Algorithm is reported. The FORTRAN code is used to identify limit cycles in multiple path and nonlinearity systems while retaining the effects of several harmonic components.

Modification of LAMPF's magnet-mapping code for offsets of center coordinates

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

Hurd, J.W.; Gomulka, S.; Merrill, F.

1991-01-01

One of the magnet measurements performed at LAMPF is the determination of the cylindrical harmonics of a quadrupole magnet using a rotating coil. The data are analyzed with the code HARMAL to derive the amplitudes of the harmonics. Initially, the origin of the polar coordinate system is the axis of the rotating coil. A new coordinate system is found by a simple translation of the old system such that the dipole moment in the new system is zero. The origin of this translated system is referred to as the magnetic center. Given this translation, the code calculates the coefficients ofmore » the cylindrical harmonics in the new system. The code has been modified to use an analytical calculation to determine these new coefficients. The method of calculation is described and some implications of this formulation are presented. 8 refs., 2 figs.« less

Fan Flutter Computations Using the Harmonic Balance Method

NASA Technical Reports Server (NTRS)

Bakhle, Milind A.; Thomas, Jeffrey P.; Reddy, T.S.R.

2009-01-01

An experimental forward-swept fan encountered flutter at part-speed conditions during wind tunnel testing. A new propulsion aeroelasticity code, based on a computational fluid dynamics (CFD) approach, was used to model the aeroelastic behavior of this fan. This threedimensional code models the unsteady flowfield due to blade vibrations using a harmonic balance method to solve the Navier-Stokes equations. This paper describes the flutter calculations and compares the results to experimental measurements and previous results from a time-accurate propulsion aeroelasticity code.

Quasilinear Line Broadened Model for Energetic Particle Transport

NASA Astrophysics Data System (ADS)

Ghantous, Katy; Gorelenkov, Nikolai; Berk, Herbert

2011-10-01

We present a self-consistent quasi-linear model that describes wave-particle interaction in toroidal geometry and computes fast ion transport during TAE mode evolution. The model bridges the gap between single mode resonances, where it predicts the analytically expected saturation levels, and the case of multiple modes overlapping, where particles diffuse across phase space. Results are presented in the large aspect ratio limit where analytic expressions are used for Fourier harmonics of the power exchange between waves and particles, . Implemention of a more realistic mode structure calculated by NOVAK code are also presented. This work is funded by DOE contract DE-AC02-09CH11466.

An Enhanced GINGERSimulation Code with Harmonic Emission and HDF5IO Capabilities

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

Fawley, William M.

GINGER [1] is an axisymmetric, polychromatic (r-z-t) FEL simulation code originally developed in the mid-1980's to model the performance of single-pass amplifiers. Over the past 15 years GINGER's capabilities have been extended to include more complicated configurations such as undulators with drift spaces, dispersive sections, and vacuum chamber wakefield effects; multi-pass oscillators; and multi-stage harmonic cascades. Its coding base has been tuned to permit running effectively on platforms ranging from desktop PC's to massively parallel processors such as the IBM-SP. Recently, we have made significant changes to GINGER by replacing the original predictor-corrector field solver with a new direct implicitmore » algorithm, adding harmonic emission capability, and switching to the HDF5 IO library [2] for output diagnostics. In this paper, we discuss some details regarding these changes and also present simulation results for LCLS SASE emission at {lambda} = 0.15 nm and higher harmonics.« less

Nonlinear evolution of Mack modes in a hypersonic boundary layer

NASA Astrophysics Data System (ADS)

Chokani, Ndaona

2005-01-01

In hypersonic boundary layer flows the nonlinear disturbance evolution occurs relatively slowly over a very long length scale and has a profound effect on boundary layer transition. In the case of low-level freestream disturbances and negligible surface roughness, the transition is due to the modal growth of exponentially growing Mack modes that are destabilized by wall cooling. Cross-bicoherence measurements, derived from hot-wire data acquired in a quiet hypersonic tunnel, are used to identify and quantify phase-locked, quadratic sum and difference interactions involving the Mack modes. In the early stages of the nonlinear disturbance evolution, cross-bicoherence measurements indicate that the energy exchange between the Mack mode and the mean flow first occurs to broaden the sidebands; this is immediately followed by a sum interaction of the Mack mode to generate the first harmonic. In the next stages of the nonlinear disturbance evolution, there is a difference interaction of the first harmonic, which is also thought to contribute to the mean flow distortion. This difference interaction, in the latter stages, is also accompanied by a difference interaction between Mack mode and first harmonic, and a sum interaction, which forces the second harmonic. Analysis using the digital complex demodulation technique, shows that the low-frequency, phase-locked interaction that is identified in the cross bicoherence when the Mack mode and first harmonic have large amplitudes, arises due to the amplitude modulation of Mack mode and first harmonic.

40 CFR Appendix K to Subpart A of... - Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled Substances K Appendix K to Subpart A of...) PROTECTION OF STRATOSPHERIC OZONE Production and Consumption Controls Pt. 82, Subpt. A, App. K Appendix K to...

40 CFR Appendix K to Subpart A of... - Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled Substances K Appendix K to Subpart A of...) PROTECTION OF STRATOSPHERIC OZONE Production and Consumption Controls Pt. 82, Subpt. A, App. K Appendix K to...

40 CFR Appendix K to Subpart A of... - Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled...

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled Substances K Appendix K to Subpart A of...) PROTECTION OF STRATOSPHERIC OZONE Production and Consumption Controls Pt. 82, Subpt. A, App. K Appendix K to...

40 CFR Appendix K to Subpart A of... - Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled Substances K Appendix K To Subpart A Of...) PROTECTION OF STRATOSPHERIC OZONE Production and Consumption Controls Pt. 82, Subpt. A, App. K Appendix K To...

40 CFR Appendix K to Subpart A of... - Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Commodity Codes From the Harmonized Tariff Schedule for Controlled Substances and Used Controlled Substances K Appendix K to Subpart A of...) PROTECTION OF STRATOSPHERIC OZONE Production and Consumption Controls Pt. 82, Subpt. A, App. K Appendix K to...

Calculation of spherical harmonics and Wigner d functions by FFT. Applications to fast rotational matching in molecular replacement and implementation into AMoRe.

PubMed

Trapani, Stefano; Navaza, Jorge

2006-07-01

The FFT calculation of spherical harmonics, Wigner D matrices and rotation function has been extended to all angular variables in the AMoRe molecular replacement software. The resulting code avoids singularity issues arising from recursive formulas, performs faster and produces results with at least the same accuracy as the original code. The new code aims at permitting accurate and more rapid computations at high angular resolution of the rotation function of large particles. Test calculations on the icosahedral IBDV VP2 subviral particle showed that the new code performs on the average 1.5 times faster than the original code.

75 FR 34682 - Bulk Solid Hazardous Materials: Harmonization With the International Maritime Solid Bulk Cargoes...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-18

...] RIN 1625-AB47 Bulk Solid Hazardous Materials: Harmonization With the International Maritime Solid Bulk... on June 17, 2010, entitled ``Bulk Solid Hazardous Materials: Harmonization With the International Maritime Solid Bulk Cargoes (IMSBC) Code.'' This correction provides correct information with regard to the...

Superharmonic imaging with chirp coded excitation: filtering spectrally overlapped harmonics.

PubMed

Harput, Sevan; McLaughlan, James; Cowell, David M J; Freear, Steven

2014-11-01

Superharmonic imaging improves the spatial resolution by using the higher order harmonics generated in tissue. The superharmonic component is formed by combining the third, fourth, and fifth harmonics, which have low energy content and therefore poor SNR. This study uses coded excitation to increase the excitation energy. The SNR improvement is achieved on the receiver side by performing pulse compression with harmonic matched filters. The use of coded signals also introduces new filtering capabilities that are not possible with pulsed excitation. This is especially important when using wideband signals. For narrowband signals, the spectral boundaries of the harmonics are clearly separated and thus easy to filter; however, the available imaging bandwidth is underused. Wideband excitation is preferable for harmonic imaging applications to preserve axial resolution, but it generates spectrally overlapping harmonics that are not possible to filter in time and frequency domains. After pulse compression, this overlap increases the range side lobes, which appear as imaging artifacts and reduce the Bmode image quality. In this study, the isolation of higher order harmonics was achieved in another domain by using the fan chirp transform (FChT). To show the effect of excitation bandwidth in superharmonic imaging, measurements were performed by using linear frequency modulated chirp excitation with varying bandwidths of 10% to 50%. Superharmonic imaging was performed on a wire phantom using a wideband chirp excitation. Results were presented with and without applying the FChT filtering technique by comparing the spatial resolution and side lobe levels. Wideband excitation signals achieved a better resolution as expected, however range side lobes as high as -23 dB were observed for the superharmonic component of chirp excitation with 50% fractional bandwidth. The proposed filtering technique achieved >50 dB range side lobe suppression and improved the image quality without affecting the axial resolution.

Simulation of nonlinear propagation of biomedical ultrasound using PZFlex and the KZK Texas code

NASA Astrophysics Data System (ADS)

Qiao, Shan; Jackson, Edward; Coussios, Constantin-C.; Cleveland, Robin

2015-10-01

In biomedical ultrasound nonlinear acoustics can be important in both diagnostic and therapeutic applications and robust simulations tools are needed in the design process but also for day-to-day use such as treatment planning. For most biomedical application the ultrasound sources generate focused sound beams of finite amplitude. The KZK equation is a common model as it accounts for nonlinearity, absorption and paraxial diffraction and there are a number of solvers available, primarily developed by research groups. We compare the predictions of the KZK Texas code (a finite-difference time-domain algorithm) to an FEM-based commercial software, PZFlex. PZFlex solves the continuity equation and momentum conservation equation with a correction for nonlinearity in the equation of state incorporated using an incrementally linear, 2nd order accurate, explicit algorithm in time domain. Nonlinear ultrasound beams from two transducers driven at 1 MHz and 3.3 MHz respectively were simulated by both the KZK Texas code and PZFlex, and the pressure field was also measured by a fibre-optic hydrophone to validate the models. Further simulations were carried out a wide range of frequencies. The comparisons showed good agreement for the fundamental frequency for PZFlex, the KZK Texas code and the experiments. For the harmonic components, the KZK Texas code was in good agreement with measurements but PZFlex underestimated the amplitude: 32% for the 2nd harmonic and 66% for the 3rd harmonic. The underestimation of harmonics by PZFlex was more significant when the fundamental frequency increased. Furthermore non-physical oscillations in the axial profile of harmonics occurred in the PZFlex results when the amplitudes were relatively low. These results suggest that careful benchmarking of nonlinear simulations is important.

Simulation of nonlinear propagation of biomedical ultrasound using PZFlex and the KZK Texas code

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

Qiao, Shan, E-mail: shan.qiao@eng.ox.ac.uk; Jackson, Edward; Coussios, Constantin-C

In biomedical ultrasound nonlinear acoustics can be important in both diagnostic and therapeutic applications and robust simulations tools are needed in the design process but also for day-to-day use such as treatment planning. For most biomedical application the ultrasound sources generate focused sound beams of finite amplitude. The KZK equation is a common model as it accounts for nonlinearity, absorption and paraxial diffraction and there are a number of solvers available, primarily developed by research groups. We compare the predictions of the KZK Texas code (a finite-difference time-domain algorithm) to an FEM-based commercial software, PZFlex. PZFlex solves the continuity equationmore » and momentum conservation equation with a correction for nonlinearity in the equation of state incorporated using an incrementally linear, 2nd order accurate, explicit algorithm in time domain. Nonlinear ultrasound beams from two transducers driven at 1 MHz and 3.3 MHz respectively were simulated by both the KZK Texas code and PZFlex, and the pressure field was also measured by a fibre-optic hydrophone to validate the models. Further simulations were carried out a wide range of frequencies. The comparisons showed good agreement for the fundamental frequency for PZFlex, the KZK Texas code and the experiments. For the harmonic components, the KZK Texas code was in good agreement with measurements but PZFlex underestimated the amplitude: 32% for the 2nd harmonic and 66% for the 3rd harmonic. The underestimation of harmonics by PZFlex was more significant when the fundamental frequency increased. Furthermore non-physical oscillations in the axial profile of harmonics occurred in the PZFlex results when the amplitudes were relatively low. These results suggest that careful benchmarking of nonlinear simulations is important.« less

Can temporal fine structure represent the fundamental frequency of unresolved harmonics?

PubMed

Oxenham, Andrew J; Micheyl, Christophe; Keebler, Michael V

2009-04-01

At least two modes of pitch perception exist: in one, the fundamental frequency (F0) of harmonic complex tones is estimated using the temporal fine structure (TFS) of individual low-order resolved harmonics; in the other, F0 is derived from the temporal envelope of high-order unresolved harmonics that interact in the auditory periphery. Pitch is typically more accurate in the former than in the latter mode. Another possibility is that pitch can sometimes be coded via the TFS from unresolved harmonics. A recent study supporting this third possibility [Moore et al. (2006a). J. Acoust. Soc. Am. 119, 480-490] based its conclusion on a condition where phase interaction effects (implying unresolved harmonics) accompanied accurate F0 discrimination (implying TFS processing). The present study tests whether these results were influenced by audible distortion products. Experiment 1 replicated the original results, obtained using a low-level background noise. However, experiments 2-4 found no evidence for the use of TFS cues with unresolved harmonics when the background noise level was raised, or the stimulus level was lowered, to render distortion inaudible. Experiment 5 measured the presence and phase dependence of audible distortion products. The results provide no evidence that TFS cues are used to code the F0 of unresolved harmonics.

Higher Harmonics in Heavy Ion Collisions

NASA Astrophysics Data System (ADS)

Jeon, Sangyong

2013-03-01

As the QGP expands and cools, it carries much information on its creation and evolution imprinted on the patterns of higher harmonic flow. In this proceeding we report on the progress in simulating and understanding the higher harmonics by the McGill group using the 3+1D event-by-event viscous hydrodynamics simulation suite named MUSIC.

KvN mechanics approach to the time-dependent frequency harmonic oscillator.

PubMed

Ramos-Prieto, Irán; Urzúa-Pineda, Alejandro R; Soto-Eguibar, Francisco; Moya-Cessa, Héctor M

2018-05-30

Using the Ermakov-Lewis invariants appearing in KvN mechanics, the time-dependent frequency harmonic oscillator is studied. The analysis builds upon the operational dynamical model, from which it is possible to infer quantum or classical dynamics; thus, the mathematical structure governing the evolution will be the same in both cases. The Liouville operator associated with the time-dependent frequency harmonic oscillator can be transformed using an Ermakov-Lewis invariant, which is also time dependent and commutes with itself at any time. Finally, because the solution of the Ermakov equation is involved in the evolution of the classical state vector, we explore some analytical and numerical solutions.

The Development of the World Anti-Doping Code.

PubMed

Young, Richard

2017-01-01

This chapter addresses both the development and substance of the World Anti-Doping Code, which came into effect in 2003, as well as the subsequent Code amendments, which came into effect in 2009 and 2015. Through an extensive process of stakeholder input and collaboration, the World Anti-Doping Code has transformed the hodgepodge of inconsistent and competing pre-2003 anti-doping rules into a harmonized and effective approach to anti-doping. The Code, as amended, is now widely recognized worldwide as the gold standard in anti-doping. The World Anti-Doping Code originally went into effect on January 1, 2004. The first amendments to the Code went into effect on January 1, 2009, and the second amendments on January 1, 2015. The Code and the related international standards are the product of a long and collaborative process designed to make the fight against doping more effective through the adoption and implementation of worldwide harmonized rules and best practices. © 2017 S. Karger AG, Basel.

The effect of shot noise on the start up of the fundamental and harmonics in free-electron lasers

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

Freund, H. P.; Miner, W. H. Jr.; Giannessi, L.

2008-12-15

The problem of radiation start up in free-electron lasers (FELs) is important in the simulation of virtually all FEL configurations including oscillators and amplifiers in both seeded master oscillator power amplifier (MOPA) and self-amplified spontaneous emission (SASE) modes. Both oscillators and SASE FELs start up from spontaneous emission due to shot noise on the electron beam, which arises from the random fluctuations in the phase distribution of the electrons. The injected power in a MOPA is usually large enough to overwhelm the shot noise. However, this noise must be treated correctly in order to model the initial start up ofmore » the harmonics. In this paper, we discuss and compare two different shot noise models that are implemented in both one-dimensional wiggler-averaged (PERSEO) and non-wiggler-averaged (MEDUSA1D) simulation codes, and a three-dimensional non-wiggler-averaged (MEDUSA) formulation. These models are compared for examples describing both SASE and MOPA configurations in one dimension, in steady-state, and time-dependent simulations. Remarkable agreement is found between PERSEO and MEDUSA1D for the evolution of the fundamental and harmonics. In addition, three-dimensional correction factors have been included in the MEDUSA1D and PERSEO, which show reasonable agreement with MEDUSA for a sample MOPA in steady-state and time-dependent simulations.« less

An idealised study for the long term evolution of crescentic bars

NASA Astrophysics Data System (ADS)

Chen, W. L.; Dodd, N.; Tiessen, M. C. H.; Calvete, D.

2018-01-01

An idealised study that identifies the mechanisms in the long term evolution of crescentic bar systems in nature is presented. Growth to finite amplitude (i.e., equilibration, sometimes referred to as saturation) and higher harmonic interaction are hypothesised to be the leading nonlinear effects in long-term evolution of these systems. These nonlinear effects are added to a linear stability model and used to predict crescentic bar development along a beach in Duck, North Carolina (USA) over a 2-month period. The equilibration prolongs the development of bed patterns, thus allowing the long term evolution. Higher harmonic interaction enables the amplitude to be transferred from longer to shorter lengthscales, which leads to the dominance of shorter lengthscales in latter post-storm stages, as observed at Duck. The comparison with observations indicates the importance of higher harmonic interaction in the development of nearshore crescentic bar systems in nature. Additionally, it is concluded that these nonlinear effects should be included in models simulating the development of different bed patterns, and that this points a way forward for long-term morphodynamical modelling in general.

Spherical harmonic results for the 3D Kobayashi Benchmark suite

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

Brown, P N; Chang, B; Hanebutte, U R

1999-03-02

Spherical harmonic solutions are presented for the Kobayashi benchmark suite. The results were obtained with Ardra, a scalable, parallel neutron transport code developed at Lawrence Livermore National Laboratory (LLNL). The calculations were performed on the IBM ASCI Blue-Pacific computer at LLNL.

Simulating The Prompt Electromagnetic Pulse In 3D Using Vector Spherical Harmonics

NASA Astrophysics Data System (ADS)

Friedman, Alex; Cohen, Bruce I.; Eng, Chester D.; Farmer, William A.; Grote, David P.; Kruger, Hans W.; Larson, David J.

2017-10-01

We describe a new, efficient code for simulating the prompt electromagnetic pulse. In SHEMP (``Spherical Harmonic EMP''), we extend to 3-D the methods pioneered in C. Longmire's CHAP code. The geomagnetic field and air density are consistent with CHAP's assumed spherical symmetry only for narrow domains of influence about the line of sight, limiting validity to very early times. Also, we seek to model inherently 3-D situations. In CHAP and our own CHAP-lite, the independent coordinates are r (the distance from the source) and τ = t-r/c; the pulse varies slowly with r at fixed τ, so a coarse radial grid suffices. We add non-spherically-symmetric physics via a vector spherical harmonic decomposition. For each (l,m) harmonic, the radial equation is similar to that in CHAP and CHAP-lite. We present our methodology and results on model problems. This work was performed under the auspices of the U.S. DOE by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Characteristics of a KA-band third-harmonic peniotron driven by a high-quality linear axis-encircling electron beam

NASA Astrophysics Data System (ADS)

Zhao, Xiaoyun; Tuo, Xianguo; Ge, Qing; Peng, Ying

2017-12-01

We employ a high-quality linear axis-encircling electron beam generated by a Cuccia coupler to drive a Ka-band third-harmonic peniotron and develop a self-consistent nonlinear calculation code to numerically analyze the characteristics of the designed peniotron. It is demonstrated that through a Cuccia coupler, a 6 kV, 0.5 A pencil beam and an input microwave power of 16 kW at 10 GHz can generate a 37 kV, 0.5 A linear axis-encircling beam, and it is characterized by a very low velocity spread. Moreover, the electron beam guiding center deviation can be adjusted easily. Driven by such a beam, a 30 GHz, Ka-band third-harmonic peniotron is predicted to achieve a conversion efficiency of 51.0% and a microwave output power of 9.44 kW; the results are in good agreement with the Magic3D simulation. Using this code, we studied the factors influencing the peniotron performance, and it can provide some guidelines for the design of a Ka-band third-harmonic peniotron driven by a linear electron beam and can promote the application of high-harmonic peniotrons in practice.

Design of Phoneme MIDI Codes Using the MIDI Encoding Tool “Auto-F” and Realizing Voice Synthesizing Functions Based on Musical Sounds

NASA Astrophysics Data System (ADS)

Modegi, Toshio

Using our previously developed audio to MIDI code converter tool “Auto-F”, from given vocal acoustic signals we can create MIDI data, which enable to playback the voice-like signals with a standard MIDI synthesizer. Applying this tool, we are constructing a MIDI database, which consists of previously converted simple harmonic structured MIDI codes from a set of 71 Japanese male and female syllable recorded signals. And we are developing a novel voice synthesizing system based on harmonically synthesizing musical sounds, which can generate MIDI data and playback voice signals with a MIDI synthesizer by giving Japanese plain (kana) texts, referring to the syllable MIDI code database. In this paper, we propose an improved MIDI converter tool, which can produce temporally higher-resolution MIDI codes. Then we propose an algorithm separating a set of 20 consonant and vowel phoneme MIDI codes from 71 syllable MIDI converted codes in order to construct a voice synthesizing system. And, we present the evaluation results of voice synthesizing quality between these separated phoneme MIDI codes and their original syllable MIDI codes by our developed 4-syllable word listening tests.

76 FR 40306 - Harmonizing Schedule I Drug Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-08

... [Docket No. FMCSA-2011-0073] RIN 2126-AB35 Harmonizing Schedule I Drug Requirements AGENCY: Federal Motor... instructions for the medical examination report to clarify that drivers may not use Schedule I drugs and be.... Abbreviations CAA Clean Air Act. CFR Code of Federal Regulations. CMV Commercial Motor Vehicle. DEA Drug...

Process Timing and Its Relation to the Coding of Tonal Harmony

ERIC Educational Resources Information Center

Aksentijevic, Aleksandar; Barber, Paul J.; Elliott, Mark A.

2011-01-01

Advances in auditory research suggest that gamma-band synchronization of frequency-specific cortical loci could be responsible for the integration of pure tones (harmonics) into harmonic complex tones. Thus far, evidence for such a mechanism has been revealed in neurophysiological studies, with little corroborative psychophysical evidence. In six…

76 FR 8658 - Bulk Solid Hazardous Materials: Harmonization With the International Maritime Solid Bulk Cargoes...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-15

... Solid Hazardous Materials: Harmonization With the International Maritime Solid Bulk Cargoes (IMSBC) Code..., the Coast Guard amended its regulations governing the carriage of solid hazardous materials in bulk to... hazardous bulk solid materials not addressed in the amended regulations. This notice announces that the...

76 FR 26194 - Metarhizium anisopliae Strain F52; Exemption From the Requirement of a Tolerance

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-06

... sensitization--guinea pig (Harmonized Guideline 870.2600; MRID No. 448447-15). An acceptable dermal... pesticide manufacturer. Potentially affected entities may include, but are not limited to: Crop production (NAICS code 111). Animal production (NAICS code 112). Food manufacturing (NAICS code 311). Pesticide...

Nonlinearly driven harmonics of Alfvén modes

NASA Astrophysics Data System (ADS)

Zhang, B.; Breizman, B. N.; Zheng, L. J.; Berk, H. L.

2014-01-01

In order to study the leading order nonlinear magneto-hydrodynamic (MHD) harmonic response of a plasma in realistic geometry, the AEGIS code has been generalized to account for inhomogeneous source terms. These source terms are expressed in terms of the quadratic corrections that depend on the functional form of a linear MHD eigenmode, such as the Toroidal Alfvén Eigenmode. The solution of the resultant equation gives the second order harmonic response. Preliminary results are presented here.

LETTER: Study of combined NBI and ICRF enhancement of the D-3He fusion yield with a Fokker-Planck code

NASA Astrophysics Data System (ADS)

Azoulay, M.; George, M. A.; Burger, A.; Collins, W. E.; Silberman, E.

A two-dimensional bounce averaged Fokker-Planck code is used to study the fusion yield and the wave absorption by residual hydrogen ions in higher harmonic ICRF heating of D (120 keV) and 3He (80 keV) beams in the JT-60U tokamak. Both for the fourth harmonic resonance of 3He (ω = 4ωc3He(0), which is accompanied by the third harmonic resonance of hydrogen (ω = 3ωcH) at the low field side, and for the third harmonic resonance of 3He (ω = 4ωcD(0) = 3ωc3He(0)) = 2ωcH(0)), a few per cent of hydrogen ions are found to absorb a large fraction of the ICRF power and to degrade the fusion output power. In the latter case, D beam acceleration due to the fourth harmonic resonance in the 3He(D) regime can enhance the fusion yield more effectively. A discussion is given of the effect of D beam acceleration due to the fifth harmonic resonance (ω = 5ωcD) at the high field side in the case of ω = 4ωc3He(0) and of the optimization of the fusion yield in the case of lower electron density and higher electron temperature

Simulation of free-electron lasers seeded with broadband radiation

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

Bajlekov, Svetoslav; Fawley, William; Schroeder, Carl

2011-03-10

The longitudinal coherence of free-electron laser (FEL) radiation can be enhanced by seeding the FEL with high harmonics of an optical laser pulse. The radiation produced by high-harmonic generation (HHG), however, has a fast-varying temporal profile that can violate the slowly varying envelope approximation and limited frequency window that is employed in conventional free-electron laser simulation codes. Here we investigate the implications of violating this approximation on the accuracy of simulations. On the basis of both analytical considerations and 1D numerical studies, it is concluded that, for most realistic scenarios, conventional FEL codes are capable of accurately simulating the FELmore » process even when the seed radiation violates the slowly varying envelope approximation. We additionally discuss the significance of filtering the harmonic content of broadband HHG seeds.« less

Self-accelerating parabolic beams in quadratic nonlinear media

NASA Astrophysics Data System (ADS)

Dolev, Ido; Libster, Ana; Arie, Ady

2012-09-01

We present experimental observation of self-accelerating parabolic beams in quadratic nonlinear media. We show that the intensity peaks of the first and second harmonics are asynchronous with respect to one another in the two transverse coordinates. In addition, the two coupled harmonics have the same acceleration within and after the nonlinear medium. We also study the evolution of second harmonic accelerating beams inside the quadratic media and their correlation with theoretical beams.

Evidence for Harmonic Content and Frequency Evolution of Oscillations During the Rising Phase of X-ray Bursts From 4U 1636-536

NASA Technical Reports Server (NTRS)

Bgattacharyya, Sudip; Strohmayer, E.

2005-01-01

We report on a study of the evolution of burst oscillation properties during the rising phase of X-ray bursts from 4U 1636-536 observed with the proportional counter array (PCA) on board the Rossi X-Ray Timing Explorer (RXTE) . We present evidence for significant harmonic structure of burst oscillation pulses during the early rising phases of bursts. This is the first such detection in burst rise oscillations, and is very important for constraining neutron star structure parameters and the equation of state models of matter at the core of a neutron star. The detection of harmonic content only during the initial portions of the burst rise is consistent with the theoretical expectation that with time the thermonuclear burning region becomes larger, and hence the fundamental and harmonic amplitudes both diminish. We also find, for the first time from this source, strong evidence of oscillation frequency increase during the burst rise. The timing behavior of harmonic content, amplitude, and frequency of burst rise oscillations may be important in understanding the spreading of thermonuclear flames under the extreme physical conditions on neutron star surfaces.

Spatial Evolution of Resonant Harmonic Mode Triads in a Blasius Boundary Layer

NASA Technical Reports Server (NTRS)

Davila, Jose B.; King, Rudolph A.

2007-01-01

Blasius boundary layer evolution is studies by means of bicoherence calculations. The layer is acoustically excited at the T-S frequency to provide a controlled transition. Measurements are made using a smooth surface as well as various roughness patterns. The bicoherence calculations are used to determine the extent to which frequency resonant velocity fluctuation waves can participate in energy exchange. The emphasis is on downstream variation of the individual interactions among harmonic modes. A limited picture of the role of quadratic wave interactions is revealed.

Elementary derivation of the quantum propagator for the harmonic oscillator

NASA Astrophysics Data System (ADS)

Shao, Jiushu

2016-10-01

Operator algebra techniques are employed to derive the quantum evolution operator for the harmonic oscillator. The derivation begins with the construction of the annihilation and creation operators and the determination of the wave function for the coherent state as well as its time-dependent evolution, and ends with the transformation of the propagator in a mixed position-coherent-state representation to the desired one in configuration space. Throughout the entire procedure, besides elementary operator manipulations, it is only necessary to solve linear differential equations and to calculate Gaussian integrals.

Dynamic divertor control using resonant mixed toroidal harmonic magnetic fields during ELM suppression in DIII-D

NASA Astrophysics Data System (ADS)

Jia, M.; Sun, Y.; Paz-Soldan, C.; Nazikian, R.; Gu, S.; Liu, Y. Q.; Abrams, T.; Bykov, I.; Cui, L.; Evans, T.; Garofalo, A.; Guo, W.; Gong, X.; Lasnier, C.; Logan, N. C.; Makowski, M.; Orlov, D.; Wang, H. H.

2018-05-01

Experiments using Resonant Magnetic Perturbations (RMPs), with a rotating n = 2 toroidal harmonic combined with a stationary n = 3 toroidal harmonic, have validated predictions that divertor heat and particle flux can be dynamically controlled while maintaining Edge Localized Mode (ELM) suppression in the DIII-D tokamak. Here, n is the toroidal mode number. ELM suppression over one full cycle of a rotating n = 2 RMP that was mixed with a static n = 3 RMP field has been achieved. Prominent heat flux splitting on the outer divertor has been observed during ELM suppression by RMPs in low collisionality regime in DIII-D. Strong changes in the three dimensional heat and particle flux footprint in the divertor were observed during the application of the mixed toroidal harmonic magnetic perturbations. These results agree well with modeling of the edge magnetic field structure using the TOP2D code, which takes into account the plasma response from the MARS-F code. These results expand the potential effectiveness of the RMP ELM suppression technique for the simultaneous control of divertor heat and particle load required in ITER.

Continuous variable quantum optical simulation for time evolution of quantum harmonic oscillators

PubMed Central

Deng, Xiaowei; Hao, Shuhong; Guo, Hong; Xie, Changde; Su, Xiaolong

2016-01-01

Quantum simulation enables one to mimic the evolution of other quantum systems using a controllable quantum system. Quantum harmonic oscillator (QHO) is one of the most important model systems in quantum physics. To observe the transient dynamics of a QHO with high oscillation frequency directly is difficult. We experimentally simulate the transient behaviors of QHO in an open system during time evolution with an optical mode and a logical operation system of continuous variable quantum computation. The time evolution of an atomic ensemble in the collective spontaneous emission is analytically simulated by mapping the atomic ensemble onto a QHO. The measured fidelity, which is used for quantifying the quality of the simulation, is higher than its classical limit. The presented simulation scheme provides a new tool for studying the dynamic behaviors of QHO. PMID:26961962

Easily extensible unix software for spectral analysis, display, modification, and synthesis of musical sounds

NASA Astrophysics Data System (ADS)

Beauchamp, James W.

2002-11-01

Software has been developed which enables users to perform time-varying spectral analysis of individual musical tones or successions of them and to perform further processing of the data. The package, called sndan, is freely available in source code, uses EPS graphics for display, and is written in ansi c for ease of code modification and extension. Two analyzers, a fixed-filter-bank phase vocoder (''pvan'') and a frequency-tracking analyzer (''mqan'') constitute the analysis front end of the package. While pvan's output consists of continuous amplitudes and frequencies of harmonics, mqan produces disjoint ''tracks.'' However, another program extracts a fundamental frequency and separates harmonics from the tracks, resulting in a continuous harmonic output. ''monan'' is a program used to display harmonic data in a variety of formats, perform various spectral modifications, and perform additive resynthesis of the harmonic partials, including possible pitch-shifting and time-scaling. Sounds can also be synthesized according to a musical score using a companion synthesis language, Music 4C. Several other programs in the sndan suite can be used for specialized tasks, such as signal display and editing. Applications of the software include producing specialized sounds for music compositions or psychoacoustic experiments or as a basis for developing new synthesis algorithms.

The DANTE Boltzmann transport solver: An unstructured mesh, 3-D, spherical harmonics algorithm compatible with parallel computer architectures

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

McGhee, J.M.; Roberts, R.M.; Morel, J.E.

1997-06-01

A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner formore » scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated.« less

Effect of second harmonic in pulse-width-modulation-based DAC for feedback of digital fluxgate magnetometer

NASA Astrophysics Data System (ADS)

Belyayev, Serhiy; Ivchenko, Nickolay

2018-04-01

Digital fluxgate magnetometers employ processing of the measured pickup signal to produce the value of the compensation current. Using pulse-width modulation with filtering for digital to analog conversion is a convenient approach, but it can introduce an intrinsic source of nonlinearity, which we discuss in this design note. A code shift of one least significant bit changes the second harmonic content of the pulse train, which feeds into the pick-up signal chain despite the heavy filtering. This effect produces a code-dependent nonlinearity. This nonlinearity can be overcome by the specific design of the timing of the pulse train signal. The second harmonic is suppressed if the first and third quarters of the excitation period pulse train are repeated in the second and fourth quarters. We demonstrate this principle on a digital magnetometer, achieving a magnetometer noise level corresponding to that of the sensor itself.

“SLIMPLECTIC” INTEGRATORS: VARIATIONAL INTEGRATORS FOR GENERAL NONCONSERVATIVE SYSTEMS

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

Tsang, David; Turner, Alec; Galley, Chad R.

2015-08-10

Symplectic integrators are widely used for long-term integration of conservative astrophysical problems due to their ability to preserve the constants of motion; however, they cannot in general be applied in the presence of nonconservative interactions. In this Letter, we develop the “slimplectic” integrator, a new type of numerical integrator that shares many of the benefits of traditional symplectic integrators yet is applicable to general nonconservative systems. We utilize a fixed-time-step variational integrator formalism applied to the principle of stationary nonconservative action developed in Galley et al. As a result, the generalized momenta and energy (Noether current) evolutions are well-tracked. Wemore » discuss several example systems, including damped harmonic oscillators, Poynting–Robertson drag, and gravitational radiation reaction, by utilizing our new publicly available code to demonstrate the slimplectic integrator algorithm. Slimplectic integrators are well-suited for integrations of systems where nonconservative effects play an important role in the long-term dynamical evolution. As such they are particularly appropriate for cosmological or celestial N-body dynamics problems where nonconservative interactions, e.g., gas interactions or dissipative tides, can play an important role.« less

Interaction between high harmonic fast waves and fast ions in NSTX/NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Bertelli, N.; Valeo, E. J.; Gorelenkova, M.; Green, D. L.; RF SciDAC Team

2016-10-01

Fast wave (FW) heating in the ion cyclotron range of frequency (ICRF) has been successfully used to sustain and control the fusion plasma performance, and it will likely play an important role in the ITER experiment. As demonstrated in the NSTX and DIII-D experiments the interactions between fast waves and fast ions can be so strong to significantly modify the fast ion population from neutral beam injection. In fact, it has been recently found in NSTX that FWs can modify and, under certain conditions, even suppress the energetic particle driven instabilities, such as toroidal Alfvén eigenmodes and global Alfvén eigenmodes and fishbones. This paper examines such interactions in NSTX/NSTX-U plasmas by using the recent extension of the RF full-wave code TORIC to include non-Maxwellian ions distribution functions. Particular attention is given to the evolution of the fast ions distribution function w/ and w/o RF. Tests on the RF kick-operator implemented in the Monte-Carlo particle code NUBEAM is also discussed in order to move towards a self consistent evaluation of the RF wave-field and the ion distribution functions in the TRANSP code. Work supported by US DOE Contract DE-AC02-09CH11466.

KINETIC-J: A computational kernel for solving the linearized Vlasov equation applied to calculations of the kinetic, configuration space plasma current for time harmonic wave electric fields

NASA Astrophysics Data System (ADS)

Green, David L.; Berry, Lee A.; Simpson, Adam B.; Younkin, Timothy R.

2018-04-01

We present the KINETIC-J code, a computational kernel for evaluating the linearized Vlasov equation with application to calculating the kinetic plasma response (current) to an applied time harmonic wave electric field. This code addresses the need for a configuration space evaluation of the plasma current to enable kinetic full-wave solvers for waves in hot plasmas to move beyond the limitations of the traditional Fourier spectral methods. We benchmark the kernel via comparison with the standard k →-space forms of the hot plasma conductivity tensor.

TRANSP-based Trajectory Optimization of the Current Profile Evolution to Facilitate Robust Non-inductive Ramp-up in NSTX-U

NASA Astrophysics Data System (ADS)

Wehner, William; Schuster, Eugenio; Poli, Francesca

2016-10-01

Initial progress towards the design of non-inductive current ramp-up scenarios in the National Spherical Torus Experiment Upgrade (NSTX-U) has been made through the use of TRANSP predictive simulations. The strategy involves, first, ramping the plasma current with high harmonic fast waves (HHFW) to about 400 kA, and then further ramping to 900 kA with neutral beam injection (NBI). However, the early ramping of neutral beams and application of HHFW leads to an undesirably peaked current profile making the plasma unstable to ballooning modes. We present an optimization-based control approach to improve on the non-inductive ramp-up strategy. We combine the TRANSP code with an optimization algorithm based on sequential quadratic programming to search for time evolutions of the NBI powers, the HHFW powers, and the line averaged density that define an open-loop actuator strategy that maximizes the non-inductive current while satisfying constraints associated with the current profile evolution for MHD stable plasmas. This technique has the potential of playing a critical role in achieving robustly stable non-inductive ramp-up, which will ultimately be necessary to demonstrate applicability of the spherical torus concept to larger devices without sufficient room for a central coil. Supported by the US DOE under the SCGSR Program.

Exact dynamics of a one dimensional Bose gas in a periodic time-dependent harmonic trap

NASA Astrophysics Data System (ADS)

Scopa, Stefano; Unterberger, Jéremie; Karevski, Dragi

2018-05-01

We study the unitary dynamics of a 1D gas of hard-core bosons trapped into a harmonic potential which varies periodically in time with frequency . Such periodic systems can be classified into orbits of different monodromies corresponding to two different physical situations, namely the case in which the bosonic cloud remains stable during the time-evolution and the case where it turns out to be unstable. In the present work we derive in the large particle number limit exact results for the stroboscopic evolution of the energy and particle densities in both physical situations.

Instability modes excited by natural screech tones in a supersonic rectangular jet

NASA Technical Reports Server (NTRS)

Raman, Ganesh; Rice, Edward J.

1993-01-01

The evolution of hydrodynamic instability modes self-excited by harmonically related natural screech tones was experimentally investigated. A convergent rectangular nozzle with an aspect ratio of 9.63 was used to produce a supersonic shock containing jet. Measurements in the flow-field were made using standard hot-film probes positioned only in the subsonic (outer) portions of the flow. The hydrodynamic instability mode observed in the shear layer at the screech frequency was observed to be antisymmetric (sinuous) about the smaller dimension of the jet, whereas its harmonic was observed to be symmetric (varicose). In addition, the near-field noise measurements indicated that the radiated screech tone noise was out of phase on either side of the small jet dimension whereas its harmonic was in phase over the same region. To our knowledge such an observation on the nature of the harmonic has thus far gone unreported and therefore is the focus of the present work. The hydrodynamic instability modes occurring at the screech frequency and its harmonic satisfied the conditions for resonance. Detailed measurements of the coherent wave evolution in the streamwise and spanwise directions indicated that strong spanwise variations were present beyond x/h = 8. Details of the screech noise radiated by the coherent instability modes are also presented in this paper.

Pulse compression of harmonic chirp signals using the fractional fourier transform.

PubMed

Arif, M; Cowell, D M J; Freear, S

2010-06-01

In ultrasound harmonic imaging with chirp-coded excitation, a harmonic matched filter (HMF) is typically used on the received signal to perform pulse compression of the second harmonic component (SHC) to recover signal axial resolution. Designing the HMF for the compression of the SHC is a problematic issue because it requires optimal window selection. In the compressed second harmonic signal, the sidelobe level may increase and the mainlobe width (MLW) widen under a mismatched condition, resulting in loss of axial resolution. We propose the use of the fractional Fourier transform (FrFT) as an alternative tool to perform compression of the chirp-coded SHC generated as a result of the nonlinear propagation of an ultrasound signal. Two methods are used to experimentally assess the performance benefits of the FrFT technique over the HMF techniques. The first method uses chirp excitation with central frequency of 2.25 MHz and bandwidth of 1 MHz. The second method uses chirp excitation with pulse inversion to increase the bandwidth to 2 MHz. In this study, experiments were performed in a water tank with a single-element transducer mounted coaxially with a hydrophone in a pitch-catch configuration. Results are presented that indicate that the FrFT can perform pulse compression of the second harmonic chirp component, with a 14% reduction in the MLW of the compressed signal when compared with the HMF. Also, the FrFT provides at least 23% reduction in the MLW of the compressed signal when compared with the harmonic mismatched filter (HMMF). The FrFT maintains comparable peak and integrated sidelobe levels when compared with the HMF and HMMF techniques. Copyright 2010 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Aeroacoustic Codes For Rotor Harmonic and BVI Noise--CAMRAD.Mod1/HIRES

NASA Technical Reports Server (NTRS)

Brooks, Thomas F.; Boyd, D. Douglas, Jr.; Burley, Casey L.; Jolly, J. Ralph, Jr.

1996-01-01

This paper presents a status of non-CFD aeroacoustic codes at NASA Langley Research Center for the prediction of helicopter harmonic and Blade-Vortex Interaction (BVI) noise. The prediction approach incorporates three primary components: CAMRAD.Mod1 - a substantially modified version of the performance/trim/wake code CAMRAD; HIRES - a high resolution blade loads post-processor; and WOPWOP - an acoustic code. The functional capabilities and physical modeling in CAMRAD.Mod1/HIRES will be summarized and illustrated. A new multi-core roll-up wake modeling approach is introduced and validated. Predictions of rotor wake and radiated noise are compared with to the results of the HART program, a model BO-105 windtunnel test at the DNW in Europe. Additional comparisons are made to results from a DNW test of a contemporary design four-bladed rotor, as well as from a Langley test of a single proprotor (tiltrotor) three-bladed model configuration. Because the method is shown to help eliminate the necessity of guesswork in setting code parameters between different rotor configurations, it should prove useful as a rotor noise design tool.

Initial applications of the non-Maxwellian extension of the full-wave TORIC v.5 code in the mid/high harmonic and minority heating regimes

NASA Astrophysics Data System (ADS)

Bertelli, N.; Valeo, E. J.; Phillips, C. K.

2015-11-01

A non Maxwellian extension of the full wave TORIC v.5 code in the mid/high harmonic and minority heating regimes has been revisited. In both regimes the treatment of the non-Maxwellian ions is needed in order to improve the analysis of combined fast wave (FW) and neutral beam injection (NBI) heated discharges in the current fusion devices. Additionally, this extension is also needed in time-dependent analysis where the combined heating experiments are generally considered. Initial numerical cases with thermal ions and with a non-Maxwellian ions are presented for both regimes. The simulations are then compared with results from the AORSA code, which has already been extended to include non-Maxwellian ions. First attempts to apply this extension in a self-consistent way with the NUBEAM module, which is included in the TRANSP code, are also discussed. Work supported by US DOE Contracts # DE-FC02-01ER54648 and DE-AC02-09CH11466.

ArtDeco: a beam-deconvolution code for absolute cosmic microwave background measurements

NASA Astrophysics Data System (ADS)

Keihänen, E.; Reinecke, M.

2012-12-01

We present a method for beam-deconvolving cosmic microwave background (CMB) anisotropy measurements. The code takes as input the time-ordered data along with the corresponding detector pointings and known beam shapes, and produces as output the harmonic aTlm, aElm, and aBlm coefficients of the observed sky. From these one can derive temperature and Q and U polarisation maps. The method is applicable to absolute CMB measurements with wide sky coverage, and is independent of the scanning strategy. We tested the code with extensive simulations, mimicking the resolution and data volume of Planck 30 GHz and 70 GHz channels, but with exaggerated beam asymmetry. We applied it to multipoles up to l = 1700 and examined the results in both pixel space and harmonic space. We also tested the method in presence of white noise. The code is released under the terms of the GNU General Public License and can be obtained from http://sourceforge.net/projects/art-deco/

electromagnetics, eddy current, computer codes

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

Gartling, David

TORO Version 4 is designed for finite element analysis of steady, transient and time-harmonic, multi-dimensional, quasi-static problems in electromagnetics. The code allows simulation of electrostatic fields, steady current flows, magnetostatics and eddy current problems in plane or axisymmetric, two-dimensional geometries. TORO is easily coupled to heat conduction and solid mechanics codes to allow multi-physics simulations to be performed.

Using music to study the evolution of cognitive mechanisms relevant to language.

PubMed

Patel, Aniruddh D

2017-02-01

This article argues that music can be used in cross-species research to study the evolution of cognitive mechanisms relevant to spoken language. This is because music and language share certain cognitive processing mechanisms and because music offers specific advantages for cross-species research. Music has relatively simple building blocks (tones without semantic properties), yet these building blocks are combined into rich hierarchical structures that engage complex cognitive processing. I illustrate this point with regard to the processing of musical harmonic structure. Because the processing of musical harmonic structure has been shown to interact with linguistic syntactic processing in humans, it is of interest to know if other species can acquire implicit knowledge of harmonic structure through extended exposure to music during development (vs. through explicit training). I suggest that domestic dogs would be a good species to study in addressing this question.

Three-dimensional simulation of free-electron laser harmonics with FRED

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

Sharp, W.M.; Scharlemann, E.T.; Fawley, W.M.

1989-11-20

FRED3D, a single-mode three-dimensional version of the FEL simulation code FRED, has been modified to follow the growth of signal components at the fundamental frequency and at even and odd harmonics. The Wiggle-averaged particle and field equations for this multi-mode formulation are derived here, and their implementation in FRED3D is discussed. 12 refs.

Vector solitons in harmonic mode-locked erbium-doped fiber lasers

NASA Astrophysics Data System (ADS)

Habruseva, Tatiana; Mkhitaryan, Mkhitar; Mou, Chengbo; Rozhin, Aleksey; Turitsyn, Sergei K.; Sergeyev, Sergey V.

2014-05-01

We report experimental study of vector solitons for the fundamental and harmonic mode-locked operation in erbiumdoper fiber lasers with carbon nanotubes based saturable absorbers and anomalous dispersion cavities. We measure evolution of the output pulses polarization and demonstrate vector solitons with various polarization attractors, including locked polarization, periodic polarization switching, and polarization precession.

The Generalized Uncertainty Principle and Harmonic Interaction in Three Spatial Dimensions

NASA Astrophysics Data System (ADS)

Hassanabadi, H.; Hooshmand, P.; Zarrinkamar, S.

2015-01-01

In three spatial dimensions, the generalized uncertainty principle is considered under an isotropic harmonic oscillator interaction in both non-relativistic and relativistic regions. By using novel transformations and separations of variables, the exact analytical solution of energy eigenvalues as well as the wave functions is obtained. Time evolution of the non-relativistic region is also reported.

The oscillatory entrainment of virtual pitch perception

PubMed Central

Aksentijevic, Aleksandar; Northeast, Anthony; Canty, Daniel; Elliott, Mark A.

2013-01-01

Evidence suggests that synchronized brain oscillations in the low gamma range (around 33 Hz) are involved in the perceptual integration of harmonic complex tones. This process involves the binding of harmonic components into “harmonic templates” – neural structures responsible for pitch coding in the brain. We investigated the hypothesis that oscillatory harmonic binding promotes a change in pitch perception style from spectral (frequency) to virtual (relational). Using oscillatory priming we asked 24 participants to judge as rapidly as possible, the direction of an ambiguous target with ascending spectral and descending virtual contour. They made significantly more virtual responses when primed at 29, 31, and 33 Hz and when the first target tone was harmonically related to the prime, suggesting that neural synchronization in the low gamma range could facilitate a shift toward virtual pitch processing. PMID:23630515

Ultrashort pulse chirp measurement via transverse second-harmonic generation in strontium barium niobate crystal

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

Trull, J.; Wang, B.; Parra, A.

2015-06-01

Pulse compression in dispersive strontium barium niobate crystal with a random size and distribution of the anti-parallel orientated nonlinear domains is observed via transverse second harmonic generation. The dependence of the transverse width of the second harmonic trace along the propagation direction allows for the determination of the initial chirp and duration of pulses in the femtosecond regime. This technique permits a real-time analysis of the pulse evolution and facilitates fast in-situ correction of pulse chirp acquired in the propagation through an optical system.

A Comparative Analysis of Digital and Passive Filters for IFOC based Induction Motor Drive (EV) fed through ZSI

NASA Astrophysics Data System (ADS)

Bedi, Tarun; Heema, Dave; Singh, Dheerendra

2018-03-01

It is known that harmonics are generated in any power electronics based application. Since presence of harmonics is not desirable, it is necessary to remove the harmonics. The IFOC is based on stator current regulation, and the stator currents are sensed and used in the speed control algorithm. The current needs to be free from noise and harmonics for accurate further processing. In this paper, a passive analog filter, as well as a 50th order FIR filter is designed in MATLAB and implemented in Code Composer Studio to remove noise and distortion, and a comparative analysis has been done, for the speed control of an induction motor fed through ZSI, for electric vehicle application.

Second International Workshop on Harmonic Oscillators

NASA Technical Reports Server (NTRS)

Han, Daesoo (Editor); Wolf, Kurt Bernardo (Editor)

1995-01-01

The Second International Workshop on Harmonic Oscillators was held at the Hotel Hacienda Cocoyoc from March 23 to 25, 1994. The Workshop gathered 67 participants; there were 10 invited lecturers, 30 plenary oral presentations, 15 posters, and plenty of discussion divided into the five sessions of this volume. The Organizing Committee was asked by the chairman of several Mexican funding agencies what exactly was meant by harmonic oscillators, and for what purpose the new research could be useful. Harmonic oscillators - as we explained - is a code name for a family of mathematical models based on the theory of Lie algebras and groups, with applications in a growing range of physical theories and technologies: molecular, atomic, nuclear and particle physics; quantum optics and communication theory.

Rooted tRNAomes and evolution of the genetic code

PubMed Central

Pak, Daewoo; Du, Nan; Kim, Yunsoo; Sun, Yanni

2018-01-01

ABSTRACT We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code. PMID:29372672

Exact harmonic solutions to Guyer-Krumhansl-type equation and application to heat transport in thin films

NASA Astrophysics Data System (ADS)

Zhukovsky, K.; Oskolkov, D.

2018-03-01

A system of hyperbolic-type inhomogeneous differential equations (DE) is considered for non-Fourier heat transfer in thin films. Exact harmonic solutions to Guyer-Krumhansl-type heat equation and to the system of inhomogeneous DE are obtained in Cauchy- and Dirichlet-type conditions. The contribution of the ballistic-type heat transport, of the Cattaneo heat waves and of the Fourier heat diffusion is discussed and compared with each other in various conditions. The application of the study to the ballistic heat transport in thin films is performed. Rapid evolution of the ballistic quasi-temperature component in low-dimensional systems is elucidated and compared with slow evolution of its diffusive counterpart. The effect of the ballistic quasi-temperature component on the evolution of the complete quasi-temperature is explored. In this context, the influence of the Knudsen number and of Cauchy- and Dirichlet-type conditions on the evolution of the temperature distribution is explored. The comparative analysis of the obtained solutions is performed.

Thermonuclear targets for direct-drive ignition by a megajoule laser pulse

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

Bel’kov, S. A.; Bondarenko, S. V.; Vergunova, G. A.

2015-10-15

Central ignition of a thin two-layer-shell fusion target that is directly driven by a 2-MJ profiled pulse of Nd laser second-harmonic radiation has been studied. The parameters of the target were selected so as to provide effective acceleration of the shell toward the center, which was sufficient for the onset of ignition under conditions of increased hydrodynamic stability of the ablator acceleration and compression. The aspect ratio of the inner deuterium-tritium layer of the shell does not exceed 15, provided that a major part (above 75%) of the outer layer (plastic ablator) is evaporated by the instant of maximum compression.more » The investigation is based on two series of numerical calculations that were performed using one-dimensional (1D) hydrodynamic codes. The first 1D code was used to calculate the absorption of the profiled laser-radiation pulse (including calculation of the total absorption coefficient with allowance for the inverse bremsstrahlung and resonance mechanisms) and the spatial distribution of target heating for a real geometry of irradiation using 192 laser beams in a scheme of focusing with a cubo-octahedral symmetry. The second 1D code was used for simulating the total cycle of target evolution under the action of absorbed laser radiation and for determining the thermonuclear gain that was achieved with a given target.« less

Experimental and numerical investigation of tissue harmonic imaging (THI)

NASA Astrophysics Data System (ADS)

Jing, Yuan; Yang, Xinmai; Cleveland, Robin O.

2003-04-01

In THI the probing ultrasonic pulse has enough amplitude that it undergoes nonlinear distortion and energy shifts from the fundamental frequency of the pulse into its higher harmonics. Images generated from the second harmonic (SH) have superior quality to the images formed from the fundamental frequency. Experiments with a single element focused ultrasound transducer were used to compare a line target embedded in a tissue phantom using either fundamental or SH imaging. SH imaging showed an improvement in both the axial resolution (0.70 mm vs 0.92 mm) and the lateral resolution (1.02 mm vs 2.70 mm) of the target. In addition, the contrast-to-tissue ratio of the target was 2 dB higher with SH imaging. A three-dimensional model of the forward propagation has been developed to simulate the experimental system. The model is based on a time-domain code for solving the KZK equation and accounts for arbitrary spatial variations in all tissue properties. The code was used to determine the impact of a nearfield layer of fat on the fundamental and second harmonic signals. For a 15 mm thick layer the SH side-lobes remained the same but the fundamental side-lobes increased by 2 dB. [Work supported by the NSF through the Center for Subsurface Sensing and Imaging Systems.

The evolution of hyperboloidal data with the dual foliation formalism: mathematical analysis and wave equation tests

NASA Astrophysics Data System (ADS)

Hilditch, David; Harms, Enno; Bugner, Marcus; Rüter, Hannes; Brügmann, Bernd

2018-03-01

A long-standing problem in numerical relativity is the satisfactory treatment of future null-infinity. We propose an approach for the evolution of hyperboloidal initial data in which the outer boundary of the computational domain is placed at infinity. The main idea is to apply the ‘dual foliation’ formalism in combination with hyperboloidal coordinates and the generalized harmonic gauge formulation. The strength of the present approach is that, following the ideas of Zenginoğlu, a hyperboloidal layer can be naturally attached to a central region using standard coordinates of numerical relativity applications. Employing a generalization of the standard hyperboloidal slices, developed by Calabrese et al, we find that all formally singular terms take a trivial limit as we head to null-infinity. A byproduct is a numerical approach for hyperboloidal evolution of nonlinear wave equations violating the null-condition. The height-function method, used often for fixed background spacetimes, is generalized in such a way that the slices can be dynamically ‘waggled’ to maintain the desired outgoing coordinate lightspeed precisely. This is achieved by dynamically solving the eikonal equation. As a first numerical test of the new approach we solve the 3D flat space scalar wave equation. The simulations, performed with the pseudospectral bamps code, show that outgoing waves are cleanly absorbed at null-infinity and that errors converge away rapidly as resolution is increased.

Phase locked neural activity in the human brainstem predicts preference for musical consonance.

PubMed

Bones, Oliver; Hopkins, Kathryn; Krishnan, Ananthanarayan; Plack, Christopher J

2014-05-01

When musical notes are combined to make a chord, the closeness of fit of the combined spectrum to a single harmonic series (the 'harmonicity' of the chord) predicts the perceived consonance (how pleasant and stable the chord sounds; McDermott, Lehr, & Oxenham, 2010). The distinction between consonance and dissonance is central to Western musical form. Harmonicity is represented in the temporal firing patterns of populations of brainstem neurons. The current study investigates the role of brainstem temporal coding of harmonicity in the perception of consonance. Individual preference for consonant over dissonant chords was measured using a rating scale for pairs of simultaneous notes. In order to investigate the effects of cochlear interactions, notes were presented in two ways: both notes to both ears or each note to different ears. The electrophysiological frequency following response (FFR), reflecting sustained neural activity in the brainstem synchronised to the stimulus, was also measured. When both notes were presented to both ears the perceptual distinction between consonant and dissonant chords was stronger than when the notes were presented to different ears. In the condition in which both notes were presented to the both ears additional low-frequency components, corresponding to difference tones resulting from nonlinear cochlear processing, were observable in the FFR effectively enhancing the neural harmonicity of consonant chords but not dissonant chords. Suppressing the cochlear envelope component of the FFR also suppressed the additional frequency components. This suggests that, in the case of consonant chords, difference tones generated by interactions between notes in the cochlea enhance the perception of consonance. Furthermore, individuals with a greater distinction between consonant and dissonant chords in the FFR to individual harmonics had a stronger preference for consonant over dissonant chords. Overall, the results provide compelling evidence for the role of neural temporal coding in the perception of consonance, and suggest that the representation of harmonicity in phase locked neural firing drives the perception of consonance. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Partition-free approach to open quantum systems in harmonic environments: An exact stochastic Liouville equation

NASA Astrophysics Data System (ADS)

McCaul, G. M. G.; Lorenz, C. D.; Kantorovich, L.

2017-03-01

We present a partition-free approach to the evolution of density matrices for open quantum systems coupled to a harmonic environment. The influence functional formalism combined with a two-time Hubbard-Stratonovich transformation allows us to derive a set of exact differential equations for the reduced density matrix of an open system, termed the extended stochastic Liouville-von Neumann equation. Our approach generalizes previous work based on Caldeira-Leggett models and a partitioned initial density matrix. This provides a simple, yet exact, closed-form description for the evolution of open systems from equilibriated initial conditions. The applicability of this model and the potential for numerical implementations are also discussed.

The harmonic organization of auditory cortex.

