Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Time Series Data-fMRI Study.

PubMed

Eslami, Taban; Saeed, Fahad

2018-04-20

Functional magnetic resonance imaging (fMRI) is a non-invasive brain imaging technique, which has been regularly used for studying brain’s functional activities in the past few years. A very well-used measure for capturing functional associations in brain is Pearson’s correlation coefficient. Pearson’s correlation is widely used for constructing functional network and studying dynamic functional connectivity of the brain. These are useful measures for understanding the effects of brain disorders on connectivities among brain regions. The fMRI scanners produce huge number of voxels and using traditional central processing unit (CPU)-based techniques for computing pairwise correlations is very time consuming especially when large number of subjects are being studied. In this paper, we propose a graphics processing unit (GPU)-based algorithm called Fast-GPU-PCC for computing pairwise Pearson’s correlation coefficient. Based on the symmetric property of Pearson’s correlation, this approach returns N ( N − 1 ) / 2 correlation coefficients located at strictly upper triangle part of the correlation matrix. Storing correlations in a one-dimensional array with the order as proposed in this paper is useful for further usage. Our experiments on real and synthetic fMRI data for different number of voxels and varying length of time series show that the proposed approach outperformed state of the art GPU-based techniques as well as the sequential CPU-based versions. We show that Fast-GPU-PCC runs 62 times faster than CPU-based version and about 2 to 3 times faster than two other state of the art GPU-based methods.

Electron number probability distributions for correlated wave functions.

PubMed

Francisco, E; Martín Pendás, A; Blanco, M A

2007-03-07

Efficient formulas for computing the probability of finding exactly an integer number of electrons in an arbitrarily chosen volume are only known for single-determinant wave functions [E. Cances et al., Theor. Chem. Acc. 111, 373 (2004)]. In this article, an algebraic method is presented that extends these formulas to the case of multideterminant wave functions and any number of disjoint volumes. The derived expressions are applied to compute the probabilities within the atomic domains derived from the space partitioning based on the quantum theory of atoms in molecules. Results for a series of test molecules are presented, paying particular attention to the effects of electron correlation and of some numerical approximations on the computed probabilities.

Accelerating the two-point and three-point galaxy correlation functions using Fourier transforms

NASA Astrophysics Data System (ADS)

Slepian, Zachary; Eisenstein, Daniel J.

2016-01-01

Though Fourier transforms (FTs) are a common technique for finding correlation functions, they are not typically used in computations of the anisotropy of the two-point correlation function (2PCF) about the line of sight in wide-angle surveys because the line-of-sight direction is not constant on the Cartesian grid. Here we show how FTs can be used to compute the multipole moments of the anisotropic 2PCF. We also show how FTs can be used to accelerate the 3PCF algorithm of Slepian & Eisenstein. In both cases, these FT methods allow one to avoid the computational cost of pair counting, which scales as the square of the number density of objects in the survey. With the upcoming large data sets of Dark Energy Spectroscopic Instrument, Euclid, and Large Synoptic Survey Telescope, FT techniques will therefore offer an important complement to simple pair or triplet counts.

Simulation of synthetic discriminant function optical implementation

NASA Astrophysics Data System (ADS)

Riggins, J.; Butler, S.

1984-12-01

The optical implementation of geometrical shape and synthetic discriminant function matched filters is computer modeled. The filter implementation utilizes the Allebach-Keegan computer-generated hologram algorithm. Signal-to-noise and efficiency measurements were made on the resultant correlation planes.