PubMed

Wang, Xiaoqin

2013-12-17

A fundamental structure of sounds encountered in the natural environment is the harmonicity. Harmonicity is an essential component of music found in all cultures. It is also a unique feature of vocal communication sounds such as human speech and animal vocalizations. Harmonics in sounds are produced by a variety of acoustic generators and reflectors in the natural environment, including vocal apparatuses of humans and animal species as well as music instruments of many types. We live in an acoustic world full of harmonicity. Given the widespread existence of the harmonicity in many aspects of the hearing environment, it is natural to expect that it be reflected in the evolution and development of the auditory systems of both humans and animals, in particular the auditory cortex. Recent neuroimaging and neurophysiology experiments have identified regions of non-primary auditory cortex in humans and non-human primates that have selective responses to harmonic pitches. Accumulating evidence has also shown that neurons in many regions of the auditory cortex exhibit characteristic responses to harmonically related frequencies beyond the range of pitch. Together, these findings suggest that a fundamental organizational principle of auditory cortex is based on the harmonicity. Such an organization likely plays an important role in music processing by the brain. It may also form the basis of the preference for particular classes of music and voice sounds.

Complete tidal evolution of Pluto-Charon

NASA Astrophysics Data System (ADS)

Cheng, W. H.; Lee, Man Hoi; Peale, S. J.

2014-05-01

Both Pluto and its satellite Charon have rotation rates synchronous with their orbital mean motion. This is the theoretical end point of tidal evolution where transfer of angular momentum has ceased. Here we follow Pluto’s tidal evolution from an initial state having the current total angular momentum of the system but with Charon in an eccentric orbit with semimajor axis a≈4RP (where RP is the radius of Pluto), consistent with its impact origin. Two tidal models are used, where the tidal dissipation function Q∝1/frequency and Q = constant, where details of the evolution are strongly model dependent. The inclusion of the gravitational harmonic coefficient C22 of both bodies in the analysis allows smooth, self consistent evolution to the dual synchronous state, whereas its omission frustrates successful evolution in some cases. The zonal harmonic J2 can also be included, but does not cause a significant effect on the overall evolution. The ratio of dissipation in Charon to that in Pluto controls the behavior of the orbital eccentricity, where a judicious choice leads to a nearly constant eccentricity until the final approach to dual synchronous rotation. The tidal models are complete in the sense that every nuance of tidal evolution is realized while conserving total angular momentum-including temporary capture into spin-orbit resonances as Charon’s spin decreases and damped librations about the same.

The Effect of Non-Harmonic Active Twist Actuation on BVI Noise

NASA Technical Reports Server (NTRS)

Fogarty, David E.; Wilbur, Matthew L.; Sekula, Martin K.

2011-01-01

The results of a computational study examining the effects of non-harmonic active-twist control on blade-vortex interaction (BVI) noise for the Apache Active Twist Rotor are presented. Rotor aeroelastic behavior was modeled using the Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics code and the rotor noise was predicted using the acoustics code PSU-WOPWOP. The application of non-harmonic active-twist inputs to the main rotor blade system comprised three parameters: azimuthal location to start actuation, azimuthal duration of actuation, and magnitude of actuation. The acoustic analysis was conducted for a single low-speed flight condition of advance ratio mu=0.14 and shaft angle-of-attack, a(sub s)=+6deg. BVI noise levels were predicted on a flat plane of observers located 1.1 rotor diameters beneath the rotor. The results indicate significant reductions of up to 10dB in BVI noise using a starting azimuthal location for actuation of 90?, an azimuthal duration of actuation of 90deg, and an actuation magnitude of +1.5 ft-lb.

International variation in the definition of ‘main condition’ in ICD-coded health data

PubMed Central

Quan, H.; Moskal, L.; Forster, A.J.; Brien, S.; Walker, R.; Romano, P.S.; Sundararajan, V.; Burnand, B.; Henriksson, G.; Steinum, O.; Droesler, S.; Pincus, H.A.; Ghali, W.A.

2014-01-01

Hospital-based medical records are abstracted to create International Classification of Disease (ICD) coded discharge health data in many countries. The ‘main condition’ is not defined in a consistent manner internationally. Some countries employ a ‘reason for admission’ rule as the basis for the main condition, while other countries employ a ‘resource use’ rule. A few countries have recently transitioned from one of these approaches to the other. The definition of ‘main condition’ in such ICD data matters when it is used to define a disease cohort to assign diagnosis-related groups and to perform risk adjustment. We propose a method of harmonizing the international definition to enable researchers and international organizations using ICD-coded health data to aggregate or compare hospital care and outcomes across countries in a consistent manner. Inter-observer reliability of alternative harmonization approaches should be evaluated before finalizing the definition and adopting it worldwide. PMID:24990594

Combined electric and acoustic hearing performance with Zebra® speech processor: speech reception, place, and temporal coding evaluation.

PubMed

Vaerenberg, Bart; Péan, Vincent; Lesbros, Guillaume; De Ceulaer, Geert; Schauwers, Karen; Daemers, Kristin; Gnansia, Dan; Govaerts, Paul J

2013-06-01

To assess the auditory performance of Digisonic(®) cochlear implant users with electric stimulation (ES) and electro-acoustic stimulation (EAS) with special attention to the processing of low-frequency temporal fine structure. Six patients implanted with a Digisonic(®) SP implant and showing low-frequency residual hearing were fitted with the Zebra(®) speech processor providing both electric and acoustic stimulation. Assessment consisted of monosyllabic speech identification tests in quiet and in noise at different presentation levels, and a pitch discrimination task using harmonic and disharmonic intonating complex sounds ( Vaerenberg et al., 2011 ). These tests investigate place and time coding through pitch discrimination. All tasks were performed with ES only and with EAS. Speech results in noise showed significant improvement with EAS when compared to ES. Whereas EAS did not yield better results in the harmonic intonation test, the improvements in the disharmonic intonation test were remarkable, suggesting better coding of pitch cues requiring phase locking. These results suggest that patients with residual hearing in the low-frequency range still have good phase-locking capacities, allowing them to process fine temporal information. ES relies mainly on place coding but provides poor low-frequency temporal coding, whereas EAS also provides temporal coding in the low-frequency range. Patients with residual phase-locking capacities can make use of these cues.

Ion absorption of the high harmonic fast wave in the National Spherical Torus Experiment

NASA Astrophysics Data System (ADS)

Rosenberg, Adam Lewis

Ion absorption of the high harmonic fast wave in a spherical torus is of critical importance to assessing the viability of the wave as a means of heating and driving current. Analysis of recent NSTX shots has revealed that under some conditions when neutral beam and RF power are injected into the plasma simultaneously, a fast ion population with energy above the beam injection energy is sustained by the wave. In agreement with modeling, these experiments find the RF-induced fast ion tail strength and neutron rate at lower B-fields to be less enhanced, likely due to a larger β profile, which promotes greater off-axis absorption where the fast ion population is small. Ion loss codes find the increased loss fraction with decreased B insufficient to account for the changes in tail strength, providing further evidence that this is an RF interaction effect. Though greater ion absorption is predicted with lower k∥, surprisingly little variation in the tail was observed, along with a neutron rate enhancement with higher k∥. Data from the neutral particle analyzer, neutron detectors, x-ray crystal spectrometer, and Thomson scattering is presented, along with results from the TRANSP transport analysis code, ray-tracing codes HPRT and CURRAY, full-wave code and AORSA, quasilinear code CQL3D, and ion loss codes EIGOL and CONBEAM.

High harmonic generation in underdense plasmas by intense laser pulses with orbital angular momentum

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

Mendonça, J. T., E-mail: josetitomend@gmail.com; Vieira, J., E-mail: jorge.vieira@ist.utl.pt

We study high harmonic generation produced by twisted laser pulses, with orbital angular momentum in the relativistic regime, for pulse propagation in underdense plasma. We consider fast time scale processes associated with an ultra-short pulse, where the ion motion can be neglected. We use both analytical models and numerical simulations using a relativistic particle-in-cell code. The present description is valid for relativistic laser intensities, when the normalized field amplitude is much larger than one, a ≫ 1. We also discuss two distinct processes associated with linear and circular polarization. Using both analytical solutions and particle-in-cell simulations, we are able tomore » show that, for laser pulses in a well defined Laguerre-Gauss mode, angular momentum conservation is observed during the process of harmonic generation. Intensity modulation of the harmonic spectrum is also verified, as imposed by the nonlinear time-scale for energy transfer between different harmonics.« less

Harmonizing clinical terminologies: driving interoperability in healthcare.

PubMed

Hamm, Russell A; Knoop, Sarah E; Schwarz, Peter; Block, Aaron D; Davis, Warren L

2007-01-01

Internationally, there are countless initiatives to build National Healthcare Information Networks (NHIN) that electronically interconnect healthcare organizations by enhancing and integrating current information technology (IT) capabilities. The realization of such NHINs will enable the simple and immediate exchange of appropriate and vital clinical data among participating organizations. In order for institutions to accurately and automatically exchange information, the electronic clinical documents must make use of established clinical codes, such as those of SNOMED-CT, LOINC and ICD-9 CM. However, there does not exist one universally accepted coding scheme that encapsulates all pertinent clinical information for the purposes of patient care, clinical research and population heatlh reporting. In this paper, we propose a combination of methods and standards that target the harmonization of clinical terminologies and encourage sustainable, interoperable infrastructure for healthcare.

Complex pitch perception mechanisms are shared by humans and a New World monkey.

PubMed

Song, Xindong; Osmanski, Michael S; Guo, Yueqi; Wang, Xiaoqin

2016-01-19

The perception of the pitch of harmonic complex sounds is a crucial function of human audition, especially in music and speech processing. Whether the underlying mechanisms of pitch perception are unique to humans, however, is unknown. Based on estimates of frequency resolution at the level of the auditory periphery, psychoacoustic studies in humans have revealed several primary features of central pitch mechanisms. It has been shown that (i) pitch strength of a harmonic tone is dominated by resolved harmonics; (ii) pitch of resolved harmonics is sensitive to the quality of spectral harmonicity; and (iii) pitch of unresolved harmonics is sensitive to the salience of temporal envelope cues. Here we show, for a standard musical tuning fundamental frequency of 440 Hz, that the common marmoset (Callithrix jacchus), a New World monkey with a hearing range similar to that of humans, exhibits all of the primary features of central pitch mechanisms demonstrated in humans. Thus, marmosets and humans may share similar pitch perception mechanisms, suggesting that these mechanisms may have emerged early in primate evolution.

Aeroacoustic Analysis of Turbofan Noise Generation

NASA Technical Reports Server (NTRS)

Meyer, Harold D.; Envia, Edmane

1996-01-01

This report provides an updated version of analytical documentation for the V072 Rotor Wake/Stator Interaction Code. It presents the theoretical derivation of the equations used in the code and, where necessary, it documents the enhancements and changes made to the original code since its first release. V072 is a package of FORTRAN computer programs which calculate the in-duct acoustic modes excited by a fan/stator stage operating in a subsonic mean flow. Sound is generated by the stator vanes interacting with the mean wakes of the rotor blades. In this updated version, only the tonal noise produced at the blade passing frequency and its harmonics, is described. The broadband noise component analysis, which was part of the original report, is not included here. The code provides outputs of modal pressure and power amplitudes generated by the rotor-wake/stator interaction. The rotor/stator stage is modeled as an ensemble of blades and vanes of zero camber and thickness enclosed within an infinite hard-walled annular duct. The amplitude of each propagating mode is computed and summed to obtain the harmonics of sound power flux within the duct for both upstream and downstream propagating modes.

The harmonic organization of auditory cortex

PubMed Central

Wang, Xiaoqin

2013-01-01

A fundamental structure of sounds encountered in the natural environment is the harmonicity. Harmonicity is an essential component of music found in all cultures. It is also a unique feature of vocal communication sounds such as human speech and animal vocalizations. Harmonics in sounds are produced by a variety of acoustic generators and reflectors in the natural environment, including vocal apparatuses of humans and animal species as well as music instruments of many types. We live in an acoustic world full of harmonicity. Given the widespread existence of the harmonicity in many aspects of the hearing environment, it is natural to expect that it be reflected in the evolution and development of the auditory systems of both humans and animals, in particular the auditory cortex. Recent neuroimaging and neurophysiology experiments have identified regions of non-primary auditory cortex in humans and non-human primates that have selective responses to harmonic pitches. Accumulating evidence has also shown that neurons in many regions of the auditory cortex exhibit characteristic responses to harmonically related frequencies beyond the range of pitch. Together, these findings suggest that a fundamental organizational principle of auditory cortex is based on the harmonicity. Such an organization likely plays an important role in music processing by the brain. It may also form the basis of the preference for particular classes of music and voice sounds. PMID:24381544

Proposed Standards for Variable Harmonization Documentation and Referencing: A Case Study Using QuickCharmStats 1.1

PubMed Central

Winters, Kristi; Netscher, Sebastian

2016-01-01

Comparative statistical analyses often require data harmonization, yet the social sciences do not have clear operationalization frameworks that guide and homogenize variable coding decisions across disciplines. When faced with a need to harmonize variables researchers often look for guidance from various international studies that employ output harmonization, such as the Comparative Survey of Election Studies, which offer recoding structures for the same variable (e.g. marital status). More problematically there are no agreed documentation standards or journal requirements for reporting variable harmonization to facilitate a transparent replication process. We propose a conceptual and data-driven digital solution that creates harmonization documentation standards for publication and scholarly citation: QuickCharmStats 1.1. It is free and open-source software that allows for the organizing, documenting and publishing of data harmonization projects. QuickCharmStats starts at the conceptual level and its workflow ends with a variable recording syntax. It is therefore flexible enough to reflect a variety of theoretical justifications for variable harmonization. Using the socio-demographic variable ‘marital status’, we demonstrate how the CharmStats workflow collates metadata while being guided by the scientific standards of transparency and replication. It encourages researchers to publish their harmonization work by providing researchers who complete the peer review process a permanent identifier. Those who contribute original data harmonization work to their discipline can now be credited through citations. Finally, we propose peer-review standards for harmonization documentation, describe a route to online publishing, and provide a referencing format to cite harmonization projects. Although CharmStats products are designed for social scientists our adherence to the scientific method ensures our products can be used by researchers across the sciences. PMID:26859494

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

Zhang, Hailong; Vibration Control Lab, School of Electrical and Automation Engineering, Nanjing Normal University, Nanjing 210042; Zhang, Ning

Magneto-rheological (MR) damper possesses inherent hysteretic characteristics. We investigate the resulting nonlinear behaviors of a two degree-of-freedom (2-DoF) MR vibration isolation system under harmonic external excitation. A MR damper is identified by employing the modified Bouc-wen hysteresis model. By numerical simulation, we characterize the nonlinear dynamic evolution of period-doubling, saddle node bifurcating and inverse period-doubling using bifurcation diagrams of variations in frequency with a fixed amplitude of the harmonic excitation. The strength of chaos is determined by the Lyapunov exponent (LE) spectrum. Semi-physical experiment on the 2-DoF MR vibration isolation system is proposed. We trace the time history and phasemore » trajectory under certain values of frequency of the harmonic excitation to verify the nonlinear dynamical evolution of period-doubling bifurcations to chaos. The largest LEs computed with the experimental data are also presented, confirming the chaotic motion in the experiment. We validate the chaotic motion caused by the hysteresis of the MR damper, and show the transitions between distinct regimes of stable motion and chaotic motion of the 2-DoF MR vibration isolation system for variations in frequency of external excitation.« less

Numerical Simulation of MIG for 42 GHz, 200 kW Gyrotron

NASA Astrophysics Data System (ADS)

Singh, Udaybir; Bera, Anirban; Kumar, Narendra; Purohit, L. P.; Sinha, Ashok K.

2010-06-01

A triode type magnetron injection gun (MIG) of a 42 GHz, 200 kW gyrotron for an Indian TOKAMAK system is designed by using the commercially available code EGUN. The operating voltages of the modulating anode and the accelerating anode are 29 kV and 65 kV respectively. The operating mode of the gyrotron is TE03 and it is operated in fundamental harmonic. The simulated results of MIG obtained with the EGUN code are validated with another trajectory code TRAK.

Comparison of computer codes for calculating dynamic loads in wind turbines

NASA Technical Reports Server (NTRS)

Spera, D. A.

1977-01-01

Seven computer codes for analyzing performance and loads in large, horizontal axis wind turbines were used to calculate blade bending moment loads for two operational conditions of the 100 kW Mod-0 wind turbine. Results were compared with test data on the basis of cyclic loads, peak loads, and harmonic contents. Four of the seven codes include rotor-tower interaction and three were limited to rotor analysis. With a few exceptions, all calculated loads were within 25 percent of nominal test data.

Comparison of mechanisms involved in image enhancement of Tissue Harmonic Imaging

NASA Astrophysics Data System (ADS)

Cleveland, Robin O.; Jing, Yuan

2006-05-01

Processes that have been suggested as responsible for the improved imaging in Tissue Harmonic Imaging (THI) include: 1) reduced sensitivity to reverberation, 2) reduced sensitivity to aberration, and 3) reduction in the amplitude of diffraction side lobes. A three-dimensional model of the forward propagation of nonlinear sound beams in media with arbitrary spatial properties (a generalized KZK equation) was developed and solved using a time-domain code. The numerical simulations were validated through experiments with tissue mimicking phantoms. The impact of aberration from tissue-like media was determined through simulations using three-dimensional maps of tissue properties derived from datasets available through the Visible Female Project. The experiments and simulations demonstrated that second harmonic imaging suffers less clutter from reverberation and side-lobes but is not immune to aberration effects. The results indicate that side lobe suppression is the most significant reason for the improvement of second harmonic imaging.

Harmonic analysis and suppression in hybrid wind & PV solar system

NASA Astrophysics Data System (ADS)

Gupta, Tripti; Namekar, Swapnil

2018-04-01

The growing demand of electricity has led to produce power through non-conventional source of energy such as solar energy, wind energy, hydro power, energy through biogas and biomass etc. Hybrid system is taken to complement the shortcoming of either sources of energy. The proposed system is grid connected hybrid wind and solar system. A 2.1 MW Doubly fed Induction Generator (DFIG) has been taken for analysis of wind farm whose rotor part is connected to two back-to-back converters. A 250 KW Photovoltaic (PV) array taken to analyze solar farm where inverter is required to convert power from DC to AC since electricity generated through solar PV is in the form of DC. Stability and reliability of the system is very important when the system is grid connected. Harmonics is the major Power quality issue which degrades the quality of power at load side. Harmonics in hybrid system arise through the use of power conversion unit. The other causes of harmonics are fluctuation in wind speed and solar irradiance. The power delivered to grid must be free from harmonics and within the limits specified by Indian grid codes. In proposed work, harmonic analysis of the hybrid system is performed in Electrical Transient Analysis program (ETAP) and single tuned harmonic filter is designed to maintain the utility grid harmonics within limits.

Modal method for Second Harmonic Generation in nanostructures

NASA Astrophysics Data System (ADS)

Héron, S.; Pardo, F.; Bouchon, P.; Pelouard, J.-L.; Haïdar, R.

2015-05-01

Nanophotonic devices show interesting features for nonlinear response enhancement but numerical tools are mandatory to fully determine their behaviour. To address this need, we present a numerical modal method dedicated to nonlinear optics calculations under the undepleted pump approximation. It is brie y explained in the frame of Second Harmonic Generation for both plane waves and focused beams. The nonlinear behaviour of selected nanostructures is then investigated to show comparison with existing analytical results and study the convergence of the code.

Numerical simulation of transonic compressor under circumferential inlet distortion and rotor/stator interference using harmonic balance method

NASA Astrophysics Data System (ADS)

Wang, Ziwei; Jiang, Xiong; Chen, Ti; Hao, Yan; Qiu, Min

2018-05-01

Simulating the unsteady flow of compressor under circumferential inlet distortion and rotor/stator interference would need full-annulus grid with a dual time method. This process is time consuming and needs a large amount of computational resources. Harmonic balance method simulates the unsteady flow in compressor on single passage grid with a series of steady simulations. This will largely increase the computational efficiency in comparison with the dual time method. However, most simulations with harmonic balance method are conducted on the flow under either circumferential inlet distortion or rotor/stator interference. Based on an in-house CFD code, the harmonic balance method is applied in the simulation of flow in the NASA Stage 35 under both circumferential inlet distortion and rotor/stator interference. As the unsteady flow is influenced by two different unsteady disturbances, it leads to the computational instability. The instability can be avoided by coupling the harmonic balance method with an optimizing algorithm. The computational result of harmonic balance method is compared with the result of full-annulus simulation. It denotes that, the harmonic balance method simulates the flow under circumferential inlet distortion and rotor/stator interference as precise as the full-annulus simulation with a speed-up of about 8 times.

Simulations and model of the nonlinear Richtmyer–Meshkov instability

DOE PAGES

Dimonte, Guy; Ramaprabhu, P.

2010-01-21

The nonlinear evolution of the Richtmyer-Meshkov (RM) instability is investigated using numerical simulations with the FLASH code in two-dimensions (2D). The purpose of the simulations is to develop an empiricial nonlinear model of the RM instability that is applicable to inertial confinement fusion (ICF) and ejecta formation, namely, at large Atwood number A and scaled initial amplitude kh o (k ≡ wavenumber) of the perturbation. The FLASH code is first validated with a variety of RM experiments that evolve well into the nonlinear regime. They reveal that bubbles stagnate when they grow by an increment of 2/k and that spikesmore » accelerate for A > 0.5 due to higher harmonics that focus them. These results are then compared with a variety of nonlinear models that are based on potential flow. We find that the models agree with simulations for moderate values of A < 0.9 and kh o< 1, but not for the larger values that characterize ICF and ejecta formation. We thus develop a new nonlinear empirical model that captures the simulation results consistent with potential flow for a broader range of A and kh o. Our hope is that such empirical models concisely capture the RM simulations and inspire more rigorous solutions.« less

Physics of tissue harmonic imaging by ultrasound

NASA Astrophysics Data System (ADS)

Jing, Yuan

Tissue Harmonic Imaging (THI) is an imaging modality that is currently deployed on diagnostic ultrasound scanners. In THI the amplitude of the ultrasonic pulse that is used to probe the tissue is large enough that the pulse undergoes nonlinear distortion as it propagates into the tissue. One result of the distortion is that as the pulse propagates energy is shifted from the fundamental frequency of the source pulse into its higher harmonics. These harmonics will scatter off objects in the tissue and images formed from the scattered higher harmonics are considered to have superior quality to the images formed from the fundamental frequency. Processes that have been suggested as possibly responsible for the improved imaging in THI include: (1) reduced sensitivity to reverberation, (2) reduced sensitivity to aberration, and (3) reduction in side lobes. By using a combination of controlled experiments and numerical simulations, these three reasons have been investigated. A single element transducer and a clinical ultrasound scanner with a phased array transducer were used to image a commercial tissue-mimicking phantom with calibrated targets. The higher image quality achieved with THI was quantified in terms of spatial resolution and "clutter" signals. A three-dimensional model of the forward propagation of nonlinear sound beams in media with arbitrary spatial properties (a generalized KZK equation) was developed. A time-domain code for solving the KZK equation was validated with measurements of the acoustic field generated by the single element transducer and the phased array transducer. The code was used to investigate the impact of aberration using tissue-like media with three-dimensional variations in all acoustic properties. The three-dimensional maps of tissue properties were derived from the datasets available through the Visible Female project. The experiments and simulations demonstrated that second harmonic imaging (1) suffers less clutter associated with reverberation; (2) is not immune to aberration effects and (3) suffers less clutter due to reduced side-lobe levels. The results indicate that side lobe suppression is the most significant reason for the improvement of second harmonic imaging.

Eolian Modeling System: Predicting Windblown Dust Hazards in Battlefield Environments

DTIC Science & Technology

2011-05-03

journals (N/A for none) Pelletier, J.D., H. Mitasova, R.S. Harmon, and M. Overton, The effects of interdune vegetation changes on eolian dune field...J.D., Controls on the height and spacing of eolian ripples and transverse dunes : A numerical modeling investigation, Geomorphology, 105, 322-333, 2009...R.S. Harmon, and M. Overton, The effects of interdune vegetation changes on eolian dune field evolution: A numerical-modeling case study at Jockey’s

Simulation of Alfvén eigenmode bursts using a hybrid code for nonlinear magnetohydrodynamics and energetic particles

NASA Astrophysics Data System (ADS)

Todo, Y.; Berk, H. L.; Breizman, B. N.

2012-03-01

A hybrid simulation code for nonlinear magnetohydrodynamics (MHD) and energetic-particle dynamics has been extended to simulate recurrent bursts of Alfvén eigenmodes by implementing the energetic-particle source, collisions and losses. The Alfvén eigenmode bursts with synchronization of multiple modes and beam ion losses at each burst are successfully simulated with nonlinear MHD effects for the physics condition similar to a reduced simulation for a TFTR experiment (Wong et al 1991 Phys. Rev. Lett. 66 1874, Todo et al 2003 Phys. Plasmas 10 2888). It is demonstrated with a comparison between nonlinear MHD and linear MHD simulation results that the nonlinear MHD effects significantly reduce both the saturation amplitude of the Alfvén eigenmodes and the beam ion losses. Two types of time evolution are found depending on the MHD dissipation coefficients, namely viscosity, resistivity and diffusivity. The Alfvén eigenmode bursts take place for higher dissipation coefficients with roughly 10% drop in stored beam energy and the maximum amplitude of the dominant magnetic fluctuation harmonic δBm/n/B ~ 5 × 10-3 at the mode peak location inside the plasma. Quadratic dependence of beam ion loss rate on magnetic fluctuation amplitude is found for the bursting evolution in the nonlinear MHD simulation. For lower dissipation coefficients, the amplitude of the Alfvén eigenmodes is at steady levels δBm/n/B ~ 2 × 10-3 and the beam ion losses take place continuously. The beam ion pressure profiles are similar among the different dissipation coefficients, and the stored beam energy is higher for higher dissipation coefficients.

Frequency-domain algorithm for the Lorenz-gauge gravitational self-force

NASA Astrophysics Data System (ADS)

Akcay, Sarp; Warburton, Niels; Barack, Leor

2013-11-01

State-of-the-art computations of the gravitational self-force (GSF) on massive particles in black hole spacetimes involve numerical evolution of the metric perturbation equations in the time domain, which is computationally very costly. We present here a new strategy based on a frequency-domain treatment of the perturbation equations, which offers considerable computational saving. The essential ingredients of our method are (i) a Fourier-harmonic decomposition of the Lorenz-gauge metric perturbation equations and a numerical solution of the resulting coupled set of ordinary equations with suitable boundary conditions; (ii) a generalized version of the method of extended homogeneous solutions [L. Barack, A. Ori, and N. Sago, Phys. Rev. D 78, 084021 (2008)] used to circumvent the Gibbs phenomenon that would otherwise hamper the convergence of the Fourier mode sum at the particle’s location; (iii) standard mode-sum regularization, which finally yields the physical GSF as a sum over regularized modal contributions. We present a working code that implements this strategy to calculate the Lorenz-gauge GSF along eccentric geodesic orbits around a Schwarzschild black hole. The code is far more efficient than existing time-domain methods; the gain in computation speed (at a given precision) is about an order of magnitude at an eccentricity of 0.2, and up to 3 orders of magnitude for circular or nearly circular orbits. This increased efficiency was crucial in enabling the recently reported calculation of the long-term orbital evolution of an extreme mass ratio inspiral [N. Warburton, S. Akcay, L. Barack, J. R. Gair, and N. Sago, Phys. Rev. D 85, 061501(R) (2012)]. Here we provide full technical details of our method to complement the above report.

Axisymmetric modes of rotating relativistic stars in the Cowling approximation

NASA Astrophysics Data System (ADS)

Font, José A.; Dimmelmeier, Harald; Gupta, Anshu; Stergioulas, Nikolaos

2001-08-01

Axisymmetric pulsations of rotating neutron stars can be excited in several scenarios, such as core collapse, crust- and core-quakes or binary mergers, and could become detectable in either gravitational waves or high-energy radiation. Here, we present a comprehensive study of all low-order axisymmetric modes of uniformly and rapidly rotating relativistic stars. Initial stationary configurations are appropriately perturbed and are numerically evolved using an axisymmetric, non-linear relativistic hydrodynamics code, assuming time-independence of the gravitational field (Cowling approximation). The simulations are performed using a high-resolution shock-capturing finite-difference scheme accurate enough to maintain the initial rotation law for a large number of rotational periods, even for stars at the mass-shedding limit. Through Fourier transforms of the time evolution of selected fluid variables, we compute the frequencies of quasi-radial and non-radial modes with spherical harmonic indices l=0, 1, 2 and 3, for a sequence of rotating stars from the non-rotating limit to the mass-shedding limit. The frequencies of the axisymmetric modes are affected significantly by rotation only when the rotation rate exceeds about 50 per cent of the maximum allowed. As expected, at large rotation rates, apparent mode crossings between different modes appear. In addition to the above modes, several axisymmetric inertial modes are also excited in our numerical evolutions.

IUTAM Symposium on Statistical Energy Analysis, 8-11 July 1997, Programme

DTIC Science & Technology

1997-01-01

distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (Maximum200 words) This was the first international scientific gathering devoted...energy flow, continuum dynamics, vibrational energy, statistical energy analysis (SEA) 15. NUMBER OF PAGES 16. PRICE CODE INSECURITY... correlation v=V(ɘ ’• • determination of the correlation n^, =11^, (<?). When harmonic motion and time-average are considered, the following I

Coupled 2-dimensional cascade theory for noise and unsteady aerodynamics of blade row interaction in turbofans. Volume 1: Theory development and parametric studies

NASA Technical Reports Server (NTRS)

Hanson, Donald B.

1994-01-01

Typical analytical models for interaction between rotor and stator in a turbofan analyze the effect of wakes from the rotor impinging on the stator, producing unsteady loading, and thereby generating noise. Reflection/transmission characteristics of the rotor are sometimes added in a separate calculation. In those models, there is a one-to-one relationship between wake harmonics and noise harmonics; that is, the BPF (blade passing frequency) wake harmonic causes only the BPF noise harmonic, etc. This report presents a more complete model in which flow tangency boundary conditions are satisfied on two cascades in relative motion for several harmonics simultaneously. By an extension of S.N. Smith's code for two dimensional flat plate cascades, the noise generation/frequency scattering/blade row reflection problem is solved in a single matrix inversion. It is found that the BPF harmonic excitation of the stator scatters considerable energy in the higher BPF harmonics due to relative motion between the blade rows. Furthermore, when swirl between the rotor and stator is modeled, a 'mode trapping' effect occurs which explains observations on fans operating at rotational speeds below BFP cuton: the BPF mode amplifies between blade rows by multiple reflections but cannot escape to the inlet and exit ducts. However, energy scattered into higher harmonics does propagate and dominates the spectrum at two and three times BPF. This report presents the complete derivation of the theory, comparison with a previous (more limited) coupled rotor/stator interaction theory due to Kaji and Okazaki, exploration of the mode trapping phenomenon, and parametric studies showing the effects of vane/blade ratio and rotor/stator interaction. For generality, the analysis applies to stages where the rotor is either upstream or downstream of the stator and to counter rotation stages. The theory has been coded in a FORTRAN program called CUP2D, documented in Volume 2 of this report. It is concluded that the new features of this analysis - unsteady coupling, frequency scattering, and flow turning between rotor and stator - have a profound effect on noise generation caused by rotor/stator interaction. Treating rotors and stators as isolated cascades is not adequate for noise analysis and prediction.

Lack of harmonization in sweat testing for cystic fibrosis - a national survey.

PubMed

Christiansen, Anne Lindegaard; Nybo, Mads

2014-11-01

Sweat testing is used in the diagnosis of cystic fibrosis. Interpretation of the sweat test depends, however, on the method performed since conductivity, osmolality and chloride concentration all can be measured as part of a sweat test. The aim of this study was to investigate how performance of the test is organized in Denmark. Departments conducting the sweat test were contacted and interviewed following a premade questionnaire. They were asked about methods performed, applied NPU (Nomenclature for Properties and Units) code, reference interval, recommended interpretation and referred literature. 14 departments performed the sweat test. One department measured chloride and sodium concentration, while 13 departments measured conductivity. One department used a non-existing NPU code, two departments applied NPU codes inconsistent with the method performed, four departments applied no NPU code and seven applied a correct NPU code. Ten of the departments measuring conductivity applied reference intervals. Nine departments measuring conductivity had recommendations of a normal area, a grey zone and a pathological value, while four departments only applied a normal and grey zone or a pathological value. Cut-off values for normal, grey and pathological areas were like the reference intervals inconsistent. There is inconsistent use of NPU codes, reference intervals and interpretation of sweat conductivity used in the process of diagnosing cystic fibrosis. Because diagnosing cystic fibrosis is a combined effort between local pediatric departments, biochemical and genetic departments and cystic fibrosis centers, a national harmonization is necessary to assure correct clinical use.

Design and simulation of a ~390 GHz seventh harmonic gyrotron using a large orbit electron beam

NASA Astrophysics Data System (ADS)

Li, Fengping; He, Wenlong; Cross, Adrian W.; Donaldson, Craig R.; Zhang, Liang; Phelps, Alan D. R.; Ronald, Kevin

2010-04-01

A ~390 GHz harmonic gyrotron based on a cusp electron gun has been designed and numerically modelled. The gyrotron operates at the seventh harmonic of the electron cyclotron frequency with the beam interacting with a TE71 waveguide mode. Theoretical as well as numerical simulation results using the 3D particle-in-cell code MAGIC are presented. The cusp gun generated an axis-encircling, annular shaped electron beam of energy 40 keV, current 1.5 A with a velocity ratio α of 3. Smooth cylindrical waveguides have been studied as the interaction cavities and their cavity Q optimized for 390 GHz operation. In the simulations ~600 W of output power at the design frequency has been demonstrated.

International variation in the definition of 'main condition' in ICD-coded health data.

PubMed

Quan, H; Moskal, L; Forster, A J; Brien, S; Walker, R; Romano, P S; Sundararajan, V; Burnand, B; Henriksson, G; Steinum, O; Droesler, S; Pincus, H A; Ghali, W A

2014-10-01

Hospital-based medical records are abstracted to create International Classification of Disease (ICD) coded discharge health data in many countries. The 'main condition' is not defined in a consistent manner internationally. Some countries employ a 'reason for admission' rule as the basis for the main condition, while other countries employ a 'resource use' rule. A few countries have recently transitioned from one of these approaches to the other. The definition of 'main condition' in such ICD data matters when it is used to define a disease cohort to assign diagnosis-related groups and to perform risk adjustment. We propose a method of harmonizing the international definition to enable researchers and international organizations using ICD-coded health data to aggregate or compare hospital care and outcomes across countries in a consistent manner. Inter-observer reliability of alternative harmonization approaches should be evaluated before finalizing the definition and adopting it worldwide. © The Author 2014. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

CoCoNuT: General relativistic hydrodynamics code with dynamical space-time evolution

NASA Astrophysics Data System (ADS)

Dimmelmeier, Harald; Novak, Jérôme; Cerdá-Durán, Pablo

2012-02-01

CoCoNuT is a general relativistic hydrodynamics code with dynamical space-time evolution. The main aim of this numerical code is the study of several astrophysical scenarios in which general relativity can play an important role, namely the collapse of rapidly rotating stellar cores and the evolution of isolated neutron stars. The code has two flavors: CoCoA, the axisymmetric (2D) magnetized version, and CoCoNuT, the 3D non-magnetized version.

Wide-band doubler and sine wave quadrature generator

NASA Technical Reports Server (NTRS)

Crow, R. B.

1969-01-01

Phase-locked loop with photoresistive control, which provides both sine and cosine outputs for subcarrier demodulation, serves as a telemetry demodulator signal conditioner with a second harmonic signal for synchronization with the locally generated code.

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Simulation of Vortex Structure in Supersonic Free Shear Layer Using Pse Method

NASA Astrophysics Data System (ADS)

Guo, Xin; Wang, Qiang

The method of parabolized stability equations (PSE) are applied in the analysis of nonlinear stability and the simulation of flow structure in supersonic free shear layer. High accuracy numerical techniques including self-similar basic flow, high order differential method, appropriate transformation and decomposition of nonlinear terms are adopted and developed to solve the PSE effectively for free shear layer. The spatial evolving unstable waves which dominate the flow structure are investigated through nonlinear coupling spatial marching methods. The nonlinear interactions between harmonic waves are further analyzed and instantaneous flow field are obtained by adding the harmonic waves into basic flow. Relevant data agree well with that of DNS. The results demonstrate that T-S wave does not keeping growing exponential as the linear evolution, the energy transfer to high order harmonic modes and finally all harmonic modes get saturation due to the nonlinear interaction; Mean flow distortion is produced by the nonlinear interaction between the harmonic and its conjugate harmonic, makes great change to the average flow and increases the thickness of shear layer; PSE methods can well capture the large scale nonlinear flow structure in the supersonic free shear layer such as vortex roll-up, vortex pairing and nonlinear saturation.

78 FR 49412 - Personal Flotation Devices Labeling and Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-14

...The Coast Guard proposes to remove references to type codes in its regulations on the carriage and labeling of Coast Guard-approved personal flotation devices (PFDs). PFD type codes are unique to Coast Guard approval and are not well understood by the public. Removing these type codes from our regulations would facilitate future incorporation by reference of new industry consensus standards for PFD labeling that will more effectively convey safety information, and is a step toward harmonization of our regulations with PFD requirements in Canada and in other countries.

Some simple solutions of Schrödinger's equation for a free particle or for an oscillator

NASA Astrophysics Data System (ADS)

Andrews, Mark

2018-05-01

For a non-relativistic free particle, we show that the evolution of some simple initial wave functions made up of linear segments can be expressed in terms of Fresnel integrals. Examples include the square wave function and the triangular wave function. The method is then extended to wave functions made from quadratic elements. The evolution of all these initial wave functions can also be found for the harmonic oscillator by a transformation of the free evolutions.

Simulation of nonlinear propagation of biomedical ultrasound using pzflex and the Khokhlov-Zabolotskaya-Kuznetsov Texas code

PubMed Central

Qiao, Shan; Jackson, Edward; Coussios, Constantin C.; Cleveland, Robin O.

2016-01-01

Nonlinear acoustics plays an important role in both diagnostic and therapeutic applications of biomedical ultrasound and a number of research and commercial software packages are available. In this manuscript, predictions of two solvers available in a commercial software package, pzflex, one using the finite-element-method (FEM) and the other a pseudo-spectral method, spectralflex, are compared with measurements and the Khokhlov-Zabolotskaya-Kuznetsov (KZK) Texas code (a finite-difference time-domain algorithm). The pzflex methods solve the continuity equation, momentum equation and equation of state where they account for nonlinearity to second order whereas the KZK code solves a nonlinear wave equation with a paraxial approximation for diffraction. Measurements of the field from a single element 3.3 MHz focused transducer were compared with the simulations and there was good agreement for the fundamental frequency and the harmonics; however the FEM pzflex solver incurred a high computational cost to achieve equivalent accuracy. In addition, pzflex results exhibited non-physical oscillations in the spatial distribution of harmonics when the amplitudes were relatively low. It was found that spectralflex was able to accurately capture the nonlinear fields at reasonable computational cost. These results emphasize the need to benchmark nonlinear simulations before using codes as predictive tools. PMID:27914432

Simulation of nonlinear propagation of biomedical ultrasound using pzflex and the Khokhlov-Zabolotskaya-Kuznetsov Texas code.

PubMed

Qiao, Shan; Jackson, Edward; Coussios, Constantin C; Cleveland, Robin O

2016-09-01

Nonlinear acoustics plays an important role in both diagnostic and therapeutic applications of biomedical ultrasound and a number of research and commercial software packages are available. In this manuscript, predictions of two solvers available in a commercial software package, pzflex, one using the finite-element-method (FEM) and the other a pseudo-spectral method, spectralflex, are compared with measurements and the Khokhlov-Zabolotskaya-Kuznetsov (KZK) Texas code (a finite-difference time-domain algorithm). The pzflex methods solve the continuity equation, momentum equation and equation of state where they account for nonlinearity to second order whereas the KZK code solves a nonlinear wave equation with a paraxial approximation for diffraction. Measurements of the field from a single element 3.3 MHz focused transducer were compared with the simulations and there was good agreement for the fundamental frequency and the harmonics; however the FEM pzflex solver incurred a high computational cost to achieve equivalent accuracy. In addition, pzflex results exhibited non-physical oscillations in the spatial distribution of harmonics when the amplitudes were relatively low. It was found that spectralflex was able to accurately capture the nonlinear fields at reasonable computational cost. These results emphasize the need to benchmark nonlinear simulations before using codes as predictive tools.

Non-linear hydrodynamical evolution of rotating relativistic stars: numerical methods and code tests

NASA Astrophysics Data System (ADS)

Font, José A.; Stergioulas, Nikolaos; Kokkotas, Kostas D.

2000-04-01

We present numerical hydrodynamical evolutions of rapidly rotating relativistic stars, using an axisymmetric, non-linear relativistic hydrodynamics code. We use four different high-resolution shock-capturing (HRSC) finite-difference schemes (based on approximate Riemann solvers) and compare their accuracy in preserving uniformly rotating stationary initial configurations in long-term evolutions. Among these four schemes, we find that the third-order piecewise parabolic method scheme is superior in maintaining the initial rotation law in long-term evolutions, especially near the surface of the star. It is further shown that HRSC schemes are suitable for the evolution of perturbed neutron stars and for the accurate identification (via Fourier transforms) of normal modes of oscillation. This is demonstrated for radial and quadrupolar pulsations in the non-rotating limit, where we find good agreement with frequencies obtained with a linear perturbation code. The code can be used for studying small-amplitude or non-linear pulsations of differentially rotating neutron stars, while our present results serve as testbed computations for three-dimensional general-relativistic evolution codes.

Evolution of the heteroharmonic strategy for target-range computation in the echolocation of Mormoopidae

PubMed Central

Mora, Emanuel C.; Macías, Silvio; Hechavarría, Julio; Vater, Marianne; Kössl, Manfred

2013-01-01

Echolocating bats use the time elapsed from biosonar pulse emission to the arrival of echo (defined as echo-delay) to assess target-distance. Target-distance is represented in the brain by delay-tuned neurons that are classified as either “heteroharmonic” or “homoharmormic.” Heteroharmonic neurons respond more strongly to pulse-echo pairs in which the timing of the pulse is given by the fundamental biosonar harmonic while the timing of echoes is provided by one (or several) of the higher order harmonics. On the other hand, homoharmonic neurons are tuned to the echo delay between similar harmonics in the emitted pulse and echo. It is generally accepted that heteroharmonic computations are advantageous over homoharmonic computations; i.e., heteroharmonic neurons receive information from call and echo in different frequency-bands which helps to avoid jamming between pulse and echo signals. Heteroharmonic neurons have been found in two species of the family Mormoopidae (Pteronotus parnellii and Pteronotus quadridens) and in Rhinolophus rouxi. Recently, it was proposed that heteroharmonic target-range computations are a primitive feature of the genus Pteronotus that was preserved in the evolution of the genus. Here, we review recent findings on the evolution of echolocation in Mormoopidae, and try to link those findings to the evolution of the heteroharmonic computation strategy (HtHCS). We stress the hypothesis that the ability to perform heteroharmonic computations evolved separately from the ability of using long constant-frequency echolocation calls, high duty cycle echolocation, and Doppler Shift Compensation. Also, we present the idea that heteroharmonic computations might have been of advantage for categorizing prey size, hunting eared insects, and living in large conspecific colonies. We make five testable predictions that might help future investigations to clarify the evolution of the heteroharmonic echolocation in Mormoopidae and other families. PMID:23781209

Monitoring microstructural evolution of alloy 617 with non-linear acoustics for remaining useful life prediction; multiaxial creep-fatigue and creep-ratcheting

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

Lissenden, Cliff; Hassan, Tasnin; Rangari, Vijaya

The research built upon a prior investigation to develop a unified constitutive model for design-­by-­analysis of the intermediate heat exchanger (IHX) for a very high temperature reactor (VHTR) design of next generation nuclear plants (NGNPs). Model development requires a set of failure data from complex mechanical experiments to characterize the material behavior. Therefore uniaxial and multiaxial creep-­fatigue and creep-­ratcheting tests were conducted on the nickel-­base Alloy 617 at 850 and 950°C. The time dependence of material behavior, and the interaction of time dependent behavior (e.g., creep) with ratcheting, which is an increase in the cyclic mean strain under load-­controlled cycling,more » are major concerns for NGNP design. This research project aimed at characterizing the microstructure evolution mechanisms activated in Alloy 617 by mechanical loading and dwell times at elevated temperature. The acoustic harmonic generation method was researched for microstructural characterization. It is a nonlinear acoustics method with excellent potential for nondestructive evaluation, and even online continuous monitoring once high temperature sensors become available. It is unique because it has the ability to quantitatively characterize microstructural features well before macroscale defects (e.g., cracks) form. The nonlinear acoustics beta parameter was shown to correlate with microstructural evolution using a systematic approach to handle the complexity of multiaxial creep-­fatigue and creep-­ratcheting deformation. Mechanical testing was conducted to provide a full spectrum of data for: thermal aging, tensile creep, uniaxial fatigue, uniaxial creep-­fatigue, uniaxial creep-ratcheting, multiaxial creep-fatigue, and multiaxial creep-­ratcheting. Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), and Optical Microscopy were conducted to correlate the beta parameter with individual microstructure mechanisms. We researched application of the harmonic generation method to tubular mechanical test specimens and pipes for nondestructive evaluation. Tubular specimens and pipes act as waveguides, thus we applied the acoustic harmonic generation method to guided waves in both plates and shells. Magnetostrictive transducers were used to generate and receive guided wave modes in the shell sample and the received signals were processed to show the sensitivity of higher harmonic generation to microstructure evolution. Modeling was initiated to correlate higher harmonic generation with the microstructure that will lead to development of a life prediction model that is informed by the nonlinear acoustics measurements.« less

Analysis of rotor vibratory loads using higher harmonic pitch control

NASA Technical Reports Server (NTRS)

Quackenbush, Todd R.; Bliss, Donald B.; Boschitsch, Alexander H.; Wachspress, Daniel A.

1992-01-01

Experimental studies of isolated rotors in forward flight have indicated that higher harmonic pitch control can reduce rotor noise. These tests also show that such pitch inputs can generate substantial vibratory loads. The modification is summarized of the RotorCRAFT (Computation of Rotor Aerodynamics in Forward flighT) analysis of isolated rotors to study the vibratory loading generated by high frequency pitch inputs. The original RotorCRAFT code was developed for use in the computation of such loading, and uses a highly refined rotor wake model to facilitate this task. The extended version of RotorCRAFT incorporates a variety of new features including: arbitrary periodic root pitch control; computation of blade stresses and hub loads; improved modeling of near wake unsteady effects; and preliminary implementation of a coupled prediction of rotor airloads and noise. Correlation studies are carried out with existing blade stress and vibratory hub load data to assess the performance of the extended code.

Conical Euler solution for a highly-swept delta wing undergoing wing-rock motion

NASA Technical Reports Server (NTRS)

Lee, Elizabeth M.; Batina, John T.

1990-01-01

Modifications to an unsteady conical Euler code for the free-to-roll analysis of highly-swept delta wings are described. The modifications involve the addition of the rolling rigid-body equation of motion for its simultaneous time-integration with the governing flow equations. The flow solver utilized in the Euler code includes a multistage Runge-Kutta time-stepping scheme which uses a finite-volume spatial discretization on an unstructured mesh made up of triangles. Steady and unsteady results are presented for a 75 deg swept delta wing at a freestream Mach number of 1.2 and an angle of attack of 30 deg. The unsteady results consist of forced harmonic and free-to-roll calculations. The free-to-roll case exhibits a wing rock response produced by unsteady aerodynamics consistent with the aerodynamics of the forced harmonic results. Similarities are shown with a wing-rock time history from a low-speed wind tunnel test.

Calculation of the Transition Matrix for the Scattering of Acoustic Waves from a Thin Elastic Spherical Shell Using the ATILA Finite Element Code

DTIC Science & Technology

1994-03-01

products of radial Hankel functions and spherical harmonics. The chosen driving frequency was 474 Hz, corresponding to a value of ka 1, where k is the...spherical harmonics. The chosen driving frequency was 474 Hz, corresponding to a value of ka = 1, where k is the wavenumber of sound in water and a is...wife Adriana for her support, understanding, and for her help in typing this thesis. vi I. INTRODUCTION The utilization of sonar systems in

Density- and wavefunction-normalized Cartesian spherical harmonics for l ≤ 20

DOE PAGES

Michael, J. Robert; Volkov, Anatoliy

2015-03-01

The widely used pseudoatom formalism in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of aspherical deformations of the atomic electron density in molecules and crystals. The analytical form of the density-normalized Cartesian spherical harmonic functions for up to l ≤ 7 and the corresponding normalization coefficients were reported previously by Paturle & Coppens. It was shown that the analytical form for normalization coefficients is available primarily forl ≤ 4. Only in very special cases it is possible to derive an analytical representation of the normalization coefficients for 4 < l ≤ 7.more » In most cases for l > 4 the density normalization coefficients were calculated numerically to within seven significant figures. In this study we review the literature on the density-normalized spherical harmonics, clarify the existing notations, use the Paturle–Coppens method in the Wolfram Mathematicasoftware to derive the Cartesian spherical harmonics for l ≤ 20 and determine the density normalization coefficients to 35 significant figures, and computer-generate a Fortran90 code. The article primarily targets researchers who work in the field of experimental X-ray electron density, but may be of some use to all who are interested in Cartesian spherical harmonics.« less

Theoretical study of a dual harmonic system and its application to the CSNS/RCS

NASA Astrophysics Data System (ADS)

Yuan, Yao-Shuo; Wang, Na; Xu, Shou-Yan; Yuan, Yue; Wang, Sheng

2015-12-01

Dual harmonic systems have been widely used in high intensity proton synchrotrons to suppress the space charge effect, as well as reduce the beam loss. To investigate the longitudinal beam dynamics in a dual rf system, the potential well, the sub-buckets in the bunch and the multi-solutions of the phase equation are studied theoretically in this paper. Based on these theoretical studies, optimization of bunching factor and rf voltage waveform are made for the dual harmonic rf system in the upgrade phase of the China Spallation Neutron Source Rapid Cycling Synchrotron (CSNS/RCS). In the optimization process, the simulation with space charge effect is done using a newly developed code, C-SCSIM. Supported by National Natural Science Foundation of China (11175193)

Fenestration system energy performance research, implementation, and international harmonization

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

McGowan, Raymond F

The research conducted by the NFRC and its contractors adds significantly to the understanding of several areas of investigation. NFRC enables manufacturers to rate fenestration energy performance to comply with building energy codes, participate in ENERGY STAR, and compete fairly. NFRC continuously seeks to improve its ratings and also seeks to simplify the rating process. Several research projects investigated rating improvement potential such as • Complex Product VT Rating Research • Window 6 and Therm 6 Validation Research Project • Complex Product VT Rating Research Conclusions from these research projects led to important changes and increased confidence in the existingmore » NFRC rating process. Conclusions from the Window 6/Therm 6 project will enable window manufacturers to rate an expanded array of products and improve existing ratings. Some research lead to an improved new rating method called the Component Modeling Approach. A primary goal of the CMA was a simplification of the commercial energy rating process to increase participation and make the commercial industry more competitive and code compliant. The project below contributed towards CMA development: • Component Modeling Approach Condensation Resistance Research NFRC continues to implement the Component Modeling Approach program. The program includes the CMA software tool, CMAST, and several procedural documents to govern the certification process. This significant accomplishment was a response the commercial fenestration industry’s need for a simplification of the present NFRC energy rating method (named site built). To date, most commercial fenestration is self-rated by a variety of techniques. The CMA enables commercial fenestration manufacturers to rate according to the NFRC 100/200 as most commercial energy codes require. International Harmonization NFRC achieved significant international harmonization success by continuing its licensing agreements with the Australian Fenestration Rating Council and the Association of Architectural Aluminum Manufacturers of South Africa (AAAMSA) to produce NFRC certified product ratings in their respective nations. NFRC worked in several other nations to introduce the NFRC ratings system: • India • China • Japan • Canada • Thailand • South Africa • Brazil • Korea NFRC attended or hosted several meetings in each of these nations establishing academic, commercial, industrial, and governmental contacts. NFRC presented the NFRC process and then necessary infrastructure steps necessary to achieve harmonization with the NFRC labeling system. NFRC looks forward to continued work toward harmonization in these nations and potentially others.« less

Designs and numerical calculations for echo-enabled harmonic generation at very high harmonics

NASA Astrophysics Data System (ADS)

Penn, G.; Reinsch, M.

2011-09-01

The echo-enabled harmonic generation (EEHG) scheme for driving an FEL using two seeded energy modulations at much longer wavelengths than the output wavelength is a promising concept for future seeded FELs. There are many competing requirements in the design of an EEHG beamline which need careful optimization. Furthermore, revised simulation tools and methods are necessary because of both the high harmonic numbers simulated and the complicated nature of the phase space manipulations which are intrinsic to the scheme. This paper explores the constraints on performance and the required tolerances for reaching wavelengths well below 1/100th of that of the seed lasers, and describes some of the methodology for designing such a beamline. Numerical tools, developed both for the GENESIS and GINGER FEL codes, are presented and used here for more accurate study of the scheme beyond a time-averaged model. In particular, the impact of the local structure in peak current and bunching, which is an inherent part of the EEHG scheme, is evaluated.

U.S. exports and imports transshipped via Canadian ports 1993

DOT National Transportation Integrated Search

1994-01-01

This report summarizes U.S. cargo which moved via Canada in 1993. Summaries are : provided showing transshipped cargo through Canada, in historical perspective, : by customs district, by country and by leading Harmonized 4-digit commodity code. Appen...

Automated UMLS-Based Comparison of Medical Forms

PubMed Central

Dugas, Martin; Fritz, Fleur; Krumm, Rainer; Breil, Bernhard

2013-01-01

Medical forms are very heterogeneous: on a European scale there are thousands of data items in several hundred different systems. To enable data exchange for clinical care and research purposes there is a need to develop interoperable documentation systems with harmonized forms for data capture. A prerequisite in this harmonization process is comparison of forms. So far – to our knowledge – an automated method for comparison of medical forms is not available. A form contains a list of data items with corresponding medical concepts. An automatic comparison needs data types, item names and especially item with these unique concept codes from medical terminologies. The scope of the proposed method is a comparison of these items by comparing their concept codes (coded in UMLS). Each data item is represented by item name, concept code and value domain. Two items are called identical, if item name, concept code and value domain are the same. Two items are called matching, if only concept code and value domain are the same. Two items are called similar, if their concept codes are the same, but the value domains are different. Based on these definitions an open-source implementation for automated comparison of medical forms in ODM format with UMLS-based semantic annotations was developed. It is available as package compareODM from http://cran.r-project.org. To evaluate this method, it was applied to a set of 7 real medical forms with 285 data items from a large public ODM repository with forms for different medical purposes (research, quality management, routine care). Comparison results were visualized with grid images and dendrograms. Automated comparison of semantically annotated medical forms is feasible. Dendrograms allow a view on clustered similar forms. The approach is scalable for a large set of real medical forms. PMID:23861827

Fast Scattering Code (FSC) User's Manual: Version 2

NASA Technical Reports Server (NTRS)

Tinetti, Ana F.; Dun, M. H.; Pope, D. Stuart

2006-01-01

The Fast Scattering Code (version 2.0) is a computer program for predicting the three-dimensional scattered acoustic field produced by the interaction of known, time-harmonic, incident sound with aerostructures in the presence of potential background flow. The FSC has been developed for use as an aeroacoustic analysis tool for assessing global effects on noise radiation and scattering caused by changes in configuration (geometry, component placement) and operating conditions (background flow, excitation frequency).

Possibilities for the evolution of the genetic code from a preceding form

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1973-01-01

Analysis of the interaction between mRNA codons and tRNA anticodons suggests a model for the evolution of the genetic code. Modification of the nucleic acid following the anticodon is at present essential in both eukaryotes and prokaryotes to ensure fidelity of translation of codons starting with A, and the amino acids which could be coded for before the evolution of the modifying enzymes can be deduced.

Characteristic Evolution and Matching

NASA Astrophysics Data System (ADS)

Winicour, Jeffrey

2012-01-01

I review the development of numerical evolution codes for general relativity based upon the characteristic initial-value problem. Progress in characteristic evolution is traced from the early stage of 1D feasibility studies to 2D-axisymmetric codes that accurately simulate the oscillations and gravitational collapse of relativistic stars and to current 3D codes that provide pieces of a binary black-hole spacetime. Cauchy codes have now been successful at simulating all aspects of the binary black-hole problem inside an artificially constructed outer boundary. A prime application of characteristic evolution is to extend such simulations to null infinity where the waveform from the binary inspiral and merger can be unambiguously computed. This has now been accomplished by Cauchy-characteristic extraction, where data for the characteristic evolution is supplied by Cauchy data on an extraction worldtube inside the artificial outer boundary. The ultimate application of characteristic evolution is to eliminate the role of this outer boundary by constructing a global solution via Cauchy-characteristic matching. Progress in this direction is discussed.

Using AORSA to simulate helicon waves in DIIID and ITER

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

Lau, Cornwall H; Jaeger, E. F.; Berry, Lee Alan

2014-01-01

Recent efforts by Vdovin [1] and Prater [2] have shown that helicon waves (fast waves at ~30 ion cyclotron frequency harmonic) may be an attractive option for driving efficient off-axis current drive during non-inductive tokamak operation for DIIID, ITER and DEMO. For DIIID scenarios, the ray tracing code GENRAY has been extensively used to study helicon current drive efficiency and location as a function many plasma parameters. has some limitations on absorption at high cyclotron harmonics, so the full wave code AORSA, which is applicable to arbitrary Larmor radius and can therefore resolve high ion cyclotron harmonics, has been recentlymore » used to validate the GENRAY model. It will be shown that the GENRAY and AORSA driven current drive profiles are comparable for the envisioned high temperature and density advanced scenarios for DIIID, where there is high single pass absorption due to electron Landau damping. AORSA results will be shown for various plasma parameters for DIIID and for ITER. Computational difficulties in achieving these AORSA results will also be discussed. * Work supported by USDOE Contract No. DE-AC05-00OR22725 [1] V. L. Vdovin, Plasma Physics Reports, V.39, No.2, 2013 [2] R. Prater et al, Nucl. Fusion, 52, 083024, 2014« less

Calculation of four-particle harmonic-oscillator transformation brackets

NASA Astrophysics Data System (ADS)

Germanas, D.; Kalinauskas, R. K.; Mickevičius, S.

2010-02-01

A procedure for precise calculation of the three- and four-particle harmonic-oscillator (HO) transformation brackets is presented. The analytical expressions of the four-particle HO transformation brackets are given. The computer code for the calculations of HO transformation brackets proves to be quick, efficient and produces results with small numerical uncertainties. Program summaryProgram title: HOTB Catalogue identifier: AEFQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1247 No. of bytes in distributed program, including test data, etc.: 6659 Distribution format: tar.gz Programming language: FORTRAN 90 Computer: Any computer with FORTRAN 90 compiler Operating system: Windows, Linux, FreeBSD, True64 Unix RAM: 8 MB Classification: 17.17 Nature of problem: Calculation of the three-particle and four-particle harmonic-oscillator transformation brackets. Solution method: The method is based on compact expressions of the three-particle harmonics oscillator brackets, presented in [1] and expressions of the four-particle harmonics oscillator brackets, presented in this paper. Restrictions: The three- and four-particle harmonic-oscillator transformation brackets up to the e=28. Unusual features: Possibility of calculating the four-particle harmonic-oscillator transformation brackets. Running time: Less than one second for the single harmonic-oscillator transformation bracket. References:G.P. Kamuntavičius, R.K. Kalinauskas, B.R. Barret, S. Mickevičius, D. Germanas, Nuclear Physics A 695 (2001) 191.

Suppression and nonlinear excitation of parasitic modes in second harmonic gyrotrons operating in a very high order mode

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

Nusinovich, Gregory S.; Pu, Ruifeng; Granatstein, Victor L.

2015-07-06

In recent years, there was an active development of high-power, sub-terahertz (sub-THz) gyrotrons for numerous applications. For example, a 0.67 THz gyrotron delivering more than 200 kW with about 20% efficiency was developed. This record high efficiency was achieved because the gyrotron operated in a high-order TE{sub 31,8}-mode with the power of ohmic losses less than 10% of the power of outgoing radiation. That gyrotron operated at the fundamental cyclotron resonance, and a high magnetic field of about 27 T was created by a pulse solenoid. For numerous applications, it is beneficial to use gyrotrons at cyclotron harmonics which can operate inmore » available cryomagnets with fields not exceeding 15 T. However, typically, the gyrotron operation at harmonics faces severe competition from parasitic modes at the fundamental resonance. In the present paper, we consider a similar 0.67 THz gyrotron designed for operation in the same TE{sub 31,8}-mode, but at the second harmonic. We focus on two nonlinear effects typical for interaction between the fundamental and second harmonic modes, viz., the mode suppression and the nonlinear excitation of the mode at the fundamental harmonic by the second harmonic oscillations. Our study includes both the analytical theory and numerical simulations performed with the self-consistent code MAGY. The simulations show that stable second harmonic operation in the TE{sub 31,8} mode is possible with only modest sacrifice of efficiency and power.« less

Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

PubMed

Santos, José; Monteagudo, Ángel

2017-03-27

The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.

Harmonic plasma waves excitation and structure evolution of intense ion beams in background plasmas

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

Hu, Zhang-Hu, E-mail: zhanghu@dlut.edu.cn; Wang, You-Nian

2016-08-15

The long-term dynamic evolutions of intense ion beams in plasmas have been investigated with two-dimensional electromagnetic particle simulations, taking into account the effect of the two-stream instability between beam ions and plasma electrons. Depending on the initial beam radial density profile and velocity distribution, ring structures may be formed in the beam edge regions. At the later stage of beam-plasma interactions, the ion beams are strongly modulated by the two-stream instability and multiple density spikes are formed in the longitudinal direction. The formation of these density spikes is shown to result from the excitation of harmonic plasma waves when themore » instability gets saturated. Comparisons between the beam cases with initial flat-top and Gaussian radial density profiles are made, and a higher instability growth rate is observed for the flat-top profile case.« less

Numerical Study of HHFW Heating in FRC Plasmas

NASA Astrophysics Data System (ADS)

Ceccherini, Francesco; Galeotti, Laura; Brambilla, Marco; Dettrick, Sean; Yang, Xiaokang; TAE Team

2017-10-01

The TriAlpha Energy (TAE) code RF-Pisa is a Finite Larmor Radius (FLR) full wave code developed over the years to study RF heating in the Field Reversed Configuration (FRC) in both the ion and electron cyclotron regimes. The FLR approximation is perfectly adequate to address RF propagation and absorption at the fundamental and second harmonic frequencies (as in the minority heating scheme), but it is not able to describe higher order processes such as high-harmonic fast waves (HHFW). The latter ones have frequencies lying between the ion cyclotron and lower hybrid resonances and they may represent a viable path to develop an efficient method to deposit energy inside the FRC separatrix, as suggested by recent results obtained at NSTX. A significant upgrade of RF-Pisa to include HHFW has been undertaken. In particular, the so-called ``quasi local approximation'' originally proposed for toroidal geometries has been re-derived for the cylindrical geometry and a new HHFW version of RF-Pisa concurrent to the FLR version has been developed. Here we present the first results of the application of the new code to FRC equilibria and we discuss the features of the dispersion relations and the absorption processes which characterize this novel regime.

Phenotypic Graphs and Evolution Unfold the Standard Genetic Code as the Optimal

NASA Astrophysics Data System (ADS)

Zamudio, Gabriel S.; José, Marco V.

2018-03-01

In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions.

Modeling TAE Response To Nonlinear Drives

NASA Astrophysics Data System (ADS)

Zhang, Bo; Berk, Herbert; Breizman, Boris; Zheng, Linjin

2012-10-01

Experiment has detected the Toroidal Alfven Eigenmodes (TAE) with signals at twice the eigenfrequency.These harmonic modes arise from the second order perturbation in amplitude of the MHD equation for the linear modes that are driven the energetic particle free energy. The structure of TAE in realistic geometry can be calculated by generalizing the linear numerical solver (AEGIS package). We have have inserted all the nonlinear MHD source terms, where are quadratic in the linear amplitudes, into AEGIS code. We then invert the linear MHD equation at the second harmonic frequency. The ratio of amplitudes of the first and second harmonic terms are used to determine the internal field amplitude. The spatial structure of energy and density distribution are investigated. The results can be directly employed to compare with experiments and determine the Alfven wave amplitude in the plasma region.

Global Harmonization of Maximum Residue Limits for Pesticides.

PubMed

Ambrus, Árpád; Yang, Yong Zhen

2016-01-13

International trade plays an important role in national economics. The Codex Alimentarius Commission develops harmonized international food standards, guidelines, and codes of practice to protect the health of consumers and to ensure fair practices in the food trade. The Codex maximum residue limits (MRLs) elaborated by the Codex Committee on Pesticide Residues are based on the recommendations of the FAO/WHO Joint Meeting on Pesticides (JMPR). The basic principles applied currently by the JMPR for the evaluation of experimental data and related information are described together with some of the areas in which further developments are needed.

77 FR 49167 - Hazardous Materials: Harmonization with International Standards (RRR)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-15

...PHMSA proposes to amend the Hazardous Materials Regulations to maintain alignment with international standards by incorporating various amendments, including changes to proper shipping names, hazard classes, packing groups, special provisions, packaging authorizations, air transport quantity limitations, and vessel stowage requirements. These revisions are necessary to harmonize the Hazardous Materials Regulations with recent changes made to the International Maritime Dangerous Goods Code, the International Civil Aviation Organization's Technical Instructions for the Safe Transport of Dangerous Goods by Air, and the United Nations Recommendations on the Transport of Dangerous Goods--Model Regulations and subsequently address a petition for rulemaking.

Understanding and predicting the dynamics of tokamak discharges during startup and rampdown

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

Jackson, G. L.; Politzer, P. A.; Humphreys, D. A.

Understanding the dynamics of plasma startup and termination is important for present tokamaks and for predictive modeling of future burning plasma devices such as ITER. We report on experiments in the DIII-D tokamak that explore the plasma startup and rampdown phases and on the benchmarking of transport models. Key issues have been examined such as plasma initiation and burnthrough with limited inductive voltage and achieving flattop and maximum burn within the technical limits of coil systems and their actuators while maintaining the desired q profile. Successful rampdown requires scenarios consistent with technical limits, including controlled H-L transitions, while avoiding verticalmore » instabilities, additional Ohmic transformer flux consumption, and density limit disruptions. Discharges were typically initiated with an inductive electric field typical of ITER, 0.3 V/m, most with second harmonic electron cyclotron assist. A fast framing camera was used during breakdown and burnthrough of low Z impurity charge states to study the formation physics. An improved 'large aperture' ITER startup scenario was developed, and aperture reduction in rampdown was found to be essential to avoid instabilities. Current evolution using neoclassical conductivity in the CORSICA code agrees with rampup experiments, but the prediction of the temperature and internal inductance evolution using the Coppi-Tang model for electron energy transport is not yet accurate enough to allow extrapolation to future devices.« less

Study regarding the density evolution of messages and the characteristic functions associated of a LDPC code

NASA Astrophysics Data System (ADS)

Drăghici, S.; Proştean, O.; Răduca, E.; Haţiegan, C.; Hălălae, I.; Pădureanu, I.; Nedeloni, M.; (Barboni Haţiegan, L.

2017-01-01

In this paper a method with which a set of characteristic functions are associated to a LDPC code is shown and also functions that represent the evolution density of messages that go along the edges of a Tanner graph. Graphic representations of the density evolution are shown respectively the study and simulation of likelihood threshold that render asymptotic boundaries between which there are decodable codes were made using MathCad V14 software.

3D unstructured-mesh radiation transport codes

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

Morel, J.

1997-12-31

Three unstructured-mesh radiation transport codes are currently being developed at Los Alamos National Laboratory. The first code is ATTILA, which uses an unstructured tetrahedral mesh in conjunction with standard Sn (discrete-ordinates) angular discretization, standard multigroup energy discretization, and linear-discontinuous spatial differencing. ATTILA solves the standard first-order form of the transport equation using source iteration in conjunction with diffusion-synthetic acceleration of the within-group source iterations. DANTE is designed to run primarily on workstations. The second code is DANTE, which uses a hybrid finite-element mesh consisting of arbitrary combinations of hexahedra, wedges, pyramids, and tetrahedra. DANTE solves several second-order self-adjoint forms of the transport equation including the even-parity equation, the odd-parity equation, and a new equation called the self-adjoint angular flux equation. DANTE also offers three angular discretization options:more » $$S{_}n$$ (discrete-ordinates), $$P{_}n$$ (spherical harmonics), and $$SP{_}n$$ (simplified spherical harmonics). DANTE is designed to run primarily on massively parallel message-passing machines, such as the ASCI-Blue machines at LANL and LLNL. The third code is PERICLES, which uses the same hybrid finite-element mesh as DANTE, but solves the standard first-order form of the transport equation rather than a second-order self-adjoint form. DANTE uses a standard $$S{_}n$$ discretization in angle in conjunction with trilinear-discontinuous spatial differencing, and diffusion-synthetic acceleration of the within-group source iterations. PERICLES was initially designed to run on workstations, but a version for massively parallel message-passing machines will be built. The three codes will be described in detail and computational results will be presented.« less

Evolution of a dark soliton in a parabolic potential: Application to Bose-Einstein condensates

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

Brazhnyi, V.A.; Konotop, V.V.

2003-10-01

Evolution of a dark soliton in a one-dimensional Bose-Einstein condensate trapped by a harmonic potential is studied analytically and numerically. In the case of a deep soliton, main characteristics of its motion such as frequency and amplitude of oscillations are calculated by means of the perturbation theory which in the leading order results in a Newtonian dynamics, corrections to which are computed as well.

Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.

PubMed

Ruan, Jiangxing; Cheng, Jian; Zhang, Tongcun; Jiang, Huifeng

2017-01-01

Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.

Using AORSA to simulate helicon waves in DIII-D

NASA Astrophysics Data System (ADS)

Lau, C.; Jaeger, E. F.; Bertelli, N.; Berry, L. A.; Blazevski, D.; Green, D. L.; Murakami, M.; Park, J. M.; Pinsker, R. I.; Prater, R.

2015-12-01

Recent efforts have shown that helicon waves (fast waves at > 20ωci) may be an attractive option for driving efficient off-axis current drive during non-inductive tokamak operation for DIII-D, ITER and DEMO. For DIII-D scenarios, the ray tracing code, GENRAY, has been extensively used to study helicon current drive efficiency and location as a function of many plasma parameters. The full wave code, AORSA, which is applicable to arbitrary Larmor radius and can resolve arbitrary ion cyclotron harmonic order, has been recently used to validate the ray tracing technique at these high cyclotron harmonics. If the SOL is ignored, it will be shown that the GENRAY and AORSA calculated current drive profiles are comparable for the envisioned high beta advanced scenarios for DIII-D, where there is high single pass absorption due to electron Landau damping and minimal ion damping. AORSA is also been used to estimate possible SOL effects on helicon current drive coupling and SOL absorption due to collisional and slow wave effects.

Congenital amusia: a cognitive disorder limited to resolved harmonics and with no peripheral basis.

PubMed

Cousineau, Marion; Oxenham, Andrew J; Peretz, Isabelle

2015-01-01

Pitch plays a fundamental role in audition, from speech and music perception to auditory scene analysis. Congenital amusia is a neurogenetic disorder that appears to affect primarily pitch and melody perception. Pitch is normally conveyed by the spectro-temporal fine structure of low harmonics, but some pitch information is available in the temporal envelope produced by the interactions of higher harmonics. Using 10 amusic subjects and 10 matched controls, we tested the hypothesis that amusics suffer exclusively from impaired processing of spectro-temporal fine structure. We also tested whether the inability of amusics to process acoustic temporal fine structure extends beyond pitch by measuring sensitivity to interaural time differences, which also rely on temporal fine structure. Further tests were carried out on basic intensity and spectral resolution. As expected, pitch perception based on spectro-temporal fine structure was impaired in amusics; however, no significant deficits were observed in amusics' ability to perceive the pitch conveyed via temporal-envelope cues. Sensitivity to interaural time differences was also not significantly different between the amusic and control groups, ruling out deficits in the peripheral coding of temporal fine structure. Finally, no significant differences in intensity or spectral resolution were found between the amusic and control groups. The results demonstrate a pitch-specific deficit in fine spectro-temporal information processing in amusia that seems unrelated to temporal or spectral coding in the auditory periphery. These results are consistent with the view that there are distinct mechanisms dedicated to processing resolved and unresolved harmonics in the general population, the former being altered in congenital amusia while the latter is spared. Copyright © 2014 Elsevier Ltd. All rights reserved.

Shuttle Global Positioning System (GPS) system design study

NASA Technical Reports Server (NTRS)

Nilsen, P. W.

1979-01-01

The various integration problems in the Shuttle GPS system were investigated. The analysis of the Shuttle GPS link was studied. A preamplifier was designed since the Shuttle GPS antennas must be located remotely from the receiver. Several GPS receiver architecture trade-offs were discussed. The Shuttle RF harmonics and intermode that fall within the GPS receiver bandwidth were analyzed. The GPS PN code acquisition was examined. Since the receiver clock strongly affects both GPS carrier and code acquisition performance, a clock model was developed.

Analytic Reflected Lightcurves for Exoplanets

NASA Astrophysics Data System (ADS)

Haggard, Hal M.; Cowan, Nicolas B.

2018-04-01

The disk-integrated reflected brightness of an exoplanet changes as a function of time due to orbital and rotational motion coupled with an inhomogeneous albedo map. We have previously derived analytic reflected lightcurves for spherical harmonic albedo maps in the special case of a synchronously-rotating planet on an edge-on orbit (Cowan, Fuentes & Haggard 2013). In this letter, we present analytic reflected lightcurves for the general case of a planet on an inclined orbit, with arbitrary spin period and non-zero obliquity. We do so for two different albedo basis maps: bright points (δ-maps), and spherical harmonics (Y_l^m-maps). In particular, we use Wigner D-matrices to express an harmonic lightcurve for an arbitrary viewing geometry as a non-linear combination of harmonic lightcurves for the simpler edge-on, synchronously rotating geometry. These solutions will enable future exploration of the degeneracies and information content of reflected lightcurves, as well as fast calculation of lightcurves for mapping exoplanets based on time-resolved photometry. To these ends we make available Exoplanet Analytic Reflected Lightcurves (EARL), a simple open-source code that allows rapid computation of reflected lightcurves.

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

Yang, X. H.; Fu, J. N.; Zha, Q., E-mail: jnfu@bnu.edu.cn

Time-series photometric observations were made for the SX Phoenicis star XX Cyg between 2007 and 2011 at the Xinglong Station of National Astronomical Observatories of China. With the light curves derived from the new observations, we do not detect any secondary maximum in the descending portion of the light curves of XX Cyg, as reported in some previous work. Frequency analysis of the light curves confirms a fundamental frequency f{sub 0} = 7.4148 cycles day{sup -1} and up to 19 harmonics, 11 of which are newly detected. However, no secondary mode of pulsation is detected from the light curves. Themore » O-C diagram, produced from 46 newly determined times of maximum light combined with those derived from the literature, reveals a continuous period increase with the rate of (1/P)(dP/dt) = 1.19(13) Multiplication-Sign 10{sup -8} yr{sup -1}. Theoretical rates of period change due to the stellar evolution were calculated with a modeling code. The result shows that the observed rate of period change is fully consistent with period change caused by evolutionary behavior predicted by standard theoretical models.« less

Self-Channelling of a Short Laser Pulse at Relativistic Intensity in Near Critical Underdense Plasma

NASA Astrophysics Data System (ADS)

Willi, O.; Borghesi, M.; MacKinnon, A. J.; Barringer, L.; Gaillard, R.; Meyer, C.; Gizzi, L.; Pukhov, A.; Meyer-Ter-Vehn, J.

1996-11-01

Self channelling of a picosecond pulse at relativistic intensities has been observed in near critical underdense plasmas. The plasma was preformed by laser heating of a thin film. The interaction pulse (1-3 ps duration, 1.054 μm) was focused onto the plasma at irradiances above 5 × 10^18 W/cm^2. Self-channelling of the pulse was detected via second harmonic and optical probe measurements. Intense, localised 2ω emission suggests the formation of channel structures of less than 5 μm in diameter, extending for several Rayleigh lengths. The temporal evolution of the electron density profile across the channel was measured via interferometry with picosecond temporal resolution. PIC code simulations, performed for the conditions of the experiment, predict the formation of similar channel structures. In this model, in addition to relativistic and ponderomotive self-focusing mechanisms, pinching by large self-generated magnetic fields also contributes to the single channel formation. Measurements of magnetic fields were also performed that seem to be consistent with the computational model.

The influence of a local wall deformation on the development of natural instabilities in a laminar boundary layer

NASA Technical Reports Server (NTRS)

Burnel, S.; Gougat, P.; Martin, F.

1981-01-01

The natural instabilities which propagate in the laminar boundary layer of a flat plate composed of intermittent wave trains are described. A spectral analysis determines the frequency range and gives a frequency and the harmonic 2 only if there is a wall deformation. This analysis provides the amplitude modulation spectrum of the instabilities. Plots of the evolution of power spectral density are compared with the numerical results obtained from the resolve of the Orr-Sommerfeld equation, while the harmonic is related to a micro-recirculating flow near the wall deformation.

Nonlinear wave vacillation in the atmosphere

NASA Technical Reports Server (NTRS)

Antar, Basil N.

1987-01-01

The problem of vacillation in a baroclinically unstable flow field is studied through the time evolution of a single nonlinearly unstable wave. To this end a computer code is being developed to solve numerically for the time evolution of the amplitude of such a wave. The final working code will be the end product resulting from the development of a heirarchy of codes with increasing complexity. The first code in this series was completed and is undergoing several diagnostic analyses to verify its validity. The development of this code is detailed.

Algorithm for loading shot noise microbunching in multi-dimensional, free-electron laser simulation codes

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

Fawley, William M.

We discuss the underlying reasoning behind and the details of the numerical algorithm used in the GINGER free-electron laser(FEL) simulation code to load the initial shot noise microbunching on the electron beam. In particular, we point out that there are some additional subtleties which must be followed for multi-dimensional codes which are not necessary for one-dimensional formulations. Moreover, requiring that the higher harmonics of the microbunching also be properly initialized with the correct statistics leads to additional complexities. We present some numerical results including the predicted incoherent, spontaneous emission as tests of the shot noise algorithm's correctness.

Harmonic cascade FEL designs for LUX

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

Penn, G.; Reinsch, M.; Wurtele, J.

LUX is a design concept for an ultrafast X-ray science facility, based on an electron beam accelerated to GeV energies in are circulating linac. Included in the design are short duration (200 fs or shorter FWHM) light sources using multiple stages of higher harmonic generation, seeded by a 200-250 nm laser of similar duration. This laser modulates the energy of a group of electrons within the electron bunch; this section of the electron bunch then produces radiation at a higher harmonic after entering a second, differently tuned undulator. Repeated stages in a cascade yield increasing photon energies up to 1more » keV. Most of the undulators in the cascade operate in the low-gain FEL regime. Harmonic cascades have been designed for each pass of the recirculating linac up to a final electron beam energy of 3.1 GeV. For a given cascade, the photon energy can be selected over a wide range by varying the seed laser frequency and the field strength in the undulators. We present simulation results using the codes GENESIS and GINGER, as well as the results of analytical models which predict FEL performance. We discuss lattice considerations pertinent for harmonic cascade FELs, as well as sensitivity studies and requirements on the electron beam.« less

The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs.

PubMed

Ning, Qianqian; Li, Yixue; Wang, Zhen; Zhou, Songwen; Sun, Hong; Yu, Guangjun

2017-03-27

Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.

Studying the laws of software evolution in a long-lived FLOSS project.

PubMed

Gonzalez-Barahona, Jesus M; Robles, Gregorio; Herraiz, Israel; Ortega, Felipe

2014-07-01

Some free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case. © 2013 The Authors. Journal of Software: Evolution and Process published by John Wiley & Sons Ltd.

Studying the laws of software evolution in a long-lived FLOSS project

PubMed Central

Gonzalez-Barahona, Jesus M; Robles, Gregorio; Herraiz, Israel; Ortega, Felipe

2014-01-01

Some free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case. © 2013 The Authors. Journal of Software: Evolution and Process published by John Wiley & Sons Ltd. PMID:25893093

31 CFR 592.307 - Kimberley Process Certificate.

Code of Federal Regulations, 2010 CFR

2010-07-01

...- and forgery-resistant document that bears the following information in any language, provided that an... shipment; (k) Relevant Harmonized Commodity Description and Coding System; and (l) Validation by the exporting authority. Note to paragraph (l): See § 592.301(a)(4) for procedures governing the validation of...

ASTM and ASME-BPE Standards--Complying with the Needs of the Pharmaceutical Industry.

PubMed

Huitt, William M

2011-01-01

Designing and building a pharmaceutical facility requires the owner, engineer of record, and constructor to be knowledgeable with regard to the industry codes and standards that apply to this effort. Up until 1997 there were no industry standards directed at the needs and requirements of the pharmaceutical industry. Prior to that time it was a patchwork effort at resourcing and adopting nonpharmaceutical-related codes and standards and then modifying them in order to meet the more stringent requirements of the Food and Drug Administration (FDA). In 1997 the American Society of Mechanical Engineers (ASME) published the first Bioprocessing Equipment (BPE) Standard. Through harmonization efforts this relatively new standard has brought together, scrutinized, and refined industry accepted methodologies together with FDA compliance requirements, and has established an American National Standard that provides a comprehensive set of standards that are integral to the pharmaceutical industry. This article describes various American National Standards, including those developed and published by the American Society for Testing and Materials (ASTM), and how they apply to the pharmaceutical industry. It goes on to discuss the harmonization effort that takes place between the various standards developers in an attempt to prevent conflicts and omissions between the many standards. Also included are examples of tables and figures taken from the ASME-BPE Standard. These examples provide the reader with insight to the relevant content of the ASME-BPE Standard. Designing and building a pharmaceutical facility requires the owner, engineer of record, and constructor to be knowledgeable with regard to the industry codes and standards that apply to this effort. Up until 1997 there were no industry standards directed at the needs and requirements of the pharmaceutical industry. Prior to that time it was a patchwork effort at resourcing and adopting nonpharmaceutical-related codes and standards and then modifying them in order to meet the more stringent requirements of the Food and Drug Administration (FDA). In 1997 the American Society of Mechanical Engineers (ASME) published the first Bioprocessing Equipment (BPE) Standard. In its initial development and ongoing maintenance it works with other American National Standards developers to harmonize the many standards associated with the design, engineering, and construction of bioprocessing facilities. This harmonization effort has established a comprehensive set of standards for the betterment of the pharmaceutical industry at large. This effort is, and will remain, very important as technology, along with new and improved product and processes, evolve into the future.

Physical Model for the Evolution of the Genetic Code

NASA Astrophysics Data System (ADS)

Yamashita, Tatsuro; Narikiyo, Osamu

2011-12-01

Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.

Mass change from GRACE: a simulated comparison of Level-1B analysis techniques

NASA Astrophysics Data System (ADS)

Andrews, Stuart B.; Moore, Philip; King, Matt. A.

2015-01-01

Spherical harmonic and mascon parameters have both been successfully applied in the recovery of time-varying gravity fields from Gravity Recovery and Climate Experiment (GRACE). However, direct comparison of any mass flux is difficult with solutions generated by different groups using different codes and algorithms. It is therefore opportune to compare these methodologies, within a common software base, to understand potential limitations associated with each technique. Here we use simulations to recover a known monthly surface mass distribution from GRACE KBRR data. The ability of spherical harmonic and mascon parameters to resolve basin-level mass change is quantified with an assessment of how the noise and errors, inherent in GRACE solutions, are handled. Recovery of a noise and error free GLDAS anomaly revealed no quantifiable difference between spherical harmonic and mascon parameters. Expansion of the GLDAS anomaly to degree and order 120 shows that both spherical harmonic and mascon parameters are affected by comparable omission errors. However, the inclusion of realistic KBRR noise and errors in the simulations reveals the advantage of the mascon parameters over spherical harmonics at reducing noise and errors in the higher degree and order harmonics with an rms (cm of EWH) to the GLDAS anomaly of 10.0 for the spherical harmonic solution and 8.8 (8.6) for the 4°(2°) mascon solutions. The introduction of a constraint matrix in the mascon solution based on parameters that share geophysical similarities is shown to further reduce the signal lost at all degrees. The recovery of a simulated Antarctic mass loss signal shows that the mascon methodology is superior to spherical harmonics for this region with an rms (cm of EWH) of 8.7 for the 2° mascon solution compared to 10.0 for the spherical harmonic solution. Investigating the noise and errors for a month when the satellites were in resonance revealed both the spherical harmonic and mascon methodologies are able to recover the GLDAS and Antarctic mass loss signal with either a comparable (spherical harmonic) or improved (mascon) rms compared to non-resonance periods.

The Evolution of a Coding Schema in a Paced Program of Research

ERIC Educational Resources Information Center

Winters, Charlene A.; Cudney, Shirley; Sullivan, Therese

2010-01-01

A major task involved in the management, analysis, and integration of qualitative data is the development of a coding schema to facilitate the analytic process. Described in this paper is the evolution of a coding schema that was used in the analysis of qualitative data generated from online forums of middle-aged women with chronic conditions who…

GENERIC Integrators: Structure Preserving Time Integration for Thermodynamic Systems

NASA Astrophysics Data System (ADS)

Öttinger, Hans Christian

2018-04-01

Thermodynamically admissible evolution equations for non-equilibrium systems are known to possess a distinct mathematical structure. Within the GENERIC (general equation for the non-equilibrium reversible-irreversible coupling) framework of non-equilibrium thermodynamics, which is based on continuous time evolution, we investigate the possibility of preserving all the structural elements in time-discretized equations. Our approach, which follows Moser's [1] construction of symplectic integrators for Hamiltonian systems, is illustrated for the damped harmonic oscillator. Alternative approaches are sketched.

Direct Simulation of Evolution and Control of Three-Dimensional Instabilities in Attachment-Line Boundary Layers

NASA Technical Reports Server (NTRS)

Joslin, Ronald D.

1995-01-01

The spatial evolution of three-dimensional disturbances in an attachment-line boundary layer is computed by direct numerical simulation of the unsteady, incompressible Navier-Stokes equations. Disturbances are introduced into the boundary layer by harmonic sources that involve unsteady suction and blowing through the wall. Various harmonic- source generators are implemented on or near the attachment line, and the disturbance evolutions are compared. Previous two-dimensional simulation results and nonparallel theory are compared with the present results. The three-dimensional simulation results for disturbances with quasi-two-dimensional features indicate growth rates of only a few percent larger than pure two-dimensional results; however, the results are close enough to enable the use of the more computationally efficient, two-dimensional approach. However, true three-dimensional disturbances are more likely in practice and are more stable than two-dimensional disturbances. Disturbances generated off (but near) the attachment line spread both away from and toward the attachment line as they evolve. The evolution pattern is comparable to wave packets in at-plate boundary-layer flows. Suction stabilizes the quasi-two-dimensional attachment-line instabilities, and blowing destabilizes these instabilities; these results qualitatively agree with the theory. Furthermore, suction stabilizes the disturbances that develop off the attachment line. Clearly, disturbances that are generated near the attachment line can supply energy to attachment-line instabilities, but suction can be used to stabilize these instabilities.

78 FR 987 - Hazardous Materials: Harmonization with International Standards (RRR)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-07

...PHMSA is amending the Hazardous Materials Regulations to maintain alignment with international standards by incorporating various amendments, including changes to proper shipping names, hazard classes, packing groups, special provisions, packaging authorizations, air transport quantity limitations, and vessel stowage requirements. These revisions are necessary to harmonize the Hazardous Materials Regulations (HMR) with recent changes made to the International Maritime Dangerous Goods (IMDG) Code, the International Civil Aviation Organization's Technical Instructions for the Safe Transport of Dangerous Goods by Air (ICAO Technical Instructions), and the United Nations Recommendations on the Transport of Dangerous Goods--Model Regulations (UN Model Regulations) and address a petition for rulemaking.

The Evolution of the Phase Lags Associated with the Type-C Quasi-periodic Oscillation in GX 339–4 during the 2006/2007 Outburst

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

Zhang, Liang; Chen, Li; Wang, Yanan

2017-08-20

We present the evolution of the phase lags associated with the type-C QPO in GX 339–4 during the rising phase of the 2006/2007 outburst. We find that the phase lags at the QPO frequency are always positive (hard) and show very different behavior between QPOs with frequencies below and above ∼1.7 Hz: when the QPO frequency is below ∼1.7 Hz, the phase lags increase both with QPO frequency and energy, while when the QPO frequency is above ∼1.7 Hz, the phase lags remain more or less constant. When the QPO frequency is higher than ∼1.7 Hz, a broad feature ismore » always present in the lag–energy spectra at around 6.5 keV, suggesting that the reflection component may have a significant contribution to the phase lags. Below ∼1.7 Hz, the QPO rms first decreases with energy and then turns to almost flat, while above ∼1.7 Hz, the QPO rms increases with energy. During the transition from the low-hard state to the hard-intermediate state, the second harmonic and subharmonic of this QPO appear in the power density spectra. The second-harmonic and subharmonic phase lags show very similar evolutions for their centroid frequencies. However, the energy dependence of the second-harmonic and subharmonic phase lags are quite different. Our results suggest that, at different phases of the outburst, different mechanisms may be responsible for the phase lags of the QPO. We briefly discuss the possible scenarios for producing the lags.« less

The Evolution of the Phase Lags Associated with the Type-C Quasi-periodic Oscillation in GX 339-4 during the 2006/2007 Outburst

NASA Astrophysics Data System (ADS)

Zhang, Liang; Wang, Yanan; Méndez, Mariano; Chen, Li; Qu, Jinlu; Altamirano, Diego; Belloni, Tomaso

2017-08-01

We present the evolution of the phase lags associated with the type-C QPO in GX 339-4 during the rising phase of the 2006/2007 outburst. We find that the phase lags at the QPO frequency are always positive (hard) and show very different behavior between QPOs with frequencies below and above ˜1.7 Hz: when the QPO frequency is below ˜1.7 Hz, the phase lags increase both with QPO frequency and energy, while when the QPO frequency is above ˜1.7 Hz, the phase lags remain more or less constant. When the QPO frequency is higher than ˜1.7 Hz, a broad feature is always present in the lag-energy spectra at around 6.5 keV, suggesting that the reflection component may have a significant contribution to the phase lags. Below ˜1.7 Hz, the QPO rms first decreases with energy and then turns to almost flat, while above ˜1.7 Hz, the QPO rms increases with energy. During the transition from the low-hard state to the hard-intermediate state, the second harmonic and subharmonic of this QPO appear in the power density spectra. The second-harmonic and subharmonic phase lags show very similar evolutions for their centroid frequencies. However, the energy dependence of the second-harmonic and subharmonic phase lags are quite different. Our results suggest that, at different phases of the outburst, different mechanisms may be responsible for the phase lags of the QPO. We briefly discuss the possible scenarios for producing the lags.

Ultrafast Plasmonic Control of Second Harmonic Generation

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

Davidson, Roderick B.; Yanchenko, Anna; Ziegler, Jed I.

Efficient frequency conversion techniques are crucial to the development of plasmonic metasurfaces for information processing and signal modulation. In principle, nanoscale electric-field confinement in nonlinear materials enables higher harmonic conversion efficiencies per unit volume than those attainable in bulk materials. Here we demonstrate efficient second-harmonic generation (SHG) in a serrated nanogap plasmonic geometry that generates steep electric field gradients on a dielectric metasurface. An ultrafast control pulse is used to control plasmon-induced electric fields in a thin-film material with inversion symmetry that, without plasmonic enhancement, does not exhibit an even-order nonlinear optical response. The temporal evolution of the plasmonic near-fieldmore » is characterized with ~100 as resolution using a novel nonlinear interferometric technique. The serrated nanogap is a unique platform in which to investigate optically controlled, plasmonically enhanced harmonic generation in dielectric materials on an ultrafast time scale. Lastly, this metamaterial geometry can also be readily extended to all-optical control of other nonlinear phenomena, such as four-wave mixing and sum- and difference-frequency generation, in a wide variety of dielectric materials.« less

Ultrafast Plasmonic Control of Second Harmonic Generation

DOE PAGES

Davidson, Roderick B.; Yanchenko, Anna; Ziegler, Jed I.; ...

2016-06-01

Efficient frequency conversion techniques are crucial to the development of plasmonic metasurfaces for information processing and signal modulation. In principle, nanoscale electric-field confinement in nonlinear materials enables higher harmonic conversion efficiencies per unit volume than those attainable in bulk materials. Here we demonstrate efficient second-harmonic generation (SHG) in a serrated nanogap plasmonic geometry that generates steep electric field gradients on a dielectric metasurface. An ultrafast control pulse is used to control plasmon-induced electric fields in a thin-film material with inversion symmetry that, without plasmonic enhancement, does not exhibit an even-order nonlinear optical response. The temporal evolution of the plasmonic near-fieldmore » is characterized with ~100 as resolution using a novel nonlinear interferometric technique. The serrated nanogap is a unique platform in which to investigate optically controlled, plasmonically enhanced harmonic generation in dielectric materials on an ultrafast time scale. Lastly, this metamaterial geometry can also be readily extended to all-optical control of other nonlinear phenomena, such as four-wave mixing and sum- and difference-frequency generation, in a wide variety of dielectric materials.« less

7 CFR 1206.30 - Establishment and membership.

Code of Federal Regulations, 2014 CFR

2014-01-01

... INFORMATION Mango Promotion, Research, and Information Order Definitions National Mango Promotion Board § 1206... name and Code Number as defined in the Harmonized Tariff Schedule of the United States. The initial allocation will be two seats for District I, three seats for District II, two seats for District III, and one...

7 CFR 1206.30 - Establishment and membership.

Code of Federal Regulations, 2012 CFR

2012-01-01

... INFORMATION Mango Promotion, Research, and Information Order Definitions National Mango Promotion Board § 1206... name and Code Number as defined in the Harmonized Tariff Schedule of the United States. The initial allocation will be two seats for District I, three seats for District II, two seats for District III, and one...

Generation of a tunable environment for electrical oscillator systems.

PubMed

León-Montiel, R de J; Svozilík, J; Torres, Juan P

2014-07-01

Many physical, chemical, and biological systems can be modeled by means of random-frequency harmonic oscillator systems. Even though the noise-free evolution of harmonic oscillator systems can be easily implemented, the way to experimentally introduce, and control, noise effects due to a surrounding environment remains a subject of lively interest. Here, we experimentally demonstrate a setup that provides a unique tool to generate a fully tunable environment for classical electrical oscillator systems. We illustrate the operation of the setup by implementing the case of a damped random-frequency harmonic oscillator. The high degree of tunability and control of our scheme is demonstrated by gradually modifying the statistics of the oscillator's frequency fluctuations. This tunable system can readily be used to experimentally study interesting noise effects, such as noise-induced transitions in systems driven by multiplicative noise, and noise-induced transport, a phenomenon that takes place in quantum and classical coupled oscillator networks.

Radiative transfer code SHARM for atmospheric and terrestrial applications

NASA Astrophysics Data System (ADS)

Lyapustin, A. I.

2005-12-01

An overview of the publicly available radiative transfer Spherical Harmonics code (SHARM) is presented. SHARM is a rigorous code, as accurate as the Discrete Ordinate Radiative Transfer (DISORT) code, yet faster. It performs simultaneous calculations for different solar zenith angles, view zenith angles, and view azimuths and allows the user to make multiwavelength calculations in one run. The Δ-M method is implemented for calculations with highly anisotropic phase functions. Rayleigh scattering is automatically included as a function of wavelength, surface elevation, and the selected vertical profile of one of the standard atmospheric models. The current version of the SHARM code does not explicitly include atmospheric gaseous absorption, which should be provided by the user. The SHARM code has several built-in models of the bidirectional reflectance of land and wind-ruffled water surfaces that are most widely used in research and satellite data processing. A modification of the SHARM code with the built-in Mie algorithm designed for calculations with spherical aerosols is also described.

Radiative transfer code SHARM for atmospheric and terrestrial applications.

PubMed

Lyapustin, A I

2005-12-20

An overview of the publicly available radiative transfer Spherical Harmonics code (SHARM) is presented. SHARM is a rigorous code, as accurate as the Discrete Ordinate Radiative Transfer (DISORT) code, yet faster. It performs simultaneous calculations for different solar zenith angles, view zenith angles, and view azimuths and allows the user to make multiwavelength calculations in one run. The Delta-M method is implemented for calculations with highly anisotropic phase functions. Rayleigh scattering is automatically included as a function of wavelength, surface elevation, and the selected vertical profile of one of the standard atmospheric models. The current version of the SHARM code does not explicitly include atmospheric gaseous absorption, which should be provided by the user. The SHARM code has several built-in models of the bidirectional reflectance of land and wind-ruffled water surfaces that are most widely used in research and satellite data processing. A modification of the SHARM code with the built-in Mie algorithm designed for calculations with spherical aerosols is also described.

Temperature dependence of the symmetry energy and neutron skins in Ni, Sn, and Pb isotopic chains

NASA Astrophysics Data System (ADS)

Antonov, A. N.; Kadrev, D. N.; Gaidarov, M. K.; Sarriguren, P.; de Guerra, E. Moya

2017-02-01

The temperature dependence of the symmetry energy for isotopic chains of even-even Ni, Sn, and Pb nuclei is investigated in the framework of the local density approximation (LDA). The Skyrme energy density functional with two Skyrme-class effective interactions, SkM* and SLy4, is used in the calculations. The temperature-dependent proton and neutron densities are calculated through the hfbtho code that solves the nuclear Skyrme-Hartree-Fock-Bogoliubov problem by using the cylindrical transformed deformed harmonic-oscillator basis. In addition, two other density distributions of 208Pb, namely the Fermi-type density determined within the extended Thomas-Fermi (TF) method and symmetrized-Fermi local density obtained within the rigorous density functional approach, are used. The kinetic energy densities are calculated either by the hfbtho code or, for a comparison, by the extended TF method up to second order in temperature (with T2 term). Alternative ways to calculate the symmetry energy coefficient within the LDA are proposed. The results for the thermal evolution of the symmetry energy coefficient in the interval T =0 -4 MeV show that its values decrease with temperature. The temperature dependence of the neutron and proton root-mean-square radii and corresponding neutron skin thickness is also investigated, showing that the effect of temperature leads mainly to a substantial increase of the neutron radii and skins, especially in the more neutron-rich nuclei, a feature that may have consequences on astrophysical processes and neutron stars.

Comparisons of Flutter Analyses for an Experimental Fan

NASA Technical Reports Server (NTRS)

Bakhle, Milind A.; Reddy, T. S. R.; Stefko, George L.

2010-01-01

Two propulsion aeroelasticity codes were used to model the aeroelastic characteristics of an experimental forward-swept fan that encountered flutter during wind tunnel testing. Both of these three-dimensional codes model the unsteady flowfield due to blade vibrations using the Navier-Stokes equations. In the first approach, the unsteady flow equations are solved using an implicit time-marching approach. In the second approach, the unsteady flow equations are converted to a harmonic balance form and solved using a pseudo-time marching method. This paper describes the flutter calculations and compares the results to experimental measurements.

Analytic reflected light curves for exoplanets

NASA Astrophysics Data System (ADS)

Haggard, Hal M.; Cowan, Nicolas B.

2018-07-01

The disc-integrated reflected brightness of an exoplanet changes as a function of time due to orbital and rotational motions coupled with an inhomogeneous albedo map. We have previously derived analytic reflected light curves for spherical harmonic albedo maps in the special case of a synchronously rotating planet on an edge-on orbit (Cowan, Fuentes & Haggard). In this paper, we present analytic reflected light curves for the general case of a planet on an inclined orbit, with arbitrary spin period and non-zero obliquity. We do so for two different albedo basis maps: bright points (δ-maps), and spherical harmonics (Y_ l^m-maps). In particular, we use Wigner D-matrices to express an harmonic light curve for an arbitrary viewing geometry as a non-linear combination of harmonic light curves for the simpler edge-on, synchronously rotating geometry. These solutions will enable future exploration of the degeneracies and information content of reflected light curves, as well as fast calculation of light curves for mapping exoplanets based on time-resolved photometry. To these ends, we make available Exoplanet Analytic Reflected Lightcurves, a simple open-source code that allows rapid computation of reflected light curves.

Energetic particle modes of q = 1 high-order harmonics in tokamak plasmas with monotonic weak magnetic shear

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

Ren, Zhen-Zhen; Wang, Feng; Fu, G. Y.

Linear and nonlinear simulations of high-order harmonics q=1 energetic particle modes excited by trapped energetic particles in tokamaks are carried out using kinetic/magnetohydrodynamic hybrid code M3D-K. It is found that with a flat safety factor profile in the core region, the linear growth rate of high-order harmonics (m=n>1) driven by energetic trapped particles can be higher than the m/n=1/1 component. The high m=n>1 modes become more unstable when the pressure of energetic particles becomes higher. Moreover, it is shown that there exist multiple resonant locations satisfying different resonant conditions in the phase space of energetic particles for the high-order harmonicsmore » modes, whereas there is only one precessional resonance for the m/n=1/1 harmonics. The fluid nonlinearity reduces the saturation level of the n=1 component, while it hardly affects those of the high n components, especially the modes with m=n=3,4. The frequency of these modes does not chirp significantly, which is different with the typical fishbone driven by trapped particles. Lastly, in addition, the flattening region of energetic particle distribution due to high-order harmonics excitation is wider than that due to m/n=1/1 component, although the m/n=1/1 component has a higher saturation amplitude.« less

Energetic particle modes of q = 1 high-order harmonics in tokamak plasmas with monotonic weak magnetic shear

DOE PAGES

Ren, Zhen-Zhen; Wang, Feng; Fu, G. Y.; ...

2017-04-24

Linear and nonlinear simulations of high-order harmonics q=1 energetic particle modes excited by trapped energetic particles in tokamaks are carried out using kinetic/magnetohydrodynamic hybrid code M3D-K. It is found that with a flat safety factor profile in the core region, the linear growth rate of high-order harmonics (m=n>1) driven by energetic trapped particles can be higher than the m/n=1/1 component. The high m=n>1 modes become more unstable when the pressure of energetic particles becomes higher. Moreover, it is shown that there exist multiple resonant locations satisfying different resonant conditions in the phase space of energetic particles for the high-order harmonicsmore » modes, whereas there is only one precessional resonance for the m/n=1/1 harmonics. The fluid nonlinearity reduces the saturation level of the n=1 component, while it hardly affects those of the high n components, especially the modes with m=n=3,4. The frequency of these modes does not chirp significantly, which is different with the typical fishbone driven by trapped particles. Lastly, in addition, the flattening region of energetic particle distribution due to high-order harmonics excitation is wider than that due to m/n=1/1 component, although the m/n=1/1 component has a higher saturation amplitude.« less

On the Relevance of Natural Stimuli for the Study of Brainstem Correlates: The Example of Consonance Perception

PubMed Central

Cousineau, Marion; Bidelman, Gavin M.; Peretz, Isabelle; Lehmann, Alexandre

2015-01-01

Some combinations of musical tones sound pleasing to Western listeners, and are termed consonant, while others sound discordant, and are termed dissonant. The perceptual phenomenon of consonance has been traced to the acoustic property of harmonicity. It has been repeatedly shown that neural correlates of consonance can be found as early as the auditory brainstem as reflected in the harmonicity of the scalp-recorded frequency-following response (FFR). “Neural Pitch Salience” (NPS) measured from FFRs—essentially a time-domain equivalent of the classic pattern recognition models of pitch—has been found to correlate with behavioral judgments of consonance for synthetic stimuli. Following the idea that the auditory system has evolved to process behaviorally relevant natural sounds, and in order to test the generalizability of this finding made with synthetic tones, we recorded FFRs for consonant and dissonant intervals composed of synthetic and natural stimuli. We found that NPS correlated with behavioral judgments of consonance and dissonance for synthetic but not for naturalistic sounds. These results suggest that while some form of harmonicity can be computed from the auditory brainstem response, the general percept of consonance and dissonance is not captured by this measure. It might either be represented in the brainstem in a different code (such as place code) or arise at higher levels of the auditory pathway. Our findings further illustrate the importance of using natural sounds, as a complementary tool to fully-controlled synthetic sounds, when probing auditory perception. PMID:26720000

75 FR 35104 - Sunshine Act Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-21

... Announcement: 75 FR 34183, June 16, 2010. STATUS: Open Meeting. PLACE: 100 F Street, NE., Washington, DC. DATE...: Cancellation of Meeting. The Open Meeting scheduled for Friday, June 18, 2010 at 10 a.m. has been cancelled..., 2010. Florence E. Harmon, Deputy Secretary. [FR Doc. 2010-15011 Filed 6-17-10; 11:15 am] BILLING CODE P ...

Traditional Chinese medicine and the positive correlation with homeostatic evolution of human being: based on medical perspective.

PubMed

Wang, Jie-Hua

2012-08-01

Adaptation is an eternal theme of biological evolution. The paper aims at exploring the conception of positive correlation between traditional Chinese medicine (TCM) and human homeostatic evolution based on medical perspective. Discussions mainly involve TCM conforming to natural laws and natural evolution of life, spontaneous harmonization of yin and yang and operating system of human self-healing, modern human immunology and human endogenous immune function in TCM, self-homeostasis of human micro-ecological state and balance mechanism on regulating base in TCM, as well as adaptation-eternal theme of biological evolution and safeguarding adaptability-value of TCM. In perspective of medicine, theory and practice of TCM are in positive correlation with human homeostatic evolution, and what TCM tries to maintain is human intrinsic adaptive capability to disease and nature. Therefore, it is the core value of TCM, which is to be further studied, explored, realized and known to the world.

Using AORSA to simulate helicon waves in DIII-D

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

Lau, C., E-mail: lauch@ornl.gov; Blazevski, D.; Green, D. L.

2015-12-10

Recent efforts have shown that helicon waves (fast waves at > 20ω{sub ci}) may be an attractive option for driving efficient off-axis current drive during non-inductive tokamak operation for DIII-D, ITER and DEMO. For DIII-D scenarios, the ray tracing code, GENRAY, has been extensively used to study helicon current drive efficiency and location as a function of many plasma parameters. The full wave code, AORSA, which is applicable to arbitrary Larmor radius and can resolve arbitrary ion cyclotron harmonic order, has been recently used to validate the ray tracing technique at these high cyclotron harmonics. If the SOL is ignored,more » it will be shown that the GENRAY and AORSA calculated current drive profiles are comparable for the envisioned high beta advanced scenarios for DIII-D, where there is high single pass absorption due to electron Landau damping and minimal ion damping. AORSA is also been used to estimate possible SOL effects on helicon current drive coupling and SOL absorption due to collisional and slow wave effects.« less

Using AORSA to simulate helicon waves in DIII-D

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

Lau, Cornwall H; Jaeger, E. F.; Bertelli, Nicola

2015-01-01

Recent efforts have shown that helicon waves (fast waves at >20 omega(ci)) may be an attractive option for driving efficient off-axis current drive during non-inductive tokamak operation for DIII-D, ITER and DEMO. For DIII-D scenarios, the ray tracing code, GENRAY, has been extensively used to study helicon current drive efficiency and location as a function of many plasma parameters. The full wave code, AORSA, which is applicable to arbitrary Larmor radius and can resolve arbitrary ion cyclotron harmonic order, has been recently used to validate the ray tracing technique at these high cyclotron harmonics. If the SOL is ignored, itmore » will be shown that the GENRAY and AORSA calculated current drive profiles are comparable for the envisioned high beta advanced scenarios for DIII-D, where there is high single pass absorption due to electron Landau damping and minimal ion damping. AORSA is also been used to estimate possible SOL effects on helicon current drive coupling and SOL absorption due to collisional and slow wave effects.« less

Rotational Shear Effects on Edge Harmonic Oscillations in DIII-D Quiescent H-mode Discharges

NASA Astrophysics Data System (ADS)

Chen, Xi; Burrell, K. H.; Ferraro, N. M.; Osborne, T. H.; Austin, M. E.; Garofalo, A. M.; Groebner, R. J.; Kramer, G. J.; Luhmann, N. C., Jr.; McKee, G. R.; Muscatello, C. M.; Nazikian, R.; Ren, X.; Snyder, P. B.; Solomon, Wm.; Tobias, B. J.; Yan, Z.

2015-11-01

In quiescent H-mode (QH) regime, the edge harmonic oscillations (EHO) play an important role in avoiding the transient ELM power fluxes by providing benign and continuous edge particle transport. A detailed theoretical, experimental and modeling comparison has been made of low-n (n <= 5) EHO in DIII-D QH-mode plasmas. The calculated linear eigenmode structure from the extended MHD code M3D-C1 matches closely the coherent EHO properties from external magnetics data and internal measurements using the ECE, BES, ECE-I and MIR diagnostics, as well as the kink/peeling mode properties of the ideal MHD code ELITE. The numerical investigations indicate that the low-n EHO-like solutions from M3D-C1 are destabilized by the toroidal rotational shear while high-n modes are stabilized. This effect is independent of the rotation direction, suggesting that the low-n EHO can be destabilized in principle with rotation in both directions. These modeling results are consistent with experimental observations of the EHO and support the proposed theory of the EHO as a rotational shear driven kink/peeling mode.

Evolution of structural distortion in BiFeO3 thin films probed by second-harmonic generation

NASA Astrophysics Data System (ADS)

Jin, Kuijuan; Wang, Jiesu; Gu, Junxing; L03 Group in Institute of Physics, Chinese Academy of Sciences Team

BiFeO3 thin films have drawn much attention due to its potential applications for novel magnetoelectric devices and fundamental physics in magnetoelectric coupling. However, the structural evolution of BiFeO3 films with thickness remains controversial. Here we use an optical second-harmonic generation technique to explore the phase-related symmetry evolution of BiFeO3 thin films with the variation of thickness. The crystalline structures for 60 and 180-nm-thick BiFeO3 thin films were characterized by high-resolution X-ray diffractometry reciprocal space mapping and the local piezoelectric response for 60-nm-thick BiFeO3 thin films was characterized by piezoresponse force microscopy. The present results show that the symmetry of BiFeO3 thin films with a thickness below 60 nm belongs to the point group 4mm. We conclude that the disappearance of fourfold rotational symmetry in SHG s-out pattern implies for the appearance of R-phase. The fact that the thinner the film is, the closer to 1 the tensor element ratio χ31/ χ15 tends, indicates an increase of symmetry with the decrease of thickness for BiFeO3 thin films. email: kjjin@iphy.ac.cn

Evolution of structural distortion in BiFeO3 thin films probed by second-harmonic generation.

PubMed

Wang, Jie-Su; Jin, Kui-Juan; Guo, Hai-Zhong; Gu, Jun-Xing; Wan, Qian; He, Xu; Li, Xiao-Long; Xu, Xiu-Lai; Yang, Guo-Zhen

2016-12-01

BiFeO 3 thin films have drawn much attention due to its potential applications for novel magnetoelectric devices and fundamental physics in magnetoelectric coupling. However, the structural evolution of BiFeO 3 films with thickness remains controversial. Here we use an optical second-harmonic generation technique to explore the phase-related symmetry evolution of BiFeO 3 thin films with the variation of thickness. The crystalline structures for 60 and 180-nm-thick BiFeO 3 thin films were characterized by high-resolution X-ray diffractometry reciprocal space mapping and the local piezoelectric response for 60-nm-thick BiFeO 3 thin films was characterized by piezoresponse force microscopy. The present results show that the symmetry of BiFeO 3 thin films with a thickness below 60 nm belongs to the point group 4 mm. We conclude that the disappearance of fourfold rotational symmetry in SHG s-out pattern implies for the appearance of R-phase. The fact that the thinner the film is, the closer to 1 the tensor element ratio χ 31 /χ 15 tends, indicates an increase of symmetry with the decrease of thickness for BiFeO 3 thin films.

Evolution of structural distortion in BiFeO3 thin films probed by second-harmonic generation

PubMed Central

Wang, Jie-su; Jin, Kui-juan; Guo, Hai-zhong; Gu, Jun-xing; Wan, Qian; He, Xu; Li, Xiao-long; Xu, Xiu-lai; Yang, Guo-zhen

2016-01-01

BiFeO3 thin films have drawn much attention due to its potential applications for novel magnetoelectric devices and fundamental physics in magnetoelectric coupling. However, the structural evolution of BiFeO3 films with thickness remains controversial. Here we use an optical second-harmonic generation technique to explore the phase-related symmetry evolution of BiFeO3 thin films with the variation of thickness. The crystalline structures for 60 and 180-nm-thick BiFeO3 thin films were characterized by high-resolution X-ray diffractometry reciprocal space mapping and the local piezoelectric response for 60-nm-thick BiFeO3 thin films was characterized by piezoresponse force microscopy. The present results show that the symmetry of BiFeO3 thin films with a thickness below 60 nm belongs to the point group 4 mm. We conclude that the disappearance of fourfold rotational symmetry in SHG s-out pattern implies for the appearance of R-phase. The fact that the thinner the film is, the closer to 1 the tensor element ratio χ31/χ15 tends, indicates an increase of symmetry with the decrease of thickness for BiFeO3 thin films. PMID:27905565

Transport and equilibrium in field-reversed mirrors

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

Boyd, J.K.

Two plasma models relevant to compact torus research have been developed to study transport and equilibrium in field reversed mirrors. In the first model for small Larmor radius and large collision frequency, the plasma is described as an adiabatic hydromagnetic fluid. In the second model for large Larmor radius and small collision frequency, a kinetic theory description has been developed. Various aspects of the two models have been studied in five computer codes ADB, AV, NEO, OHK, RES. The ADB code computes two dimensional equilibrium and one dimensional transport in a flux coordinate. The AV code calculates orbit average integralsmore » in a harmonic oscillator potential. The NEO code follows particle trajectories in a Hill's vortex magnetic field to study stochasticity, invariants of the motion, and orbit average formulas. The OHK code displays analytic psi(r), B/sub Z/(r), phi(r), E/sub r/(r) formulas developed for the kinetic theory description. The RES code calculates resonance curves to consider overlap regions relevant to stochastic orbit behavior.« less

Project MANTIS: A MANTle Induction Simulator for coupling geodynamic and electromagnetic modeling

NASA Astrophysics Data System (ADS)

Weiss, C. J.

2009-12-01

A key component to testing geodynamic hypotheses resulting from the 3D mantle convection simulations is the ability to easily translate the predicted physiochemical state to the model space relevant for an independent geophysical observation, such as earth's seismic, geodetic or electromagnetic response. In this contribution a new parallel code for simulating low-frequency, global-scale electromagnetic induction phenomena is introduced that has the same Earth discretization as the popular CitcomS mantle convection code. Hence, projection of the CitcomS model into the model space of electrical conductivity is greatly simplified, and focuses solely on the node-to-node, physics-based relationship between these Earth parameters without the need for "upscaling", "downscaling", averaging or harmonizing with some other model basis such as spherical harmonics. Preliminary performance tests of the MANTIS code on shared and distributed memory parallel compute platforms shows favorable scaling (>70% efficiency) for up to 500 processors. As with CitcomS, an OpenDX visualization widget (VISMAN) is also provided for 3D rendering and interactive interrogation of model results. Details of the MANTIS code will be briefly discussed here, focusing on compatibility with CitcomS modeling, as will be preliminary results in which the electromagnetic response of a CitcomS model is evaluated. VISMAN rendering of electrical tomography-derived electrical conductivity model overlain by an a 1x1 deg crustal conductivity map. Grey scale represents the log_10 magnitude of conductivity [S/m]. Arrows are horiztonal components of a hypothetical magnetospheric source field used to electromagnetically excite the conductivity model.

Supporting Source Code Comprehension during Software Evolution and Maintenance

ERIC Educational Resources Information Center

Alhindawi, Nouh

2013-01-01

This dissertation addresses the problems of program comprehension to support the evolution of large-scale software systems. The research concerns how software engineers locate features and concepts along with categorizing changes within very large bodies of source code along with their versioned histories. More specifically, advanced Information…

Secondary School Students' Reasoning about Evolution

ERIC Educational Resources Information Center

To, Cheryl; Tenenbaum, Harriet R.; Hogh, Henriette

2017-01-01

This study examined age differences in young people's understanding of evolution theory in secondary school. A second aim of this study was to propose a new coding scheme that more accurately described students' conceptual understanding about evolutionary theory. We argue that coding schemes adopted in previous research may have overestimated…

Nada: A new code for studying self-gravitating tori around black holes

NASA Astrophysics Data System (ADS)

Montero, Pedro J.; Font, José A.; Shibata, Masaru

2008-09-01

We present a new two-dimensional numerical code called Nada designed to solve the full Einstein equations coupled to the general relativistic hydrodynamics equations. The code is mainly intended for studies of self-gravitating accretion disks (or tori) around black holes, although it is also suitable for regular spacetimes. Concerning technical aspects the Einstein equations are formulated and solved in the code using a formulation of the standard 3+1 Arnowitt-Deser-Misner canonical formalism system, the so-called Baumgarte-Shapiro Shibata-Nakamura approach. A key feature of the code is that derivative terms in the spacetime evolution equations are computed using a fourth-order centered finite difference approximation in conjunction with the Cartoon method to impose the axisymmetry condition under Cartesian coordinates (the choice in Nada), and the puncture/moving puncture approach to carry out black hole evolutions. Correspondingly, the general relativistic hydrodynamics equations are written in flux-conservative form and solved with high-resolution, shock-capturing schemes. We perform and discuss a number of tests to assess the accuracy and expected convergence of the code, namely, (single) black hole evolutions, shock tubes, and evolutions of both spherical and rotating relativistic stars in equilibrium, the gravitational collapse of a spherical relativistic star leading to the formation of a black hole. In addition, paving the way for specific applications of the code, we also present results from fully general relativistic numerical simulations of a system formed by a black hole surrounded by a self-gravitating torus in equilibrium.