Effective correlator for RadioAstron project

NASA Astrophysics Data System (ADS)

Sergeev, Sergey

This paper presents the implementation of programme FX-correlator for Very Long Baseline Interferometry, adapted for the project "RadioAstron". Software correlator implemented for heterogeneous computing systems using graphics accelerators. It is shown that for the task interferometry implementation of the graphics hardware has a high efficiency. The host processor of heterogeneous computing system, performs the function of forming the data flow for graphics accelerators, the number of which corresponds to the number of frequency channels. So, for the Radioastron project, such channels is seven. Each accelerator is perform correlation matrix for all bases for a single frequency channel. Initial data is converted to the floating-point format, is correction for the corresponding delay function and computes the entire correlation matrix simultaneously. Calculation of the correlation matrix is performed using the sliding Fourier transform. Thus, thanks to the compliance of a solved problem for architecture graphics accelerators, managed to get a performance for one processor platform Kepler, which corresponds to the performance of this task, the computing cluster platforms Intel on four nodes. This task successfully scaled not only on a large number of graphics accelerators, but also on a large number of nodes with multiple accelerators.

Report on 3 and 4-point correlation statistics in the COBE DMR anisotrophy maps

NASA Technical Reports Server (NTRS)

Hinshaw, Gary (Principal Investigator); Gorski, Krzystof M.; Banday, Anthony J.; Bennett, Charles L.

1996-01-01

As part of the work performed under NASA contract # NAS5-32648, we have computed the 3-point and 4-point correlation functions of the COBE-DNIR 2-year and 4-year anisotropy maps. The motivation for this study was to search for evidence of non-Gaussian statistical fluctuations in the temperature maps: skewness or asymmetry in the case of the 3-point function, kurtosis in the case of the 4-point function. Such behavior would have very significant implications for our understanding of the processes of galaxy formation, because our current models of galaxy formation predict that non-Gaussian features should not be present in the DMR maps. The results of our work showed that the 3-point correlation function is consistent with zero and that the 4-point function is not a very sensitive probe of non-Gaussian behavior in the COBE-DMR data. Our computation and analysis of 3-point correlations in the 2-year DMR maps was published in the Astrophysical Journal Letters, volume 446, page L67, 1995. Our computation and analysis of 3-point correlations in the 4-year DMR maps will be published, together with some additional tests, in the June 10, 1996 issue of the Astrophysical Journal Letters. Copies of both of these papers are attached as an appendix to this report.

Correlation energy functional within the GW -RPA: Exact forms, approximate forms, and challenges

NASA Astrophysics Data System (ADS)

Ismail-Beigi, Sohrab

2010-05-01

In principle, the Luttinger-Ward Green’s-function formalism allows one to compute simultaneously the total energy and the quasiparticle band structure of a many-body electronic system from first principles. We present approximate and exact expressions for the correlation energy within the GW -random-phase approximation that are more amenable to computation and allow for developing efficient approximations to the self-energy operator and correlation energy. The exact form is a sum over differences between plasmon and interband energies. The approximate forms are based on summing over screened interband transitions. We also demonstrate that blind extremization of such functionals leads to unphysical results: imposing physical constraints on the allowed solutions (Green’s functions) is necessary. Finally, we present some relevant numerical results for atomic systems.

Colour-dressed hexagon tessellations for correlation functions and non-planar corrections

NASA Astrophysics Data System (ADS)

Eden, Burkhard; Jiang, Yunfeng; le Plat, Dennis; Sfondrini, Alessandro

2018-02-01

We continue the study of four-point correlation functions by the hexagon tessellation approach initiated in [38] and [39]. We consider planar tree-level correlation functions in N=4 supersymmetric Yang-Mills theory involving two non-protected operators. We find that, in order to reproduce the field theory result, it is necessary to include SU( N) colour factors in the hexagon formalism; moreover, we find that the hexagon approach as it stands is naturally tailored to the single-trace part of correlation functions, and does not account for multi-trace admixtures. We discuss how to compute correlators involving double-trace operators, as well as more general 1 /N effects; in particular we compute the whole next-to-leading order in the large- N expansion of tree-level BMN two-point functions by tessellating a torus with punctures. Finally, we turn to the issue of "wrapping", Lüscher-like corrections. We show that SU( N) colour-dressing reproduces an earlier empirical rule for incorporating single-magnon wrapping, and we provide a direct interpretation of such wrapping processes in terms of N=2 supersymmetric Feynman diagrams.