Regional TEC dynamic modeling based on Slepian functions

NASA Astrophysics Data System (ADS)

Sharifi, Mohammad Ali; Farzaneh, Saeed

2015-09-01

In this work, the three-dimensional state of the ionosphere has been estimated by integrating the spherical Slepian harmonic function and Kalman filter. The spherical Slepian harmonic functions have been used to establish the observation equations because of their properties in local modeling. Spherical harmonics are poor choices to represent or analyze geophysical processes without perfect global coverage but the Slepian functions afford spatial and spectral selectivity. The Kalman filter has been utilized to perform the parameter estimation due to its suitable properties in processing the GPS measurements in the real-time mode. The proposed model has been applied to the real data obtained from the ground-based GPS observations across some portion of the IGS network in Europe. Results have been compared with the estimated TECs by the CODE, ESA, IGS centers and IRI-2012 model. The results indicated that the proposed model which takes advantage of the Slepian basis and Kalman filter is efficient and allows for the generation of the near-real-time regional TEC map.

Wide tracking range, auto ranging, low jitter phase lock loop for swept and fixed frequency systems

DOEpatents

Kerner, Thomas M.

2001-01-01

The present invention provides a wide tracking range phase locked loop (PLL) circuit that achieves minimal jitter in a recovered clock signal, regardless of the source of the jitter (i.e. whether it is in the source or the transmission media). The present invention PLL has automatic harmonic lockout detection circuitry via a novel lock and seek control logic in electrical communication with a programmable frequency discriminator and a code balance detector. (The frequency discriminator enables preset of a frequency window of upper and lower frequency limits to derive a programmable range within which signal acquisition is effected. The discriminator works in combination with the code balance detector circuit to minimize the sensitivity of the PLL circuit to random data in the data stream). In addition, the combination of a differential loop integrator with the lock and seek control logic obviates a code preamble and guarantees signal acquisition without harmonic lockup. An adaptive cable equalizer is desirably used in combination with the present invention PLL to recover encoded transmissions containing a clock and/or data. The equalizer automatically adapts to equalize short haul cable lengths of coaxial and twisted pair cables or wires and provides superior jitter performance itself. The combination of the equalizer with the present invention PLL is desirable in that such combination permits the use of short haul wires without significant jitter.

A Finite-Orbit-Width Fokker-Planck solver for modeling of energetic particle interactions with waves, with application to Helicons in ITER

NASA Astrophysics Data System (ADS)

Petrov, Yuri V.; Harvey, R. W.

2017-10-01

The bounce-average (BA) finite-difference Fokker-Planck (FP) code CQL3D [1,2] now includes the essential physics to describe the RF heating of Finite-Orbit-Width (FOW) ions in tokamaks. The FP equation is reformulated in terms of Constants-Of-Motion coordinates, which we select to be particle speed, pitch angle, and major radius on the equatorial plane thus obtaining the distribution function directly at this location. Full-orbit, low collisionality neoclassical radial transport emerges from averaging the local friction and diffusion coefficients along guiding center orbits. Similarly, the BA of local quasilinear RF diffusion terms gives rise to additional radial transport. The local RF electric field components needed for the BA operator are usually obtained by a ray-tracing code, such as GENRAY, or in conjunction with full-wave codes. As a new, practical application, the CQL3D-FOW version is used for simulation of alpha-particle heating by high-harmonic waves in ITER. Coupling of high harmonic or helicon fast waves power to electrons is a promising current drive (CD) scenario for high beta plasmas. However, the efficiency of current drive can be diminished by parasitic channeling of RF power into fast ions, such as alphas, through finite Larmor-radius effects. We investigate possibilities to reduce the fast ion heating in CD scenarios.

Azimuthally differential pion femtoscopy relative to the second and third harmonic in Pb-Pb 2.76 TeV collision from ALICE

NASA Astrophysics Data System (ADS)

Saleh, Mohammad; Alice Collaboration

2017-11-01

Azimuthally differential femtoscopic measurements, being sensitive to spatio-temporal characteristics of the source as well as to the collective velocity fields at freeze-out, provide very important information on the nature and dynamics of the system evolution. While the HBT radii modulations relative to the second harmonic event plane reflect mostly the spatial geometry of the source, the third harmonic results are mostly defined by the velocity fields [S. A. Voloshin, J. Phys. G38 (2011) 124097. arXiv:arxiv:arXiv:1106.5830, doi:http://dx.doi.org/10.1088/0954-3899/38/12/124097]. Radii variations with respect to the third harmonic event plane unambiguously signal a collective expansion and anisotropy in the flow fields. Event shape engineering (ESE) is a technique proposed to select events corresponding to a particular shape. Azimuthally differential HBT combined with ESE allows for a detailed analysis of the relation between initial geometry, anisotropic flow and the deformation of source shape. We present azimuthally differential pion femtoscopy with respect to second and third harmonic event planes as a function of the pion transverse momentum for different collision centralities in Pb-Pb collisions at √{sNN} = 2.76 TeV. All these results are compared to existing models. The effects of the selection of the events with high elliptic or triangular flow are also presented.

Anharmonic phonons and second-order phase-transitions by the stochastic self-consistent harmonic approximation

NASA Astrophysics Data System (ADS)

Mauri, Francesco

Anharmonic effects can generally be treated within perturbation theory. Such an approach breaks down when the harmonic solution is dynamically unstable or when the anharmonic corrections of the phonon energies are larger than the harmonic frequencies themselves. This situation occurs near lattice-related second-order phase-transitions such as charge-density-wave (CDW) or ferroelectric instabilities or in H-containing materials, where the large zero-point motion of the protons results in a violation of the harmonic approximation. Interestingly, even in these cases, phonons can be observed, measured, and used to model transport properties. In order to treat such cases, we developed a stochastic implementation of the self-consistent harmonic approximation valid to treat anharmonicity in the nonperturbative regime and to obtain, from first-principles, the structural, thermodynamic and vibrational properties of strongly anharmonic systems. I will present applications to the ferroelectric transitions in SnTe, to the CWD transitions in NbS2 and NbSe2 (in bulk and monolayer) and to the hydrogen-bond symmetrization transition in the superconducting hydrogen sulfide system, that exhibits the highest Tc reported for any superconductor so far. In all cases we are able to predict the transition temperature (pressure) and the evolution of phonons with temperature (pressure). This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant agreement No. 696656 GrapheneCore1.

Investigation of Non-linear Chirp Coding for Improved Second Harmonic Pulse Compression.

PubMed

Arif, Muhammad; Ali, Muhammad Asim; Shaikh, Muhammad Mujtaba; Freear, Steven

2017-08-01

Non-linear frequency-modulated (NLFM) chirp coding was investigated to improve the pulse compression of the second harmonic chirp signal by reducing the range side lobe level. The problem of spectral overlap between the fundamental component and second harmonic component (SHC) was also investigated. Therefore, two methods were proposed: method I for the non-overlap condition and method II with the pulse inversion technique for the overlap harmonic condition. In both methods, the performance of the NLFM chirp was compared with that of the reference LFM chirp signals. Experiments were performed using a 2.25 MHz transducer mounted coaxially at a distance of 5 cm with a 1 mm hydrophone in a water tank, and the peak negative pressure of 300 kPa was set at the receiver. Both simulations and experimental results revealed that the peak side lobe level (PSL) of the compressed SHC of the NLFM chirp was improved by at least 13 dB in method I and 5 dB in method II when compared with the PSL of LFM chirps. Similarly, the integrated side lobe level (ISL) of the compressed SHC of the NLFM chirp was improved by at least 8 dB when compared with the ISL of LFM chirps. In both methods, the axial main lobe width of the compressed NLFM chirp was comparable to that of the LFM signals. The signal-to-noise ratio of the SHC of NLFM was improved by as much as 0.8 dB, when compared with the SHC of the LFM signal having the same energy level. The results also revealed the robustness of the NLFM chirp under a frequency-dependent attenuation of 0.5 dB/cm·MHz up to a penetration depth of 5 cm and a Doppler shift up to 12 kHz. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Positional stability and radial dynamics of sonoluminescent bubbles under bi-harmonic driving: Effect of the high-frequency component and its relative phase.

PubMed

Rosselló, J M; Dellavale, D; Bonetto, F J

2016-07-01

The use of bi-frequency driving in sonoluminescence has proved to be an effective way to avoid the spatial instability (pseudo-orbits) developed by bubbles in systems with high viscous liquids like sulfuric or phosphoric acids. In this work, we present extensive experimental and numerical evidence in order to assess the effect of the high frequency component (PAc(HF)) of a bi-harmonic acoustic pressure field on the dynamic of sonoluminescent bubbles in an aqueous solution of sulfuric acid. The present study is mainly focused on the role of the harmonic frequency (Nf0) and the relative phase between the two frequency components (φb) of the acoustic field on the spatial, positional and diffusive stability of the bubbles. The results presented in this work were analyzed by means of three different approaches. First, we discussed some qualitative considerations about the changes observed in the radial dynamics, and the stability of similar bubbles under distinct bi-harmonic drivings. Later, we have investigated, through a series of numerical simulations, how the use of high frequency harmonic components of different order N, affects the positional stability of the SL bubbles. Furthermore, the influence of φb in their radius temporal evolution is systematically explored for harmonics ranging from the second to the fifteenth harmonic (N=2-15). Finally, a multivariate analysis based on the covariance method is performed to study the dependences among the parameters characterizing the SL bubble. Both experimental and numerical results indicate that the impact of PAc(HF) on the positional instability and the radial dynamics turns to be progressively negligible as the order of the high frequency harmonic component grows (i.e. N ≫ 1), however its effectiveness on the reduction of the spatial instability remains unaltered or even improved. Copyright © 2016 Elsevier B.V. All rights reserved.

Multicascade X-Ray Free-Electron Laser with Harmonic Multiplier and Two-Frequency Undulator

NASA Astrophysics Data System (ADS)

Zhukovsky, K. V.

2018-06-01

The feasibility of generation of powerful x-ray radiation by a cascade free-electron laser (FEL) with amplification of higher harmonics using a two-frequency undulator is studied. To analyze the FEL operation, a complex phenomenological single-pass FEL model is developed and used. It describes linear and nonlinear generation of harmonics in the FEL with seed laser that takes into account initial electron beam noise and describes all main losses of each harmonic in each FEL cascade. The model is also calibrated against and approved by the experimental FEL data and available results of three-dimensional numerical simulation. The electron beam in the undulator is assumed to be matched and focused, and the dynamics of power in the singlepass FEL with cascade harmonic multipliers is investigated to obtain x-ray laser radiation in the FEL having the shortest length, beam energy, and frequency of the seed laser as low as possible. In this context, the advantages of the two-frequency undulator used for generation of harmonics are demonstrated. The evolution of harmonics in a multicascade FEL with multiplication of harmonics is investigated. The operation of the cascade FEL at the wavelength λ = 1.14 nm, generating 30 MW already on 38 m with the seed laser operating at a wavelength of 11.43 nm corresponding to the maximal reflectivity of the multilayered mirror MoRu/Be coating is investigated. In addition, the operation of the multicascade FEL with accessible seed UVlaser operating at a wavelength of 157 nm (F2 excimer UV-laser) and electron beam with energy of 0.5 GeV is investigated. X-ray radiation simulated in it at the wavelength λ 3.9 nm reaches power of 50 MW already at 27 m, which is by two orders of magnitude shorter than 3.4 km of the x-ray FEL recently put into operation in Europe.

Reference results for time-like evolution up to

NASA Astrophysics Data System (ADS)

Bertone, Valerio; Carrazza, Stefano; Nocera, Emanuele R.

2015-03-01

We present high-precision numerical results for time-like Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution in the factorisation scheme, for the first time up to next-to-next-to-leading order accuracy in quantum chromodynamics. First, we scrutinise the analytical expressions of the splitting functions available in the literature, in both x and N space, and check their mutual consistency. Second, we implement time-like evolution in two publicly available, entirely independent and conceptually different numerical codes, in x and N space respectively: the already existing APFEL code, which has been updated with time-like evolution, and the new MELA code, which has been specifically developed to perform the study in this work. Third, by means of a model for fragmentation functions, we provide results for the evolution in different factorisation schemes, for different ratios between renormalisation and factorisation scales and at different final scales. Our results are collected in the format of benchmark tables, which could be used as a reference for global determinations of fragmentation functions in the future.

CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

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

Saitoh, Takayuki R., E-mail: saitoh@elsi.jp

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of thesemore » quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.« less

Code comparison for accelerator design and analysis

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

Parsa, Z.

1988-01-01

We present a comparison between results obtained from standard accelerator physics codes used for the design and analysis of synchrotrons and storage rings, with programs SYNCH, MAD, HARMON, PATRICIA, PATPET, BETA, DIMAD, MARYLIE and RACE-TRACK. In our analysis we have considered 5 (various size) lattices with large and small angles including AGS Booster (10/degree/ bend), RHIC (2.24/degree/), SXLS, XLS (XUV ring with 45/degree/ bend) and X-RAY rings. The differences in the integration methods used and the treatment of the fringe fields in these codes could lead to different results. The inclusion of nonlinear (e.g., dipole) terms may be necessary inmore » these calculations specially for a small ring. 12 refs., 6 figs., 10 tabs.« less

Interval singing links to phenotypic quality in a songbird

PubMed Central

2016-01-01

Darwin was fascinated by melodic performances of insects, fish, birds, mammals, and men. He considered the ability to produce musical notes without direct use the most mysterious endowment of mankind. Bird song is attributed to sexual selection, but it remains unknown how the expected relationship between melodic performance and phenotypic quality arises. Melodies consist of sequences of notes, and both Pythagoras and music theorists in the Middle Ages found that their tonal frequencies form simple ratios that correspond to small-integer proportions derived from the harmonic series. Harmonics are acoustically predictable, and thus form the basis of the natural, just tuning system in music. Here I analyze the songs of the great tit (Parus major), a bird with a stereotyped song of typically two notes, and test the prediction that the deviations of the intervals from small-integer frequency ratios based on the harmonic series are related to the quality of the singer. I show that the birds with the smallest deviations from small-integer ratios possess the largest melanin-based black ventral tie, a signal that has been demonstrated to indicate social status and dominance, past exposure to parasites, and reproductive potential. The singing of notes with exact frequency relationships requires high levels of motor control and auditory sensory feedback. The finding provides a missing link between melodic precision and phenotypic quality of individuals, which is key for understanding the evolution of vocal melodic expression in animals, and elucidates pathways for the evolution of melodic expression in music. PMID:27791124

Characterization of quantum interference control of injected currents in LT-GaAs for carrier-envelope phase measurements.

PubMed

Roos, Peter; Quraishi, Qudsia; Cundiff, Steven; Bhat, Ravi; Sipe, J

2003-08-25

We use two mutually coherent, harmonically related pulse trains to experimentally characterize quantum interference control (QIC) of injected currents in low-temperature-grown gallium arsenide. We observe real-time QIC interference fringes, optimize the QIC signal fidelity, uncover critical signal dependences regarding beam spatial position on the sample, measure signal dependences on the fundamental and second harmonic average optical powers, and demonstrate signal characteristics that depend on the focused beam spot sizes. Following directly from our motivation for this study, we propose an initial experiment to measure and ultimately control the carrier-envelope phase evolution of a single octave-spanning pulse train using the QIC phenomenon.

Gaussian ancillary bombardment

NASA Astrophysics Data System (ADS)

Grimmer, Daniel; Brown, Eric; Kempf, Achim; Mann, Robert B.; Martín-Martínez, Eduardo

2018-05-01

We analyze in full detail the time evolution of an open Gaussian quantum system rapidly bombarded by Gaussian ancillae. As a particular case this analysis covers the thermalization (or not) of a harmonic oscillator coupled to a thermal reservoir made of harmonic oscillators. We derive general results for this scenario and apply them to the problem of thermalization. We show that only a particular family of system-environment couplings will cause the system to thermalize to the temperature of its environment. We discuss that if we want to understand thermalization as ensuing from the Markovian interaction of a system with the individual microconstituents of its (thermal) environment then the process of thermalization is not as robust as one might expect.

A Mathematica program for the calculation of five-body Moshinsky brackets

NASA Astrophysics Data System (ADS)

Xiao, Shuyuan; Mu, Xueli; Liu, Tingting; Chen, Hong

2016-06-01

Five-body Moshinsky brackets that relate harmonic oscillator wavefunctions in two different sets of Jacobi coordinates make it straightforward to calculate some matrix elements in the variational calculations of five-body systems. The analytical expression of these transformation coefficients and the computer code written in the Mathematica language are presented here for accurate calculations.

Different evolution dynamics of vector solitons depending on their polarization states

NASA Astrophysics Data System (ADS)

Chen, Wei-Cheng; Chen, Guo-Jie

2014-03-01

There are three types of temporal evolution dynamics of vector solitons observed in a ring fiber laser with a semiconductor saturable absorption mirror (SESAM) as a mode-locker. It is found that the polarization property of vector solitons is an important factor for achieving different evolution dynamics. The vector soliton with a uniform polarization state across the whole pulse profile and zero polarization extinction ratio operates at a fundamental repetition rate with a single pulse profile. The elliptically polarized vector soliton with a larger polarization extinction ratio exhibits a harmonic pulse train. The soliton bunching with multi-peak structures exists between the above two states and shows elliptical polarization with a small polarization extinction ratio.

UCLA Final Technical Report for the "Community Petascale Project for Accelerator Science and Simulation”.

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

Mori, Warren

The UCLA Plasma Simulation Group is a major partner of the “Community Petascale Project for Accelerator Science and Simulation”. This is the final technical report. We include an overall summary, a list of publications, progress for the most recent year, and individual progress reports for each year. We have made tremendous progress during the three years. SciDAC funds have contributed to the development of a large number of skeleton codes that illustrate how to write PIC codes with a hierarchy of parallelism. These codes cover 2D and 3D as well as electrostatic solvers (which are used in beam dynamics codesmore » and quasi-static codes) and electromagnetic solvers (which are used in plasma based accelerator codes). We also used these ideas to develop a GPU enabled version of OSIRIS. SciDAC funds were also contributed to the development of strategies to eliminate the Numerical Cerenkov Instability (NCI) which is an issue when carrying laser wakefield accelerator (LWFA) simulations in a boosted frame and when quantifying the emittance and energy spread of self-injected electron beams. This work included the development of a new code called UPIC-EMMA which is an FFT based electromagnetic PIC code and to new hybrid algorithms in OSIRIS. A new hybrid (PIC in r-z and gridless in φ) algorithm was implemented into OSIRIS. In this algorithm the fields and current are expanded into azimuthal harmonics and the complex amplitude for each harmonic is calculated separately. The contributions from each harmonic are summed and then used to push the particles. This algorithm permits modeling plasma based acceleration with some 3D effects but with the computational load of an 2D r-z PIC code. We developed a rigorously charge conserving current deposit for this algorithm. Very recently, we made progress in combining the speed up from the quasi-3D algorithm with that from the Lorentz boosted frame. SciDAC funds also contributed to the improvement and speed up of the quasi-static PIC code QuickPIC. We have also used our suite of PIC codes to make scientific discovery. Highlights include supporting FACET experiments which achieved the milestones of showing high beam loading and energy transfer efficiency from a drive electron beam to a witness electron beam and the discovery of a self-loading regime a for high gradient acceleration of a positron beam. Both of these experimental milestones were published in Nature together with supporting QuickPIC simulation results. Simulation results from QuickPIC were used on the cover of Nature in one case. We are also making progress on using highly resolved QuickPIC simulations to show that ion motion may not lead to catastrophic emittance growth for tightly focused electron bunches loaded into nonlinear wakefields. This could mean that fully self-consistent beam loading scenarios are possible. This work remains in progress. OSIRIS simulations were used to discover how 200 MeV electron rings are formed in LWFA experiments, on how to generate electrons that have a series of bunches on nanometer scale, and how to transport electron beams from (into) plasma sections into (from) conventional beam optic sections.« less

AAPM/RSNA physics tutorial for residents. Topics in US: B-mode US: basic concepts and new technology.

PubMed

Hangiandreou, Nicholas J

2003-01-01

Ultrasonography (US) has been used in medical imaging for over half a century. Current US scanners are based largely on the same basic principles used in the initial devices for human imaging. Modern equipment uses a pulse-echo approach with a brightness-mode (B-mode) display. Fundamental aspects of the B-mode imaging process include basic ultrasound physics, interactions of ultrasound with tissue, ultrasound pulse formation, scanning the ultrasound beam, and echo detection and signal processing. Recent technical innovations that have been developed to improve the performance of modern US equipment include the following: tissue harmonic imaging, spatial compound imaging, extended field of view imaging, coded pulse excitation, electronic section focusing, three-dimensional and four-dimensional imaging, and the general trend toward equipment miniaturization. US is a relatively inexpensive, portable, safe, and real-time modality, all of which make it one of the most widely used imaging modalities in medicine. Although B-mode US is sometimes referred to as a mature technology, this modality continues to experience a significant evolution in capability with even more exciting developments on the horizon. Copyright RSNA, 2003

Quantum dynamics of a plane pendulum

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

Leibscher, Monika; Schmidt, Burkhard

A semianalytical approach to the quantum dynamics of a plane pendulum is developed, based on Mathieu functions which appear as stationary wave functions. The time-dependent Schroedinger equation is solved for pendular analogs of coherent and squeezed states of a harmonic oscillator, induced by instantaneous changes of the periodic potential energy function. Coherent pendular states are discussed between the harmonic limit for small displacements and the inverted pendulum limit, while squeezed pendular states are shown to interpolate between vibrational and free rotational motion. In the latter case, full and fractional revivals as well as spatiotemporal structures in the time evolution ofmore » the probability densities (quantum carpets) are quantitatively analyzed. Corresponding expressions for the mean orientation are derived in terms of Mathieu functions in time. For periodic double well potentials, different revival schemes, and different quantum carpets are found for the even and odd initial states forming the ground tunneling doublet. Time evolution of the mean alignment allows the separation of states with different parity. Implications for external (rotational) and internal (torsional) motion of molecules induced by intense laser fields are discussed.« less

Development of heavy-flavour flow-harmonics in high-energy nuclear collisions

NASA Astrophysics Data System (ADS)

Beraudo, Andrea; De Pace, Arturo; Monteno, Marco; Nardi, Marzia; Prino, Francesco

2018-02-01

We employ the POWLANG transport setup, developed over the last few years, to provide new predictions for several heavy-flavour observables in relativistic heavy-ion collisions from RHIC to LHC center-of-mass energies. In particular, we focus on the development of the flow-harmonics v 2 and v 3 arising from the initial geometric asymmetry in the initial conditions and its associated event-by-event fluctuations. Within the same transport framework, for the sake of consistency, we also compare the nuclear modification factor of the p T spectra of charm and beauty quarks, heavy hadrons and their decay electrons. We compare our findings to the most recent data from the experimental collaborations. We also study in detail the contribution to the flow harmonics from the quarks decoupling from the fireball during the various stages of its evolution: although not directly accessible to the experiments, this information can shed light on the major sources of the final measured effect.

Second-harmonic generation of ZnO nanoparticles synthesized by laser ablation of solids in liquids

NASA Astrophysics Data System (ADS)

Rocha-Mendoza, Israel; Camacho-López, Santiago; Luna-Palacios, Yryx Y.; Esqueda-Barrón, Yasmín; Camacho-López, Miguel A.; Camacho-López, Marco; Aguilar, Guillermo

2018-02-01

We report the synthesis of small zinc oxide nanoparticles (ZnO NPs) based colloidal suspensions and the study of second-harmonic generation from aggregated ZnO NPs deposited on glass substrates. The colloidal suspensions were obtained using the laser ablation of solids in liquids technique, ablating a Zn solid target immersed in acetone as the liquid medium, with ns-laser pulses (1064 nm) of a Nd-YAG laser. The per pulse laser fluence, the laser repetition rate frequency and the ablation time were kept constant. The absorption evolution of the obtained suspensions was optically characterized through absorption spectroscopy until stabilization. Raman spectroscopy, SEM and HRTEM were used to provide evidence of the ZnO NPs structure. HRTEM results showed that 5-8 nm spheroids ZnO NPs were obtained. Strong second-harmonic signal is obtained from random ZnO monocrystalline NPs and from aggregated ZnO NPs, suggesting that the high efficiency of the nonlinear process may not depend on the NPs size or aggregation state.

Computing element evolution towards Exascale and its impact on legacy simulation codes

NASA Astrophysics Data System (ADS)

Colin de Verdière, Guillaume J. L.

2015-12-01

In the light of the current race towards the Exascale, this article highlights the main features of the forthcoming computing elements that will be at the core of next generations of supercomputers. The market analysis, underlying this work, shows that computers are facing a major evolution in terms of architecture. As a consequence, it is important to understand the impacts of those evolutions on legacy codes or programming methods. The problems of dissipated power and memory access are discussed and will lead to a vision of what should be an exascale system. To survive, programming languages had to respond to the hardware evolutions either by evolving or with the creation of new ones. From the previous elements, we elaborate why vectorization, multithreading, data locality awareness and hybrid programming will be the key to reach the exascale, implying that it is time to start rewriting codes.

Compact single-pass X-ray FEL with harmonic multiplication cascades

NASA Astrophysics Data System (ADS)

Zhukovsky, K.

2018-07-01

The generation of X-ray radiation in cascaded single-pass free electron laser (FEL), which amplifies high harmonics of a two-frequency undulator, is studied. Power dynamics of FEL harmonics is explored with the help of the phenomenological model of a single pass FEL. The model describes both linear and non-linear harmonic generation, starting from a coherent seed laser and initial shot noise with account for main loss factors for each harmonic in each cascade individually: the energy spread and beam divergence, the coupling losses between FEL cascades, the diffraction etc. The model was validated with the experiment and with relevant 3-D simulations. It is employed for modeling the cascaded FELs with harmonic multiplication and analyzing the evolution of FEL harmonic power with the aim to obtain the maximum high harmonic power in the X-ray band at the shortest possible FEL length with the lowest possible seed frequency. The advantages of two-frequency undulators in HGHG FELs are elucidated. The requirements for the electron beam are studied; the need for low energy spread is evidenced: our evaluations yield σe < 2 × 10-4. Several cascaded HGHG FELs with two-frequency undulators are modeled. Generation of soft X-ray radiation at λ = 2 . 71 nm, reaching ∼50 MW power with I0 ∼ 100 A in a cascaded FEL at just 40 m with 13.51 nm seed, matching peak reflectivity of Mo/Si, is demonstrated. The generation of 40 MW radiation power at λ = 2 . 27 nm with the beam current I0 ∼ 100 A, energy E = 950 MeV and the energy spread σe = 2 × 10-4 is studied, using second and third harmonics in three-stage 45 m long FEL. The multistage FEL is modeled for generating radiation in nanometer band: ∼40 MW power at λ ∼ 2 . 6 nm with I0 ∼ 175 A current in just ∼40 m long FEL with commercially available F2 excimer UV laser seed at 157 nm. The peak radiation power rises to ∼0.5 GW for ∼1 kA beam current.

Density- and wavefunction-normalized Cartesian spherical harmonics for l ≤ 20.

PubMed

Michael, J Robert; Volkov, Anatoliy

2015-03-01

The widely used pseudoatom formalism [Stewart (1976). Acta Cryst. A32, 565-574; Hansen & Coppens (1978). Acta Cryst. A34, 909-921] in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of aspherical deformations of the atomic electron density in molecules and crystals. The analytical form of the density-normalized Cartesian spherical harmonic functions for up to l ≤ 7 and the corresponding normalization coefficients were reported previously by Paturle & Coppens [Acta Cryst. (1988), A44, 6-7]. It was shown that the analytical form for normalization coefficients is available primarily for l ≤ 4 [Hansen & Coppens, 1978; Paturle & Coppens, 1988; Coppens (1992). International Tables for Crystallography, Vol. B, Reciprocal space, 1st ed., edited by U. Shmueli, ch. 1.2. Dordrecht: Kluwer Academic Publishers; Coppens (1997). X-ray Charge Densities and Chemical Bonding. New York: Oxford University Press]. Only in very special cases it is possible to derive an analytical representation of the normalization coefficients for 4 < l ≤ 7 (Paturle & Coppens, 1988). In most cases for l > 4 the density normalization coefficients were calculated numerically to within seven significant figures. In this study we review the literature on the density-normalized spherical harmonics, clarify the existing notations, use the Paturle-Coppens (Paturle & Coppens, 1988) method in the Wolfram Mathematica software to derive the Cartesian spherical harmonics for l ≤ 20 and determine the density normalization coefficients to 35 significant figures, and computer-generate a Fortran90 code. The article primarily targets researchers who work in the field of experimental X-ray electron density, but may be of some use to all who are interested in Cartesian spherical harmonics.

Neural Representation of Concurrent Harmonic Sounds in Monkey Primary Auditory Cortex: Implications for Models of Auditory Scene Analysis

PubMed Central

Steinschneider, Mitchell; Micheyl, Christophe

2014-01-01

The ability to attend to a particular sound in a noisy environment is an essential aspect of hearing. To accomplish this feat, the auditory system must segregate sounds that overlap in frequency and time. Many natural sounds, such as human voices, consist of harmonics of a common fundamental frequency (F0). Such harmonic complex tones (HCTs) evoke a pitch corresponding to their F0. A difference in pitch between simultaneous HCTs provides a powerful cue for their segregation. The neural mechanisms underlying concurrent sound segregation based on pitch differences are poorly understood. Here, we examined neural responses in monkey primary auditory cortex (A1) to two concurrent HCTs that differed in F0 such that they are heard as two separate “auditory objects” with distinct pitches. We found that A1 can resolve, via a rate-place code, the lower harmonics of both HCTs, a prerequisite for deriving their pitches and for their perceptual segregation. Onset asynchrony between the HCTs enhanced the neural representation of their harmonics, paralleling their improved perceptual segregation in humans. Pitches of the concurrent HCTs could also be temporally represented by neuronal phase-locking at their respective F0s. Furthermore, a model of A1 responses using harmonic templates could qualitatively reproduce psychophysical data on concurrent sound segregation in humans. Finally, we identified a possible intracortical homolog of the “object-related negativity” recorded noninvasively in humans, which correlates with the perceptual segregation of concurrent sounds. Findings indicate that A1 contains sufficient spectral and temporal information for segregating concurrent sounds based on differences in pitch. PMID:25209282

Hierarchical neurocomputations underlying concurrent sound segregation: connecting periphery to percept.

PubMed

Bidelman, Gavin M; Alain, Claude

2015-02-01

Natural soundscapes often contain multiple sound sources at any given time. Numerous studies have reported that in human observers, the perception and identification of concurrent sounds is paralleled by specific changes in cortical event-related potentials (ERPs). Although these studies provide a window into the cerebral mechanisms governing sound segregation, little is known about the subcortical neural architecture and hierarchy of neurocomputations that lead to this robust perceptual process. Using computational modeling, scalp-recorded brainstem/cortical ERPs, and human psychophysics, we demonstrate that a primary cue for sound segregation, i.e., harmonicity, is encoded at the auditory nerve level within tens of milliseconds after the onset of sound and is maintained, largely untransformed, in phase-locked activity of the rostral brainstem. As then indexed by auditory cortical responses, (in)harmonicity is coded in the signature and magnitude of the cortical object-related negativity (ORN) response (150-200 ms). The salience of the resulting percept is then captured in a discrete, categorical-like coding scheme by a late negativity response (N5; ~500 ms latency), just prior to the elicitation of a behavioral judgment. Subcortical activity correlated with cortical evoked responses such that weaker phase-locked brainstem responses (lower neural harmonicity) generated larger ORN amplitude, reflecting the cortical registration of multiple sound objects. Studying multiple brain indices simultaneously helps illuminate the mechanisms and time-course of neural processing underlying concurrent sound segregation and may lead to further development and refinement of physiologically driven models of auditory scene analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Position specific variation in the rate of evolution in transcription factor binding sites

PubMed Central

Moses, Alan M; Chiang, Derek Y; Kellis, Manolis; Lander, Eric S; Eisen, Michael B

2003-01-01

Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Results Here we analyse the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikatae to study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms. Conclusion As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative sequence data in the identification of transcription factor binding sites and is an important step toward understanding the evolution of functional non-coding DNA. PMID:12946282

Impact of toroidal and poloidal mode spectra on the control of non-axisymmetric fields in tokamaks

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

Lanctot, Matthew J.; Park, J. -K.; Piovesan, Paolo

In several tokamaks, non-axisymmetric magnetic field studies show that applied magnetic fields with a toroidal harmonic n = 2 can lead to disruptive n = 1 locked modes. In Ohmic plasmas, n = 2 magnetic reconnection thresholds in otherwise stable discharges are readily accessed at edge safety factors q ~ 3, low density, and low rotation. Similar to previous studies with n = 1 fields, the thresholds are correlated with the “overlap” field computed with the IPEC code. The overlap field quantifies the plasma-mediated coupling of the external field to the resonant field. Remarkably, the “critical overlap fields” at whichmore » magnetic islands form are similar for applied n =1 and 2 fields. The critical overlap field increases with plasma density and edge safety factor but is independent of the toroidal field. Poloidal harmonics m > nq dominate the drive for resonant fields while m < nq harmonics have a negligible impact. This contrasts with previous results in H-mode discharges at high plasma pressure in which the toroidal angular momentum is sensitive to low poloidal harmonics. Altogether, these results highlight unique requirements for n > 1 field control including the need for multiple rows of coils to control selected plasma parameters for specific functions (e.g., rotation control or ELM suppression).« less

Impact of toroidal and poloidal mode spectra on the control of non-axisymmetric fields in tokamaks

DOE PAGES

Lanctot, Matthew J.; Park, J. -K.; Piovesan, Paolo; ...

2017-05-18

In several tokamaks, non-axisymmetric magnetic field studies show that applied magnetic fields with a toroidal harmonic n = 2 can lead to disruptive n = 1 locked modes. In Ohmic plasmas, n = 2 magnetic reconnection thresholds in otherwise stable discharges are readily accessed at edge safety factors q ~ 3, low density, and low rotation. Similar to previous studies with n = 1 fields, the thresholds are correlated with the “overlap” field computed with the IPEC code. The overlap field quantifies the plasma-mediated coupling of the external field to the resonant field. Remarkably, the “critical overlap fields” at whichmore » magnetic islands form are similar for applied n =1 and 2 fields. The critical overlap field increases with plasma density and edge safety factor but is independent of the toroidal field. Poloidal harmonics m > nq dominate the drive for resonant fields while m < nq harmonics have a negligible impact. This contrasts with previous results in H-mode discharges at high plasma pressure in which the toroidal angular momentum is sensitive to low poloidal harmonics. Altogether, these results highlight unique requirements for n > 1 field control including the need for multiple rows of coils to control selected plasma parameters for specific functions (e.g., rotation control or ELM suppression).« less

A description of the tides in the Eastern North Atlantic

NASA Astrophysics Data System (ADS)

Fanjul, Enrique Alvarez; Gómez, Begoña Pérez; Sánchez-Arévalo, Ignacio Rodríguez

A description of the Eastern North Atlantic tidal dynamics (in a region spanning from 20°N to 48°N in latitude and from 34°W to 0° in longitude) is obtained by means of new in situ measurements and numerical modelling based on TOPEX/POSEIDON-derived data sets. The main source of measurements is the tide gauge network REDMAR (RED de MAReógrafos de Puertos del Estado), operative since July 1992 and managed by Clima Marítimo (Puertos del Estado). Results derived from the harmonic analysis of the first years of measurements are presented and compared with model results. In order to obtain a global picture of the tides in the region, a large compilation of harmonic constants obtained from other institutes is included. The availability of new TOPEX/POSEIDON-derived harmonic constants data sets provides a chance to include the benefits derived from satellite altimetry in high resolution regional applications of numerical models. Richard Ray's tidal model (Ray et al., 1994), based on a response type tidal analysis of TOPEX/POSEIDON data, was employed within a model of the studied area. The numerical model employed is HAMSOM, a 3-D finite difference code developed both by the Institut für Meereskunde (Hamburg University) and Clima Marítimo. Results from simulations of seven major harmonics are presented, providing a comprehensive view of tidal dynamics, including current information. The results of tidal simulations show good agreement between semidiurnal harmonic components and the values measured by both coastal and pelagic tidal gauges and by current meters. The modelled diurnal constituents show larger relative differences with measurements than semidiurnal harmonics, especially concerning the phase lags. The non-linear transfer of energy from semidiurnal to higher order harmonics, such as M 4 and M 6, was mapped. Those transfers were found to be important only in two areas: the French continental shelf in the Bay of Biscay and the widest part of the African shelf, south of Cabo Bojador.

Numerical Simulation of a Double-anode Magnetron Injection Gun for 110 GHz, 1 MW Gyrotron

NASA Astrophysics Data System (ADS)

Singh, Udaybir; Kumar, Nitin; Purohit, L. P.; Sinha, Ashok K.

2010-07-01

A 40 A double-anode magnetron injection gun for a 1 MW, 110 GHz gyrotron has been designed. The preliminary design has been obtained by using some trade-off equations. The electron beam analysis has been performed by using the commercially available code EGUN and the in-house developed code MIGANS. The operating mode of the gyrotron is TE22,6 and it is operated in the fundamental harmonic. The electron beam with a low transverse velocity spread ( δ {β_{ bot max }} = 2.26% ) and the transverse-to-axial velocity ratio of the electron beam (α) = 1.37 is obtained. The simulated results of the MIG obtained with the EGUN code have been validated with another trajectory code TRAK. The results on the design output parameters obtained by both the codes are in good agreement. The sensitivity analysis has been carried out by changing the different gun parameters to decide the fabrication tolerance.

The Fast Scattering Code (FSC): Validation Studies and Program Guidelines

NASA Technical Reports Server (NTRS)

Tinetti, Ana F.; Dunn, Mark H.

2011-01-01

The Fast Scattering Code (FSC) is a frequency domain noise prediction program developed at the NASA Langley Research Center (LaRC) to simulate the acoustic field produced by the interaction of known, time harmonic incident sound with bodies of arbitrary shape and surface impedance immersed in a potential flow. The code uses the equivalent source method (ESM) to solve an exterior 3-D Helmholtz boundary value problem (BVP) by expanding the scattered acoustic pressure field into a series of point sources distributed on a fictitious surface placed inside the actual scatterer. This work provides additional code validation studies and illustrates the range of code parameters that produce accurate results with minimal computational costs. Systematic noise prediction studies are presented in which monopole generated incident sound is scattered by simple geometric shapes - spheres (acoustically hard and soft surfaces), oblate spheroids, flat disk, and flat plates with various edge topologies. Comparisons between FSC simulations and analytical results and experimental data are presented.

Coupled Harmonic Bases for Longitudinal Characterization of Brain Networks

PubMed Central

Hwang, Seong Jae; Adluru, Nagesh; Collins, Maxwell D.; Ravi, Sathya N.; Bendlin, Barbara B.; Johnson, Sterling C.; Singh, Vikas

2016-01-01

There is a great deal of interest in using large scale brain imaging studies to understand how brain connectivity evolves over time for an individual and how it varies over different levels/quantiles of cognitive function. To do so, one typically performs so-called tractography procedures on diffusion MR brain images and derives measures of brain connectivity expressed as graphs. The nodes correspond to distinct brain regions and the edges encode the strength of the connection. The scientific interest is in characterizing the evolution of these graphs over time or from healthy individuals to diseased. We pose this important question in terms of the Laplacian of the connectivity graphs derived from various longitudinal or disease time points — quantifying its progression is then expressed in terms of coupling the harmonic bases of a full set of Laplacians. We derive a coupled system of generalized eigenvalue problems (and corresponding numerical optimization schemes) whose solution helps characterize the full life cycle of brain connectivity evolution in a given dataset. Finally, we show a set of results on a diffusion MR imaging dataset of middle aged people at risk for Alzheimer’s disease (AD), who are cognitively healthy. In such asymptomatic adults, we find that a framework for characterizing brain connectivity evolution provides the ability to predict cognitive scores for individual subjects, and for estimating the progression of participant’s brain connectivity into the future. PMID:27812274

A Finite-Orbit-Width Fokker-Planck solver for modeling of RF Current Drive in ITER

NASA Astrophysics Data System (ADS)

Petrov, Yu. V.; Harvey, R. W.

2017-10-01

The bounce-average (BA) finite-difference Fokker-Planck (FP) code CQL3D now includes the essential physics to describe the RF heating of Finite-Orbit-Width (FOW) ions in tokamaks. The FP equation is reformulated in terms of constants-of-motion coordinates, which we select to be particle speed, pitch angle, and major radius on the equatorial plane thus obtaining the distribution function directly at this location. A recent development is the capability to obtain solution simultaneously for FOW ions and Zero-Orbit-Width (ZOW) electrons. As a practical application, the code is used for simulation of alpha-particle heating by high-harmonic waves in ITER scenarios. Coupling of high harmonic or helicon fast waves power to electrons is a promising current drive (CD) scenario for high beta plasmas. However, the efficiency of current drive can be diminished by parasitic channeling of RF power into fast ions such as alphas or NBI-produced deuterons, through finite Larmor-radius effects. Based on simulations, we formulate conditions where the fast ions absorb less than 10% of RF power. Supported by USDOE Grants ER54649, ER54744, and SC0006614.

Development of a linearized unsteady Euler analysis for turbomachinery blade rows

NASA Technical Reports Server (NTRS)

Verdon, Joseph M.; Montgomery, Matthew D.; Kousen, Kenneth A.

1995-01-01

A linearized unsteady aerodynamic analysis for axial-flow turbomachinery blading is described in this report. The linearization is based on the Euler equations of fluid motion and is motivated by the need for an efficient aerodynamic analysis that can be used in predicting the aeroelastic and aeroacoustic responses of blade rows. The field equations and surface conditions required for inviscid, nonlinear and linearized, unsteady aerodynamic analyses of three-dimensional flow through a single, blade row operating within a cylindrical duct, are derived. An existing numerical algorithm for determining time-accurate solutions of the nonlinear unsteady flow problem is described, and a numerical model, based upon this nonlinear flow solver, is formulated for the first-harmonic linear unsteady problem. The linearized aerodynamic and numerical models have been implemented into a first-harmonic unsteady flow code, called LINFLUX. At present this code applies only to two-dimensional flows, but an extension to three-dimensions is planned as future work. The three-dimensional aerodynamic and numerical formulations are described in this report. Numerical results for two-dimensional unsteady cascade flows, excited by prescribed blade motions and prescribed aerodynamic disturbances at inlet and exit, are also provided to illustrate the present capabilities of the LINFLUX analysis.

Euler flow predictions for an oscillating cascade using a high resolution wave-split scheme

NASA Technical Reports Server (NTRS)

Huff, Dennis L.; Swafford, Timothy W.; Reddy, T. S. R.

1991-01-01

A compressible flow code that can predict the nonlinear unsteady aerodynamics associated with transonic flows over oscillating cascades is developed and validated. The code solves the two dimensional, unsteady Euler equations using a time-marching, flux-difference splitting scheme. The unsteady pressures and forces can be determined for arbitrary input motions, although only harmonic pitching and plunging motions are addressed. The code solves the flow equations on a H-grid which is allowed to deform with the airfoil motion. Predictions are presented for both flat plate cascades and loaded airfoil cascades. Results are compared to flat plate theory and experimental data. Predictions are also presented for several oscillating cascades with strong normal shocks where the pitching amplitudes, cascade geometry and interblade phase angles are varied to investigate nonlinear behavior.

The Evolution of the Council of Academic Hospitals of Ontario Statement of Principles--A Successful Harmonization Initiative

ERIC Educational Resources Information Center

Porter, Katie; Lampson, Sarah

2011-01-01

To improve efficiency, consistency and transparency in clinical trial contract negotiations with industry sponsors, a Council of Academic Hospitals of Ontario (CAHO) committee facilitated the development of standard principles for member hospitals to follow during contract negotiation. Hospitals were encouraged to provide a link to the CAHO…

Inventory development for perfluorooctane sulfonic acid (PFOS) in Turkey: challenges to control chemicals in articles and products.

PubMed

Korucu, M Kemal; Gedik, Kadir; Weber, Roland; Karademir, Aykan; Kurt-Karakus, Perihan Binnur

2015-10-01

Perfluorooctane sulfonic acid (PFOS) and related substances have been listed as persistent organic pollutants (POPs) in the Stockholm Convention. Countries which have ratified the Convention need to take appropriate actions to control PFOS use and release. This study compiles and enhances the findings of the first inventory of PFOS and related substances use in Turkey conducted within the frame of the Stockholm Convention National Implementation Plan (NIP) update. The specific Harmonized Commodity Description and Coding System (Harmonized System (HS)) codes of imported and exported goods that possibly contain PFOS and 165 of Chemical Abstracts Service (CAS) numbers of PFOS-related substances were assessed for acquiring information from customs and other authorities. However, with the current approaches available, no useful information could be compiled since HS codes are not specific enough and CAS numbers are not used by customs. Furthermore, the cut-off volume in chemical databases in Turkey and the reporting limit in the HS system (0.1 %) are too high for controlling PFOS. The attempt of modeling imported volumes by a Monte Carlo simulation did not also result in a satisfactory estimate, giving an upper-bound estimate above the global production volumes. The replies to questionnaires were not satisfactory, highlighting that an elaborated approach is needed in the communication with potentially PFOS-using stakeholders. The experience of the challenges of gathering information on PFOS in articles and products revealed the gaps of controlling highly hazardous substances in products and articles and the need of improvements.

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

Calero, C.; Knorowski, C.; Travesset, A.

We investigate a general method to calculate the free energy of crystalline solids by considering the harmonic approximation and quasistatically switching the anharmonic contribution. The advantage of this method is that the harmonic approximation provides an already very accurate estimate of the free energy, and therefore the anharmonic term is numerically very small and can be determined to high accuracy. We further show that the anharmonic contribution to the free energy satisfies a number of exact inequalities that place constraints on its magnitude and allows approximate but fast and accurate estimates. The method is implemented into a readily available generalmore » software by combining the code HOODLT (Highly Optimized Object Oriented Dynamic Lattice Theory) for the harmonic part and the molecular dynamics (MD) simulation package HOOMD-blue for the anharmonic part. We use the method to calculate the low temperature phase diagram for Lennard-Jones particles. We demonstrate that hcp is the equilibrium phase at low temperature and pressure and obtain the coexistence curve with the fcc phase, which exhibits reentrant behavior. Furthermore, several implications of the method are discussed.« less

Determination of anharmonic free energy contributions: Low temperature phases of the Lennard-Jones system

DOE PAGES

Calero, C.; Knorowski, C.; Travesset, A.

2016-03-22

We investigate a general method to calculate the free energy of crystalline solids by considering the harmonic approximation and quasistatically switching the anharmonic contribution. The advantage of this method is that the harmonic approximation provides an already very accurate estimate of the free energy, and therefore the anharmonic term is numerically very small and can be determined to high accuracy. We further show that the anharmonic contribution to the free energy satisfies a number of exact inequalities that place constraints on its magnitude and allows approximate but fast and accurate estimates. The method is implemented into a readily available generalmore » software by combining the code HOODLT (Highly Optimized Object Oriented Dynamic Lattice Theory) for the harmonic part and the molecular dynamics (MD) simulation package HOOMD-blue for the anharmonic part. We use the method to calculate the low temperature phase diagram for Lennard-Jones particles. We demonstrate that hcp is the equilibrium phase at low temperature and pressure and obtain the coexistence curve with the fcc phase, which exhibits reentrant behavior. Furthermore, several implications of the method are discussed.« less

Aeroelastic analysis for helicopter rotors with blade appended pendulum vibration absorbers. Mathematical derivations and program user's manual

NASA Technical Reports Server (NTRS)

Bielawa, R. L.

1982-01-01

Mathematical development is presented for the expanded capabilities of the United Technologies Research Center (UTRC) G400 Rotor Aeroelastic Analysis. This expanded analysis, G400PA, simulates the dynamics of teetered rotors, blade pendulum vibration absorbers and the higher harmonic excitations resulting from prescribed vibratory hub motions and higher harmonic blade pitch control. Formulations are also presented for calculating the rotor impedance matrix appropriate to these higher harmonic blade excitations. This impedance matrix and the associated vibratory hub loads are intended as the rotor blade characteristics elements for use in the Simplified Coupled Rotor/Fuselage Vibration Analysis (SIMVIB). Sections are included presenting updates to the development of the original G400 theory, and material appropriate to the user of the G400PA computer program. This material includes: (1) a general descriptionof the tructuring of the G400PA FORTRAN coding, (2) a detaild description of the required input data and other useful information for successfully running the program, and (3) a detailed description of the output results.

An approach for spherical harmonic analysis of non-smooth data

NASA Astrophysics Data System (ADS)

Wang, Hansheng; Wu, Patrick; Wang, Zhiyong

2006-12-01

A method is proposed to evaluate the spherical harmonic coefficients of a global or regional, non-smooth, observable dataset sampled on an equiangular grid. The method is based on an integration strategy using new recursion relations. Because a bilinear function is used to interpolate points within the grid cells, this method is suitable for non-smooth data; the slope of the data may be piecewise continuous, with extreme changes at the boundaries. In order to validate the method, the coefficients of an axisymmetric model are computed, and compared with the derived analytical expressions. Numerical results show that this method is indeed reasonable for non-smooth models, and that the maximum degree for spherical harmonic analysis should be empirically determined by several factors including the model resolution and the degree of non-smoothness in the dataset, and it can be several times larger than the total number of latitudinal grid points. It is also shown that this method is appropriate for the approximate analysis of a smooth dataset. Moreover, this paper provides the program flowchart and an internet address where the FORTRAN code with program specifications are made available.

Spherical nanoindentation stress-strain analysis, Version 1

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

Weaver, Jordan S.; Turner, David; Miller, Calvin

Nanoindentation is a tool that allows the mechanical response of a variety of materials at the nano to micron length scale to be measured. Recent advances in spherical nanoindentation techniques have allowed for a more reliable and meaningful characterization of the mechanical response from nanoindentation experiments in the form on an indentation stress-strain curve. This code base, Spin, is written in MATLAB (The Mathworks, Inc.) and based on the analysis protocols developed by S.R. Kalidindi and S. Pathak [1, 2]. The inputs include the displacement, load, harmonic contact stiffness, harmonic displacement, and harmonic load from spherical nanoindentation tests in themore » form of an Excel (Microsoft) spreadsheet. The outputs include indentation stress-strain curves and indentation properties as well their variance due to the uncertainty of the zero-point correction in the form of MATLAB data (.mat) and figures (.png). [1] S. Pathak, S.R. Kalidindi. Spherical nanoindentation stress–strain curves, Mater. Sci. Eng R-Rep 91 (2015). [2] S.R. Kalidindi, S. Pathak. Determination of the effective zero-point and the extraction of spherical nanoindentation stress-strain curves, Acta Materialia 56 (2008) 3523-3532.« less

Optimization Studies of the FERMI at ELETTRA FEL Design

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

De Ninno, Giovanni; Fawley, William M.; Penn, Gregory E.

The FERMI at ELETTRA project at Sincotrone Trieste involves two FEL's, each based upon the principle of seeded harmonic generation and using the existing ELETTRA injection linac at 1.2 GeV beam energy. Scheduled to be completed in 2008, FEL-1 will operate in 40-100 nm wavelength range and will involve one stage of harmonic up-conversion. The second undulator line, FEL-2, will begin operation two years later in the 10-40 nm wavelength range and use two harmonic stages operating as a cascade. The FEL design assumes continuous wavelength tunability over the full wavelength range, and polarization tunability of the output radiation includingmore » vertical or horizontal linear as well as helical polarization. The design considers focusing properties and segmentation of realizable undulators and available input seed lasers. We review the studies that have led to our current design. We present results of simulations using GENESIS and GINGER simulation codes including studies of various shot-to-shot fluctuations and undulator errors. Findings for the expected output radiation in terms of the power, transverse and longitudinal coherence are reported.« less

Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

PubMed

Pang, Erli; Wu, Xiaomei; Lin, Kui

2016-06-01

Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution.

Improving 1D Stellar Models with 3D Atmospheres

NASA Astrophysics Data System (ADS)

Mosumgaard, Jakob Rørsted; Silva Aguirre, Víctor; Weiss, Achim; Christensen-Dalsgaard, Jørgen; Trampedach, Regner

2017-10-01

Stellar evolution codes play a major role in present-day astrophysics, yet they share common issues. In this work we seek to remedy some of those by the use of results from realistic and highly detailed 3D hydrodynamical simulations of stellar atmospheres. We have implemented a new temperature stratification extracted directly from the 3D simulations into the Garching Stellar Evolution Code to replace the simplified atmosphere normally used. Secondly, we have implemented the use of a variable mixing-length parameter, which changes as a function of the stellar surface gravity and temperature - also derived from the 3D simulations. Furthermore, to make our models consistent, we have calculated new opacity tables to match the atmospheric simulations. Here, we present the modified code and initial results on stellar evolution using it.

The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape.

PubMed

Yousaf, Aisha; Sohail Raza, Muhammad; Ali Abbasi, Amir

2015-08-06

Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates' conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water-land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods' enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Comparison of Three Elliptical Galaxy Photochemical Evolution Codes

NASA Astrophysics Data System (ADS)

Gibson, Brad K.

1996-09-01

Working within the classic supernovae-driven wind framework for elliptical galaxy evolution, We perform a systematic investigation into the discrepancies between the predictions of three contemporary codes (by Arimoto & Yoshii, Bressan et al., and Gibson). By being primarily concerned with reproducing the present-day color-metallicity-luminosity (CML) relations among elliptical galaxies, the approaches taken in the theoretical modeling have managed to obscure many of the hidden differences between the codes. Targeting the timescale for the onset of the initial galactic wind, t_GW_, as a primary "difference" indicator, We demonstrate exactly how and why each code is able to claim successful reproduction of the CML relations, despite possessing apparently incompatible input ingredients.

On the evolution of primitive genetic codes.

PubMed

Weberndorfer, Günter; Hofacker, Ivo L; Stadler, Peter F

2003-10-01

The primordial genetic code probably has been a drastically simplified ancestor of the canonical code that is used by contemporary cells. In order to understand how the present-day code came about we first need to explain how the language of the building plan can change without destroying the encoded information. In this work we introduce a minimal organism model that is based on biophysically reasonable descriptions of RNA and protein, namely secondary structure folding and knowledge based potentials. The evolution of a population of such organism under competition for a common resource is simulated explicitly at the level of individual replication events. Starting with very simple codes, and hence greatly reduced amino acid alphabets, we observe a diversification of the codes in most simulation runs. The driving force behind this effect is the possibility to produce fitter proteins when the repertoire of amino acids is enlarged.

Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.

PubMed

Seligmann, Hervé

2018-05-01

Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections. Copyright © 2018 Elsevier B.V. All rights reserved.

Hyperspectral retrieval of surface reflectances: A new scheme

NASA Astrophysics Data System (ADS)

Thelen, Jean-Claude; Havemann, Stephan

2013-05-01

Here, we present a new prototype algorithm for the simultaneous retrieval of the atmospheric profiles (temperature, humidity, ozone and aerosol) and the surface reflectance from hyperspectral radiance measurements obtained from air/space borne, hyperspectral imagers. The new scheme, proposed here, consists of a fast radiative transfer code, based on empirical orthogonal functions (EOFs), in conjunction with a 1D-Var retrieval scheme. The inclusion of an 'exact' scattering code based on spherical harmonics, allows for an accurate treatment of Rayleigh scattering and scattering by aerosols, water droplets and ice-crystals, thus making it possible to also retrieve cloud and aerosol optical properties, although here we will concentrate on non-cloudy scenes.

Axially deformed solution of the Skyrme–Hartree–Fock–Bogolyubov equations using the transformed harmonic oscillator basis (III) hfbtho (v3.00): A new version of the program

DOE PAGES

Perez, R. Navarro; Schunck, N.; Lasseri, R. -D.; ...

2017-07-05

Here, we describe the new version 3.00 of the code hfbtho that solves the nuclear Hartree–Fock (HF) or Hartree–Fock–Bogolyubov (HFB) problem by using the cylindrical transformed deformed harmonic oscillator basis. In the new version, we have implemented the following features: (i) the full Gogny force in both particle–hole and particle–particle channels, (ii) the calculation of the nuclear collective inertia at the perturbative cranking approximation, (iii) the calculation of fission fragment charge, mass and deformations based on the determination of the neck, (iv) the regularization of zero-range pairing forces, (v) the calculation of localization functions, (vi) a MPI interface for large-scalemore » mass table calculations.« less

Demonstration of Johnson noise thermometry with all-superconducting quantum voltage noise source

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

Yamada, Takahiro, E-mail: yamada-takahiro@aist.go.jp; Urano, Chiharu; Maezawa, Masaaki

We present a Johnson noise thermometry (JNT) system based on an integrated quantum voltage noise source (IQVNS) that has been fully implemented using superconducting circuit technology. To enable precise measurement of Boltzmann's constant, an IQVNS chip was designed to produce intrinsically calculable pseudo-white noise to calibrate the JNT system. On-chip real-time generation of pseudo-random codes via simple circuits produced pseudo-voltage noise with a harmonic tone interval of less than 1 Hz, which was one order of magnitude finer than the harmonic tone interval of conventional quantum voltage noise sources. We estimated a value for Boltzmann's constant experimentally by performing JNT measurementsmore » at the temperature of the triple point of water using the IQVNS chip.« less

Quaternionic representation of the genetic code.

PubMed

Carlevaro, C Manuel; Irastorza, Ramiro M; Vericat, Fernando

2016-03-01

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Precise and efficient evaluation of gravimetric quantities at arbitrarily scattered points in space

NASA Astrophysics Data System (ADS)

Ivanov, Kamen G.; Pavlis, Nikolaos K.; Petrushev, Pencho

2017-12-01

Gravimetric quantities are commonly represented in terms of high degree surface or solid spherical harmonics. After EGM2008, such expansions routinely extend to spherical harmonic degree 2190, which makes the computation of gravimetric quantities at a large number of arbitrarily scattered points in space using harmonic synthesis, a very computationally demanding process. We present here the development of an algorithm and its associated software for the efficient and precise evaluation of gravimetric quantities, represented in high degree solid spherical harmonics, at arbitrarily scattered points in the space exterior to the surface of the Earth. The new algorithm is based on representation of the quantities of interest in solid ellipsoidal harmonics and application of the tensor product trigonometric needlets. A FORTRAN implementation of this algorithm has been developed and extensively tested. The capabilities of the code are demonstrated using as examples the disturbing potential T, height anomaly ζ , gravity anomaly Δ g , gravity disturbance δ g , north-south deflection of the vertical ξ , east-west deflection of the vertical η , and the second radial derivative T_{rr} of the disturbing potential. After a pre-computational step that takes between 1 and 2 h per quantity, the current version of the software is capable of computing on a standard PC each of these quantities in the range from the surface of the Earth up to 544 km above that surface at speeds between 20,000 and 40,000 point evaluations per second, depending on the gravimetric quantity being evaluated, while the relative error does not exceed 10^{-6} and the memory (RAM) use is 9.3 GB.

XTRAN2L - A PROGRAM FOR SOLVING THE GENERAL-FREQUENCY UNSTEADY TWO-DIMENSIONAL TRANSONIC SMALL-DISTURBANCE EQUATIONS

NASA Technical Reports Server (NTRS)

Seidel, D. A.

1994-01-01

The Program for Solving the General-Frequency Unsteady Two-Dimensional Transonic Small-Disturbance Equation, XTRAN2L, is used to calculate time-accurate, finite-difference solutions of the nonlinear, small-disturbance potential equation for two- dimensional transonic flow about airfoils. The code can treat forced harmonic, pulse, or aeroelastic transient type motions. XTRAN2L uses a transonic small-disturbance equation that incorporates a time accurate finite-difference scheme. Airfoil flow tangency boundary conditions are defined to include airfoil contour, chord deformation, nondimensional plunge displacement, pitch, and trailing edge control surface deflection. Forced harmonic motion can be based on: 1) coefficients of harmonics based on information from each quarter period of the last cycle of harmonic motion; or 2) Fourier analyses of the last cycle of motion. Pulse motion (an alternate to forced harmonic motion) in which the airfoil is given a small prescribed pulse in a given mode of motion, and the aerodynamic transients are calculated. An aeroelastic transient capability is available within XTRAN2L, wherein the structural equations of motion are coupled with the aerodynamic solution procedure for simultaneous time-integration. The wake is represented as a slit downstream of the airfoil trailing edge. XTRAN2L includes nonreflecting farfield boundary conditions. XTRAN2L was developed on a CDC CYBER mainframe running under NOS 2.4. It is written in FORTRAN 5 and uses overlays to minimize storage requirements. The program requires 120K of memory in overlayed form. XTRAN2L was developed in 1987.

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

PubMed Central

Reinhardt, Josephine A.; Wanjiru, Betty M.; Brant, Alicia T.; Saelao, Perot; Begun, David J.; Jones, Corbin D.

2013-01-01

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important. PMID:24146629

Dynamic Monte Carlo simulations of radiatively accelerated GRB fireballs

NASA Astrophysics Data System (ADS)

Chhotray, Atul; Lazzati, Davide

2018-05-01

We present a novel Dynamic Monte Carlo code (DynaMo code) that self-consistently simulates the Compton-scattering-driven dynamic evolution of a plasma. We use the DynaMo code to investigate the time-dependent expansion and acceleration of dissipationless gamma-ray burst fireballs by varying their initial opacities and baryonic content. We study the opacity and energy density evolution of an initially optically thick, radiation-dominated fireball across its entire phase space - in particular during the Rph < Rsat regime. Our results reveal new phases of fireball evolution: a transition phase with a radial extent of several orders of magnitude - the fireball transitions from Γ ∝ R to Γ ∝ R0, a post-photospheric acceleration phase - where fireballs accelerate beyond the photosphere and a Thomson-dominated acceleration phase - characterized by slow acceleration of optically thick, matter-dominated fireballs due to Thomson scattering. We quantify the new phases by providing analytical expressions of Lorentz factor evolution, which will be useful for deriving jet parameters.

Design of the central region for axial injection in the VINCY cyclotron

NASA Astrophysics Data System (ADS)

Milinković, Ljiljana; Toprek, Dragan

1996-02-01

This paper describes the design of the central region for h = 1, h = 2 and h = 4 modes of acceleration in the VINCY cyclotron. The result which is worth reported in that the central region is unique and compatible with the three above mentioned harmonic modes of operation. Only one spiral type inflector will be used. The central region is designed to operate with two external ion sources: (a) an ECR ion source with the maximum extraction voltage of 25 kV for heavy ions, and (b) a multicusp ion source with the maximum extraction voltage of 30 kV for H - and D - ions. Heavy ions will be accelerated by the second and fourth harmonics, D - ions by the second harmonic and H - ions by the first harmonic of the RF field. The central region is equipped with an axial injection system. The electric field distribution in the inflector and in the four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region were studied by using the programs CASINO and CYCLONE respectively. We have also made an effort to minimize the inflector fringe field using the RELAX3D program.

Implementation of a hybrid particle code with a PIC description in r–z and a gridless description in ϕ into OSIRIS

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

Davidson, A., E-mail: davidsoa@physics.ucla.edu; Tableman, A., E-mail: Tableman@physics.ucla.edu; An, W., E-mail: anweiming@ucla.edu

2015-01-15

For many plasma physics problems, three-dimensional and kinetic effects are very important. However, such simulations are very computationally intensive. Fortunately, there is a class of problems for which there is nearly azimuthal symmetry and the dominant three-dimensional physics is captured by the inclusion of only a few azimuthal harmonics. Recently, it was proposed [1] to model one such problem, laser wakefield acceleration, by expanding the fields and currents in azimuthal harmonics and truncating the expansion. The complex amplitudes of the fundamental and first harmonic for the fields were solved on an r–z grid and a procedure for calculating the complexmore » current amplitudes for each particle based on its motion in Cartesian geometry was presented using a Marder's correction to maintain the validity of Gauss's law. In this paper, we describe an implementation of this algorithm into OSIRIS using a rigorous charge conserving current deposition method to maintain the validity of Gauss's law. We show that this algorithm is a hybrid method which uses a particles-in-cell description in r–z and a gridless description in ϕ. We include the ability to keep an arbitrary number of harmonics and higher order particle shapes. Examples for laser wakefield acceleration, plasma wakefield acceleration, and beam loading are also presented and directions for future work are discussed.« less

Molecular vibrational states during a collision

NASA Technical Reports Server (NTRS)

Recamier, Jose A.; Jauregui, Rocio

1995-01-01

Alternative algebraic techniques to approximate a given Hamiltonian by a harmonic oscillator are described both for time-independent and time-dependent systems. We apply them to the description of a one dimensional atom-diatom collision. From the resulting evolution operator, we evaluate vibrational transition probabilities as well as other time-dependent properties. As expected, the ground vibrational state becomes a squeezed state during the collision.

The physics of symbols: bridging the epistemic cut.

PubMed

Pattee, H H

2001-01-01

Evolution requires the genotype-phenotype distinction, a primeval epistemic cut that separates energy-degenerate, rate-independent genetic symbols from the rate-dependent dynamics of construction that they control. This symbol-matter or subject-object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code. The converse of control is measurement in which a rate-dependent dynamical state is coded into quiescent symbols. Non-integrable constraints are one necessary condition for bridging the epistemic cut by measurement, control, and coding. Additional properties of heteropolymer constraints are necessary for biological evolution.

Coding strategies for cochlear implants under adverse environments

NASA Astrophysics Data System (ADS)

Tahmina, Qudsia

Cochlear implants are electronic prosthetic devices that restores partial hearing in patients with severe to profound hearing loss. Although most coding strategies have significantly improved the perception of speech in quite listening conditions, there remains limitations on speech perception under adverse environments such as in background noise, reverberation and band-limited channels, and we propose strategies that improve the intelligibility of speech transmitted over the telephone networks, reverberated speech and speech in the presence of background noise. For telephone processed speech, we propose to examine the effects of adding low-frequency and high- frequency information to the band-limited telephone speech. Four listening conditions were designed to simulate the receiving frequency characteristics of telephone handsets. Results indicated improvement in cochlear implant and bimodal listening when telephone speech was augmented with high frequency information and therefore this study provides support for design of algorithms to extend the bandwidth towards higher frequencies. The results also indicated added benefit from hearing aids for bimodal listeners in all four types of listening conditions. Speech understanding in acoustically reverberant environments is always a difficult task for hearing impaired listeners. Reverberated sounds consists of direct sound, early reflections and late reflections. Late reflections are known to be detrimental to speech intelligibility. In this study, we propose a reverberation suppression strategy based on spectral subtraction to suppress the reverberant energies from late reflections. Results from listening tests for two reverberant conditions (RT60 = 0.3s and 1.0s) indicated significant improvement when stimuli was processed with SS strategy. The proposed strategy operates with little to no prior information on the signal and the room characteristics and therefore, can potentially be implemented in real-time CI speech processors. For speech in background noise, we propose a mechanism underlying the contribution of harmonics to the benefit of electroacoustic stimulations in cochlear implants. The proposed strategy is based on harmonic modeling and uses synthesis driven approach to synthesize the harmonics in voiced segments of speech. Based on objective measures, results indicated improvement in speech quality. This study warrants further work into development of algorithms to regenerate harmonics of voiced segments in the presence of noise.

An evaluation of a computer code based on linear acoustic theory for predicting helicopter main rotor noise

NASA Astrophysics Data System (ADS)

Davis, S. J.; Egolf, T. A.

1980-07-01

Acoustic characteristics predicted using a recently developed computer code were correlated with measured acoustic data for two helicopter rotors. The analysis, is based on a solution of the Ffowcs-Williams-Hawkings (FW-H) equation and includes terms accounting for both the thickness and loading components of the rotational noise. Computations are carried out in the time domain and assume free field conditions. Results of the correlation show that the Farrassat/Nystrom analysis, when using predicted airload data as input, yields fair but encouraging correlation for the first 6 harmonics of blade passage. It also suggests that although the analysis represents a valuable first step towards developing a truly comprehensive helicopter rotor noise prediction capability, further work remains to be done identifying and incorporating additional noise mechanisms into the code.

Function and Evolution of Vibrato-like Frequency Modulation in Mammals.

PubMed

Charlton, Benjamin D; Taylor, Anna M; Reby, David

2017-09-11

Why do distantly related mammals like sheep, giant pandas, and fur seals produce bleats that are characterized by vibrato-like fundamental frequency (F0) modulation? To answer this question, we used psychoacoustic tests and comparative analyses to investigate whether this distinctive vocal feature has evolved to improve the perception of formants, key acoustic components of animal calls that encode important information about the caller's size and identity [1]. Psychoacoustic tests on humans confirmed that vibrato-like F0 modulation improves the ability of listeners to detect differences in the formant patterns of synthetic bleat-like stimuli. Subsequent phylogenetically controlled comparative analyses revealed that vibrato-like F0 modulation has evolved independently in six mammalian orders in vocal signals with relatively high F0 and, therefore, low spectral density (i.e., less harmonic overtones). We also found that mammals modulate the vibrato in these calls over greater frequency extents when the number of harmonic overtones per formant is low, suggesting that this is a mechanism to improve formant perception in calls with low spectral density. Our findings constitute the first evidence that formant perception in non-speech sounds is improved by fundamental frequency modulation and provide a mechanism for the convergent evolution of bleat-like calls in mammals. They also indicate that selection pressures for animals to transmit important information encoded by formant frequencies (on size and identity, for example) are likely to have been a key driver in the evolution of mammal vocal diversity. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the coupled evolution of oceanic internal waves and quasi-geostrophic flow

NASA Astrophysics Data System (ADS)

Wagner, Gregory LeClaire

Oceanic motion outside thin boundary layers is primarily a mixture of quasi-geostrophic flow and internal waves with either near-inertial frequencies or the frequency of the semidiurnal lunar tide. This dissertation seeks a deeper understanding of waves and flow through reduced models that isolate their nonlinear and coupled evolution from the Boussinesq equations. Three physical-space models are developed: an equation that describes quasi-geostrophic evolution in an arbitrary and prescribed field of hydrostatic internal waves; a three-component model that couples quasi-geostrophic flow to both near-inertial waves and the near-inertial second harmonic; and a model for the slow evolution of hydrostatic internal tides in quasi-geostrophic flow of near-arbitrary scale. This slow internal tide equation opens the path to a coupled model for the energetic interaction of quasi-geostrophic flow and oceanic internal tides. Four results emerge. First, the wave-averaged quasi-geostrophic equation reveals that finite-amplitude waves give rise to a mean flow that advects quasi-geostrophic potential vorticity. Second is the definition of a new material invariant: Available Potential Vorticity, or APV. APV isolates the part of Ertel potential vorticity available for balanced-flow evolution in Eulerian frames and proves necessary in the separating waves and quasi-geostrophic flow. The third result, hashed out for near-inertial waves and quasi-geostrophic flow, is that wave-flow interaction leads to energy exchange even under conditions of weak nonlinearity. For storm-forced oceanic near-inertial waves the interaction often energizes waves at the expense of flow. We call this extraction of balanced quasi-geostrophic energy 'stimulated generation' since it requires externally-forced rather than spontaneously-generated waves. The fourth result is that quasi-geostrophic flow can encourage or 'catalyze' a nonlinear interaction between a near-inertial wave field and its second harmonic that transfers energy to the small near-inertial vertical scales of wave breaking and mixing.

Progenitors of Core-Collapse Supernovae

NASA Astrophysics Data System (ADS)

Hirschi, R.; Arnett, D.; Cristini, A.; Georgy, C.; Meakin, C.; Walkington, I.

2017-02-01

Massive stars have a strong impact on their surroundings, in particular when they produce a core-collapse supernova at the end of their evolution. In these proceedings, we review the general evolution of massive stars and their properties at collapse as well as the transition between massive and intermediate-mass stars. We also summarise the effects of metallicity and rotation. We then discuss some of the major uncertainties in the modelling of massive stars, with a particular emphasis on the treatment of convection in 1D stellar evolution codes. Finally, we present new 3D hydrodynamic simulations of convection in carbon burning and list key points to take from 3D hydrodynamic studies for the development of new prescriptions for convective boundary mixing in 1D stellar evolution codes.

Electron scattering in large water clusters from photoelectron imaging with high harmonic radiation.

PubMed

Gartmann, Thomas E; Hartweg, Sebastian; Ban, Loren; Chasovskikh, Egor; Yoder, Bruce L; Signorell, Ruth

2018-06-06

Low-energy electron scattering in water clusters (H2O)n with average cluster sizes of n < 700 is investigated by angle-resolved photoelectron spectroscopy using high harmonic radiation at photon energies of 14.0, 20.3, and 26.5 eV for ionization from the three outermost valence orbitals. The measurements probe the evolution of the photoelectron anisotropy parameter β as a function of cluster size. A remarkably steep decrease of β with increasing cluster size is observed, which for the largest clusters reaches liquid bulk values. Detailed electron scattering calculations reveal that neither gas nor condensed phase scattering can explain the cluster data. Qualitative agreement between experiment and simulations is obtained with scattering calculations that treat cluster scattering as an intermediate case between gas and condensed phase scattering.

Explanatory Parent-Child Conversation Predominates at an Evolution Exhibit

ERIC Educational Resources Information Center

Tare, Medha; French, Jason; Frazier, Brandy N.; Diamond, Judy; Evans, E. Margaret

2011-01-01

To investigate how parents support children's learning at an exhibit on evolution, the conversations of 12 families were recorded, transcribed, and coded (6,263 utterances). Children (mean age 9.6 years) and parents visited Explore Evolution, which conveyed current research about the evolution of seven organisms. Families were engaged with the…

Coding of DNA samples and data in the pharmaceutical industry: current practices and future directions--perspective of the I-PWG.

PubMed

Franc, M A; Cohen, N; Warner, A W; Shaw, P M; Groenen, P; Snapir, A

2011-04-01

DNA samples collected in clinical trials and stored for future research are valuable to pharmaceutical drug development. Given the perceived higher risk associated with genetic research, industry has implemented complex coding methods for DNA. Following years of experience with these methods and with addressing questions from institutional review boards (IRBs), ethics committees (ECs) and health authorities, the industry has started reexamining the extent of the added value offered by these methods. With the goal of harmonization, the Industry Pharmacogenomics Working Group (I-PWG) conducted a survey to gain an understanding of company practices for DNA coding and to solicit opinions on their effectiveness at protecting privacy. The results of the survey and the limitations of the coding methods are described. The I-PWG recommends dialogue with key stakeholders regarding coding practices such that equal standards are applied to DNA and non-DNA samples. The I-PWG believes that industry standards for privacy protection should provide adequate safeguards for DNA and non-DNA samples/data and suggests a need for more universal standards for samples stored for future research.

Mesh-based Monte Carlo code for fluorescence modeling in complex tissues with irregular boundaries

NASA Astrophysics Data System (ADS)

Wilson, Robert H.; Chen, Leng-Chun; Lloyd, William; Kuo, Shiuhyang; Marcelo, Cynthia; Feinberg, Stephen E.; Mycek, Mary-Ann

2011-07-01

There is a growing need for the development of computational models that can account for complex tissue morphology in simulations of photon propagation. We describe the development and validation of a user-friendly, MATLAB-based Monte Carlo code that uses analytically-defined surface meshes to model heterogeneous tissue geometry. The code can use information from non-linear optical microscopy images to discriminate the fluorescence photons (from endogenous or exogenous fluorophores) detected from different layers of complex turbid media. We present a specific application of modeling a layered human tissue-engineered construct (Ex Vivo Produced Oral Mucosa Equivalent, EVPOME) designed for use in repair of oral tissue following surgery. Second-harmonic generation microscopic imaging of an EVPOME construct (oral keratinocytes atop a scaffold coated with human type IV collagen) was employed to determine an approximate analytical expression for the complex shape of the interface between the two layers. This expression can then be inserted into the code to correct the simulated fluorescence for the effect of the irregular tissue geometry.

Effects of sensorineural hearing loss on temporal coding of harmonic and inharmonic tone complexes in the auditory nerve

PubMed Central

Kale, Sushrut; Micheyl, Christophe; Heinz, Michael G.

2013-01-01

Listeners with sensorineural hearing loss (SNHL) often show poorer thresholds for fundamental-frequency (F0) discrimination, and poorer discrimination between harmonic and frequency-shifted (inharmonic) complex tones, than normal-hearing (NH) listeners—especially when these tones contain resolved or partially resolved components. It has been suggested that these perceptual deficits reflect reduced access to temporal-fine-structure (TFS) information, and could be due to degraded phase-locking in the auditory nerve (AN) with SNHL. In the present study, TFS and temporal-envelope (ENV) cues in single AN-fiber responses to bandpass-filtered harmonic and inharmonic complex tones were measured in chinchillas with either normal hearing or noise-induced SNHL. The stimuli were comparable to those used in recent psychophysical studies of F0 and harmonic/inharmonic discrimination. As in those studies, the rank of the center component was manipulated to produce different resolvability conditions, different phase relationships (cosine and random phase) were tested, and background noise was present. Neural TFS and ENV cues were quantified using cross-correlation coefficients computed using shuffled cross-correlograms between neural responses to REF (harmonic) and TEST (F0- or frequency-shifted) stimuli. In animals with SNHL, AN-fiber tuning curves showed elevated thresholds, broadened tuning, best-frequency shifts, and downward shifts in the dominant TFS response component; however, no significant degradation in the ability of AN fibers to encode TFS or ENV cues was found. Consistent with optimal-observer analyses, the results indicate that TFS and ENV cues depended only on the relevant frequency shift in Hz and thus were not degraded because phase-locking remained intact. These results suggest that perceptual “TFS-processing” deficits do not simply reflect degraded phase-locking at the level of the AN. To the extent that performance in F0 and harmonic/inharmonic discrimination tasks depend on TFS cues, it is likely through a more complicated (sub-optimal) decoding mechanism, which may involve “spatiotemporal” (place-time) neural representations. PMID:23716215

Construction of SO(5)⊃SO(3) spherical harmonics and Clebsch-Gordan coefficients

NASA Astrophysics Data System (ADS)

Caprio, M. A.; Rowe, D. J.; Welsh, T. A.

2009-07-01

The SO(5)⊃SO(3) spherical harmonics form a natural basis for expansion of nuclear collective model angular wave functions. They underlie the recently-proposed algebraic method for diagonalization of the nuclear collective model Hamiltonian in an SU(1,1)×SO(5) basis. We present a computer code for explicit construction of the SO(5)⊃SO(3) spherical harmonics and use them to compute the Clebsch-Gordan coefficients needed for collective model calculations in an SO(3)-coupled basis. With these Clebsch-Gordan coefficients it becomes possible to compute the matrix elements of collective model observables by purely algebraic methods. Program summaryProgram title: GammaHarmonic Catalogue identifier: AECY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 346 421 No. of bytes in distributed program, including test data, etc.: 16 037 234 Distribution format: tar.gz Programming language: Mathematica 6 Computer: Any which supports Mathematica Operating system: Any which supports Mathematica; tested under Microsoft Windows XP and Linux Classification: 4.2 Nature of problem: Explicit construction of SO(5) ⊃ SO(3) spherical harmonics on S. Evaluation of SO(3)-reduced matrix elements and SO(5) ⊃ SO(3) Clebsch-Gordan coefficients (isoscalar factors). Solution method: Construction of SO(5) ⊃ SO(3) spherical harmonics by orthonormalization, obtained from a generating set of functions, according to the method of Rowe, Turner, and Repka [1]. Matrix elements and Clebsch-Gordan coefficients follow by construction and integration of SO(3) scalar products. Running time: Depends strongly on the maximum SO(5) and SO(3) representation labels involved. A few minutes for the calculation in the Mathematica notebook. References: [1] D.J. Rowe, P.S. Turner, J. Repka, J. Math. Phys. 45 (2004) 2761.

Delay-Encoded Harmonic Imaging (DE-HI) in Multiplane-Wave Compounding.

PubMed

Gong, Ping; Song, Pengfei; Chen, Shigao

2017-04-01

The development of ultrafast ultrasound imaging brings great opportunities to improve imaging technologies such as shear wave elastography and ultrafast Doppler imaging. In ultrafast imaging, several tilted plane or diverging wave images are coherently combined to form a compounded image, leading to trade-offs among image signal-to-noise ratio (SNR), resolution, and post-compounded frame rate. Multiplane wave (MW) imaging is proposed to solve this trade-off by encoding multiple plane waves with Hadamard matrix during one transmission event (i.e. pulse-echo event), to improve image SNR without sacrificing the resolution or frame rate. However, it suffers from stronger reverberation artifacts in B-mode images compared to standard plane wave compounding due to longer transmitted pulses. If harmonic imaging can be combined with MW imaging, the reverberation artifacts and other clutter noises such as sidelobes and multipath scattering clutters should be suppressed. The challenge, however, is that the Hadamard codes used in MW imaging cannot encode the 2 nd harmonic component by inversing the pulse polarity. In this paper, we propose a delay-encoded harmonic imaging (DE-HI) technique to encode the 2 nd harmonic with a one quarter period delay calculated at the transmit center frequency, rather than reversing the pulse polarity during multiplane wave emissions. Received DE-HI signals can then be decoded in the frequency domain to recover the signals as in single plane wave emissions, but mainly with improved SNR at the 2 nd harmonic component instead of the fundamental component. DE-HI was tested experimentally with a point target, a B-mode imaging phantom, and in-vivo human liver imaging. Improvements in image contrast-to-noise ratio (CNR), spatial resolution, and lesion-signal-to-noise ratio ( l SNR) have been achieved compared to standard plane wave compounding, MW imaging, and standard harmonic imaging (maximal improvement of 116% on CNR and 115% on l SNR as compared to standard HI around 55 mm depth in the B-mode imaging phantom study). The potential high frame rate and the stability of encoding and decoding processes of DE-HI were also demonstrated, which made DE-HI promising for a wide spectrum of imaging applications.

Adaptive Precoded MIMO for LTE Wireless Communication

NASA Astrophysics Data System (ADS)

Nabilla, A. F.; Tiong, T. C.

2015-04-01

Long-Term Evolution (LTE) and Long Term Evolution-Advanced (ATE-A) have provided a major step forward in mobile communication capability. The objectives to be achieved are high peak data rates in high spectrum bandwidth and high spectral efficiencies. Technically, pre-coding means that multiple data streams are emitted from the transmit antenna with independent and appropriate weightings such that the link throughput is maximized at the receiver output thus increasing or equalizing the received signal to interference and noise (SINR) across the multiple receiver terminals. However, it is not reliable enough to fully utilize the information transfer rate to fit the condition of channel according to the bandwidth size. Thus, adaptive pre-coding is proposed. It applies pre-coding matrix indicator (PMI) channel state making it possible to change the pre-coding codebook accordingly thus improving the data rate higher than fixed pre-coding.

Dynamics and manipulation of entanglement in coupled harmonic systems with many degrees of freedom

NASA Astrophysics Data System (ADS)

Plenio, M. B.; Hartley, J.; Eisert, J.

2004-03-01

We study the entanglement dynamics of a system consisting of a large number of coupled harmonic oscillators in various configurations and for different types of nearest-neighbour interactions. For a one-dimensional chain, we provide compact analytical solutions and approximations to the dynamical evolution of the entanglement between spatially separated oscillators. Key properties such as the speed of entanglement propagation, the maximum amount of transferred entanglement and the efficiency for the entanglement transfer are computed. For harmonic oscillators coupled by springs, corresponding to a phonon model, we observe a non-monotonic transfer efficiency in the initially prepared amount of entanglement, i.e. an intermediate amount of initial entanglement is transferred with the highest efficiency. In contrast, within the framework of the rotating-wave approximation (as appropriate, e.g. in quantum optical settings) one finds a monotonic behaviour. We also study geometrical configurations that are analogous to quantum optical devices (such as beamsplitters and interferometers) and observe characteristic differences when initially thermal or squeezed states are entering these devices. We show that these devices may be switched on and off by changing the properties of an individual oscillator. They may therefore be used as building blocks of large fixed and pre-fabricated but programmable structures in which quantum information is manipulated through propagation. We discuss briefly possible experimental realizations of systems of interacting harmonic oscillators in which these effects may be confirmed experimentally.

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

Vassilevska, Tanya

This is the first code, designed to run on a desktop, which models the intracellular replication and the cell-to-cell infection and demonstrates virus evolution at the molecular level. This code simulates the infection of a population of "idealized biological cells" (represented as objects that do not divide or have metabolism) with "virus" (represented by its genetic sequence), the replication and simultaneous mutation of the virus which leads to evolution of the population of genetically diverse viruses. The code is built to simulate single-stranded RNA viruses. The input for the code is 1. the number of biological cells in the culture,more » 2. the initial composition of the virus population, 3. the reference genome of the RNA virus, 4. the coordinates of the genome regions and their significance and, 5. parameters determining the dynamics of virus replication, such as the mutation rate. The simulation ends when all cells have been infected or when no more infections occurs after a given number of attempts. The code has the ability to simulate the evolution of the virus in serial passage of cell "cultures", i.e. after the end of a simulation, a new one is immediately scheduled with a new culture of infected cells. The code outputs characteristics of the resulting virus population dynamics and genetic composition of the virus population, such as the top dominant genomes, percentage of a genome with specific characteristics.« less

Critical roles for a genetic code alteration in the evolution of the genus Candida.

PubMed

Silva, Raquel M; Paredes, João A; Moura, Gabriela R; Manadas, Bruno; Lima-Costa, Tatiana; Rocha, Rita; Miranda, Isabel; Gomes, Ana C; Koerkamp, Marian J G; Perrot, Michel; Holstege, Frank C P; Boucherie, Hélian; Santos, Manuel A S

2007-10-31

During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross-protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation.

Superconducting Cavity Development for Free Electron Lasers.

DTIC Science & Technology

1986-06-30

effects have been modeled extensively using the code PARMELA, including finite space charge . The conflict is resolved through the use of harmonically...depends on the specifics of how the whole accelerator is run, i.e., bunch length, interpulse spacing , macrobunch length, charge per bunch, external...this indicates that the bunch length should be as long as possible. 2.4 OPTIMUM BUNCH LENGTH 20 Although wakefield, HOM excitation and space charge

Perception and Neural Coding of Harmonic Fusion in Ferrets

DTIC Science & Technology

2004-01-01

distinct percepts that come under the rubric of pitch, be- cause periodicity pitch underlies speakers’ voices and speech prosody, as well as musical ...spectral fusion is unclear for sounds having predominantly low-frequency spectra such as speech, music , and many animal vocalizations. In summary...84, 560–565. von Helmholtz, H. (1863). Die Lehre von den Tonempfindungen als physiologische Grundlage fr die Theorie der Musik . (Vieweg und Sohn

Ozone data and mission sampling analysis

NASA Technical Reports Server (NTRS)

Robbins, J. L.

1980-01-01

A methodology was developed to analyze discrete data obtained from the global distribution of ozone. Statistical analysis techniques were applied to describe the distribution of data variance in terms of empirical orthogonal functions and components of spherical harmonic models. The effects of uneven data distribution and missing data were considered. Data fill based on the autocorrelation structure of the data is described. Computer coding of the analysis techniques is included.

Rotational shear effects on edge harmonic oscillations in DIII-D quiescent H-mode discharges

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

Chen, Xi; Burrell, Keith H.; Ferraro, Nathaniel M.

In the quiescent H-mode (QH-mode) regime, edge harmonic oscillations (EHO) play an important role in avoiding transient edge localized mode (ELM) power fluxes by providing benign and continuous edge particle transport. A detailed theoretical, experimental and modeling comparison has been made of low-n (n ≤ 5) EHO in DIII-D QH-mode plasmas. The calculated linear eigenmode structure from the extended MHD code M3D-C1 matches closely the coherent EHO properties from external magnetics data and internal measurements using the ECE, BES, ECE-Imaging and microwave imaging reflectometer (MIR) diagnostics, as well as the kink/peeling mode properties found by the ideal MHD code ELITE.more » Numerical investigations indicate that the low-n EHO-like solutions from M3D-C1 are destabilized by the rotational shear while high-n modes are stabilized. This effect is independent of the rotation direction, suggesting that EHO can be destabilized in principle with rotation in either direction. Furthermore, the modeling results are consistent with observations of the EHO, support the proposed theory of the EHO as a rotational shear driven kink/peeling mode, and improve our understanding and confidence in creating and sustaining QH-mode in present and future devices.« less

Spherical Harmonic Solutions to the 3D Kobayashi Benchmark Suite

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

Brown, P.N.; Chang, B.; Hanebutte, U.R.

1999-12-29

Spherical harmonic solutions of order 5, 9 and 21 on spatial grids containing up to 3.3 million cells are presented for the Kobayashi benchmark suite. This suite of three problems with simple geometry of pure absorber with large void region was proposed by Professor Kobayashi at an OECD/NEA meeting in 1996. Each of the three problems contains a source, a void and a shield region. Problem 1 can best be described as a box in a box problem, where a source region is surrounded by a square void region which itself is embedded in a square shield region. Problems 2more » and 3 represent a shield with a void duct. Problem 2 having a straight and problem 3 a dog leg shaped duct. A pure absorber and a 50% scattering case are considered for each of the three problems. The solutions have been obtained with Ardra, a scalable, parallel neutron transport code developed at Lawrence Livermore National Laboratory (LLNL). The Ardra code takes advantage of a two-level parallelization strategy, which combines message passing between processing nodes and thread based parallelism amongst processors on each node. All calculations were performed on the IBM ASCI Blue-Pacific computer at LLNL.« less

Rotational shear effects on edge harmonic oscillations in DIII-D quiescent H-mode discharges

DOE PAGES

Chen, Xi; Burrell, Keith H.; Ferraro, Nathaniel M.; ...

2016-06-21

In the quiescent H-mode (QH-mode) regime, edge harmonic oscillations (EHO) play an important role in avoiding transient edge localized mode (ELM) power fluxes by providing benign and continuous edge particle transport. A detailed theoretical, experimental and modeling comparison has been made of low-n (n ≤ 5) EHO in DIII-D QH-mode plasmas. The calculated linear eigenmode structure from the extended MHD code M3D-C1 matches closely the coherent EHO properties from external magnetics data and internal measurements using the ECE, BES, ECE-Imaging and microwave imaging reflectometer (MIR) diagnostics, as well as the kink/peeling mode properties found by the ideal MHD code ELITE.more » Numerical investigations indicate that the low-n EHO-like solutions from M3D-C1 are destabilized by the rotational shear while high-n modes are stabilized. This effect is independent of the rotation direction, suggesting that EHO can be destabilized in principle with rotation in either direction. Furthermore, the modeling results are consistent with observations of the EHO, support the proposed theory of the EHO as a rotational shear driven kink/peeling mode, and improve our understanding and confidence in creating and sustaining QH-mode in present and future devices.« less

Rotational shear effects on edge harmonic oscillations in DIII-D quiescent H-mode discharges

NASA Astrophysics Data System (ADS)

Chen, Xi; Burrell, K. H.; Ferraro, N. M.; Osborne, T. H.; Austin, M. E.; Garofalo, A. M.; Groebner, R. J.; Kramer, G. J.; Luhmann, N. C., Jr.; McKee, G. R.; Muscatello, C. M.; Nazikian, R.; Ren, X.; Snyder, P. B.; Solomon, W. M.; Tobias, B. J.; Yan, Z.

2016-07-01

In the quiescent H-mode (QH-mode) regime, edge harmonic oscillations (EHOs) play an important role in avoiding transient edge localized mode (ELM) power fluxes by providing benign and continuous edge particle transport. A detailed theoretical, experimental and modeling comparison has been made of low-n (n  ⩽  5) EHO in DIII-D QH-mode plasmas. The calculated linear eigenmode structure from the extended magentoohydrodynamics (MHD) code M3D-C1 matches closely the coherent EHO properties from external magnetics data and internal measurements using the ECE, BES, ECE-Imaging and microwave imaging reflectometer (MIR) diagnostics, as well as the kink/peeling mode properties found by the ideal MHD code ELITE. Numerical investigations indicate that the low-n EHO-like solutions from M3D-C1 are destabilized by rotation and/or rotational shear while high-n modes are stabilized. This effect is independent of the rotation direction, suggesting that EHOs can be destabilized in principle with rotation in either direction. The modeling results are consistent with observations of EHO, support the proposed theory of the EHO as a low-n kink/peeling mode destabilized by edge E  ×  B rotational shear, and improve our understanding and confidence in creating and sustaining QH-mode in present and future devices.

High accuracy binary black hole simulations with an extended wave zone

NASA Astrophysics Data System (ADS)

Pollney, Denis; Reisswig, Christian; Schnetter, Erik; Dorband, Nils; Diener, Peter

2011-02-01

We present results from a new code for binary black hole evolutions using the moving-puncture approach, implementing finite differences in generalized coordinates, and allowing the spacetime to be covered with multiple communicating nonsingular coordinate patches. Here we consider a regular Cartesian near-zone, with adapted spherical grids covering the wave zone. The efficiencies resulting from the use of adapted coordinates allow us to maintain sufficient grid resolution to an artificial outer boundary location which is causally disconnected from the measurement. For the well-studied test case of the inspiral of an equal-mass nonspinning binary (evolved for more than 8 orbits before merger), we determine the phase and amplitude to numerical accuracies better than 0.010% and 0.090% during inspiral, respectively, and 0.003% and 0.153% during merger. The waveforms, including the resolved higher harmonics, are convergent and can be consistently extrapolated to r→∞ throughout the simulation, including the merger and ringdown. Ringdown frequencies for these modes (to (ℓ,m)=(6,6)) match perturbative calculations to within 0.01%, providing a strong confirmation that the remnant settles to a Kerr black hole with irreducible mass Mirr=0.884355±20×10-6 and spin Sf/Mf2=0.686923±10×10-6.

Filter bank canonical correlation analysis for implementing a high-speed SSVEP-based brain-computer interface

NASA Astrophysics Data System (ADS)

Chen, Xiaogang; Wang, Yijun; Gao, Shangkai; Jung, Tzyy-Ping; Gao, Xiaorong

2015-08-01

Objective. Recently, canonical correlation analysis (CCA) has been widely used in steady-state visual evoked potential (SSVEP)-based brain-computer interfaces (BCIs) due to its high efficiency, robustness, and simple implementation. However, a method with which to make use of harmonic SSVEP components to enhance the CCA-based frequency detection has not been well established. Approach. This study proposed a filter bank canonical correlation analysis (FBCCA) method to incorporate fundamental and harmonic frequency components to improve the detection of SSVEPs. A 40-target BCI speller based on frequency coding (frequency range: 8-15.8 Hz, frequency interval: 0.2 Hz) was used for performance evaluation. To optimize the filter bank design, three methods (M1: sub-bands with equally spaced bandwidths; M2: sub-bands corresponding to individual harmonic frequency bands; M3: sub-bands covering multiple harmonic frequency bands) were proposed for comparison. Classification accuracy and information transfer rate (ITR) of the three FBCCA methods and the standard CCA method were estimated using an offline dataset from 12 subjects. Furthermore, an online BCI speller adopting the optimal FBCCA method was tested with a group of 10 subjects. Main results. The FBCCA methods significantly outperformed the standard CCA method. The method M3 achieved the highest classification performance. At a spelling rate of ˜33.3 characters/min, the online BCI speller obtained an average ITR of 151.18 ± 20.34 bits min-1. Significance. By incorporating the fundamental and harmonic SSVEP components in target identification, the proposed FBCCA method significantly improves the performance of the SSVEP-based BCI, and thereby facilitates its practical applications such as high-speed spelling.

An engineer's view on genetic information and biological evolution.

PubMed

Battail, Gérard

2004-01-01

We develop ideas on genome replication introduced in Battail [Europhys. Lett. 40 (1997) 343]. Starting with the hypothesis that the genome replication process uses error-correcting means, and the auxiliary one that nested codes are used to this end, we first review the concepts of redundancy and error-correcting codes. Then we show that these hypotheses imply that: distinct species exist with a hierarchical taxonomy, there is a trend of evolution towards complexity, and evolution proceeds by discrete jumps. At least the first two features above may be considered as biological facts so, in the absence of direct evidence, they provide an indirect proof in favour of the hypothesized error-correction system. The very high redundancy of genomes makes it possible. In order to explain how it is implemented, we suggest that soft codes and replication decoding, to be briefly described, are plausible candidates. Experimentally proven properties of long-range correlation of the DNA message substantiate this claim.

Modeling carbon production and transport during ELMs in DIII-D

NASA Astrophysics Data System (ADS)

Hogan, J.; Wade, M.; Coster, D.; Lasnier, C.

2004-11-01

Large-scale Type I ELM events could provide a significant C source in ITER, and C production rates depend on incident D flux density and surface temperature, quantities which can vary significantly during an ELM event. Recent progress on DIII-D has improved opportunities for code comparison. Fast time-scale measurements of divertor CIII evolution [1] and fast edge CER measurements of C profile evolution during low-density DIII-D LSN ELMy H-modes (type I) [2] have been modeled using the solps5.0/Eirene99 coupled edge code and time dependent thermal analysis codes. An ELM model based on characteristics of MHD peeling-ballooning modes reproduces the pedestal evolution. Qualitative agreement for the CIII evolution during an ELM event is found using the Roth et al annealing model for chemical sputtering and the sensitivity to other models is described. Significant ELM-to-ELM variations in observed maximum divertor target IR temperature during nominally identical ELMs are investigated with models for C emission from micron-scale dust particles. [1] M Groth, M Fenstermacher et al J Nucl Mater 2003, [2] M Wade, K Burrell et al PSI-16

The evolution of transcriptional regulation in eukaryotes

NASA Technical Reports Server (NTRS)

Wray, Gregory A.; Hahn, Matthew W.; Abouheif, Ehab; Balhoff, James P.; Pizer, Margaret; Rockman, Matthew V.; Romano, Laura A.

2003-01-01

Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.

Evolution of Structure and Composition in Saturn's Rings Due to Ballistic Transport of Micrometeoroid Impact Ejecta

NASA Astrophysics Data System (ADS)

Estrada, P. R.; Durisen, R. H.; Cuzzi, J. N.

2014-04-01

We introduce improved numerical techniques for simulating the structural and compositional evolution of planetary rings due to micrometeoroid bombardment and subsequent ballistic transport of impact ejecta. Our current, robust code, which is based on the original structural code of [1] and on the pollution transport code of [3], is capable of modeling structural changes and pollution transport simultaneously over long times on both local and global scales. We provide demonstrative simulations to compare with, and extend upon previous work, as well as examples of how ballistic transport can maintain the observed structure in Saturn's rings using available Cassini occultation optical depth data.

A new technique for calculations of binary stellar evolution, with application to magnetic braking

NASA Technical Reports Server (NTRS)

Rappaport, S.; Joss, P. C.; Verbunt, F.

1983-01-01

The development of appropriate computer programs has made it possible to conduct studies of stellar evolution which are more detailed and accurate than the investigations previously feasible. However, the use of such programs can also entail some serious drawbacks which are related to the time and expense required for the work. One approach for overcoming these drawbacks involves the employment of simplified stellar evolution codes which incorporate the essential physics of the problem of interest without attempting either great generality or maximal accuracy. Rappaport et al. (1982) have developed a simplified code to study the evolution of close binary stellar systems composed of a collapsed object and a low-mass secondary. The present investigation is concerned with a more general, but still simplified, technique for calculating the evolution of close binary systems with collapsed binaries and mass-losing secondaries.

Long-time efficacy of the surface code in the presence of a super-Ohmic environment

NASA Astrophysics Data System (ADS)

López-Delgado, D. A.; Novais, E.; Mucciolo, E. R.; Caldeira, A. O.

2017-06-01

We study the long-time evolution of a quantum memory coupled to a bosonic environment on which quantum error correction (QEC) is performed using the surface code. The memory's evolution encompasses N QEC cycles, each of them yielding a nonerror syndrome. This assumption makes our analysis independent of the recovery process. We map the expression for the time evolution of the memory onto the partition function of an equivalent statistical-mechanical spin system. In the super-Ohmic dissipation case the long-time evolution of the memory has the same behavior as the time evolution for just one QEC cycle. For this case we find analytical expressions for the critical parameters of the order-disorder phase transition of an equivalent spin system. These critical parameters determine the threshold value for the system-environment coupling below which it is possible to preserve the memory's state.

The response of phospholipid-encapsulated microbubbles to chirp-coded excitation: Implications for high-frequency nonlinear imaging

PubMed Central

Shekhar, Himanshu; Doyley, Marvin M.

2013-01-01

The current excitation strategy for harmonic and subharmonic imaging (HI and SHI) uses short sine-bursts. However, alternate pulsing strategies may be useful for enhancing nonlinear emissions from ultrasound contrast agents. The goal of this study was to corroborate the hypothesis that chirp-coded excitation can improve the performance of high-frequency HI and SHI. A secondary goal was to understand the mechanisms that govern the response of ultrasound contrast agents to chirp-coded and sine-burst excitation schemes. Numerical simulations and acoustic measurements were conducted to evaluate the response of a commercial contrast agent (Targestar-P®) to chirp-coded and sine-burst excitation (10 MHz frequency, peak pressures 290 kPa). The results of the acoustic measurements revealed an improvement in signal-to-noise ratio by 4 to 14 dB, and a two- to threefold reduction in the subharmonic threshold with chirp-coded excitation. Simulations conducted with the Marmottant model suggest that an increase in expansion-dominated radial excursion of microbubbles was the mechanism responsible for the stronger nonlinear response. Additionally, chirp-coded excitation detected the nonlinear response for a wider range of agent concentrations than sine-bursts. Therefore, chirp-coded excitation could be a viable approach for enhancing the performance of HI and SHI. PMID:23654417

The response of phospholipid-encapsulated microbubbles to chirp-coded excitation: implications for high-frequency nonlinear imaging.

PubMed

Shekhar, Himanshu; Doyley, Marvin M

2013-05-01

The current excitation strategy for harmonic and subharmonic imaging (HI and SHI) uses short sine-bursts. However, alternate pulsing strategies may be useful for enhancing nonlinear emissions from ultrasound contrast agents. The goal of this study was to corroborate the hypothesis that chirp-coded excitation can improve the performance of high-frequency HI and SHI. A secondary goal was to understand the mechanisms that govern the response of ultrasound contrast agents to chirp-coded and sine-burst excitation schemes. Numerical simulations and acoustic measurements were conducted to evaluate the response of a commercial contrast agent (Targestar-P(®)) to chirp-coded and sine-burst excitation (10 MHz frequency, peak pressures 290 kPa). The results of the acoustic measurements revealed an improvement in signal-to-noise ratio by 4 to 14 dB, and a two- to threefold reduction in the subharmonic threshold with chirp-coded excitation. Simulations conducted with the Marmottant model suggest that an increase in expansion-dominated radial excursion of microbubbles was the mechanism responsible for the stronger nonlinear response. Additionally, chirp-coded excitation detected the nonlinear response for a wider range of agent concentrations than sine-bursts. Therefore, chirp-coded excitation could be a viable approach for enhancing the performance of HI and SHI.

Design of a Double Anode Magnetron Injection Gun for Q-band Gyro-TWT Using Boundary Element Method

NASA Astrophysics Data System (ADS)

Li, Zhiliang; Feng, Jinjun; Liu, Bentian

2018-04-01

This paper presents a novel design code for double anode magnetron injection guns (MIGs) in gyro-devices based on boundary element method (BEM). The physical and mathematical models were constructed, and then the code using BEM for MIG's calculation was developed. Using the code, a double anode MIG for a Q-band gyrotron traveling-wave tube (gyro-TWT) amplifier operating in the circular TE01 mode at the fundamental cyclotron harmonic was designed. In order to verify the reliability of this code, velocity spread and guiding center radius of the MIG simulated by the BEM code were compared with these from the commonly used EGUN code, showing a reasonable agreement. Then, a Q-band gyro-TWT was fabricated and tested. The testing results show that the device has achieved an average power of 5kW and peak power ≥ 150 kW at a 3% duty cycle within bandwidth of 2 GHz, and maximum output peak power of 220 kW, with a corresponding saturated gain of 50.9 dB and efficiency of 39.8%. This paper demonstrates that the BEM code can be used as an effective approach for analysis of electron optics system in gyro-devices.

Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine

PubMed Central

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409

An evaluation of a computer code based on linear acoustic theory for predicting helicopter main rotor noise. [CH-53A and S-76 helicopters

NASA Technical Reports Server (NTRS)

Davis, S. J.; Egolf, T. A.

1980-01-01

Acoustic characteristics predicted using a recently developed computer code were correlated with measured acoustic data for two helicopter rotors. The analysis, is based on a solution of the Ffowcs-Williams-Hawkings (FW-H) equation and includes terms accounting for both the thickness and loading components of the rotational noise. Computations are carried out in the time domain and assume free field conditions. Results of the correlation show that the Farrassat/Nystrom analysis, when using predicted airload data as input, yields fair but encouraging correlation for the first 6 harmonics of blade passage. It also suggests that although the analysis represents a valuable first step towards developing a truly comprehensive helicopter rotor noise prediction capability, further work remains to be done identifying and incorporating additional noise mechanisms into the code.

The genetic code as a periodic table: algebraic aspects.

PubMed

Bashford, J D; Jarvis, P D

2000-01-01

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, A=(-1,0), C=(0,-1), G=(0,1), U=(1,0), data can be fitted as low order polynomials of the six coordinates in the 64-dimensional codon weight space. The work confirms and extends the recent studies by Siemion et al. (1995. BioSystems 36, 231-238) of the conformational parameters. Fundamental patterns in the data such as codon periodicities, and related harmonics and reflection symmetries, are here associated with the structure of the set of basis monomials chosen for fitting. Results are plotted using the Siemion one-step mutation ring scheme, and variants thereof. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

Surface retrievals from Hyperion EO1 using a new, fast, 1D-Var based retrieval code

NASA Astrophysics Data System (ADS)

Thelen, Jean-Claude; Havemann, Stephan; Wong, Gerald

2015-05-01

We have developed a new algorithm for the simultaneous retrieval of the atmospheric profiles (temperature, humidity, ozone and aerosol) and the surface reflectance from hyperspectral radiance measurements obtained from air/space-borne, hyperspectral imagers such as Hyperion EO-1. The new scheme, proposed here, consists of a fast radiative transfer code, based on empirical orthogonal functions (EOFs), in conjunction with a 1D-Var retrieval scheme. The inclusion of an 'exact' scattering code based on spherical harmonics, allows for an accurate treatment of Rayleigh scattering and scattering by aerosols, water droplets and ice-crystals, thus making it possible to also retrieve cloud and aerosol optical properties, although here we will concentrate on non-cloudy scenes. We successfully tested this new approach using hyperspectral images taken by Hyperion EO-1, an experimental pushbroom imaging spectrometer operated by NASA.

Axial deformed solution of the Skyrme-Hartree-Fock-Bogolyubov equations using the transformed harmonic oscillator Basis

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

Perez, R. Navarro; Schunck, N.; Lasseri, R.

2017-03-09

HFBTHO is a physics computer code that is used to model the structure of the nucleus. It is an implementation of the nuclear energy Density Functional Theory (DFT), where the energy of the nucleus is obtained by integration over space of some phenomenological energy density, which is itself a functional of the neutron and proton densities. In HFBTHO, the energy density derives either from the zero-range Dkyrme or the finite-range Gogny effective two-body interaction between nucleons. Nuclear superfluidity is treated at the Hartree-Fock-Bogoliubov (HFB) approximation, and axial-symmetry of the nuclear shape is assumed. This version is the 3rd release ofmore » the program; the two previous versions were published in Computer Physics Communications [1,2]. The previous version was released at LLNL under GPL 3 Open Source License and was given release code LLNL-CODE-573953.« less

Modeling the propagation of nonlinear three-dimensional acoustic beams in inhomogeneous media.

PubMed

Jing, Yuan; Cleveland, Robin O

2007-09-01

A three-dimensional model of the forward propagation of nonlinear sound beams in inhomogeneous media, a generalized Khokhlov-Zabolotskaya-Kuznetsov equation, is described. The Texas time-domain code (which accounts for paraxial diffraction, nonlinearity, thermoviscous absorption, and absorption and dispersion associated with multiple relaxation processes) was extended to solve for the propagation of nonlinear beams for the case where all medium properties vary in space. The code was validated with measurements of the nonlinear acoustic field generated by a phased array transducer operating at 2.5 MHz in water. A nonuniform layer of gel was employed to create an inhomogeneous medium. There was good agreement between the code and measurements in capturing the shift in the pressure distribution of both the fundamental and second harmonic due to the gel layer. The results indicate that the numerical tool described here is appropriate for propagation of nonlinear sound beams through weakly inhomogeneous media.

Design Aspects of the Rayleigh Convection Code

NASA Astrophysics Data System (ADS)

Featherstone, N. A.

2017-12-01

Understanding the long-term generation of planetary or stellar magnetic field requires complementary knowledge of the large-scale fluid dynamics pervading large fractions of the object's interior. Such large-scale motions are sensitive to the system's geometry which, in planets and stars, is spherical to a good approximation. As a result, computational models designed to study such systems often solve the MHD equations in spherical geometry, frequently employing a spectral approach involving spherical harmonics. We present computational and user-interface design aspects of one such modeling tool, the Rayleigh convection code, which is suitable for deployment on desktop and petascale-hpc architectures alike. In this poster, we will present an overview of this code's parallel design and its built-in diagnostics-output package. Rayleigh has been developed with NSF support through the Computational Infrastructure for Geodynamics and is expected to be released as open-source software in winter 2017/2018.

Frequency spectrum might act as communication code between retina and visual cortex I

PubMed Central

Yang, Xu; Gong, Bo; Lu, Jian-Wei

2015-01-01

AIM To explore changes and possible communication relationship of local potential signals recorded simultaneously from retina and visual cortex I (V1). METHODS Fourteen C57BL/6J mice were measured with pattern electroretinogram (PERG) and pattern visually evoked potential (PVEP) and fast Fourier transform has been used to analyze the frequency components of those signals. RESULTS The amplitude of PERG and PVEP was measured at about 36.7 µV and 112.5 µV respectively and the dominant frequency of PERG and PVEP, however, stay unchanged and both signals do not have second, or otherwise, harmonic generation. CONCLUSION The results suggested that retina encodes visual information in the way of frequency spectrum and then transfers it to primary visual cortex. The primary visual cortex accepts and deciphers the input visual information coded from retina. Frequency spectrum may act as communication code between retina and V1. PMID:26682156

Frequency spectrum might act as communication code between retina and visual cortex I.

PubMed

Yang, Xu; Gong, Bo; Lu, Jian-Wei

2015-01-01

To explore changes and possible communication relationship of local potential signals recorded simultaneously from retina and visual cortex I (V1). Fourteen C57BL/6J mice were measured with pattern electroretinogram (PERG) and pattern visually evoked potential (PVEP) and fast Fourier transform has been used to analyze the frequency components of those signals. The amplitude of PERG and PVEP was measured at about 36.7 µV and 112.5 µV respectively and the dominant frequency of PERG and PVEP, however, stay unchanged and both signals do not have second, or otherwise, harmonic generation. The results suggested that retina encodes visual information in the way of frequency spectrum and then transfers it to primary visual cortex. The primary visual cortex accepts and deciphers the input visual information coded from retina. Frequency spectrum may act as communication code between retina and V1.

SIGNUM: A Matlab, TIN-based landscape evolution model

NASA Astrophysics Data System (ADS)

Refice, A.; Giachetta, E.; Capolongo, D.

2012-08-01

Several numerical landscape evolution models (LEMs) have been developed to date, and many are available as open source codes. Most are written in efficient programming languages such as Fortran or C, but often require additional code efforts to plug in to more user-friendly data analysis and/or visualization tools to ease interpretation and scientific insight. In this paper, we present an effort to port a common core of accepted physical principles governing landscape evolution directly into a high-level language and data analysis environment such as Matlab. SIGNUM (acronym for Simple Integrated Geomorphological Numerical Model) is an independent and self-contained Matlab, TIN-based landscape evolution model, built to simulate topography development at various space and time scales. SIGNUM is presently capable of simulating hillslope processes such as linear and nonlinear diffusion, fluvial incision into bedrock, spatially varying surface uplift which can be used to simulate changes in base level, thrust and faulting, as well as effects of climate changes. Although based on accepted and well-known processes and algorithms in its present version, it is built with a modular structure, which allows to easily modify and upgrade the simulated physical processes to suite virtually any user needs. The code is conceived as an open-source project, and is thus an ideal tool for both research and didactic purposes, thanks to the high-level nature of the Matlab environment and its popularity among the scientific community. In this paper the simulation code is presented together with some simple examples of surface evolution, and guidelines for development of new modules and algorithms are proposed.

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.

PubMed

Shapiro, James A

2016-06-08

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

PubMed Central

Shapiro, James A.

2016-01-01

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. PMID:27338490

JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

Independent evolution of genomic characters during major metazoan transitions.

PubMed

Simakov, Oleg; Kawashima, Takeshi

2017-07-15

Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages. In this review we describe recent advances in our understanding of ancestral metazoan coding and non-coding features, as deduced from genomic comparisons. Some genomic changes such as innovations in gene and linkage content occur at different rates across metazoan clades, suggesting some level of independence among genomic characters. While their contribution to biological innovation remains largely unclear, we review recent literature about certain genomic changes that do correlate with changes to specific developmental pathways and metazoan innovations. In particular, we discuss the origins of the recently described pharyngeal cluster which is conserved across deuterostome genomes, and highlight different genomic features that have contributed to the evolution of this group. We also assess our current capacity to infer ancestral metazoan states from gene models and comparative genomics tools and elaborate on the future directions of metazoan comparative genomics relevant to evo-devo studies. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A theoretical and experimental investigation of nonlinear propagation of ultrasound through tissue mimicking media

NASA Astrophysics Data System (ADS)

Rielly, Matthew Robert

An existing numerical model (known as the Bergen code) is used to investigate finite amplitude ultrasound propagation through multiple layers of tissue-like media. This model uses a finite difference method to solve the nonlinear parabolic KZK wave equation. The code is modified to include an arbitrary frequency dependence of absorption and transmission effects for wave propagation across a plane interface at normal incidence. In addition the code is adapted to calculate the total intensity loss associated with the absorption of the fundamental and nonlinearly generated harmonics. Measurements are also taken of the axial nonlinear pressure field generated from a circular focused, 2.25 MHz source, through single and multiple layered tissue mimicking fluids, for source pressures in the range from 13 kPa to 310 kPa. Two tissue mimicking fluids are developed to provide acoustic properties similar to amniotic fluid and a typical soft tissue. The values of the nonlinearity parameter, sound velocity and frequency dependence of attenuation for both fluids are presented, and the measurement procedures employed to obtain these characteristics are described in detail. These acoustic parameters, together with the measured source conditions are used as input to the numerical model, allowing the experimental conditions to be simulated. Extensive comparisons are made between the model's predictions and the axial pressure field measurements. Results are presented in the frequency domain showing the fundamental and three subsequent harmonic amplitudes on axis, as a function of axial distance. These show that significant nonlinear distortion can occur through media with characteristics typical of tissue. Time domain waveform comparisons are also made. An excellent agreement is found between theory and experiment indicating that the model can be used to predict nonlinear ultrasound propagation through multiple layers of tissue-like media. The numerical code is also used to model the intensity loss through layered tissue mimics and results are presented illustrating the effects of altering the layered medium on the magnitude and spatial distribution of intensity loss.

Quasi-Static Evolution, Catastrophe, and Failed Eruption of Solar Flux Ropes

DTIC Science & Technology

2016-12-30

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6794--16-9710 Quasi -Static Evolution, Catastrophe, and “Failed” Eruption of Solar Flux...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Quasi -Static Evolution, Catastrophe...evolution of solar flux ropes subject to slowly increasing magnetic energy, encompassing quasi -static evolution, “catastrophic” transition to an eruptive

Investigation of local thermodynamic equilibrium of laser induced Al{sub 2}O{sub 3}–TiC plasma in argon by spatially resolved optical emission spectroscopy

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

Alnama, K.; Alkhawwam, A.; Jazmati, A. K., E-mail: pscientific5@aec.org.sy

Plasma plume of Al{sub 2}O{sub 3}–TiC is generated by third harmonic Q-switched Nd:YAG nanosecond laser. It is characterized using Optical Emission Spectroscopy (OES) at different argon background gas pressures 10, 10{sup 2}, 10{sup 3}, 10{sup 4} and 10{sup 5} Pa. Spatial evolution of excitation and ionic temperatures is deduced from spectral data analysis. Temporal evolution of Ti I emission originated from different energy states is probed. The correlation between the temporal behavior and the spatial temperature evolution are investigated under LTE condition for the possibility to use the temporal profile of Ti I emission as an indicator for LTE validitymore » in the plasma.« less

The Early Shape of the Moon

NASA Astrophysics Data System (ADS)

Garrick-Bethell, I.; Perera, V.; Nimmo, F.; Zuber, M. T.