Clinical application of calculated split renal volume using computed tomography-based renal volumetry after partial nephrectomy: Correlation with technetium-99m dimercaptosuccinic acid renal scan data.

PubMed

Lee, Chan Ho; Park, Young Joo; Ku, Ja Yoon; Ha, Hong Koo

2017-06-01

To evaluate the clinical application of computed tomography-based measurement of renal cortical volume and split renal volume as a single tool to assess the anatomy and renal function in patients with renal tumors before and after partial nephrectomy, and to compare the findings with technetium-99m dimercaptosuccinic acid renal scan. The data of 51 patients with a unilateral renal tumor managed by partial nephrectomy were retrospectively analyzed. The renal cortical volume of tumor-bearing and contralateral kidneys was measured using ImageJ software. Split estimated glomerular filtration rate and split renal volume calculated using this renal cortical volume were compared with the split renal function measured with technetium-99m dimercaptosuccinic acid renal scan. A strong correlation between split renal function and split renal volume of the tumor-bearing kidney was observed before and after surgery (r = 0.89, P < 0.001 and r = 0.94, P < 0.001). The preoperative and postoperative split estimated glomerular filtration rate of the operated kidney showed a moderate correlation with split renal function (r = 0.39, P = 0.004 and r = 0.49, P < 0.001). The correlation between reductions in split renal function and split renal volume of the operated kidney (r = 0.87, P < 0.001) was stronger than that between split renal function and percent reduction in split estimated glomerular filtration rate (r = 0.64, P < 0.001). The split renal volume calculated using computed tomography-based renal volumetry had a strong correlation with the split renal function measured using technetium-99m dimercaptosuccinic acid renal scan. Computed tomography-based split renal volume measurement before and after partial nephrectomy can be used as a single modality for anatomical and functional assessment of the tumor-bearing kidney. © 2017 The Japanese Urological Association.

Computing many-body wave functions with guaranteed precision: the first-order Møller-Plesset wave function for the ground state of helium atom.

PubMed

Bischoff, Florian A; Harrison, Robert J; Valeev, Edward F

2012-09-14

We present an approach to compute accurate correlation energies for atoms and molecules using an adaptive discontinuous spectral-element multiresolution representation for the two-electron wave function. Because of the exponential storage complexity of the spectral-element representation with the number of dimensions, a brute-force computation of two-electron (six-dimensional) wave functions with high precision was not practical. To overcome the key storage bottlenecks we utilized (1) a low-rank tensor approximation (specifically, the singular value decomposition) to compress the wave function, and (2) explicitly correlated R12-type terms in the wave function to regularize the Coulomb electron-electron singularities of the Hamiltonian. All operations necessary to solve the Schrödinger equation were expressed so that the reconstruction of the full-rank form of the wave function is never necessary. Numerical performance of the method was highlighted by computing the first-order Møller-Plesset wave function of a helium atom. The computed second-order Møller-Plesset energy is precise to ~2 microhartrees, which is at the precision limit of the existing general atomic-orbital-based approaches. Our approach does not assume special geometric symmetries, hence application to molecules is straightforward.

Functional CAR models for large spatially correlated functional datasets.

PubMed

Zhang, Lin; Baladandayuthapani, Veerabhadran; Zhu, Hongxiao; Baggerly, Keith A; Majewski, Tadeusz; Czerniak, Bogdan A; Morris, Jeffrey S

2016-01-01

We develop a functional conditional autoregressive (CAR) model for spatially correlated data for which functions are collected on areal units of a lattice. Our model performs functional response regression while accounting for spatial correlations with potentially nonseparable and nonstationary covariance structure, in both the space and functional domains. We show theoretically that our construction leads to a CAR model at each functional location, with spatial covariance parameters varying and borrowing strength across the functional domain. Using basis transformation strategies, the nonseparable spatial-functional model is computationally scalable to enormous functional datasets, generalizable to different basis functions, and can be used on functions defined on higher dimensional domains such as images. Through simulation studies, we demonstrate that accounting for the spatial correlation in our modeling leads to improved functional regression performance. Applied to a high-throughput spatially correlated copy number dataset, the model identifies genetic markers not identified by comparable methods that ignore spatial correlations.