2013-12-01

The origin and nature of the long-wavelength shape of the Moon has been a puzzle for at least 100 years [1-5]. Understanding its origin would provide insight into the patterns of mare volcanism, early thermal evolution, the history of the Moon's orientation, and the Moon's orbital evolution. Previously, we explained the shape and structure of the lunar farside highlands with a model of early tidal heating in the crust [6]. However, we left open the problem of the rest of the Moon's low-order shape, and we did not consider the lunar gravity field together with topography. To address these problems, and further assess the tidal-rotation (spherical harmonic degree-2) origins of the lunar shape, we consider three effects: the Moon's degree-1 spherical harmonics, the Moon's largest basins and mascons, and the choice of reference frame in which we analyze topography. We find that removing the degree-1 terms from a topography map helps illustrate the Moon's degree-2 shape, since the degree-1 harmonics have relatively high power. More importantly, however, when we fit spherical harmonics to topography outside of the largest lunar basins (including South-Pole Aitken, Imbrium, Serenitatis, Nectaris, and Orientale), the degree-2 coefficient values change significantly. When these best-fit harmonics are rotated into a reference frame that only contains the C2,0 and C2,2 harmonics (equivalent to the frame that would have once faced the Earth if the early Moon's shape controlled the moments of inertia), we find that gravity and topography data together imply a mixture of compensated and uncompensated degree-2 topography components. The compensated topography component can be explained by global-scale tidal heating in the early crust, while the uncompensated component can be explained by a frozen 'fossil bulge' that formed at a semi-major axis of about 32 Earth radii. To check these explanations, we can examine the ratios of the C2,0 and C2,2 harmonics for each component. We find that the values of C2,0/C2,2 are approximately equal to the values expected for each unique process: -1.3 and -1.0, for compensated (tidal-heating) and uncompensated (fossil bulge) topography components, respectively. However, if we had not removed the effects of large basins, the ratios would not be in agreement. In conclusion, a combination of early tidal heating in the crust and a frozen fossil bulge can help explain the global, pre-basin shape of the Moon. References [1] W.F. Sedgwick, On the figure of the Moon, Messenger Math. 27 (1898) 171. [2] H. Jeffreys, On the figures of the Earth and Moon, Geophys. J. Int. 4 (1937) 1-13. [3] H.C. Urey, et al., Note on the internal structure of the Moon, Ap. J. 129 (1959) 842. [4] K. Lambeck, S. Pullan, The lunar fossil bulge hypothesis revisited, Phys. Earth Planet. Inter. 22 (1980) 29-35. [5] D.J. Stevenson, Origin and implications of the degree two lunar gravity field, Proc. Lunar Sci. Conf. 32nd (2001) 1175. [6] I. Garrick-Bethell, et al., Structure and formation of the lunar farside highlands, Science 330 (2010) 949-951.

Research on ponderomotive driven Vlasov–Poisson system in electron acoustic wave parametric region

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

Xiao, C. Z.; Huang, T. W.; Liu, Z. J.

2014-03-15

Theoretical analysis and corresponding 1D Particle-in-Cell (PIC) simulations of ponderomotive driven Vlasov–Poisson system in electron acoustic wave (EAW) parametric region are demonstrated. Theoretical analysis identifies that under the resonant condition, a monochromatic EAW can be excited when the wave number of the drive ponderomotive force satisfies 0.26≲k{sub d}λ{sub D}≲0.53. If k{sub d}λ{sub D}≲0.26, nonlinear superposition of harmonic waves can be resonantly excited, called kinetic electrostatic electron nonlinear waves. Numerical simulations have demonstrated these wave excitation and evolution dynamics, in consistence with the theoretical predictions. The physical nature of these two waves is supposed to be interaction of harmonic waves, andmore » their similar phase space properties are also discussed.« less

Harmonic Bloch and dipole oscillations and their transition in elliptical optical waveguide arrays

NASA Astrophysics Data System (ADS)

Chan, Yun San; Zheng, Ming Jie; Yu, Kin Wah

2011-03-01

We have studied harmonic oscillations in an elliptical optical waveguide array in which the couplings between neighboring waveguides are varied in accord with a Kac matrix so that the propagation constant eigenvalues can take equally spaced values. As a result, the long-living optical Bloch oscillation (BO) and dipole oscillation (DO) are obtained. Moreover, when a linear gradient in the propagation constant is applied, we achieve a switching from DO to BO and vice versa by ramping up or down the gradient profile]. The various optical oscillations as well as their switching are investigated by field evolution analysis and confirmed by Hamiltonian optics. The equally spaced eigenvalues in the propagation constant allow viable applications in transmitting images, switching and routing of optical signals. Work supported by the General Research Fund of the Hong Kong SAR Government.

A Harmonic Solution for the Hyperbolic Heat Conduction Equation and Its Relationship to the Guyer-Krumhansl Equation

NASA Astrophysics Data System (ADS)

Zhukovsky, K. V.

2018-01-01

A particular solution of the hyperbolic heat-conduction equation was constructed using the method of operators. The evolution of a harmonic solution is studied, which simulates the propagation of electric signals in long wire transmission lines. The structures of the solutions of the telegraph equation and of the Guyer-Krumhansl equation are compared. The influence of the phonon heat-transfer mechanism in the environment is considered from the point of view of heat conductivity. The fulfillment of the maximum principle for the obtained solutions is considered. The frequency dependences of heat conductivity in the telegraph equation and in an equation of the Guyer-Krumhansl type are studied and compared with each other. The influence of the Knudsen number on heat conductivity in the model of thin films is studied.

Optical probing of high intensity laser interaction with micron-sized cryogenic hydrogen jets

NASA Astrophysics Data System (ADS)

Ziegler, Tim; Rehwald, Martin; Obst, Lieselotte; Bernert, Constantin; Brack, Florian-Emanuel; Curry, Chandra B.; Gauthier, Maxence; Glenzer, Siegfried H.; Göde, Sebastian; Kazak, Lev; Kraft, Stephan D.; Kuntzsch, Michael; Loeser, Markus; Metzkes-Ng, Josefine; Rödel, Christian; Schlenvoigt, Hans-Peter; Schramm, Ulrich; Siebold, Mathias; Tiggesbäumker, Josef; Wolter, Steffen; Zeil, Karl

2018-07-01

Probing the rapid dynamics of plasma evolution in laser-driven plasma interactions provides deeper understanding of experiments in the context of laser-driven ion acceleration and facilitates the interplay with complementing numerical investigations. Besides the microscopic scales involved, strong plasma (self-)emission, predominantly around the harmonics of the driver laser, often complicates the data analysis. We present the concept and the implementation of a stand-alone probe laser system that is temporally synchronized to the driver laser, providing probing wavelengths beyond the harmonics of the driver laser. The capability of this system is shown during a full-scale laser proton acceleration experiment using renewable cryogenic hydrogen jet targets. For further improvements, we studied the influence of probe color, observation angle of the probe and temporal contrast of the driver laser on the probe image quality.

Real-Time Implementation of a Speech Digitization Algorithm Combining Time-Domain Harmonic Scaling and Adaptive Residual Coding. Volume 1.

DTIC Science & Technology

1983-06-01

recomuended values are b1 - 1.79 b2 - -1.40 b3 - 0.57 b4 - -0.15 s - 0.95 abias - 0.001 g - 0.15 The bi are determined using the technique suggested by...R.A. McDonald (1966). The term, max{.), computes the biased percent change desired. The abias term helps the coefficient move from the zero level

Low-Density Parity-Check (LDPC) Codes Constructed from Protographs

NASA Astrophysics Data System (ADS)

Thorpe, J.

2003-08-01

We introduce a new class of low-density parity-check (LDPC) codes constructed from a template called a protograph. The protograph serves as a blueprint for constructing LDPC codes of arbitrary size whose performance can be predicted by analyzing the protograph. We apply standard density evolution techniques to predict the performance of large protograph codes. Finally, we use a randomized search algorithm to find good protographs.

The Evolution of Random Number Generation in MUVES

DTIC Science & Technology

2017-01-01

mathematical basis and statistical justification for algorithms used in the code. The working code provided produces results identical to the current...MUVES, includ- ing the mathematical basis and statistical justification for algorithms used in the code. The working code provided produces results...questionable numerical and statistical properties. The development of the modern system is traced through software change requests, resulting in a random number

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

Seiler, M.; Seiß, M.; Hoffmann, H.

The reconstruction of the orbital evolution of the propeller structure Blériot orbiting in Saturn’s A ring from recurrent observations in Cassini ISS images yielded a considerable offset motion from the expected Keplerian orbit. This offset motion can be composed by three sinusoidal harmonics with amplitudes and periods of 1845, 152, 58 km and 11.1, 3.7, and 2.2 years, respectively. In this paper we present results from N -body simulations, where we integrated the orbital evolution of a moonlet, which is placed at the radial position of Blériot under the gravitational action of the Saturnian satellites. Our simulations yield that, especiallymore » the gravitational interactions with Prometheus, Pandora, and Mimas are forcing the moonlet to librate with the right frequencies, but the libration amplitudes are too small to explain the observations. Thus, further mechanisms are needed to explain the amplitudes of the forced librations—e.g., moonlet–ring interactions. Here, we develop a model, where the moonlet is allowed to be slightly displaced with respect to its created gaps breaking the point symmetry and causing a repulsive force in this way. As a result, the evolution of the moonlet’s longitude can be described by a harmonic oscillator. In the presence of external forcing by the outer moons, the libration amplitudes get the more amplified the closer the forcing frequency is to the eigenfrequency of the disturbed propeller oscillator. Applying our model to Blériot, it is possible to reproduce a libration period of 13 years with an amplitude of about 2000 km.« less

A Librational Model for the Propeller Blériot in the Saturnian Ring System

NASA Astrophysics Data System (ADS)

Seiler, M.; Sremčević, M.; Seiß, M.; Hoffmann, H.; Spahn, F.

2017-05-01

The reconstruction of the orbital evolution of the propeller structure Blériot orbiting in Saturn’s A ring from recurrent observations in Cassini ISS images yielded a considerable offset motion from the expected Keplerian orbit. This offset motion can be composed by three sinusoidal harmonics with amplitudes and periods of 1845, 152, 58 km and 11.1, 3.7, and 2.2 years, respectively. In this paper we present results from N-body simulations, where we integrated the orbital evolution of a moonlet, which is placed at the radial position of Blériot under the gravitational action of the Saturnian satellites. Our simulations yield that, especially the gravitational interactions with Prometheus, Pandora, and Mimas are forcing the moonlet to librate with the right frequencies, but the libration amplitudes are too small to explain the observations. Thus, further mechanisms are needed to explain the amplitudes of the forced librations—e.g., moonlet-ring interactions. Here, we develop a model, where the moonlet is allowed to be slightly displaced with respect to its created gaps breaking the point symmetry and causing a repulsive force in this way. As a result, the evolution of the moonlet’s longitude can be described by a harmonic oscillator. In the presence of external forcing by the outer moons, the libration amplitudes get the more amplified the closer the forcing frequency is to the eigenfrequency of the disturbed propeller oscillator. Applying our model to Blériot, it is possible to reproduce a libration period of 13 years with an amplitude of about 2000 km.

Parabolized Stability Equations analysis of nonlinear interactions with forced eigenmodes to control subsonic jet instabilities

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

Itasse, Maxime, E-mail: Maxime.Itasse@onera.fr; Brazier, Jean-Philippe, E-mail: Jean-Philippe.Brazier@onera.fr; Léon, Olivier, E-mail: Olivier.Leon@onera.fr

2015-08-15

Nonlinear evolution of disturbances in an axisymmetric, high subsonic, high Reynolds number hot jet with forced eigenmodes is studied using the Parabolized Stability Equations (PSE) approach to understand how modes interact with one another. Both frequency and azimuthal harmonic interactions are analyzed by setting up one or two modes at higher initial amplitudes and various phases. While single mode excitation leads to harmonic growth and jet noise amplification, controlling the evolution of a specific mode has been made possible by forcing two modes (m{sub 1}, n{sub 1}), (m{sub 2}, n{sub 2}), such that the difference in azimuth and in frequencymore » matches the desired “target” mode (m{sub 1} − m{sub 2}, n{sub 1} − n{sub 2}). A careful setup of the initial amplitudes and phases of the forced modes, defined as the “killer” modes, has allowed the minimizing of the initially dominant instability in the near pressure field, as well as its estimated radiated noise with a 15 dB loss. Although an increase of the overall sound pressure has been found in the range of azimuth and frequency analyzed, the present paper reveals the possibility to make the initially dominant instability ineffective acoustically using nonlinear interactions with forced eigenmodes.« less

Libsharp - spherical harmonic transforms revisited

NASA Astrophysics Data System (ADS)

Reinecke, M.; Seljebotn, D. S.

2013-06-01

We present libsharp, a code library for spherical harmonic transforms (SHTs), which evolved from the libpsht library and addresses several of its shortcomings, such as adding MPI support for distributed memory systems and SHTs of fields with arbitrary spin, but also supporting new developments in CPU instruction sets like the Advanced Vector Extensions (AVX) or fused multiply-accumulate (FMA) instructions. The library is implemented in portable C99 and provides an interface that can be easily accessed from other programming languages such as C++, Fortran, Python, etc. Generally, libsharp's performance is at least on par with that of its predecessor; however, significant improvements were made to the algorithms for scalar SHTs, which are roughly twice as fast when using the same CPU capabilities. The library is available at http://sourceforge.net/projects/libsharp/ under the terms of the GNU General Public License.

Effect of Forcing Function on Nonlinear Acoustic Standing Waves

NASA Technical Reports Server (NTRS)

Finkheiner, Joshua R.; Li, Xiao-Fan; Raman, Ganesh; Daniels, Chris; Steinetz, Bruce

2003-01-01

Nonlinear acoustic standing waves of high amplitude have been demonstrated by utilizing the effects of resonator shape to prevent the pressure waves from entering saturation. Experimentally, nonlinear acoustic standing waves have been generated by shaking an entire resonating cavity. While this promotes more efficient energy transfer than a piston-driven resonator, it also introduces complicated structural dynamics into the system. Experiments have shown that these dynamics result in resonator forcing functions comprised of a sum of several Fourier modes. However, previous numerical studies of the acoustics generated within the resonator assumed simple sinusoidal waves as the driving force. Using a previously developed numerical code, this paper demonstrates the effects of using a forcing function constructed with a series of harmonic sinusoidal waves on resonating cavities. From these results, a method will be demonstrated which allows the direct numerical analysis of experimentally generated nonlinear acoustic waves in resonators driven by harmonic forcing functions.

Numerical verification of bounce-harmonic resonances in neoclassical toroidal viscosity for tokamaks.

PubMed

Kim, Kimin; Park, Jong-Kyu; Boozer, Allen H

2013-05-03

This Letter presents the first numerical verification for the bounce-harmonic (BH) resonance phenomena of the neoclassical transport in a tokamak perturbed by nonaxisymmetric magnetic fields. The BH resonances were predicted by analytic theories of neoclassical toroidal viscosity (NTV), as the parallel and perpendicular drift motions can be resonant and result in a great enhancement of the radial momentum transport. A new drift-kinetic δf guiding-center particle code, POCA, clearly verified that the perpendicular drift motions can reduce the transport by phase-mixing, but in the BH resonances the motions can form closed orbits and particles radially drift out fast. The POCA calculations on resulting NTV torque are largely consistent with analytic calculations, and show that the BH resonances can easily dominate the NTV torque when a plasma rotates in the perturbed tokamak and therefore, is a critical physics for predicting the rotation and stability in the International Thermonuclear Experimental Reactor.

Dipolar effects on propagation of ultrashort laser pulse in one-dimensional para-nitroaniline (pNA) molecules

NASA Astrophysics Data System (ADS)

Zhao, Ke; Li, Hong-Yu; Liu, Ji-Cai; Wang, Chuan-Kui; Luo, Yi

2005-12-01

The dynamic behaviour of ultrashort (femtosecond) laser pulses in a molecular medium is studied by solving the full Maxwell-Bloch equations beyond the limits of the slowly varying envelope approximation and the rotating-wave approximation under the resonant and the non-resonant conditions. A one-dimensional asymmetric charge-transfer molecule, para-nitroaniline, is used as a model molecule whose electronic properties are calculated with the time-dependent hybrid density functional theory. Under the one-photon resonant condition, 4π pulse is separated into two sub-pulses. The weight of the second-harmonic component mainly contributed by the two-photon excitation becomes stronger with longer propagation time. Under the two-photon resonant condition, the separation of 4π pulse is not induced and many higher-order spectral components beyond the second-harmonic generation occur. Interestingly, when the pulse propagates for long enough, the carrier modification becomes so significant that a continuous spectrum is generated. The Fourier transform of the high-harmonic spectrum demonstrates that an even shorter laser pulse can be produced in both resonant and non-resonant propagations. The effects of permanent dipole moments on the pulse evolution are discussed.

LIDT-DD: A New Self-Consistent Debris Disc Model Including Radiation Pressure and Coupling Dynamical and Collisional Evolution

NASA Astrophysics Data System (ADS)

Kral, Q.; Thebault, P.; Charnoz, S.

2014-01-01

The first attempt at developing a fully self-consistent code coupling dynamics and collisions to study debris discs (Kral et al. 2013) is presented. So far, these two crucial mechanisms were studied separately, with N-body and statistical collisional codes respectively, because of stringent computational constraints. We present a new model named LIDT-DD which is able to follow over long timescales the coupled evolution of dynamics (including radiation forces) and collisions in a self-consistent way.

The evolution of popular music: USA 1960-2010.

PubMed

Mauch, Matthias; MacCallum, Robert M; Levy, Mark; Leroi, Armand M

2015-05-01

In modern societies, cultural change seems ceaseless. The flux of fashion is especially obvious for popular music. While much has been written about the origin and evolution of pop, most claims about its history are anecdotal rather than scientific in nature. To rectify this, we investigate the US Billboard Hot 100 between 1960 and 2010. Using music information retrieval and text-mining tools, we analyse the musical properties of approximately 17 000 recordings that appeared in the charts and demonstrate quantitative trends in their harmonic and timbral properties. We then use these properties to produce an audio-based classification of musical styles and study the evolution of musical diversity and disparity, testing, and rejecting, several classical theories of cultural change. Finally, we investigate whether pop musical evolution has been gradual or punctuated. We show that, although pop music has evolved continuously, it did so with particular rapidity during three stylistic 'revolutions' around 1964, 1983 and 1991. We conclude by discussing how our study points the way to a quantitative science of cultural change.

Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation.

PubMed

Geller, Ron; Pechmann, Sebastian; Acevedo, Ashley; Andino, Raul; Frydman, Judith

2018-05-03

Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution. We find that Hsp90 offsets evolutionary trade-offs between protein stability and aggregation. Lower chaperone levels favor variants of reduced hydrophobicity and protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize competing constraints posed by protein stability, aggregation propensity, and translation rate on successful protein biogenesis.

A NEW HYBRID N-BODY-COAGULATION CODE FOR THE FORMATION OF GAS GIANT PLANETS

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

Bromley, Benjamin C.; Kenyon, Scott J., E-mail: bromley@physics.utah.edu, E-mail: skenyon@cfa.harvard.edu

2011-04-20

We describe an updated version of our hybrid N-body-coagulation code for planet formation. In addition to the features of our 2006-2008 code, our treatment now includes algorithms for the one-dimensional evolution of the viscous disk, the accretion of small particles in planetary atmospheres, gas accretion onto massive cores, and the response of N-bodies to the gravitational potential of the gaseous disk and the swarm of planetesimals. To validate the N-body portion of the algorithm, we use a battery of tests in planetary dynamics. As a first application of the complete code, we consider the evolution of Pluto-mass planetesimals in amore » swarm of 0.1-1 cm pebbles. In a typical evolution time of 1-3 Myr, our calculations transform 0.01-0.1 M{sub sun} disks of gas and dust into planetary systems containing super-Earths, Saturns, and Jupiters. Low-mass planets form more often than massive planets; disks with smaller {alpha} form more massive planets than disks with larger {alpha}. For Jupiter-mass planets, masses of solid cores are 10-100 M{sub +}.« less

Two fundamental questions about protein evolution.

PubMed

Penny, David; Zhong, Bojian

2015-12-01

Two basic questions are considered that approach protein evolution from different directions; the problems arising from using Markov models for the deeper divergences, and then the origin of proteins themselves. The real problem for the first question (going backwards in time) is that at deeper phylogenies the Markov models of sequence evolution must lose information exponentially at deeper divergences, and several testable methods are suggested that should help resolve these deeper divergences. For the second question (coming forwards in time) a problem is that most models for the origin of protein synthesis do not give a role for the very earliest stages of the process. From our knowledge of the importance of replication accuracy in limiting the length of a coding molecule, a testable hypothesis is proposed. The length of the code, the code itself, and tRNAs would all have prior roles in increasing the accuracy of RNA replication; thus proteins would have been formed only after the tRNAs and the length of the triplet code are already formed. Both questions lead to testable predictions. Copyright © 2014 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Phase Transitions and Domain Structure in Mixed Tetragonal-Rhombohedral BiFeO3 thin films using Raman Spectroscopy and Nonlinear Optics

NASA Astrophysics Data System (ADS)

Vlahos, E.; Kumar, A.; Denev, S.; Melville, A.; Adamo, C.; Ihlefeld, J. F.; Sheng, G.; Zeches, R. J.; Zhang, J. X.; He, Q.; Yang, C. H.; Erni, R.; Rossell, M. D.; J, A.; Hatt; Chu, Y.-H.; Wang, C. H.; Ederer, C.; Gopalan, V.; Chen, L. Q.; Schlom, D. G.; Spaldin, N. A.; Martin, L. W.; Ramesh, R.; Tenne, Dmitri

2010-03-01

We have shown that biaxially strained BiFeO3 thin films can undergo an isosymmetric phase transition from a rhombohedral-like to a tetragonal-like phase. This talk discusses the evolution of the tetragonal and the mixed phases in BiFeO3/YAlO3 thin films with varying film thickness using optical second harmonic generation (SHG) and Raman spectroscopy. 25nm, 75nm, and 225 nm thick films were studied; thinner films are dominated by the tetragonal phase, whereas thicker films exhibit both tetragonal and rhombohedral phases. The evolution of these phases as function of film thickness and temperature was experimentally determined.

Superfluid Boson-Fermion Mixture: Structure Formation and Collective Periodic Motion

NASA Astrophysics Data System (ADS)

Mitra, A.

2018-01-01

Multiple periodic domain formation due to a modulation instability in a boson-fermion mixture superfluid in the unitary regime has been studied. The periodicity of the structure evolves with time. At the early stage of evolution, bosonic domains show the periodic nature, whereas the periodicity in the fermionic (Cooper pair) domains appears at the late stage of evolution. The nature of interatomic interspecies interactions affects the domain formation. In a harmonic trap, the mixture executes an undamped oscillation. The frequency of the oscillation depends on the relative coupling strength between boson-fermion and fermion-fermion. The repulsive boson-fermion interaction reduces the oscillation frequency, whereas the attractive interaction enhances the frequency significantly.

On the possible origin and evolution of the genetic code

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1974-01-01

The genetic code is examined for indications of possible preceding codes that existed during early evolution. Eight of the 20 amino acids are coded by 'quartets' of codons with fourfold degeneracy, and 16 such quartets can exist, so that an earlier code could have provided for 15 or 16 amino acids, rather than 20. If twofold degeneracy is postulated for the first position of the codon, there could have been ten amino acids in the code. It is speculated that these may have been phenylalanine, valine, proline, alanine, histidine, glutamine, glutanic acid, aspartic acid, cysteine and glycine. There is a notable deficiency of arginine in proteins, despite the fact that it has six codons. Simultaneously, there is more lysine in proteins than would be expected from its two codons, if the four bases in mRNA are equiprobable and are arranged randomly. It is speculated that arginine is an 'intruder' into the genetic code, and that it may have displayed another amino acid such as ornithine, or may even have displayed lysine from some of its previous codon assignments. As a result, natural selection has favored lysine against the fact that it has only two codons.

Multi-photon transitions and Rabi resonance in continuous wave EPR.

PubMed

Saiko, Alexander P; Fedaruk, Ryhor; Markevich, Siarhei A

2015-10-01

The study of microwave-radiofrequency multi-photon transitions in continuous wave (CW) EPR spectroscopy is extended to a Rabi resonance condition, when the radio frequency of the magnetic-field modulation matches the Rabi frequency of a spin system in the microwave field. Using the non-secular perturbation theory based on the Bogoliubov averaging method, the analytical description of the response of the spin system is derived for all modulation frequency harmonics. When the modulation frequency exceeds the EPR linewidth, multi-photon transitions result in sidebands in absorption EPR spectra measured with phase-sensitive detection at any harmonic. The saturation of different-order multi-photon transitions is shown to be significantly different and to be sensitive to the Rabi resonance. The noticeable frequency shifts of sidebands are found to be the signatures of this resonance. The inversion of two-photon lines in some spectral intervals of the out-of-phase first-harmonic signal is predicted under passage through the Rabi resonance. The inversion indicates the transition from absorption to stimulated emission or vice versa, depending on the sideband. The manifestation of the primary and secondary Rabi resonance is also demonstrated in the time evolution of steady-state EPR signals formed by all harmonics of the modulation frequency. Our results provide a theoretical framework for future developments in multi-photon CW EPR spectroscopy, which can be useful for samples with long spin relaxation times and extremely narrow EPR lines. Copyright © 2015 Elsevier Inc. All rights reserved.

Mechanisms of high-frequency song generation in brachypterous crickets and the role of ghost frequencies.

PubMed

Robillard, Tony; Montealegre-Z, Fernando; Desutter-Grandcolas, Laure; Grandcolas, Philippe; Robert, Daniel

2013-06-01

Sound production in crickets relies on stridulation, the well-understood rubbing together of a pair of specialised wings. As the file of one wing slides over the scraper of the other, a series of rhythmic impacts causes harmonic oscillations, usually resulting in the radiation of pure tones delivered at low frequencies (2-8 kHz). In the short-winged crickets of the Lebinthini tribe, acoustic communication relies on signals with remarkably high frequencies (>8 kHz) and rich harmonic content. Using several species of the subfamily Eneopterinae, we characterised the morphological and mechanical specialisations supporting the production of high frequencies, and demonstrated that higher harmonics are exploited as dominant frequencies. These specialisations affect the structure of the stridulatory file, the motor control of stridulation and the resonance of the sound radiator. We placed these specialisations in a phylogenetic framework and show that they serve to exploit high-frequency vibrational modes pre-existing in the phylogenetic ancestor. In Eneopterinae, the lower frequency components are harmonically related to the dominant peak, suggesting they are relicts of ancestral carrier frequencies. Yet, such ghost frequencies still occur in the wings' free resonances, highlighting the fundamental mechanical constraints of sound radiation. These results support the hypothesis that such high-frequency songs evolved stepwise, by a form of punctuated evolution that could be related to functional constraints, rather than by only the progressive increase of the ancestral fundamental frequency.

Predictions for multiplicities and flow harmonics in 5.44 TeV Xe+Xe collisions at the CERN Large Hadron Collider

NASA Astrophysics Data System (ADS)

Eskola, K. J.; Niemi, H.; Paatelainen, R.; Tuominen, K.

2018-03-01

We present the event-by-event next-to-leading-order perturbative-QCD + saturation + viscous hydrodynamics (EKRT) model predictions for the centrality dependence of the charged hadron multiplicity in the pseudorapidity interval |η |≤0.5 , and for the centrality dependence of the charged hadron flow harmonics vn{2 } obtained from two-particle cumulants, in √{sN N}=5.44 TeV Xe+Xe collisions at the CERN Large Hadron Collider. Our prediction for the 0-5 % central charged multiplicity is d Nch/d η =1218 ±46 . We also predict vn{2 } in Xe+Xe collisions to increase more slowly from central towards peripheral collisions than those in a Pb+Pb system. We find that at 10 ,⋯,50 % centralities v2{2 } is smaller and v3{2 } is larger than in the Pb+Pb system while v4{2 } is of the same magnitude in both systems. We also find that the ratio of flow harmonics in Xe+Xe collisions and in Pb+Pb collisions shows a slight sensitivity to the temperature dependence of the shear-viscosity-to-entropy ratio. As we discuss here, the new nuclear mass-number systematics especially in the flow harmonics serves as a welcome further constraint for describing the space-time evolution of a heavy-ion system and for determining the shear viscosity and other transport properties of strongly interacting matter.

Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

PubMed

Galián, José A; Rosato, Marcela; Rosselló, Josep A

2014-03-01

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.

High-Speed Solution of Spacecraft Trajectory Problems Using Taylor Series Integration

NASA Technical Reports Server (NTRS)

Scott, James R.; Martini, Michael C.

2010-01-01

It has been known for some time that Taylor series (TS) integration is among the most efficient and accurate numerical methods in solving differential equations. However, the full benefit of the method has yet to be realized in calculating spacecraft trajectories, for two main reasons. First, most applications of Taylor series to trajectory propagation have focused on relatively simple problems of orbital motion or on specific problems and have not provided general applicability. Second, applications that have been more general have required use of a preprocessor, which inevitably imposes constraints on computational efficiency. The latter approach includes the work of Berryman et al., who solved the planetary n-body problem with relativistic effects. Their work specifically noted the computational inefficiencies arising from use of a preprocessor and pointed out the potential benefit of manually coding derivative routines. In this Engineering Note, we report on a systematic effort to directly implement Taylor series integration in an operational trajectory propagation code: the Spacecraft N-Body Analysis Program (SNAP). The present Taylor series implementation is unique in that it applies to spacecraft virtually anywhere in the solar system and can be used interchangeably with another integration method. SNAP is a high-fidelity trajectory propagator that includes force models for central body gravitation with N X N harmonics, other body gravitation with N X N harmonics, solar radiation pressure, atmospheric drag (for Earth orbits), and spacecraft thrusting (including shadowing). The governing equations are solved using an eighth-order Runge-Kutta Fehlberg (RKF) single-step method with variable step size control. In the present effort, TS is implemented by way of highly integrated subroutines that can be used interchangeably with RKF. This makes it possible to turn TS on or off during various phases of a mission. Current TS force models include central body gravitation with the J2 spherical harmonic, other body gravitation, thrust, constant atmospheric drag from Earth's atmosphere, and solar radiation pressure for a sphere under constant illumination. The purpose of this Engineering Note is to demonstrate the performance of TS integration in an operational trajectory analysis code and to compare it with a standard method, eighth-order RKF. Results show that TS is 16.6 times faster on average and is more accurate in 87.5% of the cases presented.

Local variations in the timing of RSV epidemics.

PubMed

Noveroske, Douglas B; Warren, Joshua L; Pitzer, Virginia E; Weinberger, Daniel M

2016-11-11

Respiratory syncytial virus (RSV) is a primary cause of hospitalizations in children worldwide. The timing of seasonal RSV epidemics needs to be known in order to administer prophylaxis to high-risk infants at the appropriate time. We used data from the Connecticut State Inpatient Database to identify RSV hospitalizations based on ICD-9 diagnostic codes. Harmonic regression analyses were used to evaluate RSV epidemic timing at the county level and ZIP code levels. Linear regression was used to investigate associations between the socioeconomic status of a locality and RSV epidemic timing. 9,740 hospitalizations coded as RSV occurred among children less than 2 years old between July 1, 1997 and June 30, 2013. The earliest ZIP code had a seasonal RSV epidemic that peaked, on average, 4.64 weeks earlier than the latest ZIP code. Earlier epidemic timing was significantly associated with demographic characteristics (higher population density and larger fraction of the population that was black). Seasonal RSV epidemics in Connecticut occurred earlier in areas that were more urban (higher population density and larger fraction of the population that was). These findings could be used to better time the administration of prophylaxis to high-risk infants.

Status and future of MUSE

NASA Astrophysics Data System (ADS)

Harfst, S.; Portegies Zwart, S.; McMillan, S.

2008-12-01

We present MUSE, a software framework for combining existing computational tools from different astrophysical domains into a single multi-physics, multi-scale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a ``Noah's Ark'' milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multi-scale and multi-physics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe two examples calculated using MUSE: the merger of two galaxies and an N-body simulation with live stellar evolution. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.

Code dependencies of pre-supernova evolution and nucleosynthesis in massive stars: evolution to the end of core helium burning

DOE PAGES

Jones, S.; Hirschi, R.; Pignatari, M.; ...

2015-01-15

We present a comparison of 15M ⊙ , 20M ⊙ and 25M ⊙ stellar models from three different codes|GENEC, KEPLER and MESA|and their nucleosynthetic yields. The models are calculated from the main sequence up to the pre-supernova (pre-SN) stage and do not include rotation. The GENEC and KEPLER models hold physics assumptions that are characteristic of the two codes. The MESA code is generally more flexible; overshooting of the convective core during the hydrogen and helium burning phases in MESA is chosen such that the CO core masses are consistent with those in the GENEC models. Full nucleosynthesis calculations aremore » performed for all models using the NuGrid post-processing tool MPPNP and the key energy-generating nuclear reaction rates are the same for all codes. We are thus able to highlight the key diferences between the models that are caused by the contrasting physics assumptions and numerical implementations of the three codes. A reasonable agreement is found between the surface abundances predicted by the models computed using the different codes, with GENEC exhibiting the strongest enrichment of H-burning products and KEPLER exhibiting the weakest. There are large variations in both the structure and composition of the models—the 15M ⊙ and 20M ⊙ in particular—at the pre-SN stage from code to code caused primarily by convective shell merging during the advanced stages. For example the C-shell abundances of O, Ne and Mg predicted by the three codes span one order of magnitude in the 15M ⊙ models. For the alpha elements between Si and Fe the differences are even larger. The s-process abundances in the C shell are modified by the merging of convective shells; the modification is strongest in the 15M ⊙ model in which the C-shell material is exposed to O-burning temperatures and the γ -process is activated. The variation in the s-process abundances across the codes is smallest in the 25M ⊙ models, where it is comparable to the impact of nuclear reaction rate uncertainties. In general the differences in the results from the three codes are due to their contrasting physics assumptions (e.g. prescriptions for mass loss and convection). The broadly similar evolution of the 25M ⊙ models gives us reassurance that different stellar evolution codes do produce similar results. For the 15M ⊙ and 20M ⊙ models, however, the different input physics and the interplay between the various convective zones lead to important differences in both the pre-supernova structure and nucleosynthesis predicted by the three codes. For the KEPLER models the core masses are different and therefore an exact match could not be expected.« less

Drift Wave Simulation in Toroidal Geometry.

NASA Astrophysics Data System (ADS)

Lebrun, Maurice Joseph, III

1988-12-01

The drift wave, a general category of plasma behavior arising from a plasma inhomogeneity, is studied using the particle simulation method. In slab geometry, the drift wave (or universal mode) is stabilized by any finite amount of magnetic shear. In toroidal geometry, however, the coupling of the poloidal harmonics gives rise to a new branch of drift wave eigenmodes called the toroidicity -induced mode, which is predicted to be unstable in some regimes. The drift wave in a toroidal system is intrinsically three-dimensional, and is sensitive to the handling of the parallel electron dynamics, the (nearly) perpendicular wave dynamics, and the radial variation of magnetic field vector (shear). A simulation study must therefore be kinetic in nature, motivating the extension of particle simulation techniques to complex geometries. From this effort a three dimensional particle code in a toroidal coordinate system has been developed and applied to the toroidal drift wave problem. The code uses an (r,theta,phi) -type coordinate system, and a nonuniform radial grid that increases resolution near the mode-rational surfaces. Full ion dynamics and electron guiding center dynamics are employed. Further, the algorithm incorporates a straightforward limiting process to cylindrical geometry and slab geometry, enabling comparison to the theoretical results in these regimes. Simulations of the density-driven modes in toroidal geometry retain a single toroidal mode number (n = 9). In this regime, the poloidal harmonics are expected to be strongly coupled, giving rise to the marginally unstable toroidicity-induced drift mode. Analysis of the simulation data reveals a strong, low-frequency response that peaks near each mode rational surface. Further, the characteristic oscillation frequencies persist from one mode rational surface to the next, which identifies them as multiple harmonics of the toroidicity-induced mode. The lowest harmonic occurs at a frequency of omega/ omega^{*} ~ 0.26, which is reasonably close to the prediction of linear theory. Interferogram analysis of these modes indicates a "ballooning" structure toward the outside of the torus. The amplitude of the potential is observed to grow exponentially for the m = 8 through m = 10 poloidal mode numbers, with a growth rate of approximately gamma/omega ^{*} ~ 0.075. Saturation occurs at time t ~ 1000 Omega_sp{i}{-1}, and may be caused by quasilinear flattening of the density profile.

Rotor Wake/Stator Interaction Noise Prediction Code Technical Documentation and User's Manual

NASA Technical Reports Server (NTRS)

Topol, David A.; Mathews, Douglas C.

2010-01-01

This report documents the improvements and enhancements made by Pratt & Whitney to two NASA programs which together will calculate noise from a rotor wake/stator interaction. The code is a combination of subroutines from two NASA programs with many new features added by Pratt & Whitney. To do a calculation V072 first uses a semi-empirical wake prediction to calculate the rotor wake characteristics at the stator leading edge. Results from the wake model are then automatically input into a rotor wake/stator interaction analytical noise prediction routine which calculates inlet aft sound power levels for the blade-passage-frequency tones and their harmonics, along with the complex radial mode amplitudes. The code allows for a noise calculation to be performed for a compressor rotor wake/stator interaction, a fan wake/FEGV interaction, or a fan wake/core stator interaction. This report is split into two parts, the first part discusses the technical documentation of the program as improved by Pratt & Whitney. The second part is a user's manual which describes how input files are created and how the code is run.

Tempest simulations of kinetic GAM mode and neoclassical turbulence

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Dimits, A. M.

2007-11-01

TEMPEST is a nonlinear five dimensional (3d2v) gyrokinetic continuum code for studies of H-mode edge plasma neoclassical transport and turbulence in real divertor geometry. The 4D TEMPEST code correctly produces frequency, collisionless damping of GAM and zonal flow with fully nonlinear Boltzmann electrons in homogeneous plasmas. For large q=4 to 9, the Tempest simulations show that a series of resonance at higher harmonics v||=φGqR0/n with n=4 become effective. The TEMPEST simulation also shows that GAM exists in edge plasma pedestal for steep density and temperature gradients, and an initial GAM relaxes to the standard neoclassical residual with neoclassical transport, rather than Rosenbluth-Hinton residual due to the presence of ion-ion collisions. The enhanced GAM damping explains experimental BES measurements on the edge q scaling of the GAM amplitude. Our 5D gyrokinetic code is built on 4D Tempest neoclassical code with extension to a fifth dimension in toroidal direction and with 3D domain decompositions. Progress on performing 5D neoclassical turbulence simulations will be reported.

Terahertz Sideband-tuned Quantum Cascade Laser Radiation

DTIC Science & Technology

2008-03-31

resolution of 2 MHz in CW regime was observed. ©2008 Optical Society of America OCIS codes: (140.5965) Semiconductor lasers , quantum cascade...diode,” Opt. Lett. 29, 1632 (2004). 6. A. Baryshev, et.al., “ Phase locking and spectral linewidth of a two-mode terahertz quantum cascade laser ,” Appl... optically pumped gas laser . With further improvements in power and spatial mode quality, it should be possible to lock a TQCL to the harmonic of an ultra

A comparison of models for supernova remnants including cosmic rays

NASA Astrophysics Data System (ADS)

Kang, Hyesung; Drury, L. O'C.

1992-11-01

A simplified model which can follow the dynamical evolution of a supernova remnant including the acceleration of cosmic rays without carrying out full numerical simulations has been proposed by Drury, Markiewicz, & Voelk in 1989. To explore the accuracy and the merits of using such a model, we have recalculated with the simplified code the evolution of the supernova remnants considered in Jones & Kang, in which more detailed and accurate numerical simulations were done using a full hydrodynamic code based on the two-fluid approximation. For the total energy transferred to cosmic rays the two codes are in good agreement, the acceleration efficiency being the same within a factor of 2 or so. The dependence of the results of the two codes on the closure parameters for the two-fluid approximation is also qualitatively similar. The agreement is somewhat degraded in those cases where the shock is smoothed out by the cosmic rays.

Calculations of Helium Bubble Evolution in the PISCES Experiments with Cluster Dynamics

NASA Astrophysics Data System (ADS)

Blondel, Sophie; Younkin, Timothy; Wirth, Brian; Lasa, Ane; Green, David; Canik, John; Drobny, Jon; Curreli, Davide

2017-10-01

Plasma surface interactions in fusion tokamak reactors involve an inherently multiscale, highly non-equilibrium set of phenomena, for which current models are inadequate to predict the divertor response to and feedback on the plasma. In this presentation, we describe the latest code developments of Xolotl, a spatially-dependent reaction diffusion cluster dynamics code to simulate the divertor surface response to fusion-relevant plasma exposure. Xolotl is part of a code-coupling effort to model both plasma and material simultaneously; the first benchmark for this effort is the series of PISCES linear device experiments. We will discuss the processes leading to surface morphology changes, which further affect erosion, as well as how Xolotl has been updated in order to communicate with other codes. Furthermore, we will show results of the sub-surface evolution of helium bubbles in tungsten as well as the material surface displacement under these conditions.

Implementation and validation of a wake model for low-speed forward flight

NASA Technical Reports Server (NTRS)

Komerath, Narayanan M.; Schreiber, Olivier A.

1987-01-01

The computer implementation and calculations of the induced velocities produced by a wake model consisting of a trailing vortex system defined from a prescribed time averaged downwash distribution are detailed. Induced velocities are computed by approximating each spiral turn by a pair of large straight vortex segments positioned at critical points relative to where the induced velocity is required. A remainder term for the rest of the spiral is added. This approach results in decreased computation time compared to classical models where each spiral turn is broken down in small straight vortex segments. The model includes features such a harmonic variation of circulation, downwash outside of the blade and/or outside the tip path plane, blade bound vorticity induced velocity with harmonic variation of circulation and time averaging. The influence of various options and parameters on the results are investigated and results are compared to experimental field measurements with which, a resonable agreement is obtained. The capabilities of the model as well as its extension possibilities are studied. The performance of the model in predicting the recently-acquired NASA Langley Inflow data base for a four-bladed rotor is compared to that of the Scully Free Wake code, a well-established program which requires much greater computational resources. It is found that the two codes predict the experimental data with essentially the same accuracy, and show the same trends.

Physical scales in the Wigner–Boltzmann equation

PubMed Central

Nedjalkov, M.; Selberherr, S.; Ferry, D.K.; Vasileska, D.; Dollfus, P.; Querlioz, D.; Dimov, I.; Schwaha, P.

2013-01-01

The Wigner–Boltzmann equation provides the Wigner single particle theory with interactions with bosonic degrees of freedom associated with harmonic oscillators, such as phonons in solids. Quantum evolution is an interplay of two transport modes, corresponding to the common coherent particle-potential processes, or to the decoherence causing scattering due to the oscillators. Which evolution mode will dominate depends on the scales of the involved physical quantities. A dimensionless formulation of the Wigner–Boltzmann equation is obtained, where these scales appear as dimensionless strength parameters. A notion called scaling theorem is derived, linking the strength parameters to the coupling with the oscillators. It is shown that an increase of this coupling is equivalent to a reduction of both the strength of the electric potential, and the coherence length. Secondly, the existence of classes of physically different, but mathematically equivalent setups of the Wigner–Boltzmann evolution is demonstrated. PMID:23504194

Finite-element time evolution operator for the anharmonic oscillator

NASA Technical Reports Server (NTRS)

Milton, Kimball A.

1995-01-01

The finite-element approach to lattice field theory is both highly accurate (relative errors approximately 1/N(exp 2), where N is the number of lattice points) and exactly unitary (in the sense that canonical commutation relations are exactly preserved at the lattice sites). In this talk I construct matrix elements for dynamical variables and for the time evolution operator for the anharmonic oscillator, for which the continuum Hamiltonian is H = p(exp 2)/2 + lambda q(exp 4)/4. Construction of such matrix elements does not require solving the implicit equations of motion. Low order approximations turn out to be extremely accurate. For example, the matrix element of the time evolution operator in the harmonic oscillator ground state gives a results for the anharmonic oscillator ground state energy accurate to better than 1 percent, while a two-state approximation reduces the error to less than 0.1 percent.

Entanglement negativity after a local quantum quench in conformal field theories

NASA Astrophysics Data System (ADS)

Wen, Xueda; Chang, Po-Yao; Ryu, Shinsei

2015-08-01

We study the time evolution of the entanglement negativity after a local quantum quench in (1 + 1)-dimensional conformal field theories (CFTs), which we introduce by suddenly joining two initially decoupled CFTs at their end points. We calculate the negativity evolution for both adjacent intervals and disjoint intervals explicitly. For two adjacent intervals, the entanglement negativity grows logarithmically in time right after the quench. After developing a plateau-like feature, the entanglement negativity drops to the ground-state value. For the case of two spatially separated intervals, a light-cone behavior is observed in the negativity evolution; in addition, a long-range entanglement, which is independent of the distance between two intervals, can be created. Our results agree with the heuristic picture that quasiparticles, which carry entanglement, are emitted from the joining point and propagate freely through the system. Our analytical results are confirmed by numerical calculations based on a critical harmonic chain.

Numerical simulation of stability and stability control of high speed compressible rotating couette flow

NASA Technical Reports Server (NTRS)

Biringen, Sedat; Hatay, Ferhat F.

1993-01-01

The nonlinear temporal evolution of disturbances in compressible flow between infinitely long, concentric cylinders is investigated through direct numerical simulations of the full, three-dimensional Navier-Stokes and energy equations. Counter-rotating cylinders separated by wide gaps are considered with supersonic velocities of the inner cylinder. Initially, the primary disturbance grows exponentially in accordance with linear stability theory. As the disturbances evolve, higher harmonics and subharmonics are generated in a cascading order eventually reaching a saturation state. Subsequent highly nonlinear stages of the evolution are governed by the interaction of the disturbance modes, particularly the axial subharmonics. Nonlinear evolution of the disturbance field is characterized by the formation of high-shear layers extending from the inner cylinder towards the center of the gap in the form of jets similar to the ejection events in transitional and turbulent wall-bounded shear flows.

Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion

NASA Astrophysics Data System (ADS)

Olšina, Jan; Kramer, Tobias; Kreisbeck, Christoph; Mančal, Tomáš

2014-10-01

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.

Stochastic modeling of mode interactions via linear parabolized stability equations

NASA Astrophysics Data System (ADS)

Ran, Wei; Zare, Armin; Hack, M. J. Philipp; Jovanovic, Mihailo

2017-11-01

Low-complexity approximations of the Navier-Stokes equations have been widely used in the analysis of wall-bounded shear flows. In particular, the parabolized stability equations (PSE) and Floquet theory have been employed to capture the evolution of primary and secondary instabilities in spatially-evolving flows. We augment linear PSE with Floquet analysis to formally treat modal interactions and the evolution of secondary instabilities in the transitional boundary layer via a linear progression. To this end, we leverage Floquet theory by incorporating the primary instability into the base flow and accounting for different harmonics in the flow state. A stochastic forcing is introduced into the resulting linear dynamics to model the effect of nonlinear interactions on the evolution of modes. We examine the H-type transition scenario to demonstrate how our approach can be used to model nonlinear effects and capture the growth of the fundamental and subharmonic modes observed in direct numerical simulations and experiments.

A New Approach to Model Pitch Perception Using Sparse Coding

PubMed Central

Furst, Miriam; Barak, Omri

2017-01-01

Our acoustical environment abounds with repetitive sounds, some of which are related to pitch perception. It is still unknown how the auditory system, in processing these sounds, relates a physical stimulus and its percept. Since, in mammals, all auditory stimuli are conveyed into the nervous system through the auditory nerve (AN) fibers, a model should explain the perception of pitch as a function of this particular input. However, pitch perception is invariant to certain features of the physical stimulus. For example, a missing fundamental stimulus with resolved or unresolved harmonics, or a low and high-level amplitude stimulus with the same spectral content–these all give rise to the same percept of pitch. In contrast, the AN representations for these different stimuli are not invariant to these effects. In fact, due to saturation and non-linearity of both cochlear and inner hair cells responses, these differences are enhanced by the AN fibers. Thus there is a difficulty in explaining how pitch percept arises from the activity of the AN fibers. We introduce a novel approach for extracting pitch cues from the AN population activity for a given arbitrary stimulus. The method is based on a technique known as sparse coding (SC). It is the representation of pitch cues by a few spatiotemporal atoms (templates) from among a large set of possible ones (a dictionary). The amount of activity of each atom is represented by a non-zero coefficient, analogous to an active neuron. Such a technique has been successfully applied to other modalities, particularly vision. The model is composed of a cochlear model, an SC processing unit, and a harmonic sieve. We show that the model copes with different pitch phenomena: extracting resolved and non-resolved harmonics, missing fundamental pitches, stimuli with both high and low amplitudes, iterated rippled noises, and recorded musical instruments. PMID:28099436

Development and Validation of an Agency for Healthcare Research and Quality Indicator for Mortality After Congenital Heart Surgery Harmonized With Risk Adjustment for Congenital Heart Surgery (RACHS-1) Methodology.

PubMed

Jenkins, Kathy J; Koch Kupiec, Jennifer; Owens, Pamela L; Romano, Patrick S; Geppert, Jeffrey J; Gauvreau, Kimberlee

2016-05-20

The National Quality Forum previously approved a quality indicator for mortality after congenital heart surgery developed by the Agency for Healthcare Research and Quality (AHRQ). Several parameters of the validated Risk Adjustment for Congenital Heart Surgery (RACHS-1) method were included, but others differed. As part of the National Quality Forum endorsement maintenance process, developers were asked to harmonize the 2 methodologies. Parameters that were identical between the 2 methods were retained. AHRQ's Healthcare Cost and Utilization Project State Inpatient Databases (SID) 2008 were used to select optimal parameters where differences existed, with a goal to maximize model performance and face validity. Inclusion criteria were not changed and included all discharges for patients <18 years with International Classification of Diseases, Ninth Revision, Clinical Modification procedure codes for congenital heart surgery or nonspecific heart surgery combined with congenital heart disease diagnosis codes. The final model includes procedure risk group, age (0-28 days, 29-90 days, 91-364 days, 1-17 years), low birth weight (500-2499 g), other congenital anomalies (Clinical Classifications Software 217, except for 758.xx), multiple procedures, and transfer-in status. Among 17 945 eligible cases in the SID 2008, the c statistic for model performance was 0.82. In the SID 2013 validation data set, the c statistic was 0.82. Risk-adjusted mortality rates by center ranged from 0.9% to 4.1% (5th-95th percentile). Congenital heart surgery programs can now obtain national benchmarking reports by applying AHRQ Quality Indicator software to hospital administrative data, based on the harmonized RACHS-1 method, with high discrimination and face validity. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

A New Approach to Model Pitch Perception Using Sparse Coding.

PubMed

Barzelay, Oded; Furst, Miriam; Barak, Omri

2017-01-01

Our acoustical environment abounds with repetitive sounds, some of which are related to pitch perception. It is still unknown how the auditory system, in processing these sounds, relates a physical stimulus and its percept. Since, in mammals, all auditory stimuli are conveyed into the nervous system through the auditory nerve (AN) fibers, a model should explain the perception of pitch as a function of this particular input. However, pitch perception is invariant to certain features of the physical stimulus. For example, a missing fundamental stimulus with resolved or unresolved harmonics, or a low and high-level amplitude stimulus with the same spectral content-these all give rise to the same percept of pitch. In contrast, the AN representations for these different stimuli are not invariant to these effects. In fact, due to saturation and non-linearity of both cochlear and inner hair cells responses, these differences are enhanced by the AN fibers. Thus there is a difficulty in explaining how pitch percept arises from the activity of the AN fibers. We introduce a novel approach for extracting pitch cues from the AN population activity for a given arbitrary stimulus. The method is based on a technique known as sparse coding (SC). It is the representation of pitch cues by a few spatiotemporal atoms (templates) from among a large set of possible ones (a dictionary). The amount of activity of each atom is represented by a non-zero coefficient, analogous to an active neuron. Such a technique has been successfully applied to other modalities, particularly vision. The model is composed of a cochlear model, an SC processing unit, and a harmonic sieve. We show that the model copes with different pitch phenomena: extracting resolved and non-resolved harmonics, missing fundamental pitches, stimuli with both high and low amplitudes, iterated rippled noises, and recorded musical instruments.

Historical Roots and Future Perspectives Related to Nursing Ethics.

ERIC Educational Resources Information Center

Freitas, Lorraine

1990-01-01

This article traces the evolution of the development and refinement of the professional code from concerns about the ethical conduct of nurses to its present state as a professional code for all nurses. The relationship of the Ethics Committee of the American Nurses' Association to the development of the code is also discussed. (Author/MLW)

Radiation from advanced solid rocket motor plumes

NASA Technical Reports Server (NTRS)

Farmer, Richard C.; Smith, Sheldon D.; Myruski, Brian L.

1994-01-01

The overall objective of this study was to develop an understanding of solid rocket motor (SRM) plumes in sufficient detail to accurately explain the majority of plume radiation test data. Improved flowfield and radiation analysis codes were developed to accurately and efficiently account for all the factors which effect radiation heating from rocket plumes. These codes were verified by comparing predicted plume behavior with measured NASA/MSFC ASRM test data. Upon conducting a thorough review of the current state-of-the-art of SRM plume flowfield and radiation prediction methodology and the pertinent data base, the following analyses were developed for future design use. The NOZZRAD code was developed for preliminary base heating design and Al2O3 particle optical property data evaluation using a generalized two-flux solution to the radiative transfer equation. The IDARAD code was developed for rapid evaluation of plume radiation effects using the spherical harmonics method of differential approximation to the radiative transfer equation. The FDNS CFD code with fully coupled Euler-Lagrange particle tracking was validated by comparison to predictions made with the industry standard RAMP code for SRM nozzle flowfield analysis. The FDNS code provides the ability to analyze not only rocket nozzle flow, but also axisymmetric and three-dimensional plume flowfields with state-of-the-art CFD methodology. Procedures for conducting meaningful thermo-vision camera studies were developed.

An introduction to wavelet analysis in oceanography and meteorology - With application to the dispersion of Yanai waves

NASA Technical Reports Server (NTRS)

Meyers, Steven D.; Kelly, B. G.; O'Brien, J. J.

1993-01-01

Wavelet analysis is a relatively new technique that is an important addition to standard signal analysis methods. Unlike Fourier analysis that yields an average amplitude and phase for each harmonic in a dataset, the wavelet transform produces an instantaneous estimate or local value for the amplitude and phase of each harmonic. This allows detailed study of nonstationary spatial or time-dependent signal characteristics. The wavelet transform is discussed, examples are given, and some methods for preprocessing data for wavelet analysis are compared. By studying the dispersion of Yanai waves in a reduced gravity equatorial model, the usefulness of the transform is demonstrated. The group velocity is measured directly over a finite range of wavenumbers by examining the time evolution of the transform. The results agree well with linear theory at higher wavenumber but the measured group velocity is reduced at lower wavenumbers, possibly due to interaction with the basin boundaries.

A Gaussian Wave Packet Propagation Approach to Vibrationally Resolved Optical Spectra at Non-Zero Temperatures.

PubMed

Reddy, Ch Sridhar; Prasad, M Durga

2016-04-28

An effective time dependent approach based on a method that is similar to the Gaussian wave packet propagation (GWP) technique of Heller is developed for the computation of vibrationally resolved electronic spectra at finite temperatures in the harmonic, Franck-Condon/Hertzberg-Teller approximations. Since the vibrational thermal density matrix of the ground electronic surface and the time evolution operator on that surface commute, it is possible to write the spectrum generating correlation function as a trace of the time evolved doorway state. In the stated approximations, the doorway state is a superposition of the harmonic oscillator zero and one quantum eigenfunctions and thus can be propagated by the GWP. The algorithm has an O(N(3)) dependence on the number of vibrational modes. An application to pyrene absorption spectrum at two temperatures is presented as a proof of the concept.

Wolf-Rayet stars, black holes and the first detected gravitational wave source

NASA Astrophysics Data System (ADS)

Bogomazov, A. I.; Cherepashchuk, A. M.; Lipunov, V. M.; Tutukov, A. V.

2018-01-01

The recently discovered burst of gravitational waves GW150914 provides a good new chance to verify the current view on the evolution of close binary stars. Modern population synthesis codes help to study this evolution from two main sequence stars up to the formation of two final remnant degenerate dwarfs, neutron stars or black holes (Masevich and Tutukov, 1988). To study the evolution of the GW150914 predecessor we use the ;Scenario Machine; code presented by Lipunov et al. (1996). The scenario modeling conducted in this study allowed to describe the evolution of systems for which the final stage is a massive BH+BH merger. We find that the initial mass of the primary component can be 100÷140M⊙ and the initial separation of the components can be 50÷350R⊙. Our calculations show the plausibility of modern evolutionary scenarios for binary stars and the population synthesis modeling based on it.

Unraveling the Complexity of the Evolution of the Sun's Photospheric Magnetic Field

NASA Astrophysics Data System (ADS)

Hathaway, David H.

2016-10-01

Given the emergence of tilted, bipolar active regions, surface flux transport has been shown to reproduce much of the complex evolution of the Sun's photospheric magnetic field. Surface flux is transported by flows in the surface shear layer - the axisymmetric differential rotation and meridional flow and the non-axisymmetric convective motions (granules, supergranules, and giant cells). We have measured these flows by correlation tracking of the magnetic elements themselves, correlation tracking of the Doppler features (supergranules), and by direct Doppler measurements using SDO/HMI data. These measurements fully constrain (with no free parameters) the flows used in our surface flux transport code - the Advective Flux Transport or AFT code. Here we show the up-to-date evolution of these flows, their impact on the detailed evolution of the Sun's photospheric magnetic field, and predictions for what the polar fields will be at the next minimum in 2020.

Biosemiotics: a new understanding of life.

PubMed

Barbieri, Marcello

2008-07-01

Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes--copying and coding--and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.

Harmonic effects on ion-bulk waves and simulation of stimulated ion-bulk-wave scattering in CH plasmas

NASA Astrophysics Data System (ADS)

Feng, Q. S.; Zheng, C. Y.; Liu, Z. J.; Cao, L. H.; Xiao, C. Z.; Wang, Q.; Zhang, H. C.; He, X. T.

2017-08-01

Ion-bulk (IBk) wave, a novel branch with a phase velocity close to the ion’s thermal velocity, discovered by Valentini et al (2011 Plasma Phys. Control. Fusion 53 105017), is recently considered as an important electrostatic activity in solar wind, and thus of great interest to space physics and also inertial confinement fusion. The harmonic effects on IBk waves has been researched by Vlasov simulation for the first time. The condition of excitation of the large-amplitude IBk waves is given. The nature of nonlinear IBk waves in the condition of k< {k}{{lor}}/2 (k lor is the wave number at loss-of-resonance point) is undamped Bernstein-Greene-Kruskal-like waves with harmonic superposition. Only when the wave number k of IBk waves satisfies {k}{{lor}}/2≲ k≤slant {k}{{lor}}, can a large-amplitude and mono-frequency IBk wave be excited. A novel stimulated scattering from IBk modes called stimulated ion-bulk-wave scattering (SIBS) or stimulated Feng scattering (SFS) has been proposed and also verified by Vlasov-Maxwell code. In CH plasmas, in addition to the stimulated Brillouin scattering from multi ion-acoustic waves, there exists SIBS simultaneously. This research gives an insight into the SIBS in the field of laser plasma interaction.

Effect of aberration on the acoustic field in tissue harmonic imaging (THI)

NASA Astrophysics Data System (ADS)

Jing, Yuan; Cleveland, Robin

2003-10-01

A numerical simulation was used to study the impact of an aberrating layer on the generation of the fundamental and second-harmonic (SH) field in a tissue harmonic imaging scenario. The simulation used a three-dimensional time-domain code for solving the KZK equation and accounted for arbitrary spatial variations in all acoustic properties. The aberration effect was modeled by assuming that the tissue consisted of two layers where the interface has a spatial variation C that acted like an effective phase screen. Initial experiments were carried out with sinusoidal-shaped interfaces. The sinusoidal interface produced grating lobes which were at least 6 dB larger for the fundamental signal than the SH. The energy outside of the main lobe was found to increase linearly as the amplitude of the interface variation increased. The location of the grating lobes was affected by the spatial period on the interface variation. The inhomogeneous nature of tissue was modeled with an interface with a random spatial variation. With the random interface the average sidelobe level for the fundamental was -30 dB whereas the SH had an average sidelobe level of -36 dB. [Work supported by the NSF through the Center for Subsurface Sensing and Imaging Systems.

Cerebral perfusion imaging with bolus harmonic imaging (Honorable Mention Poster Award)

NASA Astrophysics Data System (ADS)

Kier, Christian; Toth, Daniel; Meyer-Wiethe, Karsten; Schindler, Angela; Cangur, Hakan; Seidel, Gunter; Aach, Til

2005-04-01

Fast visualisation of cerebral microcirculation supports diagnosis of acute stroke. However, the commonly used CT/MRI-based methods are time consuming, costly and not applicable to every patient. The bolus perfusion harmonic imaging (BHI) method is an ultrasound imaging technique which makes use of the fact, that ultrasound contrast agents unlike biological tissues resonate at harmonic frequencies. Exploiting this effect, the contrast between perfused and non-perfused areas can be improved. Thus, BHI overcomes the low signal-to-noise ratio of transcranial ultrasound and the high impedance of the skull. By analysing image sequences, visualising the qualitative characteristics of an US contrast agent bolus injection becomes possible. The analysis consists of calculating four perfusion-related parameters, Local Peak Intensity, Time To Peak, Area Under Curve, and Average Rising, from the time/intensity curve and providing them as colour-coded images. For calculating these parameters the fundamental assumption is that image intensity corresponds to contrast agent concentration which in turn shows the perfusion of the corresponding brain region. In a clinical study on patients suffering from acute ischemic stroke it is shown that some of the parameters correlate significantly to the infarction area. Thus, BHI becomes a less time-consuming and inexpensive bedside method for diagnosis of cerebral perfusion deficits.

Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

USDA-ARS?s Scientific Manuscript database

Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

The Nature of the Arguments for Creationism, Intelligent Design, and Evolution

ERIC Educational Resources Information Center

Barnes, Ralph M.; Church, Rebecca A.; Draznin-Nagy, Samuel

2017-01-01

Seventy-two Internet documents promoting creationism, intelligent design (I.D.), or evolution were selected for analysis. The primary goal of each of the 72 documents was to present arguments for creationism, I.D., or evolution. We first identified all arguments in these documents. Each argument was then coded in terms of both argument type…

Directed Chemical Evolution with an Outsized Genetic Code

PubMed Central

Krusemark, Casey J.; Tilmans, Nicolas P.; Brown, Patrick O.; Harbury, Pehr B.

2016-01-01

The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution. PMID:27508294

Conference on Early Mars: Geologic and Hydrologic Evolution, Physical and Chemical Environments, and the Implications for Life

NASA Technical Reports Server (NTRS)

Clifford, S. M. (Editor); Treiman, A. H. (Editor); Newsom, H. E. (Editor); Farmer, J. D. (Editor)

1997-01-01

Topics considered include: Geology alteration and life in an extreme environment; developing a chemical code to identify magnetic biominerals; effect of impacts on early Martin geologic evolution; spectroscopic identification of minerals in Hematite-bearing soils and sediments; exopaleontology and the search for a Fossil record on Mars; geochemical evolution of the crust of Mars; geological evolution of the early earth;solar-wind-induced erosion of the Mars atmosphere. Also included geological evolution of the crust of Mars.

Study of dispersive and nonlinear effects of coastal wave dynamics with a fully nonlinear potential flow model

NASA Astrophysics Data System (ADS)

Benoit, Michel; Yates, Marissa L.; Raoult, Cécile

2017-04-01

Efficient and accurate numerical models simulating wave propagation are required for a variety of engineering projects including the evaluation of coastal risks, the design of protective coastal structures, and the estimation of the potential for marine renewable energy devices. Nonlinear and dispersive effects are particularly significant in the coastal zone where waves interact with the bottom, the shoreline, and coastal structures. The main challenge in developing a numerical models is finding a compromise between computational efficiency and the required accuracy of the simulated wave field. Here, a potential approach is selected and the (fully nonlinear) water wave problem is formulated using the Euler-Zakharov equations (Zakharov, 1968) describing the temporal evolution of the free surface elevation and velocity potential. The proposed model (Yates and Benoit, 2015) uses a spectral approach in the vertical (i.e. the vertical variation of the potential is approximated by a linear combination of the first NT+1 Chebyshev polynomials, following the work of Tian and Sato (2008)). The Zakharov equations are integrated in time using a fourth-order Runge-Kutta scheme with a constant time step. At each sub-timestep, the Laplace Boundary Value Problem (BVP) is solved to estimate the free surface vertical velocity using the spectral approach, with typical values of NT between 5 to 8 for practical applications. The 1DH version of the code is validated with comparisons to the experimental data set of Becq-Girard et al. (1999), which studied the propagation of irregular waves over a beach profile with a submerged bar. The nonlinear and dispersive capacities of the model are verified with the correct representation of wave-wave interactions, in particular the transfer of energy between different harmonic components during wave propagation (analysis of the transformation of the variance spectrum along the channel). Evolution of wave skewness, asymmetry and kurtosis along the bathymetric profile also compare well with the measured values. The statistical distributions of the free surface elevation and wave height, calculated from the simulated time series, are compared to those of the measurements, with particular attention paid to the extreme waves. To use this model for realistic cases with complex bathymetric variations and multidirectional wave fields, the model has been extended to two horizontal dimensions (2DH). The spectral approach in the vertical dimension is retained, while the horizontal plane is discretized with scattered nodes to maintain the model's flexibility. The horizontal derivatives are estimated with finite-difference type formulas using Radial Basis Functions (Wright and Fornberg, 2006). The 2DH version of the code is applied to simulate the propagation of regular waves over a semi-circular step, which acts as a focusing lens. The simulation results are compared to the experimental data set of Whalin (1971). The evolution of the higher harmonic amplitudes in the shallow-water zone demonstrates the ability of the model to simulate wave propagation over complex 2DH coastal bathymetries. References: Becq-Girard F., Forget P., Benoit M. (1999) Non-linear propagation of unidirectional wave fields over varying topography. Coastal Eng., 38, 91-113. Tian Y., Sato S. (2008) A numerical model on the interaction between nearshore nonlinear waves and strong currents. Coast. Eng. Journal, 50(4), 369-395. Whalin R.W. (1971) The limit of applicability of linear wave refraction theory in a convergence zone. Technical report, DTIC Documents. Wright G.B., Fornberg B. (2006) Scattered node compact finite difference-type formulas generated from radial basis functions. J. Comp. Phys., 212, 99-123. Yates M.L., Benoit M. (2015) Accuracy and efficiency of two numerical methods of solving the potential flow problem for highly nonlinear and dispersive water waves. Int. J. Numer. Meth. Fluids, 77, 616-640. Zakharov V.E. (1968) Stability of periodic waves of finite amplitude on the surface of a deep fluid. J. Appl. Mech. Tech. Phys., 9(2), 190-194.

Biosemiotics: a new understanding of life

NASA Astrophysics Data System (ADS)

Barbieri, Marcello

2008-07-01

Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes—copying and coding—and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.

ERRATUM: Papers published in incorrect sections

NASA Astrophysics Data System (ADS)

2004-04-01

A number of J. Phys. A: Math. Gen. articles have mistakenly been placed in the wrong subject section in recent issues of the journal. We would like to apologize to the authors of these articles for publishing their papers in the Fluid and Plasma Theory section. The correct section for each article is given below. Statistical Physics Issue 4: Microcanonical entropy for small magnetizations Behringer H 2004 J. Phys. A: Math. Gen. 37 1443 Mathematical Physics Issue 9: On the solution of fractional evolution equations Kilbas A A, Pierantozzi T, Trujillo J J and Vázquez L 2004 J. Phys. A: Math. Gen. 37 3271 Quantum Mechanics and Quantum Information Theory Issue 6: New exactly solvable isospectral partners for PT-symmetric potentials Sinha A and Roy P 2004 J. Phys. A: Math. Gen. 37 2509 Issue 9: Symplectically entangled states and their applications to coding Vourdas A 2004 J. Phys. A: Math. Gen. 37 3305 Classical and Quantum Field Theory Issue 6: Pairing of parafermions of order 2: seniority model Nelson C A 2004 J. Phys. A: Math. Gen. 37 2497 Issue 7: Jordan-Schwinger map, 3D harmonic oscillator constants of motion, and classical and quantum parameters characterizing electromagnetic wave polarization Mota R D, Xicoténcatl M A and Granados V D 2004 J. Phys. A: Math. Gen. 37 2835 Issue 9: Could only fermions be elementary? Lev F M 2004 J. Phys. A: Math. Gen. 37 3285

Aeroacoustic and Performance Simulations of a Test Scale Open Rotor

NASA Technical Reports Server (NTRS)

Claus, Russell W.

2013-01-01

This paper explores a comparison between experimental data and numerical simulations of the historical baseline F31/A31 open rotor geometry. The experimental data were obtained at the NASA Glenn Research Center s Aeroacoustic facility and include performance and noise information for a variety of flow speeds (matching take-off and cruise). The numerical simulations provide both performance and aeroacoustic results using the NUMECA s Fine-Turbo analysis code. A non-linear harmonic method is used to capture the rotor/rotor interaction.

Reciprocity Calibration in a Plane Wave Resonator.

DTIC Science & Technology

1985-12-01

300 N. Quincy St. (code 11121ELEMENT NO INO :4NO ACCESS~oN NO Arlington, Va. , zip. 22217 6 115 3N IR1108-0 384_-1 8 V0 14 351-R 7IT..E (include...room " temperature [22 deg C3 ----------------------- 66 1.7 Differential volume under consideration ----- 71 2.1 .-.Iified four port network...natural log of both sides and differentiate , V Equation 1.41 If the acoustic pressure is harmonic then it can be written as, * L 4 U j i OEquation

MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation

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

Harrison, Robert J.; Beylkin, Gregory; Bischoff, Florian A.

2016-01-01

MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods with guaranteed precision based on multiresolution analysis and separated representations. Underpinning the numerical capabilities is a powerful petascale parallel programming environment that aims to increase both programmer productivity and code scalability. This paper describes the features and capabilities of MADNESS and briefly discusses some current applications in chemistry and several areas of physics.

Electromagnetic Fields of a Uniform Sphere in a Uniform Conducting Medium with Application to Dipole Sources

DTIC Science & Technology

1991-09-01

12b. DISTRIBUTION CODE Approved for public release; distribution is unlimited. 13. ABSTRACT (Maximum 200 words) Vector spherical harmonic expansions are...electric and magnetic field vectors from E rand B - r alone. Genural expressions are given relating the scattered field expansion coefficients to the source...Prescnbed by ANSI Std. Z39-18 29W-102 NCSC TR 426-90 CONTENTS Pag o INTRODUCTION 1 BACKGROUND 1 ANGULAR MOMENTUM OPERATOR AND VECTOR SPHERICAL

Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence.

PubMed

Kim, Dong Seon; Hahn, Yoonsoo

2012-11-13

Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence. We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors) in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of SMOX gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways. Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution.

The Global Registry of Biodiversity Repositories: A Call for Community Curation.

PubMed

Schindel, David E; Miller, Scott E; Trizna, Michael G; Graham, Eileen; Crane, Adele E

2016-01-01

The Global Registry of Biodiversity Repositories is an online metadata resource for biodiversity collections, the institutions that contain them, and associated staff members. The registry provides contact and address information, characteristics of the institutions and collections using controlled vocabularies and free-text descripitons, links to related websites, unique identifiers for each institution and collection record, text fields for loan and use policies, and a variety of other descriptors. Each institution record includes an institutionCode that must be unique, and each collection record must have a collectionCode that is unique within that institution. The registry is populated with records imported from the largest similar registries and more can be harmonized and added. Doing so will require community input and curation and would produce a truly comprehensive and unifying information resource.

DAGON: a 3D Maxwell-Bloch code

NASA Astrophysics Data System (ADS)

Oliva, Eduardo; Cotelo, Manuel; Escudero, Juan Carlos; González-Fernández, Agustín.; Sanchís, Alberto; Vera, Javier; Vicéns, Sergio; Velarde, Pedro

2017-05-01

The amplification of UV radiation and high order harmonics (HOH) in plasmas is a subject of raising interest due to its different potential applications in several fields like environment and security (detection at distance), biology, materials science and industry (3D imaging) and atomic and plasma physics (pump-probe experiments). In order to develop these sources, it is necessary to properly understand the amplification process. Being the plasma an inhomogeneous medium which changes with time, it is desirable to have a full time-dependent 3D description of the interaction of UV and XUV radiation with plasmas. For these reasons, at the Instituto de Fusíon Nuclear we have developed DAGON, a 3D Maxwell-Bloch code capable of studying the full spationtemporal structure of the amplification process abovementioned.

An Advanced simulation Code for Modeling Inductive Output Tubes

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

Thuc Bui; R. Lawrence Ives

2012-04-27

During the Phase I program, CCR completed several major building blocks for a 3D large signal, inductive output tube (IOT) code using modern computer language and programming techniques. These included a 3D, Helmholtz, time-harmonic, field solver with a fully functional graphical user interface (GUI), automeshing and adaptivity. Other building blocks included the improved electrostatic Poisson solver with temporal boundary conditions to provide temporal fields for the time-stepping particle pusher as well as the self electric field caused by time-varying space charge. The magnetostatic field solver was also updated to solve for the self magnetic field caused by time changing currentmore » density in the output cavity gap. The goal function to optimize an IOT cavity was also formulated, and the optimization methodologies were investigated.« less

The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

NASA Astrophysics Data System (ADS)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

Saturation of recognition elements blocks evolution of new tRNA identities

PubMed Central

Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D.; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A.; Ribas de Pouplana, Lluís

2016-01-01

Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. PMID:27386510

History of the Nuclei Important for Cosmochemistry

NASA Technical Reports Server (NTRS)

Meyer, Bradley S.

2004-01-01

An essential aspect of studying the nuclei important for cosmochemistry is their production in stars. Over the grant period, we have further developed the Clemson/American University of Beirut stellar evolution code. Through use of a biconjugate-gradient matrix solver, we now routinely solve l0(exp 6) x l0(exp 6) sparse matrices on our desktop computers. This has allowed us to couple nucleosynthesis and convection fully in the 1-D star, which, in turn, provides better estimates of nuclear yields when the mixing and nuclear burning timescales are comparable. We also have incorporated radiation transport into our 1-D supernova explosion code. We used the stellar evolution and explosion codes to compute iron abundances in a 25 Solar mass star and compared the results to data from RIMS.

Optimal generation of spatially coherent soft X-ray isolated attosecond pulses in a gas-filled waveguide using two-color synthesized laser pulses

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

Jin, Cheng; Hong, Kyung -Han; Lin, C. D.

2016-12-08

Here, we numerically demonstrate the generation of intense, low-divergence soft X-ray isolated attosecond pulses in a gas-filled hollow waveguide using synthesized few-cycle two-color laser waveforms. The waveform is a superposition of a fundamental and its second harmonic optimized such that highest harmonic yields are emitted from each atom. We then optimize the gas pressure and the length and radius of the waveguide such that bright coherent high-order harmonics with angular divergence smaller than 1 mrad are generated, for photon energy from the extreme ultraviolet to soft X-rays. By selecting a proper spectral range enhanced isolated attosecond pulses are generated. Wemore » study how dynamic phase matching caused by the interplay among waveguide mode, neutral atomic dispersion, and plasma effect is achieved at the optimal macroscopic conditions, by performing time-frequency analysis and by analyzing the evolution of the driving laser’s electric field during the propagation. Our results, when combined with the on-going push of high-repetition-rate lasers (sub- to few MHz’s) may eventually lead to the generation of high-flux, low-divergence soft X-ray tabletop isolated attosecond pulses for applications.« less

A new method of presentation the large-scale magnetic field structure on the Sun and solar corona

NASA Technical Reports Server (NTRS)

Ponyavin, D. I.

1995-01-01

The large-scale photospheric magnetic field, measured at Stanford, has been analyzed in terms of surface harmonics. Changes of the photospheric field which occur within whole solar rotation period can be resolved by this analysis. For this reason we used daily magnetograms of the line-of-sight magnetic field component observed from Earth over solar disc. We have estimated the period during which day-to-day full disc magnetograms must be collected. An original algorithm was applied to resolve time variations of spherical harmonics that reflect time evolution of large-scale magnetic field within solar rotation period. This method of magnetic field presentation can be useful enough in lack of direct magnetograph observations due to sometimes bad weather conditions. We have used the calculated surface harmonics to reconstruct the large-scale magnetic field structure on the source surface near the sun - the origin of heliospheric current sheet and solar wind streams. The obtained results have been compared with spacecraft in situ observations and geomagnetic activity. We tried to show that proposed technique can trace shon-time variations of heliospheric current sheet and short-lived solar wind streams. We have compared also our results with those obtained traditionally from potential field approximation and extrapolation using synoptic charts as initial boundary conditions.

Real-time Monitoring Of Damage Evolution In Aerospace Materials Using Nonlinear Acoustics

NASA Astrophysics Data System (ADS)

Matikas, T. E.; Paipetis, A.; Kostopoulos, V.

2008-06-01

This work deals with the development of a novel non-destructive technique based on nonlinear acoustics, enabling real-time monitoring of material degradation in aerospace structures. When a sinusoidal ultrasonic wave of a given frequency and of sufficient amplitude is introduced into a nonlinear or an-harmonic solid, the fundamental wave distorts as it propagates, so that the second and higher harmonics of the fundamental frequency are generated. The measurement of the amplitude of these harmonics provides information on the coefficient of the second and higher order terms of the stress-strain relation for a nonlinear solid. It is demonstrated here that the material bulk nonlinear parameter for titanium alloy samples at different fatigue levels exhibits large changes compared to linear ultrasonic parameters such as velocity and attenuation. However, the use of bulk ultrasonic waves has serious disadvantages for the health monitoring of aerospace structures since it requires the placement of ultrasonic transducers on two, perfectly parallel, opposite sides of the samples. Such a setup is hardly feasible in real field conditions. For this reason, surface acoustic waves (SAW) were used in this study enabling the in-situ characterization of fatigue damage. The experimental setup for measuring the material nonlinear parameter using SAW was realised and the feasibility of the technique for health monitoring of aerospace structures was evaluated.

The evolution and challenges for the international harmonization of the regulation of pharmaceutical excipients in Taiwan.

PubMed

Chang, Lin-Chau; Kang, Jaw-Jou; Gau, Churn-Shiouh

2015-12-01

Excipients, once considered an inert component, have been shown to greatly influence the characteristics of the drug product, such as quality and safety. Functionality-related characteristics of excipients could affect the performance of the drug product. Moreover, the impact of globalization has complicated the issue and made the supervision of supply chain highly important. Taiwan, a member of the Pharmaceutical Inspection Convention and Pharmaceutical Inspection Co-operation Scheme, makes efforts to harmonize with international regulations and to strengthen the protection of patients through regulatory controls. In order to improve the harmonization and the transparency of regulatory requirements, the aim of the present study was to investigate the regulatory framework and considerations of stringent regulatory authorities and to propose the draft regulatory requirements to the Taiwan Food and Drug Administration for jurisdiction. The proposal which was extensively discussed in the expert committee includes the regulatory considerations to ensure the safety and quality of the excipients and may serve as a platform to facilitate the communication with industries about the current thinking on related issues. Moreover, through the review of the recent guidelines published by the stringent regulatory authorities, the trend of the regulatory considerations was revealed and discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Exact reconstruction with directional wavelets on the sphere

NASA Astrophysics Data System (ADS)

Wiaux, Y.; McEwen, J. D.; Vandergheynst, P.; Blanc, O.

2008-08-01

A new formalism is derived for the analysis and exact reconstruction of band-limited signals on the sphere with directional wavelets. It represents an evolution of a previously developed wavelet formalism developed by Antoine & Vandergheynst and Wiaux et al. The translations of the wavelets at any point on the sphere and their proper rotations are still defined through the continuous three-dimensional rotations. The dilations of the wavelets are directly defined in harmonic space through a new kernel dilation, which is a modification of an existing harmonic dilation. A family of factorized steerable functions with compact harmonic support which are suitable for this kernel dilation are first identified. A scale-discretized wavelet formalism is then derived, relying on this dilation. The discrete nature of the analysis scales allows the exact reconstruction of band-limited signals. A corresponding exact multi-resolution algorithm is finally described and an implementation is tested. The formalism is of interest notably for the denoising or the deconvolution of signals on the sphere with a sparse expansion in wavelets. In astrophysics, it finds a particular application for the identification of localized directional features in the cosmic microwave background data, such as the imprint of topological defects, in particular, cosmic strings, and for their reconstruction after separation from the other signal components.

When Homoplasy Is Not Homoplasy: Dissecting Trait Evolution by Contrasting Composite and Reductive Coding.

PubMed

Torres-Montúfar, Alejandro; Borsch, Thomas; Ochoterena, Helga

2018-05-01

The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs. reductive). Up to now, there is no common agreement to either code characters as complex or simple. Phylogeneticists have discussed which coding method is best but have not incorporated the heuristic process of reciprocal illumination to evaluate the coding. Composite coding allows to test whether 1) several characters were linked resulting in a structure described as a complex character or trait or 2) independently evolving characters resulted in the configuration incorrectly interpreted as a complex character. We propose that complex characters or character states should be decomposed iteratively into simpler characters when the original homology hypothesis is not corroborated by a phylogenetic analysis, and the character or character state is retrieved as homoplastic. We tested this approach using the case of fruit types within subfamily Cinchonoideae (Rubiaceae). The iterative reductive coding of characters associated with drupes allowed us to unthread fruit evolution within Cinchonoideae. Our results show that drupes and berries are not homologous. As a consequence, a more precise ontology for the Cinchonoideae drupes is required.

Physical scales in the Wigner-Boltzmann equation

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

Nedjalkov, M., E-mail: mixi@iue.tuwien.ac.at; Selberherr, S.; Ferry, D.K.

2013-01-15

The Wigner-Boltzmann equation provides the Wigner single particle theory with interactions with bosonic degrees of freedom associated with harmonic oscillators, such as phonons in solids. Quantum evolution is an interplay of two transport modes, corresponding to the common coherent particle-potential processes, or to the decoherence causing scattering due to the oscillators. Which evolution mode will dominate depends on the scales of the involved physical quantities. A dimensionless formulation of the Wigner-Boltzmann equation is obtained, where these scales appear as dimensionless strength parameters. A notion called scaling theorem is derived, linking the strength parameters to the coupling with the oscillators. Itmore » is shown that an increase of this coupling is equivalent to a reduction of both the strength of the electric potential, and the coherence length. Secondly, the existence of classes of physically different, but mathematically equivalent setups of the Wigner-Boltzmann evolution is demonstrated. - Highlights: Black-Right-Pointing-Pointer Dimensionless parameters determine the ratio of quantum or classical WB evolution. Black-Right-Pointing-Pointer The scaling theorem evaluates the decoherence effect due to scattering. Black-Right-Pointing-Pointer Evolution processes are grouped into classes of equivalence.« less

Exploring the read-write genome: mobile DNA and mammalian adaptation.

PubMed

Shapiro, James A

2017-02-01

The read-write genome idea predicts that mobile DNA elements will act in evolution to generate adaptive changes in organismal DNA. This prediction was examined in the context of mammalian adaptations involving regulatory non-coding RNAs, viviparous reproduction, early embryonic and stem cell development, the nervous system, and innate immunity. The evidence shows that mobile elements have played specific and sometimes major roles in mammalian adaptive evolution by generating regulatory sites in the DNA and providing interaction motifs in non-coding RNA. Endogenous retroviruses and retrotransposons have been the predominant mobile elements in mammalian adaptive evolution, with the notable exception of bats, where DNA transposons are the major agents of RW genome inscriptions. A few examples of independent but convergent exaptation of mobile DNA elements for similar regulatory rewiring functions are noted.

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

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

Nakamachi, Eiji; Yoshida, Takashi; Yamaguchi, Toshihiko

2014-10-06

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture andmore » hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.« less

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

NASA Astrophysics Data System (ADS)

Nakamachi, Eiji; Yoshida, Takashi; Kuramae, Hiroyuki; Morimoto, Hideo; Yamaguchi, Toshihiko; Morita, Yusuke

2014-10-01

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture and hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.

The evolution of popular music: USA 1960–2010

PubMed Central

Mauch, Matthias; MacCallum, Robert M.; Levy, Mark; Leroi, Armand M.

2015-01-01

In modern societies, cultural change seems ceaseless. The flux of fashion is especially obvious for popular music. While much has been written about the origin and evolution of pop, most claims about its history are anecdotal rather than scientific in nature. To rectify this, we investigate the US Billboard Hot 100 between 1960 and 2010. Using music information retrieval and text-mining tools, we analyse the musical properties of approximately 17 000 recordings that appeared in the charts and demonstrate quantitative trends in their harmonic and timbral properties. We then use these properties to produce an audio-based classification of musical styles and study the evolution of musical diversity and disparity, testing, and rejecting, several classical theories of cultural change. Finally, we investigate whether pop musical evolution has been gradual or punctuated. We show that, although pop music has evolved continuously, it did so with particular rapidity during three stylistic ‘revolutions’ around 1964, 1983 and 1991. We conclude by discussing how our study points the way to a quantitative science of cultural change. PMID:26064663

On the effects of higher convection modes on the thermal evolution of small planetary bodies

NASA Technical Reports Server (NTRS)

Arkani-Hamed, J.

1979-01-01

The effects of higher modes of convection on the thermal evolution of a small planetary body is investigated. Three sets of models are designed to specify an initially cold and differentiated, an initially hot and differentiated, and an initially cold and undifferentiated Moon-type body. The strong temperature dependence of viscosity enhances the thickening of lithosphere so that a lithosphere of about 400 km thickness is developed within the first billion years of the evolution of a Moon-type body. The thermally isolating effect of such a lithosphere hampers the heat flux out of the body and increases the temperature of the interior, causing the solid-state convection to occur with high velocity so that even the lower modes of convection can maintain an adiabatic temperature gradient there. It is demonstrated that the effect of solid-state convection on the thermal evolution of the models may be adequately determined by a combination of convection modes up to the third or the fourth order harmonic. The inclusion of higher modes does not affect the results significantly.

Contamination of RR Lyrae stars from Binary Evolution Pulsators

NASA Astrophysics Data System (ADS)

Karczmarek, Paulina; Pietrzyński, Grzegorz; Belczyński, Krzysztof; Stępień, Kazimierz; Wiktorowicz, Grzegorz; Iłkiewicz, Krystian

2016-06-01

Binary Evolution Pulsator (BEP) is an extremely low-mass member of a binary system, which pulsates as a result of a former mass transfer to its companion. BEP mimics RR Lyrae-type pulsations but has different internal structure and evolution history. We present possible evolution channels to produce BEPs, and evaluate the contamination value, i.e. how many objects classified as RR Lyrae stars can be undetected BEPs. In this analysis we use population synthesis code StarTrack.

ISPOR Code of Ethics 2017 (4th Edition).

PubMed

Santos, Jessica; Palumbo, Francis; Molsen-David, Elizabeth; Willke, Richard J; Binder, Louise; Drummond, Michael; Ho, Anita; Marder, William D; Parmenter, Louise; Sandhu, Gurmit; Shafie, Asrul A; Thompson, David

2017-12-01

As the leading health economics and outcomes research (HEOR) professional society, ISPOR has a responsibility to establish a uniform, harmonized international code for ethical conduct. ISPOR has updated its 2008 Code of Ethics to reflect the current research environment. This code addresses what is acceptable and unacceptable in research, from inception to the dissemination of its results. There are nine chapters: 1 - Introduction; 2 - Ethical Principles respect, beneficence and justice with reference to a non-exhaustive compilation of international, regional, and country-specific guidelines and standards; 3 - Scope HEOR definitions and how HEOR and the Code relate to other research fields; 4 - Research Design Considerations primary and secondary data related issues, e.g., participant recruitment, population and research setting, sample size/site selection, incentive/honorarium, administration databases, registration of retrospective observational studies and modeling studies; 5 - Data Considerations privacy and data protection, combining, verification and transparency of research data, scientific misconduct, etc.; 6 - Sponsorship and Relationships with Others (roles of researchers, sponsors, key opinion leaders and advisory board members, research participants and institutional review boards (IRBs) / independent ethics committees (IECs) approval and responsibilities); 7 - Patient Centricity and Patient Engagement new addition, with explanation and guidance; 8 - Publication and Dissemination; and 9 - Conclusion and Limitations. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

PubMed

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Computational methods for coupling microstructural and micromechanical materials response simulations

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

HOLM,ELIZABETH A.; BATTAILE,CORBETT C.; BUCHHEIT,THOMAS E.

2000-04-01

Computational materials simulations have traditionally focused on individual phenomena: grain growth, crack propagation, plastic flow, etc. However, real materials behavior results from a complex interplay between phenomena. In this project, the authors explored methods for coupling mesoscale simulations of microstructural evolution and micromechanical response. In one case, massively parallel (MP) simulations for grain evolution and microcracking in alumina stronglink materials were dynamically coupled. In the other, codes for domain coarsening and plastic deformation in CuSi braze alloys were iteratively linked. this program provided the first comparison of two promising ways to integrate mesoscale computer codes. Coupled microstructural/micromechanical codes were appliedmore » to experimentally observed microstructures for the first time. In addition to the coupled codes, this project developed a suite of new computational capabilities (PARGRAIN, GLAD, OOF, MPM, polycrystal plasticity, front tracking). The problem of plasticity length scale in continuum calculations was recognized and a solution strategy was developed. The simulations were experimentally validated on stockpile materials.« less

Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

NASA Astrophysics Data System (ADS)

Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

2018-01-01

Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.

Studies of Planet Formation Using a Hybrid N-Body + Planetesimal Code

NASA Technical Reports Server (NTRS)

Kenyon, Scott J.

2004-01-01

The goal of our proposal was to use a hybrid multi-annulus planetesimal/n-body code to examine the planetesimal theory, one of the two main theories of planet formation. We developed this code to follow the evolution of numerous 1 m to 1 km planetesimals as they collide, merge, and grow into full-fledged planets. Our goal was to apply the code to several well-posed, topical problems in planet formation and to derive observational consequences of the models. We planned to construct detailed models to address two fundamental issues: (1) icy planets: models for icy planet formation will demonstrate how the physical properties of debris disks - including the Kuiper Belt in our solar system - depend on initial conditions and input physics; and (2) terrestrial planets: calculations following the evolution of 1-10 km planetesimals into Earth-mass planets and rings of dust will provide a better understanding of how terrestrial planets form and interact with their environment.

Kinetic Simulations of Type II Radio Burst Emission Processes

NASA Astrophysics Data System (ADS)

Ganse, U.; Spanier, F. A.; Vainio, R. O.

2011-12-01

The fundamental emission process of Type II Radio Bursts has been under discussion for many decades. While analytic deliberations point to three wave interaction as the source for fundamental and harmonic radio emissions, sparse in-situ observational data and high computational demands for kinetic simulations have not allowed for a definite conclusion to be reached. A popular model puts the radio emission into the foreshock region of a coronal mass ejection's shock front, where shock drift acceleration can create eletrcon beam populations in the otherwise quiescent foreshock plasma. Beam-driven instabilities are then assumed to create waves, forming the starting point of three wave interaction processes. Using our kinetic particle-in-cell code, we have studied a number of emission scenarios based on electron beam populations in a CME foreshock, with focus on wave-interaction microphysics on kinetic scales. The self-consistent, fully kinetic simulations with completely physical mass-ratio show fundamental and harmonic emission of transverse electromagnetic waves and allow for detailled statistical analysis of all contributing wavemodes and their couplings.

Mathematical modeling and statistical analysis of SPE-OCDMA systems utilizing second harmonic generation effect in thick crystal receivers

NASA Astrophysics Data System (ADS)

Matinfar, Mehdi D.; Salehi, Jawad A.

2009-11-01

In this paper we analytically study and evaluate the performance of a Spectral-Phase-Encoded Optical CDMA system for different parameters such as the user's code length and the number of users in the network. In this system an advanced receiver structure in which the Second Harmonic Generation effect imposed in a thick crystal is employed as the nonlinear pre-processor prior to the conventional low speed photodetector. We consider ASE noise of the optical amplifiers, effective in low power conditions, besides the multiple access interference (MAI) noise which is the dominant source of noise in any OCDMA communications system. We use the results of the previous work which we analyzed the statistical behavior of the thick crystals in an optically amplified digital lightwave communication system to evaluate the performance of the SPE-OCDMA system with thick crystals receiver structure. The error probability is evaluated using Saddle-Point approximation and the approximation is verified by Monte-Carlo simulation.

Science and the rules governing anti-doping violations.

PubMed

Bowers, Larry D

2010-01-01

The fight against the use of performance-enhancing drugs in sports has been in effect for nearly 90 years. The formation of the World Anti-Doping Agency in 1999 was a major event because an independent agency was entrusted with harmonization of the antidoping program. In addition to sports governing bodies, governments have endorsed WADA and its programs by signing a United Nations Education, Science, and Cultural Organization Convention on Doping. The first step in the harmonization process was the development of the World Anti-Doping Program. This program consisted of five documents - the Code, the International Standard for Testing, the International Standard for Laboratories, the Prohibited List, and the International Standard for Therapeutic Use Exemptions - which unified the approach of the international federations and national antidoping agencies in applying antidoping rules. For laboratory testing, the International Standard for Laboratories establishes the performance expectations for and competence of laboratories recognized by WADA, including accreditation under ISO/IEC 17025. The antidoping rules are adjudicated by arbitration using the internationally recognized Court of Arbitration for Sport.

Libpsht - algorithms for efficient spherical harmonic transforms

NASA Astrophysics Data System (ADS)

Reinecke, M.

2011-02-01

Libpsht (or "library for performant spherical harmonic transforms") is a collection of algorithms for efficient conversion between spatial-domain and spectral-domain representations of data defined on the sphere. The package supports both transforms of scalars and spin-1 and spin-2 quantities, and can be used for a wide range of pixelisations (including HEALPix, GLESP, and ECP). It will take advantage of hardware features such as multiple processor cores and floating-point vector operations, if available. Even without this additional acceleration, the employed algorithms are among the most efficient (in terms of CPU time, as well as memory consumption) currently being used in the astronomical community. The library is written in strictly standard-conforming C90, ensuring portability to many different hard- and software platforms, and allowing straightforward integration with codes written in various programming languages like C, C++, Fortran, Python etc. Libpsht is distributed under the terms of the GNU General Public License (GPL) version 2 and can be downloaded from .

Libpsht: Algorithms for Efficient Spherical Harmonic Transforms

NASA Astrophysics Data System (ADS)

Reinecke, Martin

2010-10-01

Libpsht (or "library for Performing Spherical Harmonic Transforms") is a collection of algorithms for efficient conversion between spatial-domain and spectral-domain representations of data defined on the sphere. The package supports transforms of scalars as well as spin-1 and spin-2 quantities, and can be used for a wide range of pixelisations (including HEALPix, GLESP and ECP). It will take advantage of hardware features like multiple processor cores and floating-point vector operations, if available. Even without this additional acceleration, the employed algorithms are among the most efficient (in terms of CPU time as well as memory consumption) currently being used in the astronomical community. The library is written in strictly standard-conforming C90, ensuring portability to many different hard- and software platforms, and allowing straightforward integration with codes written in various programming languages like C, C++, Fortran, Python etc. Libpsht is distributed under the terms of the GNU General Public License (GPL) version 2. Development on this project has ended; its successor is libsharp (ascl:1402.033).

Solution of the Skyrme-Hartree–Fock–Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (VIII) HFODD (v2.73y): A new version of the program

DOE PAGES

Schunck, N.; Dobaczewski, J.; Satuła, W.; ...

2017-03-27

Here, we describe the new version (v2.73y) of the code hfodd which solves the nuclear Skyrme Hartree–Fock or Skyrme Hartree–Fock–Bogolyubov problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented the following new features: (i) full proton–neutron mixing in the particle–hole channel for Skyrme functionals, (ii) the Gogny force in both particle–hole and particle–particle channels, (iii) linear multi-constraint method at finite temperature, (iv) fission toolkit including the constraint on the number of particles in the neck between two fragments, calculation of the interaction energy between fragments, and calculation of the nuclear and Coulomb energy ofmore » each fragment, (v) the new version 200d of the code hfbtho, together with an enhanced interface between HFBTHO and HFODD, (vi) parallel capabilities, significantly extended by adding several restart options for large-scale jobs, (vii) the Lipkin translational energy correction method with pairing, (viii) higher-order Lipkin particle-number corrections, (ix) interface to a program plotting single-particle energies or Routhians, (x) strong-force isospin-symmetry-breaking terms, and (xi) the Augmented Lagrangian Method for calculations with 3D constraints on angular momentum and isospin. Finally, an important bug related to the calculation of the entropy at finite temperature and several other little significant errors of the previous published version were corrected.« less

Solution of the Skyrme-Hartree–Fock–Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (VIII) HFODD (v2.73y): A new version of the program

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

Schunck, N.; Dobaczewski, J.; Satuła, W.

Here, we describe the new version (v2.73y) of the code hfodd which solves the nuclear Skyrme Hartree–Fock or Skyrme Hartree–Fock–Bogolyubov problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented the following new features: (i) full proton–neutron mixing in the particle–hole channel for Skyrme functionals, (ii) the Gogny force in both particle–hole and particle–particle channels, (iii) linear multi-constraint method at finite temperature, (iv) fission toolkit including the constraint on the number of particles in the neck between two fragments, calculation of the interaction energy between fragments, and calculation of the nuclear and Coulomb energy ofmore » each fragment, (v) the new version 200d of the code hfbtho, together with an enhanced interface between HFBTHO and HFODD, (vi) parallel capabilities, significantly extended by adding several restart options for large-scale jobs, (vii) the Lipkin translational energy correction method with pairing, (viii) higher-order Lipkin particle-number corrections, (ix) interface to a program plotting single-particle energies or Routhians, (x) strong-force isospin-symmetry-breaking terms, and (xi) the Augmented Lagrangian Method for calculations with 3D constraints on angular momentum and isospin. Finally, an important bug related to the calculation of the entropy at finite temperature and several other little significant errors of the previous published version were corrected.« less

Structural Health Monitoring challenges on the 10-MW offshore wind turbine model

NASA Astrophysics Data System (ADS)

Di Lorenzo, E.; Kosova, G.; Musella, U.; Manzato, S.; Peeters, B.; Marulo, F.; Desmet, W.

2015-07-01

The real-time structural damage detection on large slender structures has one of its main application on offshore Horizontal Axis Wind Turbines (HAWT). The renewable energy market is continuously pushing the wind turbine sizes and performances. This is the reason why nowadays offshore wind turbines concepts are going toward a 10 MW reference wind turbine model. The aim of the work is to perform operational analyses on the 10-MW reference wind turbine finite element model using an aeroelastic code in order to obtain long-time-low- cost simulations. The aeroelastic code allows simulating the damages in several ways: by reducing the edgewise/flapwise blades stiffness, by adding lumped masses or considering a progressive mass addiction (i.e. ice on the blades). The damage detection is then performed by means of Operational Modal Analysis (OMA) techniques. Virtual accelerometers are placed in order to simulate real measurements and to estimate the modal parameters. The feasibility of a robust damage detection on the model has been performed on the HAWT model in parked conditions. The situation is much more complicated in case of operating wind turbines because the time periodicity of the structure need to be taken into account. Several algorithms have been implemented and tested in the simulation environment. They are needed in order to carry on a damage detection simulation campaign and develop a feasible real-time damage detection method. In addition to these algorithms, harmonic removal tools are needed in order to dispose of the harmonics due to the rotation.

Process and metaphors in the evolutionary paradigm

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

Ho, M.; Fox, S

1988-01-01

Presents thinking on the processes and interpretation of biological evolution, emphasizing the study of biological processes as they occur in living organisms and their communities, rather than through mechanical or statistical models. Contributors explore processes and metaphors in evolution, the origin of the genetic code, new genetic mechanisms and their implications for the formation of new species, panbiogeography, the active role of behavior in evolution, sociobiology, and more.

No cataclysmic variables missing: higher merger rate brings into agreement observed and predicted space densities

NASA Astrophysics Data System (ADS)

Belloni, Diogo; Schreiber, Matthias R.; Zorotovic, Mónica; Iłkiewicz, Krystian; Hurley, Jarrod R.; Giersz, Mirek; Lagos, Felipe

2018-06-01

The predicted and observed space density of cataclysmic variables (CVs) have been for a long time discrepant by at least an order of magnitude. The standard model of CV evolution predicts that the vast majority of CVs should be period bouncers, whose space density has been recently measured to be ρ ≲ 2 × 10-5 pc-3. We performed population synthesis of CVs using an updated version of the Binary Stellar Evolution (BSE) code for single and binary star evolution. We find that the recently suggested empirical prescription of consequential angular momentum loss (CAML) brings into agreement predicted and observed space densities of CVs and period bouncers. To progress with our understanding of CV evolution it is crucial to understand the physical mechanism behind empirical CAML. Our changes to the BSE code are also provided in details, which will allow the community to accurately model mass transfer in interacting binaries in which degenerate objects accrete from low-mass main-sequence donor stars.

Rapid Aeroelastic Analysis of Blade Flutter in Turbomachines

NASA Technical Reports Server (NTRS)

Trudell, J. J.; Mehmed, O.; Stefko, G. L.; Bakhle, M. A.; Reddy, T. S. R.; Montgomery, M.; Verdon, J.

2006-01-01

The LINFLUX-AE computer code predicts flutter and forced responses of blades and vanes in turbomachines under subsonic, transonic, and supersonic flow conditions. The code solves the Euler equations of unsteady flow in a blade passage under the assumption that the blades vibrate harmonically at small amplitudes. The steady-state nonlinear Euler equations are solved by a separate program, then equations for unsteady flow components are obtained through linearization around the steady-state solution. A structural-dynamics analysis (see figure) is performed to determine the frequencies and mode shapes of blade vibrations, a preprocessor interpolates mode shapes from the structural-dynamics mesh onto the LINFLUX computational-fluid-dynamics mesh, and an interface code is used to convert the steady-state flow solution to a form required by LINFLUX. Then LINFLUX solves the linearized equations in the frequency domain to calculate the unsteady aerodynamic pressure distribution for a given vibration mode, frequency, and interblade phase angle. A post-processor uses the unsteady pressures to calculate generalized aerodynamic forces, response amplitudes, and eigenvalues (which determine the flutter frequency and damping). In comparison with the TURBO-AE aeroelastic-analysis code, which solves the equations in the time domain, LINFLUX-AE is 6 to 7 times faster.

Exact solution for a non-Markovian dissipative quantum dynamics.

PubMed

Ferialdi, Luca; Bassi, Angelo

2012-04-27

We provide the exact analytic solution of the stochastic Schrödinger equation describing a harmonic oscillator interacting with a non-Markovian and dissipative environment. This result represents an arrival point in the study of non-Markovian dynamics via stochastic differential equations. It is also one of the few exactly solvable models for infinite-dimensional systems. We compute the Green's function; in the case of a free particle and with an exponentially correlated noise, we discuss the evolution of Gaussian wave functions.

GRABGAM Analysis of Ultra-Low-Level HPGe Gamma Spectra

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

Winn, W.G.

The GRABGAM code has been used successfully for ultra-low level HPGe gamma spectrometry analysis since its development in 1985 at Savannah River Technology Center (SRTC). Although numerous gamma analysis codes existed at that time, reviews of institutional and commercial codes indicated that none addressed all features that were desired by SRTC. Furthermore, it was recognized that development of an in-house code would better facilitate future evolution of the code to address SRTC needs based on experience with low-level spectra. GRABGAM derives its name from Gamma Ray Analysis BASIC Generated At MCA/PC.

Utilitarianism and the evolution of ecological ethics.

PubMed

Varner, Gary

2008-12-01

R.M. Hare's two-level utilitarianism provides a useful framework for understanding the evolution of codes of professional ethics. From a Harean perspective, the codes reflect both the fact that members of various professions face special kinds of ethically charged situations in the normal course of their work, and the need for people in special roles to acquire various habits of thought and action. This highlights the role of virtue in professional ethics and provides guidance to professional societies when considering modifications to their codes. From a Harean perspective, a professional society should ask both "Are there kinds of situations that members of this profession will normally encounter which members of other professions and/or the general public will not?" and "What habits of thought and action would it be good for individuals encountering such situations to have?"

A Dancing Black Hole

NASA Astrophysics Data System (ADS)

Shoemaker, Deirdre; Smith, Kenneth; Schnetter, Erik; Fiske, David; Laguna, Pablo; Pullin, Jorge

2002-04-01

Recently, stationary black holes have been successfully simulated for up to times of approximately 600-1000M, where M is the mass of the black hole. Considering that the expected burst of gravitational radiation from a binary black hole merger would last approximately 200-500M, black hole codes are approaching the point where simulations of mergers may be feasible. We will present two types of simulations of single black holes obtained with a code based on the Baumgarte-Shapiro-Shibata-Nakamura formulation of the Einstein evolution equations. One type of simulations addresses the stability properties of stationary black hole evolutions. The second type of simulations demonstrates the ability of our code to move a black hole through the computational domain. This is accomplished by shifting the stationary black hole solution to a coordinate system in which the location of the black hole is time dependent.

ASTEC—the Aarhus STellar Evolution Code

NASA Astrophysics Data System (ADS)

Christensen-Dalsgaard, Jørgen

2008-08-01

The Aarhus code is the result of a long development, starting in 1974, and still ongoing. A novel feature is the integration of the computation of adiabatic oscillations for specified models as part of the code. It offers substantial flexibility in terms of microphysics and has been carefully tested for the computation of solar models. However, considerable development is still required in the treatment of nuclear reactions, diffusion and convective mixing.

The origins and evolutionary history of human non-coding RNA regulatory networks.

PubMed

Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

A Comparison of Grid-based and SPH Binary Mass-transfer and Merger Simulations

DOE PAGES

Motl, Patrick M.; Frank, Juhan; Staff, Jan; ...

2017-03-29

There is currently a great amount of interest in the outcomes and astrophysical implications of mergers of double degenerate binaries. In a commonly adopted approximation, the components of such binaries are represented by polytropes with an index of n = 3/2. We present detailed comparisons of stellar mass-transfer and merger simulations of polytropic binaries that have been carried out using two very different numerical algorithms—a finite-volume "grid" code and a smoothed-particle hydrodynamics (SPH) code. We find that there is agreement in both the ultimate outcomes of the evolutions and the intermediate stages if the initial conditions for each code aremore » chosen to match as closely as possible. We find that even with closely matching initial setups, the time it takes to reach a concordant evolution differs between the two codes because the initial depth of contact cannot be matched exactly. There is a general tendency for SPH to yield higher mass transfer rates and faster evolution to the final outcome. Here, we also present comparisons of simulations calculated from two different energy equations: in one series, we assume a polytropic equation of state and in the other series an ideal gas equation of state. In the latter series of simulations, an atmosphere forms around the accretor, which can exchange angular momentum and cause a more rapid loss of orbital angular momentum. In the simulations presented here, the effect of the ideal equation of state is to de-stabilize the binary in both SPH and grid simulations, but the effect is more pronounced in the grid code.« less

Xenomicrobiology: a roadmap for genetic code engineering.

PubMed

Acevedo-Rocha, Carlos G; Budisa, Nediljko

2016-09-01

Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high-throughput and low-cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non-natural building blocks in living cells. In this context, genetic code engineering respectively enables the re-design of genes/genomes and proteins/proteomes with non-canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new-to-nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a 'genetic firewall' will also allow to study and understand the relation between code evolution and horizontal gene transfer. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Chemical and physical characterization of the first stages of protoplanetary disk formation

NASA Astrophysics Data System (ADS)

Hincelin, Ugo

2012-12-01

Low mass stars, like our Sun, are born from the collapse of a molecular cloud. The matter falls in the center of the cloud, creating a protoplanetary disk surrounding a protostar. Planets and other Solar System bodies will be formed in the disk. The chemical composition of the interstellar matter and its evolution during the formation of the disk are important to better understand the formation process of these objects. I studied the chemical and physical evolution of this matter, from the cloud to the disk, using the chemical gas-grain code Nautilus. A sensitivity study to some parameters of the code (such as elemental abundances and parameters of grain surface chemistry) has been done. More particularly, the updates of rate coefficients and branching ratios of the reactions of our chemical network showed their importance, such as on the abundances of some chemical species, and on the code sensitivity to others parameters. Several physical models of collapsing dense core have also been considered. The more complex and solid approach has been to interface our chemical code with the radiation-magneto-hydrodynamic model of stellar formation RAMSES, in order to model in three dimensions the physical and chemical evolution of a young disk formation. Our study showed that the disk keeps imprints of the past history of the matter, and so its chemical composition is sensitive to the initial conditions.

Million-body star cluster simulations: comparisons between Monte Carlo and direct N-body

NASA Astrophysics Data System (ADS)

Rodriguez, Carl L.; Morscher, Meagan; Wang, Long; Chatterjee, Sourav; Rasio, Frederic A.; Spurzem, Rainer

2016-12-01

We present the first detailed comparison between million-body globular cluster simulations computed with a Hénon-type Monte Carlo code, CMC, and a direct N-body code, NBODY6++GPU. Both simulations start from an identical cluster model with 106 particles, and include all of the relevant physics needed to treat the system in a highly realistic way. With the two codes `frozen' (no fine-tuning of any free parameters or internal algorithms of the codes) we find good agreement in the overall evolution of the two models. Furthermore, we find that in both models, large numbers of stellar-mass black holes (>1000) are retained for 12 Gyr. Thus, the very accurate direct N-body approach confirms recent predictions that black holes can be retained in present-day, old globular clusters. We find only minor disagreements between the two models and attribute these to the small-N dynamics driving the evolution of the cluster core for which the Monte Carlo assumptions are less ideal. Based on the overwhelming general agreement between the two models computed using these vastly different techniques, we conclude that our Monte Carlo approach, which is more approximate, but dramatically faster compared to the direct N-body, is capable of producing an accurate description of the long-term evolution of massive globular clusters even when the clusters contain large populations of stellar-mass black holes.

The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster.

PubMed

Chong, Zechen; Zhai, Weiwei; Li, Chunyan; Gao, Min; Gong, Qiang; Ruan, Jue; Li, Juan; Jiang, Lan; Lv, Xuemei; Hungate, Eric; Wu, Chung-I

2013-12-01

Studies of protein evolution have focused on amino acid substitutions with much less systematic analysis on insertion and deletions (indels) in protein coding genes. We hence surveyed 7,500 genes between Drosophila melanogaster and D. simulans, using D. yakuba as an outgroup for this purpose. The evolutionary rate of coding indels is indeed low, at only 3% of that of nonsynonymous substitutions. As coding indels follow a geometric distribution in size and tend to fall in low-complexity regions of proteins, it is unclear whether selection or mutation underlies this low rate. To resolve the issue, we collected genomic sequences from an isogenic African line of D. melanogaster (ZS30) at a high coverage of 70× and analyzed indel polymorphism between ZS30 and the reference genome. In comparing polymorphism and divergence, we found that the divergence to polymorphism ratio (i.e., fixation index) for smaller indels (size ≤ 10 bp) is very similar to that for synonymous changes, suggesting that most of the within-species polymorphism and between-species divergence for indels are selectively neutral. Interestingly, deletions of larger sizes (size ≥ 11 bp and ≤ 30 bp) have a much higher fixation index than synonymous mutations and 44.4% of fixed middle-sized deletions are estimated to be adaptive. To our surprise, this pattern is not found for insertions. Protein indel evolution appear to be in a dynamic flux of neutrally driven expansion (insertions) together with adaptive-driven contraction (deletions), and these observations provide important insights for understanding the fitness of new mutations as well as the evolutionary driving forces for genomic evolution in Drosophila species.

Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence

PubMed Central

2012-01-01

Background Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence. Results We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors) in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of SMOX gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways. Conclusions Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution. PMID:23148531

Multifrequency acoustics as a probe of mesoscopic blood coagulation dynamics

NASA Astrophysics Data System (ADS)

Ganesan, Adarsh; Rajendran, Gokulnath; Ercole, Ari; Seshia, Ashwin

2016-08-01

Coagulation is a complex enzymatic polymerisation cascade. Disordered coagulation is common in medicine and may be life-threatening yet clinical assays are typically bulky and/or provide an incomplete picture of clot mechanical evolution. We present the adaptation of an in-plane acoustic wave device: quartz crystal microbalance with dissipation at multiple harmonics to determine the time-evolution of mesoscale mechanical properties of clot formation in vitro. This approach is sensitive to changes in surface and bulk clot structure in various models of induced coagulopathy. Furthermore, we are able to show that clot formation at surfaces has different kinetics and mechanical strength to that in the bulk, which may have implications for the design of bioprosthetic materials. The "Multifrequency acoustics" approach thus enables unique capability to portray biological processes concerning blood coagulation.

Applicability of ERTS to Antarctic iceberg resources. [harvesting icebergs for fresh water

NASA Technical Reports Server (NTRS)

Hult, J. L.; Ostrander, N. C.

1974-01-01

This investigation explores the applicability of ERTS to: (1) determine the Antarctic sea ice and environmental behavior that may influence the harvesting of icebergs, and (2) monitor iceberg locations, characteristics, and evolution. Imagery sampling in the western Antarctic between the Peninsula and the Ross Sea is used in the analysis. It is found that the potential applicability of ERTS to the research, planning, and harvesting operations can contribute importantly to the glowing promise derived from broader scope studies for the use of Antarctic icebergs to relieve a growing global thirst for fresh water. Several years of comprehensive monitoring will be necessary to characterize sea-ice and environmental behavior and iceberg evolution. Live ERTS services will assist harvesting control and claiming operations and offer a means for harmonizing entitlements to iceberg resources.

Synthetic diagnostics platform for fusion plasmas (invited)

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

Shi, L., E-mail: lshi@pppl.gov; Valeo, E. J.; Tobias, B. J.

A Synthetic Diagnostics Platform (SDP) for fusion plasmas has been developed which provides state of the art synthetic reflectometry, beam emission spectroscopy, and Electron Cyclotron Emission (ECE) diagnostics. Interfaces to the plasma simulation codes GTC, XGC-1, GTS, and M3D-C{sup 1} are provided, enabling detailed validation of these codes. In this paper, we give an overview of SDP’s capabilities, and introduce the synthetic diagnostic modules. A recently developed synthetic ECE Imaging module which self-consistently includes refraction, diffraction, emission, and absorption effects is discussed in detail. Its capabilities are demonstrated on two model plasmas. The importance of synthetic diagnostics in validation ismore » shown by applying the SDP to M3D-C{sup 1} output and comparing it with measurements from an edge harmonic oscillation mode on DIII-D.« less

Synthetic diagnostics platform for fusion plasmas (invited)

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

Shi, L.; Valeo, E. J.; Tobias, B. J.

A Synthetic Diagnostics Platform (SDP) for fusion plasmas has been developed which provides state of the art synthetic reflectometry, beam emission spectroscopy, and Electron Cyclotron Emission (ECE) diagnostics. Interfaces to the plasma simulation codes GTC, XGC-1, GTS, and M3D-C-1 are provided, enabling detailed validation of these codes. In this paper, we give an overview of SDP's capabilities, and introduce the synthetic diagnostic modules. A recently developed synthetic ECE Imaging module which self-consistently includes refraction, diffraction, emission, and absorption effects is discussed in detail. Its capabilities are demonstrated on two model plasmas. Finally, the importance of synthetic diagnostics in validation ismore » shown by applying the SDP to M3D-C 1 output and comparing it with measurements from an edge harmonic oscillation mode on DIII-D.« less

Calculation of viscous effects on transonic flow for oscillating airfoils and comparisons with experiment

NASA Technical Reports Server (NTRS)

Howlett, James T.; Bland, Samuel R.

1987-01-01

A method is described for calculating unsteady transonic flow with viscous interaction by coupling a steady integral boundary-layer code with an unsteady, transonic, inviscid small-disturbance computer code in a quasi-steady fashion. Explicit coupling of the equations together with viscous -inviscid iterations at each time step yield converged solutions with computer times about double those required to obtain inviscid solutions. The accuracy and range of applicability of the method are investigated by applying it to four AGARD standard airfoils. The first-harmonic components of both the unsteady pressure distributions and the lift and moment coefficients have been calculated. Comparisons with inviscid calcualtions and experimental data are presented. The results demonstrate that accurate solutions for transonic flows with viscous effects can be obtained for flows involving moderate-strength shock waves.

Synthetic diagnostics platform for fusion plasmas (invited)

DOE PAGES

Shi, L.; Valeo, E. J.; Tobias, B. J.; ...

2016-08-26

A Synthetic Diagnostics Platform (SDP) for fusion plasmas has been developed which provides state of the art synthetic reflectometry, beam emission spectroscopy, and Electron Cyclotron Emission (ECE) diagnostics. Interfaces to the plasma simulation codes GTC, XGC-1, GTS, and M3D-C-1 are provided, enabling detailed validation of these codes. In this paper, we give an overview of SDP's capabilities, and introduce the synthetic diagnostic modules. A recently developed synthetic ECE Imaging module which self-consistently includes refraction, diffraction, emission, and absorption effects is discussed in detail. Its capabilities are demonstrated on two model plasmas. Finally, the importance of synthetic diagnostics in validation ismore » shown by applying the SDP to M3D-C 1 output and comparing it with measurements from an edge harmonic oscillation mode on DIII-D.« less

The Global Registry of Biodiversity Repositories: A Call for Community Curation

PubMed Central

Miller, Scott E.; Trizna, Michael G.; Graham, Eileen; Crane, Adele E.

2016-01-01

Abstract The Global Registry of Biodiversity Repositories is an online metadata resource for biodiversity collections, the institutions that contain them, and associated staff members. The registry provides contact and address information, characteristics of the institutions and collections using controlled vocabularies and free-text descripitons, links to related websites, unique identifiers for each institution and collection record, text fields for loan and use policies, and a variety of other descriptors. Each institution record includes an institutionCode that must be unique, and each collection record must have a collectionCode that is unique within that institution. The registry is populated with records imported from the largest similar registries and more can be harmonized and added. Doing so will require community input and curation and would produce a truly comprehensive and unifying information resource. PMID:27660523

Hybrid finite element/waveguide mode analysis of passive RF devices

NASA Astrophysics Data System (ADS)

McGrath, Daniel T.

1993-07-01

A numerical solution for time-harmonic electromagnetic fields in two-port passive radio frequency (RF) devices has been developed, implemented in a computer code, and validated. Vector finite elements are used to represent the fields in the device interior, and field continuity across waveguide apertures is enforced by matching the interior solution to a sum of waveguide modes. Consequently, the mesh may end at the aperture instead of extending into the waveguide. The report discusses the variational formulation and its reduction to a linear system using Galerkin's method. It describes the computer code, including its interface to commercial CAD software used for geometry generation. It presents validation results for waveguide discontinuities, coaxial transitions, and microstrip circuits. They demonstrate that the method is an effective and versatile tool for predicting the performance of passive RF devices.

Sexual selection drives evolution and rapid turnover of male gene expression.

PubMed

Harrison, Peter W; Wright, Alison E; Zimmer, Fabian; Dean, Rebecca; Montgomery, Stephen H; Pointer, Marie A; Mank, Judith E

2015-04-07

The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.

Evolution and molecular epidemiology of classical swine fever virus during a multi-annual outbreak amongst European wild boar.

PubMed

Goller, Katja V; Gabriel, Claudia; Dimna, Mireille Le; Le Potier, Marie-Frédérique; Rossi, Sophie; Staubach, Christoph; Merboth, Matthias; Beer, Martin; Blome, Sandra

2016-03-01

Classical swine fever is a viral disease of pigs that carries tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high-resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of classical swine fever virus strains over the years and no impact of vaccination on mutation rates. However, substitution rates varied amongst protein genes; furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers.

AX-GADGET: a new code for cosmological simulations of Fuzzy Dark Matter and Axion models

NASA Astrophysics Data System (ADS)

Nori, Matteo; Baldi, Marco

2018-05-01

We present a new module of the parallel N-Body code P-GADGET3 for cosmological simulations of light bosonic non-thermal dark matter, often referred as Fuzzy Dark Matter (FDM). The dynamics of the FDM features a highly non-linear Quantum Potential (QP) that suppresses the growth of structures at small scales. Most of the previous attempts of FDM simulations either evolved suppressed initial conditions, completely neglecting the dynamical effects of QP throughout cosmic evolution, or resorted to numerically challenging full-wave solvers. The code provides an interesting alternative, following the FDM evolution without impairing the overall performance. This is done by computing the QP acceleration through the Smoothed Particle Hydrodynamics (SPH) routines, with improved schemes to ensure precise and stable derivatives. As an extension of the P-GADGET3 code, it inherits all the additional physics modules implemented up to date, opening a wide range of possibilities to constrain FDM models and explore its degeneracies with other physical phenomena. Simulations are compared with analytical predictions and results of other codes, validating the QP as a crucial player in structure formation at small scales.

Final Technical Report for GO17004 Regulatory Logic: Codes and Standards for the Hydrogen Economy

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

Nakarado, Gary L.

The objectives of this project are to: develop a robust supporting research and development program to provide critical hydrogen behavior data and a detailed understanding of hydrogen combustion and safety across a range of scenarios, needed to establish setback distances in building codes and minimize the overall data gaps in code development; support and facilitate the completion of technical specifications by the International Organization for Standardization (ISO) for gaseous hydrogen refueling (TS 20012) and standards for on-board liquid (ISO 13985) and gaseous or gaseous blend (ISO 15869) hydrogen storage by 2007; support and facilitate the effort, led by the NFPA,more » to complete the draft Hydrogen Technologies Code (NFPA 2) by 2008; with experimental data and input from Technology Validation Program element activities, support and facilitate the completion of standards for bulk hydrogen storage (e.g., NFPA 55) by 2008; facilitate the adoption of the most recently available model codes (e.g., from the International Code Council [ICC]) in key regions; complete preliminary research and development on hydrogen release scenarios to support the establishment of setback distances in building codes and provide a sound basis for model code development and adoption; support and facilitate the development of Global Technical Regulations (GTRs) by 2010 for hydrogen vehicle systems under the United Nations Economic Commission for Europe, World Forum for Harmonization of Vehicle Regulations and Working Party on Pollution and Energy Program (ECE-WP29/GRPE); and to Support and facilitate the completion by 2012 of necessary codes and standards needed for the early commercialization and market entry of hydrogen energy technologies.« less

A Python Calculator for Supernova Remnant Evolution

NASA Astrophysics Data System (ADS)

Leahy, D. A.; Williams, J. E.

2017-05-01

A freely available Python code for modeling supernova remnant (SNR) evolution has been created. This software is intended for two purposes: to understand SNR evolution and to use in modeling observations of SNR for obtaining good estimates of SNR properties. It includes all phases for the standard path of evolution for spherically symmetric SNRs. In addition, alternate evolutionary models are available, including evolution in a cloudy ISM, the fractional energy-loss model, and evolution in a hot low-density ISM. The graphical interface takes in various parameters and produces outputs such as shock radius and velocity versus time, as well as SNR surface brightness profile and spectrum. Some interesting properties of SNR evolution are demonstrated using the program.

Evidence of birth-and-death evolution of 5S rRNA gene in Channa species (Teleostei, Perciformes).

PubMed

Barman, Anindya Sundar; Singh, Mamta; Singh, Rajeev Kumar; Lal, Kuldeep Kumar

2016-12-01

In higher eukaryotes, minor rDNA family codes for 5S rRNA that is arranged in tandem arrays and comprises of a highly conserved 120 bp long coding sequence with a variable non-transcribed spacer (NTS). Initially the 5S rDNA repeats are considered to be evolved by the process of concerted evolution. But some recent reports, including teleost fishes suggested that evolution of 5S rDNA repeat does not fit into the concerted evolution model and evolution of 5S rDNA family may be explained by a birth-and-death evolution model. In order to study the mode of evolution of 5S rDNA repeats in Perciformes fish species, nucleotide sequence and molecular organization of five species of genus Channa were analyzed in the present study. Molecular analyses revealed several variants of 5S rDNA repeats (four types of NTS) and networks created by a neighbor net algorithm for each type of sequences (I, II, III and IV) did not show a clear clustering in species specific manner. The stable secondary structure is predicted and upstream and downstream conserved regulatory elements were characterized. Sequence analyses also shown the presence of two putative pseudogenes in Channa marulius. Present study supported that 5S rDNA repeats in genus Channa were evolved under the process of birth-and-death.

OBJECT KINETIC MONTE CARLO SIMULATIONS OF MICROSTRUCTURE EVOLUTION

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

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2013-09-30

The objective is to report the development of the flexible object kinetic Monte Carlo (OKMC) simulation code KSOME (kinetic simulation of microstructure evolution) which can be used to simulate microstructure evolution of complex systems under irradiation. In this report we briefly describe the capabilities of KSOME and present preliminary results for short term annealing of single cascades in tungsten at various primary-knock-on atom (PKA) energies and temperatures.

Shallow Water Quasi-Geostrophic Theory on the Sphere

NASA Astrophysics Data System (ADS)

Schubert, Wayne H.; Taft, Richard K.; Silvers, Levi G.

2009-02-01

Quasi-geostrophic theory forms the basis for much of our understanding of mid-latitude atmospheric dynamics. The theory is typically presented in either its f-plane form or its β-plane form. However, for many applications, including diagnostic use in global climate modeling, a fully spherical version would be most useful. Such a global theory does in fact exist and has for many years, but few in the scientific community seem to have ever been aware of it. In the context of shallow water dynamics, it is shown that the spherical version of quasigeostrophic theory is easily derived (re-derived) based on a partitioning of the flow between nondivergent and irrotational components, as opposed to a partitioning between geostrophic and ageostrophic components. In this way, the invertibility principle is expressed as a relation between the streamfunction and the potential vorticity, rather than between the geopotential and the potential vorticity. This global theory is then extended by showing that the invertibility principle can be solved analytically using spheroidal harmonic transforms, an advancement that greatly improves the usefulness of this "forgotten" theory. When the governing equation for the time evolution of the potential vorticity is linearized about a state of rest, a simple Rossby-Haurwitz wave dispersion relation is derived and examined. These waves have a horizontal structure described by spheroidal harmonics, and the Rossby-Haurwitz wave frequencies are given in terms of the eigenvalues of the spheroidal harmonic operator. Except for sectoral harmonics with low zonal wavenumber, the quasi-geostrophic Rossby-Haurwitz frequencies agree very well with those calculated from the primitive equations. One of the many possible applications of spherical quasi-geostrophic theory is to the study of quasi-geostrophic turbulence on the sphere. In this context, the theory is used to derive an anisotropic Rhines barrier in three-dimensional wavenumber space.

Symmetries of the quantum damped harmonic oscillator

NASA Astrophysics Data System (ADS)

Guerrero, J.; López-Ruiz, F. F.; Aldaya, V.; Cossío, F.

2012-11-01

For the non-conservative Caldirola-Kanai system, describing a quantum damped harmonic oscillator, a couple of constant-of-motion operators generating the Heisenberg-Weyl algebra can be found. The inclusion of the standard time evolution generator (which is not a symmetry) as a symmetry in this algebra, in a unitary manner, requires a non-trivial extension of this basic algebra and hence of the physical system itself. Surprisingly, this extension leads directly to the so-called Bateman dual system, which now includes a new particle acting as an energy reservoir. In addition, the Caldirola-Kanai dissipative system can be retrieved by imposing constraints. The algebra of symmetries of the dual system is presented, as well as a quantization that implies, in particular, a first-order Schrödinger equation. As opposed to other approaches, where it is claimed that the spectrum of the Bateman Hamiltonian is complex and discrete, we obtain that it is real and continuous, with infinite degeneracy in all regimes.

Determining the strengths of HCP slip systems using harmonic analyses of lattice strain distributions

DOE PAGES

Dawson, Paul R.; Boyce, Donald E.; Park, Jun-Sang; ...

2017-10-15

A robust methodology is presented to extract slip system strengths from lattice strain distributions for polycrystalline samples obtained from high-energy x-ray diffraction (HEXD) experiments with in situ loading. The methodology consists of matching the evolution of coefficients of a harmonic expansion of the distributions from simulation to the coefficients derived from measurements. Simulation results are generated via finite element simulations of virtual polycrystals that are subjected to the loading history applied in the HEXD experiments. Advantages of the methodology include: (1) its ability to utilize extensive data sets generated by HEXD experiments; (2) its ability to capture trends in distributionsmore » that may be noisy (both measured and simulated); and (3) its sensitivity to the ratios of the family strengths. The approach is used to evaluate the slip system strengths of Ti-6Al-4V using samples having relatively equiaxed grains. These strength estimates are compared to values in the literature.« less

Alternative descriptions of wave and particle aspects of the harmonic oscillator

NASA Technical Reports Server (NTRS)

Schuch, Dieter

1993-01-01

The dynamical properties of the wave and particle aspects of the harmonic oscillator can be studied with the help of the time-dependent Schroedinger equation (SE). Especially the time-dependence of maximum and width of Gaussian wave packet solutions allow to show the evolution and connections of those two complementary aspects. The investigation of the relations between the equations describing wave and particle aspects leads to an alternative description of the considered systems. This can be achieved by means of a Newtonian equation for a complex variable in connection with a conservation law for a nonclassical angular momentum-type quantity. With the help of this complex variable, it is also possible to develop a Hamiltonian formalism for the wave aspect contained in the SE, which allows to describe the dynamics of the position and momentum uncertainties. In this case the Hamiltonian function is equivalent to the difference between the mean value of the Hamiltonian operator and the classical Hamiltonian function.

On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum

PubMed Central

2017-01-01

We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly. PMID:28489368

Mode-locking evolution in ring fiber lasers with tunable repetition rate.

PubMed

Korobko, D A; Fotiadi, A A; Zolotovskii, I O

2017-09-04

We have applied a simple approach to analyze behavior of the harmonically mode-locked fiber laser incorporating an adjustable Mach-Zehnder interferometer (MZI). Our model is able to describe key features of the laser outputs and explore limitations of physical mechanisms responsible for laser operation at different pulse repetition rates tuned over a whole GHz range. At low repetition rates the laser operates as a harmonically mode-locked soliton laser triggered by a fast saturable absorber. At high repetition rates the laser mode-locking occurs due to dissipative four-wave mixing seeded by MZI and gain spectrum filtering. However, the laser stability in this regime is rather low due to poor mode selectivity provided by MZI that is able to support the desired laser operation just near the lasing threshold. The use of a double MZI instead of a single MZI could improve the laser stability and extends the range of the laser tunability. The model predicts a gap between two repetitive rate ranges where pulse train generation is not supported.

canvasDesigner: A versatile interactive high-resolution scientific multi-panel visualization toolkit.

PubMed

Zhang, Baohong; Zhao, Shanrong; Neuhaus, Isaac

2018-05-03

We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel, and producing multi-panel publication-ready figures in PDF format simultaneously. Source code and detailed user guides are available at http://canvasxpress.org, https://baohongz.github.io/canvasDesigner, and https://baohongz.github.io/canvasDesigner/demo_video.html. isaac.neuhaus@bms.com, baohong.zhang@pfizer.com, shanrong.zhao@pfizer.com. Supplementary materials are available at https://goo.gl/1uQygs.

MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation

DOE PAGES

Harrison, Robert J.; Beylkin, Gregory; Bischoff, Florian A.; ...

2016-01-01

We present MADNESS (multiresolution adaptive numerical environment for scientific simulation) that is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods with guaranteed precision that are based on multiresolution analysis and separated representations. Underpinning the numerical capabilities is a powerful petascale parallel programming environment that aims to increase both programmer productivity and code scalability. This paper describes the features and capabilities of MADNESS and briefly discusses some current applications in chemistry and several areas of physics.

OSA Proceedings of the Topical Meeting (5th) on Short-Wave Length Coherent Radiation: Generation and Applications Held in Monterey, California on 8-10 April 1991. Volume 11

DTIC Science & Technology

1992-05-22

PIC simulation code to study several of the constraints imposed by plasma phenomena on the propagation of ultrashort high intensity laser pulses in...and radiation spectrum of free electrons in the focus of an ultrashort high intensity laser pulse is solved. Motion and radiation of electrons in a...higher harmonics. These studies are intended as a prelude to experiments with high intensity ultrashort laser pulses . To investigate the motion of

[Computer-assisted management of depots for blood products in health establishments].

PubMed

Carré, J

2008-11-01

To manage the filing of blood components at the hospital of the city of Bayeux, the laboratory uses Cursus, a dedicated software for haemovigilance. Benefits for using this software at different steps of the blood bank management are: simplification, security and harmonization of practices during receipt and issurance of blood components, securing recordings with the use of bar codes for patient identification and blood components listing, implementation of a computerized tracking system for transfusion, traceability, limitation of written documents and availability of statistics on the management of the depot.

Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability.

PubMed

Hogeweg, Paulien

2012-01-01

Most of evolutionary theory has abstracted away from how information is coded in the genome and how this information is transformed into traits on which selection takes place. While in the earliest stages of biological evolution, in the RNA world, the mapping from the genotype into function was largely predefined by the physical-chemical properties of the evolving entities (RNA replicators, e.g. from sequence to folded structure and catalytic sites), in present-day organisms, the mapping itself is the result of evolution. I will review results of several in silico evolutionary studies which examine the consequences of evolving the genetic coding, and the ways this information is transformed, while adapting to prevailing environments. Such multilevel evolution leads to long-term information integration. Through genome, network, and dynamical structuring, the occurrence and/or effect of random mutations becomes nonrandom, and facilitates rapid adaptation. This is what does happen in the in silico experiments. Is it also what did happen in biological evolution? I will discuss some data that suggest that it did. In any case, these results provide us with novel search images to tackle the wealth of biological data.

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

PubMed Central

Woltering, Joost M.; Duboule, Denis

2015-01-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. PMID:26238020

Effects of the plasma profiles on photon and pair production in ultrahigh intensity laser solid interaction

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

Tian, Y. X.; Jin, X. L., E-mail: jinxiaolin@uestc.edu.cn; Yan, W. Z.

The model of photon and pair production in strong field quantum electrodynamics is implemented into our 1D3V particle-in-cell code with Monte Carlo algorithm. Using this code, the evolution of the particles in ultrahigh intensity laser (∼10{sup 23} W/cm{sup 2}) interaction with aluminum foil target is observed. Four different initial plasma profiles are considered in the simulations. The effects of initial plasma profiles on photon and pair production, energy spectra, and energy evolution are analyzed. The results imply that one can set an optimal initial plasma profile to obtain the desired photon distributions.

Three stages in the evolution of the genetic code

NASA Technical Reports Server (NTRS)

Baumann, U.; Oro, J.

1993-01-01

A diversification of the genetic code based on the number of codons available for the proteinous amino acids is established. Three groups of amino acids during evolution of the code are distinguished. On the basis of their chemical complexity those amino acids emerging later in a translation process are derived. Codon number and chemical complexity indicate that His, Phe, Tyr, Cys and either Lys or Asn were introduced in the second stage, whereas the number of codons alone gives evidence that Trp and Met were introduced in the third stage. The amino acids of stage 1 use purine-rich codons, while all the amino acids introduced in the second stage, in contrast, use pyrimidines in the third position of their codons. A low abundance of pyrimidines during early translation is derived. This assumption is supported by experiments on non-enzymatic replication and interactions of hairpin loops with a complementary strand. A back extrapolation concludes a high purine content of the first nucleic acids, which gradually decreased during their evolution. Amino acids independently available from prebiotic synthesis were thus correlated to purine-rich codons. Implications on the prebiotic replication are discussed also in the light of recent codon usage data.

Rational harmonic mode-locking pulse quality of the dark-optical-comb injected semiconductor optical amplifier fiber ring laser.

PubMed

Lin, Gong-Ru; Lee, Chao-Kuei; Kang, Jung-Jui

2008-06-09

We study the rational harmonic mode-locking (RHML) order dependent pulse shortening force and dynamic chirp characteristics of a gain-saturated semiconductor optical amplifier fiber laser (SOAFL) under dark-optical-comb injection, and discuss the competition between mode-locking mechanisms in the SOAFL at high-gain and strong optical injection condition at higher RHML orders. The evolutions of spectra, mode-locking and continuous lasing powers by measuring the ratio of DC/pulse amplitude and the pulse shortening force (I(pulse)/P(avg)(2) ) are performed to determine the RHML capability of SOAFL. As the rational harmonic order increases up to 20, the spectral linewidth shrinks from 12 to 3 nm, the ratio of DC/pulse amplitude enlarges from 0.025 to 2.4, and the pulse-shortening force reduces from 0.9 to 0.05. At fundamental and highest RHML condition, we characterize the frequency detuning range to realize the mode-locking quality, and measure the dynamic frequency chirp of the RHML-SOAFL to distinguish the linear and nonlinear chirp after dispersion compensation. With increasing RHML order, the pulsewidth is broadened from 4.2 to 26.4 ps with corresponding chirp reducing from 0.7 to 0.2 GHz and linear/nonlinear chirp ratio changes from 4.3 to 1.3, which interprets the high-order chirp becomes dominates at higher RHML orders.

TORBEAM 2.0, a paraxial beam tracing code for electron-cyclotron beams in fusion plasmas for extended physics applications

NASA Astrophysics Data System (ADS)

Poli, E.; Bock, A.; Lochbrunner, M.; Maj, O.; Reich, M.; Snicker, A.; Stegmeir, A.; Volpe, F.; Bertelli, N.; Bilato, R.; Conway, G. D.; Farina, D.; Felici, F.; Figini, L.; Fischer, R.; Galperti, C.; Happel, T.; Lin-Liu, Y. R.; Marushchenko, N. B.; Mszanowski, U.; Poli, F. M.; Stober, J.; Westerhof, E.; Zille, R.; Peeters, A. G.; Pereverzev, G. V.

2018-04-01

The paraxial WKB code TORBEAM (Poli, 2001) is widely used for the description of electron-cyclotron waves in fusion plasmas, retaining diffraction effects through the solution of a set of ordinary differential equations. With respect to its original form, the code has undergone significant transformations and extensions, in terms of both the physical model and the spectrum of applications. The code has been rewritten in Fortran 90 and transformed into a library, which can be called from within different (not necessarily Fortran-based) workflows. The models for both absorption and current drive have been extended, including e.g. fully-relativistic calculation of the absorption coefficient, momentum conservation in electron-electron collisions and the contribution of more than one harmonic to current drive. The code can be run also for reflectometry applications, with relativistic corrections for the electron mass. Formulas that provide the coupling between the reflected beam and the receiver have been developed. Accelerated versions of the code are available, with the reduced physics goal of inferring the location of maximum absorption (including or not the total driven current) for a given setting of the launcher mirrors. Optionally, plasma volumes within given flux surfaces and corresponding values of minimum and maximum magnetic field can be provided externally to speed up the calculation of full driven-current profiles. These can be employed in real-time control algorithms or for fast data analysis.

Emergence and Evolution

PubMed Central

Bullwinkle, Tammy J.

2013-01-01

The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter. PMID:23478877

Newspaper Ethics and Managing Editors: The Evolution of APME's Code.

ERIC Educational Resources Information Center

De Mott, John

A review of the 42-year development of the professional code of ethics of the Associated Press Managing Editors (APME) demonstrates an effort to elevate newspaper ethical standards around the country. Following the example of the American Society of Newspaper Editors in establishing its "Canons of Journalism" in 1923, the APME formed a…

Confinement properties of tokamak plasmas with extended regions of low magnetic shear

NASA Astrophysics Data System (ADS)

Graves, J. P.; Cooper, W. A.; Kleiner, A.; Raghunathan, M.; Neto, E.; Nicolas, T.; Lanthaler, S.; Patten, H.; Pfefferle, D.; Brunetti, D.; Lutjens, H.

2017-10-01

Extended regions of low magnetic shear can be advantageous to tokamak plasmas. But the core and edge can be susceptible to non-resonant ideal fluctuations due to the weakened restoring force associated with magnetic field line bending. This contribution shows how saturated non-linear phenomenology, such as 1 / 1 Long Lived Modes, and Edge Harmonic Oscillations associated with QH-modes, can be modelled accurately using the non-linear stability code XTOR, the free boundary 3D equilibrium code VMEC, and non-linear analytic theory. That the equilibrium approach is valid is particularly valuable because it enables advanced particle confinement studies to be undertaken in the ordinarily difficult environment of strongly 3D magnetic fields. The VENUS-LEVIS code exploits the Fourier description of the VMEC equilibrium fields, such that full Lorenzian and guiding centre approximated differential operators in curvilinear angular coordinates can be evaluated analytically. Consequently, the confinement properties of minority ions such as energetic particles and high Z impurities can be calculated accurately over slowing down timescales in experimentally relevant 3D plasmas.

Origin and evolution of the long non-coding genes in the X-inactivation center.

PubMed

Romito, Antonio; Rougeulle, Claire

2011-11-01

Random X chromosome inactivation (XCI), the eutherian mechanism of X-linked gene dosage compensation, is controlled by a cis-acting locus termed the X-inactivation center (Xic). One of the striking features that characterize the Xic landscape is the abundance of loci transcribing non-coding RNAs (ncRNAs), including Xist, the master regulator of the inactivation process. Recent comparative genomic analyses have depicted the evolutionary scenario behind the origin of the X-inactivation center, revealing that this locus evolved from a region harboring protein-coding genes. During mammalian radiation, this ancestral protein-coding region was disrupted in the marsupial group, whilst it provided in eutherian lineage the starting material for the non-translated RNAs of the X-inactivation center. The emergence of non-coding genes occurred by a dual mechanism involving loss of protein-coding function of the pre-existing genes and integration of different classes of mobile elements, some of which modeled the structure and sequence of the non-coding genes in a species-specific manner. The rising genes started to produce transcripts that acquired function in regulating the epigenetic status of the X chromosome, as shown for Xist, its antisense Tsix, Jpx, and recently suggested for Ftx. Thus, the appearance of the Xic, which occurred after the divergence between eutherians and marsupials, was the basis for the evolution of random X inactivation as a strategy to achieve dosage compensation. Copyright © 2011. Published by Elsevier Masson SAS.

Recent evidence for evolution of the genetic code

NASA Technical Reports Server (NTRS)

Osawa, S.; Jukes, T. H.; Watanabe, K.; Muto, A.

1992-01-01

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

A Comparison of Grid-based and SPH Binary Mass-transfer and Merger Simulations

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

Motl, Patrick M.; Frank, Juhan; Clayton, Geoffrey C.

2017-04-01

There is currently a great amount of interest in the outcomes and astrophysical implications of mergers of double degenerate binaries. In a commonly adopted approximation, the components of such binaries are represented by polytropes with an index of n  = 3/2. We present detailed comparisons of stellar mass-transfer and merger simulations of polytropic binaries that have been carried out using two very different numerical algorithms—a finite-volume “grid” code and a smoothed-particle hydrodynamics (SPH) code. We find that there is agreement in both the ultimate outcomes of the evolutions and the intermediate stages if the initial conditions for each code are chosen to matchmore » as closely as possible. We find that even with closely matching initial setups, the time it takes to reach a concordant evolution differs between the two codes because the initial depth of contact cannot be matched exactly. There is a general tendency for SPH to yield higher mass transfer rates and faster evolution to the final outcome. We also present comparisons of simulations calculated from two different energy equations: in one series, we assume a polytropic equation of state and in the other series an ideal gas equation of state. In the latter series of simulations, an atmosphere forms around the accretor, which can exchange angular momentum and cause a more rapid loss of orbital angular momentum. In the simulations presented here, the effect of the ideal equation of state is to de-stabilize the binary in both SPH and grid simulations, but the effect is more pronounced in the grid code.« less

Reaction Wheel Disturbance Model Extraction Software - RWDMES

NASA Technical Reports Server (NTRS)

Blaurock, Carl

2009-01-01

The RWDMES is a tool for modeling the disturbances imparted on spacecraft by spinning reaction wheels. Reaction wheels are usually the largest disturbance source on a precision pointing spacecraft, and can be the dominating source of pointing error. Accurate knowledge of the disturbance environment is critical to accurate prediction of the pointing performance. In the past, it has been difficult to extract an accurate wheel disturbance model since the forcing mechanisms are difficult to model physically, and the forcing amplitudes are filtered by the dynamics of the reaction wheel. RWDMES captures the wheel-induced disturbances using a hybrid physical/empirical model that is extracted directly from measured forcing data. The empirical models capture the tonal forces that occur at harmonics of the spin rate, and the broadband forces that arise from random effects. The empirical forcing functions are filtered by a physical model of the wheel structure that includes spin-rate-dependent moments (gyroscopic terms). The resulting hybrid model creates a highly accurate prediction of wheel-induced forces. It accounts for variation in disturbance frequency, as well as the shifts in structural amplification by the whirl modes, as the spin rate changes. This software provides a point-and-click environment for producing accurate models with minimal user effort. Where conventional approaches may take weeks to produce a model of variable quality, RWDMES can create a demonstrably high accuracy model in two hours. The software consists of a graphical user interface (GUI) that enables the user to specify all analysis parameters, to evaluate analysis results and to iteratively refine the model. Underlying algorithms automatically extract disturbance harmonics, initialize and tune harmonic models, and initialize and tune broadband noise models. The component steps are described in the RWDMES user s guide and include: converting time domain data to waterfall PSDs (power spectral densities); converting PSDs to order analysis data; extracting harmonics; initializing and simultaneously tuning a harmonic model and a wheel structural model; initializing and tuning a broadband model; and verifying the harmonic/broadband/structural model against the measurement data. Functional operation is through a MATLAB GUI that loads test data, performs the various analyses, plots evaluation data for assessment and refinement of analysis parameters, and exports the data to documentation or downstream analysis code. The harmonic models are defined as specified functions of frequency, typically speed-squared. The reaction wheel structural model is realized as mass, damping, and stiffness matrices (typically from a finite element analysis package) with the addition of a gyroscopic forcing matrix. The broadband noise model is realized as a set of speed-dependent filters. The tuning of the combined model is performed using nonlinear least squares techniques. RWDMES is implemented as a MATLAB toolbox comprising the Fit Manager for performing the model extraction, Data Manager for managing input data and output models, the Gyro Manager for modifying wheel structural models, and the Harmonic Editor for evaluating and tuning harmonic models. This software was validated using data from Goodrich E wheels, and from GSFC Lunar Reconnaissance Orbiter (LRO) wheels. The validation testing proved that RWDMES has the capability to extract accurate disturbance models from flight reaction wheels with minimal user effort.

Analysis of quantum error-correcting codes: Symplectic lattice codes and toric codes

NASA Astrophysics Data System (ADS)

Harrington, James William

Quantum information theory is concerned with identifying how quantum mechanical resources (such as entangled quantum states) can be utilized for a number of information processing tasks, including data storage, computation, communication, and cryptography. Efficient quantum algorithms and protocols have been developed for performing some tasks (e.g. , factoring large numbers, securely communicating over a public channel, and simulating quantum mechanical systems) that appear to be very difficult with just classical resources. In addition to identifying the separation between classical and quantum computational power, much of the theoretical focus in this field over the last decade has been concerned with finding novel ways of encoding quantum information that are robust against errors, which is an important step toward building practical quantum information processing devices. In this thesis I present some results on the quantum error-correcting properties of oscillator codes (also described as symplectic lattice codes) and toric codes. Any harmonic oscillator system (such as a mode of light) can be encoded with quantum information via symplectic lattice codes that are robust against shifts in the system's continuous quantum variables. I show the existence of lattice codes whose achievable rates match the one-shot coherent information over the Gaussian quantum channel. Also, I construct a family of symplectic self-dual lattices and search for optimal encodings of quantum information distributed between several oscillators. Toric codes provide encodings of quantum information into two-dimensional spin lattices that are robust against local clusters of errors and which require only local quantum operations for error correction. Numerical simulations of this system under various error models provide a calculation of the accuracy threshold for quantum memory using toric codes, which can be related to phase transitions in certain condensed matter models. I also present a local classical processing scheme for correcting errors on toric codes, which demonstrates that quantum information can be maintained in two dimensions by purely local (quantum and classical) resources.

Numerical relativity for D dimensional axially symmetric space-times: Formalism and code tests

NASA Astrophysics Data System (ADS)

Zilhão, Miguel; Witek, Helvi; Sperhake, Ulrich; Cardoso, Vitor; Gualtieri, Leonardo; Herdeiro, Carlos; Nerozzi, Andrea

2010-04-01

The numerical evolution of Einstein’s field equations in a generic background has the potential to answer a variety of important questions in physics: from applications to the gauge-gravity duality, to modeling black hole production in TeV gravity scenarios, to analysis of the stability of exact solutions, and to tests of cosmic censorship. In order to investigate these questions, we extend numerical relativity to more general space-times than those investigated hitherto, by developing a framework to study the numerical evolution of D dimensional vacuum space-times with an SO(D-2) isometry group for D≥5, or SO(D-3) for D≥6. Performing a dimensional reduction on a (D-4) sphere, the D dimensional vacuum Einstein equations are rewritten as a 3+1 dimensional system with source terms, and presented in the Baumgarte, Shapiro, Shibata, and Nakamura formulation. This allows the use of existing 3+1 dimensional numerical codes with small adaptations. Brill-Lindquist initial data are constructed in D dimensions and a procedure to match them to our 3+1 dimensional evolution equations is given. We have implemented our framework by adapting the Lean code and perform a variety of simulations of nonspinning black hole space-times. Specifically, we present a modified moving puncture gauge, which facilitates long-term stable simulations in D=5. We further demonstrate the internal consistency of the code by studying convergence and comparing numerical versus analytic results in the case of geodesic slicing for D=5, 6.

Parallel evolution of chordate cis-regulatory code for development.

PubMed

Doglio, Laura; Goode, Debbie K; Pelleri, Maria C; Pauls, Stefan; Frabetti, Flavia; Shimeld, Sebastian M; Vavouri, Tanya; Elgar, Greg

2013-11-01

Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

Nonlinear stability of oscillatory core-annular flow: A generalized Kuramoto-Sivashinsky equation with time periodic coefficients

NASA Technical Reports Server (NTRS)

Coward, Adrian V.; Papageorgiou, Demetrios T.; Smyrlis, Yiorgos S.

1994-01-01

In this paper the nonlinear stability of two-phase core-annular flow in a pipe is examined when the acting pressure gradient is modulated by time harmonic oscillations and viscosity stratification and interfacial tension is present. An exact solution of the Navier-Stokes equations is used as the background state to develop an asymptotic theory valid for thin annular layers, which leads to a novel nonlinear evolution describing the spatio-temporal evolution of the interface. The evolution equation is an extension of the equation found for constant pressure gradients and generalizes the Kuramoto-Sivashinsky equation with dispersive effects found by Papageorgiou, Maldarelli & Rumschitzki, Phys. Fluids A 2(3), 1990, pp. 340-352, to a similar system with time periodic coefficients. The distinct regimes of slow and moderate flow are considered and the corresponding evolution is derived. Certain solutions are described analytically in the neighborhood of the first bifurcation point by use of multiple scales asymptotics. Extensive numerical experiments, using dynamical systems ideas, are carried out in order to evaluate the effect of the oscillatory pressure gradient on the solutions in the presence of a constant pressure gradient.

Observing Stellar Clusters in the Computer

NASA Astrophysics Data System (ADS)

Borch, A.; Spurzem, R.; Hurley, J.

2006-08-01

We present a new approach to combine direct N-body simulations to stellar population synthesis modeling in order to model the dynamical evolution and color evolution of globular clusters at the same time. This allows us to model the spectrum, colors and luminosities of each star in the simulated cluster. For this purpose the NBODY6++ code (Spurzem 1999) is used, which is a parallel version of the NBODY code. J. Hurley implemented simple recipes to follow the changes of stellar masses, radii, and luminosities due to stellar evolution into the NBODY6++ code (Hurley et al. 2001), in the sense that each simulation particle represents one star. These prescriptions cover all evolutionary phases and solar to globular cluster metallicities. We used the stellar parameters obtained by this stellar evolution routine and coupled them to the stellar library BaSeL 2.0 (Lejeune et al. 1997). As a first application we investigated the integrated broad band colors of simulated clusters. We modeled tidally disrupted globular clusters and compared the results with isolated globular clusters. Due to energy equipartition we expected a relative blueing of tidally disrupted clusters, because of the higher escape probability of red, low-mass stars. This behaviour we actually observe for concentrated globular clusters. The mass-to-light ratio of isolated clusters follows exactly a color-M/L correlation, similar as described in Bell and de Jong (2001) in the case of spiral galaxies. At variance to this correlation, in tidally disrupted clusters the M/L ratio becomes significantly lower at the time of cluster dissolution. Hence, for isolated clusters the behavior of the stellar population is not influenced by dynamical evolution, whereas the stellar population of tidally disrupted clusters is strongly influenced by dynamical effects.

Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae).

PubMed

Walker, Joseph F; Zanis, Michael J; Emery, Nancy C

2014-04-01

Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae. We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession. The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions. Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.

The analysis of convolutional codes via the extended Smith algorithm

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Onyszchuk, I.

1993-01-01

Convolutional codes have been the central part of most error-control systems in deep-space communication for many years. Almost all such applications, however, have used the restricted class of (n,1), also known as 'rate 1/n,' convolutional codes. The more general class of (n,k) convolutional codes contains many potentially useful codes, but their algebraic theory is difficult and has proved to be a stumbling block in the evolution of convolutional coding systems. In this article, the situation is improved by describing a set of practical algorithms for computing certain basic things about a convolutional code (among them the degree, the Forney indices, a minimal generator matrix, and a parity-check matrix), which are usually needed before a system using the code can be built. The approach is based on the classic Forney theory for convolutional codes, together with the extended Smith algorithm for polynomial matrices, which is introduced in this article.

Origin and evolution of spliceosomal introns

PubMed Central

2012-01-01

Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes. This article was reviewed by I. King Jordan, Manuel Irimia (nominated by Anthony Poole), Tobias Mourier (nominated by Anthony Poole), and Fyodor Kondrashov. For the complete reports, see the Reviewers’ Reports section. PMID:22507701

Earth-moon system: Dynamics and parameter estimation; numerical considerations and program documentation

NASA Technical Reports Server (NTRS)

Breedlove, W. J., Jr.

1976-01-01

Major activities included coding and verifying equations of motion for the earth-moon system. Some attention was also given to numerical integration methods and parameter estimation methods. Existing analytical theories such as Brown's lunar theory, Eckhardt's theory for lunar rotation, and Newcomb's theory for the rotation of the earth were coded and verified. These theories serve as checks for the numerical integration. Laser ranging data for the period January 1969 - December 1975 was collected and stored on tape. The main goal of this research is the development of software to enable physical parameters of the earth-moon system to be estimated making use of data available from the Lunar Laser Ranging Experiment and the Very Long Base Interferometry experiment of project Apollo. A more specific goal is to develop software for the estimation of certain physical parameters of the moon such as inertia ratios, and the third and fourth harmonic gravity coefficients.

Applications of surface acoustic and shallow bulk acoustic wave devices

NASA Astrophysics Data System (ADS)

Campbell, Colin K.

1989-10-01

Surface acoustic wave (SAW) device coverage includes delay lines and filters operating at selected frequencies in the range from about 10 MHz to 11 GHz; modeling with single-crystal piezoelectrics and layered structures; resonators and low-loss filters; comb filters and multiplexers; antenna duplexers; harmonic devices; chirp filters for pulse compression; coding with fixed and programmable transversal filters; Barker and quadraphase coding; adaptive filters; acoustic and acoustoelectric convolvers and correlators for radar, spread spectrum, and packet radio; acoustooptic processors for Bragg modulation and spectrum analysis; real-time Fourier-transform and cepstrum processors for radar and sonar; compressive receivers; Nyquist filters for microwave digital radio; clock-recovery filters for fiber communications; fixed-, tunable-, and multimode oscillators and frequency synthesizers; acoustic charge transport; and other SAW devices for signal processing on gallium arsenide. Shallow bulk acoustic wave device applications include gigahertz delay lines, surface-transverse-wave resonators employing energy-trapping gratings, and oscillators with enhanced performance and capability.

Comparing contribution of flexural and planar modes to thermodynamic properties

NASA Astrophysics Data System (ADS)

Mann, Sarita; Rani, Pooja; Jindal, V. K.

2017-05-01

Graphene, the most studied and explored 2D structure has unusual thermal properties such as negative thermal expansion, high thermal conductivity etc. We have already studied the thermal expansion behavior and various thermodynamic properties of pure graphene like heat capacity, entropy and free energy. The results of thermal expansion and various thermodynamic properties match well with available theoretical studies. For a deeper understanding of these properties, we analyzed the contribution of each phonon branch towards the total value of the individual property. To compute these properties, the dynamical matrix was calculated using VASP code where the density functional perturbation theory (DFPT) is employed under quasi-harmonic approximation in interface with phonopy code. It is noticed that transverse mode has major contribution to negative thermal expansion and all branches have almost same contribution towards the various thermodynamic properties with the contribution of ZA mode being the highest.

A new Gaussian MCTDH program: Implementation and validation on the levels of the water and glycine molecules

NASA Astrophysics Data System (ADS)

Skouteris, D.; Barone, V.

2014-06-01

We report the main features of a new general implementation of the Gaussian Multi-Configuration Time-Dependent Hartree model. The code allows effective computations of time-dependent phenomena, including calculation of vibronic spectra (in one or more electronic states), relative state populations, etc. Moreover, by expressing the Dirac-Frenkel variational principle in terms of an effective Hamiltonian, we are able to provide a new reliable estimate of the representation error. After validating the code on simple one-dimensional systems, we analyze the harmonic and anharmonic vibrational spectra of water and glycine showing that reliable and converged energy levels can be obtained with reasonable computing resources. The data obtained on water and glycine are compared with results of previous calculations using the vibrational second-order perturbation theory method. Additional features and perspectives are also shortly discussed.

Brief Report: Databases in the Asia-Pacific Region: The Potential for a Distributed Network Approach.

PubMed

Lai, Edward Chia-Cheng; Man, Kenneth K C; Chaiyakunapruk, Nathorn; Cheng, Ching-Lan; Chien, Hsu-Chih; Chui, Celine S L; Dilokthornsakul, Piyameth; Hardy, N Chantelle; Hsieh, Cheng-Yang; Hsu, Chung Y; Kubota, Kiyoshi; Lin, Tzu-Chieh; Liu, Yanfang; Park, Byung Joo; Pratt, Nicole; Roughead, Elizabeth E; Shin, Ju-Young; Watcharathanakij, Sawaeng; Wen, Jin; Wong, Ian C K; Yang, Yea-Huei Kao; Zhang, Yinghong; Setoguchi, Soko

2015-11-01

This study describes the availability and characteristics of databases in Asian-Pacific countries and assesses the feasibility of a distributed network approach in the region. A web-based survey was conducted among investigators using healthcare databases in the Asia-Pacific countries. Potential survey participants were identified through the Asian Pharmacoepidemiology Network. Investigators from a total of 11 databases participated in the survey. Database sources included four nationwide claims databases from Japan, South Korea, and Taiwan; two nationwide electronic health records from Hong Kong and Singapore; a regional electronic health record from western China; two electronic health records from Thailand; and cancer and stroke registries from Taiwan. We identified 11 databases with capabilities for distributed network approaches. Many country-specific coding systems and terminologies have been already converted to international coding systems. The harmonization of health expenditure data is a major obstacle for future investigations attempting to evaluate issues related to medical costs.

Adiabatic invariants in stellar dynamics. 1: Basic concepts

NASA Technical Reports Server (NTRS)

Weinberg, Martin D.

1994-01-01

The adiabatic criterion, widely used in astronomical dynamics, is based on the harmonic oscillator. It asserts that the change in action under a slowly varying perturbation is exponentially small. Recent mathematical results that precisely define the conditions for invariance show that this model does not apply in general. In particular, a slowly varying perturbation may cause significant evolution stellar dynamical systems even if its time scale is longer than any internal orbital time scale. This additional 'heating' may have serious implications for the evolution of star clusters and dwarf galaxies which are subject to long-term environmental forces. The mathematical developments leading to these results are reviewed, and the conditions for applicability to and further implications for stellar systems are discussed. Companion papers present a computational method for a general time-dependent disturbance and detailed example.

Incomplete Thermalization from Trap-Induced Integrability Breaking: Lessons from Classical Hard Rods

NASA Astrophysics Data System (ADS)

Cao, Xiangyu; Bulchandani, Vir B.; Moore, Joel E.

2018-04-01

We study a one-dimensional gas of hard rods trapped in a harmonic potential, which breaks integrability of the hard-rod interaction in a nonuniform way. We explore the consequences of such broken integrability for the dynamics of a large number of particles and find three distinct regimes: initial, chaotic, and stationary. The initial regime is captured by an evolution equation for the phase-space distribution function. For any finite number of particles, this hydrodynamics breaks down and the dynamics becomes chaotic after a characteristic timescale determined by the interparticle distance and scattering length. The system fails to thermalize over the timescale studied (1 04 natural units), but the time-averaged ensemble is a stationary state of the hydrodynamic evolution. We close by discussing logical extensions of the results to similar systems of quantum particles.

Rapid evolution of cis-regulatory sequences via local point mutations

NASA Technical Reports Server (NTRS)

Stone, J. R.; Wray, G. A.

2001-01-01

Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

PubMed

Campo, Daniel; García-Vázquez, Eva

2012-01-01

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

Testing a one-dimensional prescription of dynamical shear mixing with a two-dimensional hydrodynamic simulation

NASA Astrophysics Data System (ADS)

Edelmann, P. V. F.; Röpke, F. K.; Hirschi, R.; Georgy, C.; Jones, S.

2017-07-01

Context. The treatment of mixing processes is still one of the major uncertainties in 1D stellar evolution models. This is mostly due to the need to parametrize and approximate aspects of hydrodynamics in hydrostatic codes. In particular, the effect of hydrodynamic instabilities in rotating stars, for example, dynamical shear instability, evades consistent description. Aims: We intend to study the accuracy of the diffusion approximation to dynamical shear in hydrostatic stellar evolution models by comparing 1D models to a first-principle hydrodynamics simulation starting from the same initial conditions. Methods: We chose an initial model calculated with the stellar evolution code GENEC that is just at the onset of a dynamical shear instability but does not show any other instabilities (e.g., convection). This was mapped to the hydrodynamics code SLH to perform a 2D simulation in the equatorial plane. We compare the resulting profiles in the two codes and compute an effective diffusion coefficient for the hydro simulation. Results: Shear instabilities develop in the 2D simulation in the regions predicted by linear theory to become unstable in the 1D stellar evolution model. Angular velocity and chemical composition is redistributed in the unstable region, thereby creating new unstable regions. After a period of time, the system settles in a symmetric, steady state, which is Richardson stable everywhere in the 2D simulation, whereas the instability remains for longer in the 1D model due to the limitations of the current implementation in the 1D code. A spatially resolved diffusion coefficient is extracted by comparing the initial and final profiles of mean atomic mass. Conclusions: The presented simulation gives a first insight on hydrodynamics of shear instabilities in a real stellar environment and even allows us to directly extract an effective diffusion coefficient. We see evidence for a critical Richardson number of 0.25 as regions above this threshold remain stable for the course of the simulation. The movie of the simulation is available at http://www.aanda.org

Assessment of polarization effect on aerosol retrievals from MODIS

NASA Astrophysics Data System (ADS)

Korkin, S.; Lyapustin, A.

2010-12-01

Light polarization affects the total intensity of scattered radiation. In this work, we compare aerosol retrievals performed by code MAIAC [1] with and without taking polarization into account. The MAIAC retrievals are based on the look-up tables (LUT). For this work, MAIAC was run using two different LUTs, the first one generated using the scalar code SHARM [2], and the second one generated with the vector code Modified Vector Discrete Ordinates Method (MVDOM). MVDOM is a new code suitable for computations with highly anisotropic phase functions, including cirrus clouds and snow [3]. To this end, the solution of the vector radiative transfer equation (VRTE) is represented as a sum of anisotropic and regular components. The anisotropic component is evaluated in the Small Angle Modification of the Spherical Harmonics Method (MSH) [4]. The MSH is formulated in the frame of reference of the solar beam where z-axis lies along the solar beam direction. In this case, the MSH solution for anisotropic part is nearly symmetric in azimuth, and is computed analytically. In scalar case, this solution coincides with the Goudsmit-Saunderson small-angle approximation [5]. To correct for an analytical separation of the anisotropic part of the signal, the transfer equation for the regular part contains a correction source function term [6]. Several examples of polarization impact on aerosol retrievals over different surface types will be presented. 1. Lyapustin A., Wang Y., Laszlo I., Kahn R., Korkin S., Remer L., Levy R., and Reid J. S. Multi-Angle Implementation of Atmospheric Correction (MAIAC): Part 2. Aerosol Algorithm. J. Geophys. Res., submitted (2010). 2. Lyapustin A., Muldashev T., Wang Y. Code SHARM: fast and accurate radiative transfer over spatially variable anisotropic surfaces. In: Light Scattering Reviews 5. Chichester: Springer, 205 - 247 (2010). 3. Budak, V.P., Korkin S.V. On the solution of a vectorial radiative transfer equation in an arbitrary three-dimensional turbid medium with anisotropic scattering. JQSRT, 109, 220-234 (2008). 4. Budak V.P., Sarmin S.E. Solution of radiative transfer equation by the method of spherical harmonics in the small angle modification. Atmospheric and Oceanic Optics, 3, 898-903 (1990). 5. Goudsmit S., Saunderson J.L. Multiple scattering of electrons. Phys. Rev., 57, 24-29 (1940). 6. Budak V.P, Klyuykov D.A., Korkin S.V. Convergence acceleration of radiative transfer equation solution at strongly anisotropic scattering. In: Light Scattering Reviews 5. Chichester: Springer, 147 - 204 (2010).

Jet and electromagnetic tomography (JET) of extreme phases of matter in heavy-ion collisions

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

Heinz, Ulrich

2015-08-31

The Ohio State University (OSU) group contributed to the deliverables of the JET Collaboration three major products: 1. The code package iEBE-VISHNU for modeling the dynamical evolution of the soft medium created in relativistic heavy-ion collisions, from its creation all the way to final freeze-out using a hybrid approach that interfaces a free-streaming partonic pre-equilbrium stage with a (2+1)-dimensional viscous relativistic fluid dynamical stage for the quark-gluon plasma (QGP) phase and the microscopic hadron cascade UrQMD for the hadronic rescattering and freeze-out stage. Except for UrQMD, all dynamical evolution components and interfaces were developed at OSU and tested and implementedmore » in collaboration with the Duke University group. 2. An electromagnetic radiation module for the calculation of thermal photon emission from the QGP and hadron resonance gas stages of a heavy-ion collision, with emission rates that have been corrected for viscous effects in the expanding medium consistent with the bulk evolution. The electromagnetic radiation module was developed under OSU leadership in collaboration with the McGill group and has been integrated in the iEBE-VISHNU code package. 3. An interface between the Monte Carlo jet shower evolution and hadronization codes developed by the Wayne State University (WSU), McGill and Texas A&M groups and the iEBE-VISHNU bulk evolution code, for performing jet quenching and jet shape modification studies in a realistically modeled evolving medium that was tuned to measured soft hadron data. Building on work performed at OSU for the theoretical framework used to describe the interaction of jets with the medium, initial work on the jet shower Monte Carlo was started at OSU and moved to WSU when OSU Visiting Assistant Professor Abhijit Majumder accepted a tenure track faculty position at WSU in September 2011. The jet-hydro interface was developed at OSU and WSU and tested and implemented in collaboration with the McGill, Texas A&M, and LBNL groups.« less

Plutonium shipments - a supplement

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

Kwiatkowska, B.; Soons, A.

1994-10-01

By means of a supplement to the stimulating analysis found in the comprehensive article by Professor Jon Van Dyke on `Sea Shipment of Japanese Plutonium under International Law`, published in Volume 24 of this journal, we feel that the following clarifications and additions are appropriate. Radioactive wastes are not covered by the 1989 Basel Convention on the Control of Transboundary Movements of Hazardous Wastes and Their Disposal. Fir this reason, the Basel Conference adopted on March 22, 1989, along with the convention, Resolution 5 on Harmonization of Procedures of the Basel Convention and the Code of Practice for International Transactionsmore » Involving Nuclear Wastes. In accordance with Resolution 5, the provisions of the Basel Convention were taken into full account during the elaboration of the IAEA code, which ultimately was adopted by Resolution GC(XXXIV)/530 of the General Conference on Code of Practice on the International Transboundary Movement of Radioactive Waste (TMRW) of September 21, 1990. The IAEA code of practice and the respective regional instruments affirm, with respect to TMRW, the general principles of the Basel Convention, including the critical regime of prior notification and prior informed consent (PIC) that extend the scope of duties of notification, environmental impact assessment, and consultation with respect to transboundary interference as the duties have evolved under existing customary law.« less

Modulation of spike coding by subthreshold extracellular electric fields and neuronal morphology

NASA Astrophysics Data System (ADS)

Wei, Xile; Li, Bingjie; Lu, Meili; Yi, Guosheng; Wang, Jiang

2015-07-01

We use a two-compartment model, which includes soma and dendrite, to explore how extracellular subthreshold sinusoidal electric fields (EFs) influence the spike coding of an active neuron. By changing the intensity and the frequency of subthreshold EFs, we find that subthreshold EFs indeed affect neuronal coding remarkably within several stimulus frequency windows where the field effects on spike timing are stronger than that on spiking rate. The field effects are maximized at several harmonics of the intrinsic spiking frequency of an active neuron. Our findings implicate the potential resonance mechanism underlying subthreshold field effects. We also discuss how neuronal morphologic properties constrain subthreshold EF effects on spike timing. The morphologic properties are represented by two parameters, gc and p, where gc is the internal conductance between soma and dendrite and geometric factor p characterizes the proportion of area occupied by soma. We find that the contribution to field effects from the variation of p is stronger than that from gc, which suggests that neuronal geometric features play a crucial role in subthreshold field effects. Theoretically, these insights into how subthreshold sinusoidal EFs modulate ongoing neuron behaviors could contribute to uncovering the relevant mechanism of subthreshold sinusoidal EFs effects on neuronal coding. Furthermore, they are useful in rationally designing noninvasive brain stimulation strategies and developing electromagnetic stimulus techniques.

Experimental study on the resonance frequencies of a cantilevered plate in air flow

NASA Astrophysics Data System (ADS)

Cros, Anne; Arellano Castro, Rocío F.

2016-02-01

The present experimental work focuses on the resonances exhibited by a cantilevered plate immersed in airflow. The flexible plate is clamped at its leading edge and submitted to a small, lateral harmonic displacement. Throughout this work, our two control parameters are the forcing frequency and the air velocity. We determine experimentally the evolution of the first three resonant frequencies as air velocity is increased. Our results are in agreement with the Eloy et al. (2007) [1] and Michelin and Llewellyn-Smith (2009) [2] linear theoretical predictions.

Enforcing dust mass conservation in 3D simulations of tightly coupled grains with the PHANTOM SPH code

NASA Astrophysics Data System (ADS)

Ballabio, G.; Dipierro, G.; Veronesi, B.; Lodato, G.; Hutchison, M.; Laibe, G.; Price, D. J.

2018-06-01

We describe a new implementation of the one-fluid method in the SPH code PHANTOM to simulate the dynamics of dust grains in gas protoplanetary discs. We revise and extend previously developed algorithms by computing the evolution of a new fluid quantity that produces a more accurate and numerically controlled evolution of the dust dynamics. Moreover, by limiting the stopping time of uncoupled grains that violate the assumptions of the terminal velocity approximation, we avoid fatal numerical errors in mass conservation. We test and validate our new algorithm by running 3D SPH simulations of a large range of disc models with tightly and marginally coupled grains.

New Directions in Giant Planet Formation

NASA Astrophysics Data System (ADS)

Youdin, Andrew

The proposed research will explore the limits of the core accretion mechanism for forming giant planets, both in terms of timescale and orbital distance. This theoretical research will be useful in interpreting the results of ongoing exoplanet searches. The effects of radiogenic heating and aerodynamic accretion of pebbles and boulders will be included in time-dependent models of atmospheric structure and growth. To investigate these issues, we will develop and publicly share a protoplanet atmospheric evolution code as an extension of the MESA stellar evolution code. By focusing on relevant processes in the early stages of giant planet formation, we can refine model predictions for exoplanet searches at a wide range of stellar ages and distances from the host star.

Industry and Occupation in the Electronic Health Record: An Investigation of the National Institute for Occupational Safety and Health Industry and Occupation Computerized Coding System.

PubMed

Schmitz, Matthew; Forst, Linda

2016-02-15

Inclusion of information about a patient's work, industry, and occupation, in the electronic health record (EHR) could facilitate occupational health surveillance, better health outcomes, prevention activities, and identification of workers' compensation cases. The US National Institute for Occupational Safety and Health (NIOSH) has developed an autocoding system for "industry" and "occupation" based on 1990 Bureau of Census codes; its effectiveness requires evaluation in conjunction with promoting the mandatory addition of these variables to the EHR. The objective of the study was to evaluate the intercoder reliability of NIOSH's Industry and Occupation Computerized Coding System (NIOCCS) when applied to data collected in a community survey conducted under the Affordable Care Act; to determine the proportion of records that are autocoded using NIOCCS. Standard Occupational Classification (SOC) codes are used by several federal agencies in databases that capture demographic, employment, and health information to harmonize variables related to work activities among these data sources. There are 359 industry and occupation responses that were hand coded by 2 investigators, who came to a consensus on every code. The same variables were autocoded using NIOCCS at the high and moderate criteria level. Kappa was .84 for agreement between hand coders and between the hand coder consensus code versus NIOCCS high confidence level codes for the first 2 digits of the SOC code. For 4 digits, NIOCCS coding versus investigator coding ranged from kappa=.56 to .70. In this study, NIOCCS was able to achieve production rates (ie, to autocode) 31%-36% of entered variables at the "high confidence" level and 49%-58% at the "medium confidence" level. Autocoding (production) rates are somewhat lower than those reported by NIOSH. Agreement between manually coded and autocoded data are "substantial" at the 2-digit level, but only "fair" to "good" at the 4-digit level. This work serves as a baseline for performance of NIOCCS by investigators in the field. Further field testing will clarify NIOCCS effectiveness in terms of ability to assign codes and coding accuracy and will clarify its value as inclusion of these occupational variables in the EHR is promoted.

Lie algebraic approach to the time-dependent quantum general harmonic oscillator and the bi-dimensional charged particle in time-dependent electromagnetic fields

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

Ibarra-Sierra, V.G.; Sandoval-Santana, J.C.; Cardoso, J.L.

We discuss the one-dimensional, time-dependent general quadratic Hamiltonian and the bi-dimensional charged particle in time-dependent electromagnetic fields through the Lie algebraic approach. Such method consists in finding a set of generators that form a closed Lie algebra in terms of which it is possible to express a quantum Hamiltonian and therefore the evolution operator. The evolution operator is then the starting point to obtain the propagator as well as the explicit form of the Heisenberg picture position and momentum operators. First, the set of generators forming a closed Lie algebra is identified for the general quadratic Hamiltonian. This algebra ismore » later extended to study the Hamiltonian of a charged particle in electromagnetic fields exploiting the similarities between the terms of these two Hamiltonians. These results are applied to the solution of five different examples: the linear potential which is used to introduce the Lie algebraic method, a radio frequency ion trap, a Kanai–Caldirola-like forced harmonic oscillator, a charged particle in a time dependent magnetic field, and a charged particle in constant magnetic field and oscillating electric field. In particular we present exact analytical expressions that are fitting for the study of a rotating quadrupole field ion trap and magneto-transport in two-dimensional semiconductor heterostructures illuminated by microwave radiation. In these examples we show that this powerful method is suitable to treat quadratic Hamiltonians with time dependent coefficients quite efficiently yielding closed analytical expressions for the propagator and the Heisenberg picture position and momentum operators. -- Highlights: •We deal with the general quadratic Hamiltonian and a particle in electromagnetic fields. •The evolution operator is worked out through the Lie algebraic approach. •We also obtain the propagator and Heisenberg picture position and momentum operators. •Analytical expressions for a rotating quadrupole field ion trap are presented. •Exact solutions for magneto-transport in variable electromagnetic fields are shown.« less