Power Series Approximation for the Correlation Kernel Leading to Kohn-Sham Methods Combining Accuracy, Computational Efficiency, and General Applicability

NASA Astrophysics Data System (ADS)

Erhard, Jannis; Bleiziffer, Patrick; Görling, Andreas

2016-09-01

A power series approximation for the correlation kernel of time-dependent density-functional theory is presented. Using this approximation in the adiabatic-connection fluctuation-dissipation (ACFD) theorem leads to a new family of Kohn-Sham methods. The new methods yield reaction energies and barriers of unprecedented accuracy and enable a treatment of static (strong) correlation with an accuracy of high-level multireference configuration interaction methods but are single-reference methods allowing for a black-box-like handling of static correlation. The new methods exhibit a better scaling of the computational effort with the system size than rivaling wave-function-based electronic structure methods. Moreover, the new methods do not suffer from the problem of singularities in response functions plaguing previous ACFD methods and therefore are applicable to any type of electronic system.

Two-body Schrödinger wave functions in a plane-wave basis via separation of dimensions

NASA Astrophysics Data System (ADS)

Jerke, Jonathan; Poirier, Bill

2018-03-01

Using a combination of ideas, the ground and several excited electronic states of the helium atom and the hydrogen molecule are computed to chemical accuracy—i.e., to within 1-2 mhartree or better. The basic strategy is very different from the standard electronic structure approach in that the full two-electron six-dimensional (6D) problem is tackled directly, rather than starting from a single-electron Hartree-Fock approximation. Electron correlation is thus treated exactly, even though computational requirements remain modest. The method also allows for exact wave functions to be computed, as well as energy levels. From the full-dimensional 6D wave functions computed here, radial distribution functions and radial correlation functions are extracted—as well as a 2D probability density function exhibiting antisymmetry for a single Cartesian component. These calculations support a more recent interpretation of Hund's rule, which states that the lower energy of the higher spin-multiplicity states is actually due to reduced screening, rather than reduced electron-electron repulsion. Prospects for larger systems and/or electron dynamics applications appear promising.

Two-body Schrödinger wave functions in a plane-wave basis via separation of dimensions.

PubMed

Jerke, Jonathan; Poirier, Bill

2018-03-14

Using a combination of ideas, the ground and several excited electronic states of the helium atom and the hydrogen molecule are computed to chemical accuracy-i.e., to within 1-2 mhartree or better. The basic strategy is very different from the standard electronic structure approach in that the full two-electron six-dimensional (6D) problem is tackled directly, rather than starting from a single-electron Hartree-Fock approximation. Electron correlation is thus treated exactly, even though computational requirements remain modest. The method also allows for exact wave functions to be computed, as well as energy levels. From the full-dimensional 6D wave functions computed here, radial distribution functions and radial correlation functions are extracted-as well as a 2D probability density function exhibiting antisymmetry for a single Cartesian component. These calculations support a more recent interpretation of Hund's rule, which states that the lower energy of the higher spin-multiplicity states is actually due to reduced screening, rather than reduced electron-electron repulsion. Prospects for larger systems and/or electron dynamics applications appear promising.

Ways to improve your correlation functions

NASA Technical Reports Server (NTRS)

Hamilton, A. J. S.

1993-01-01

This paper describes a number of ways to improve on the standard method for measuring the two-point correlation function of large scale structure in the Universe. Issues addressed are: (1) the problem of the mean density, and how to solve it; (2) how to estimate the uncertainty in a measured correlation function; (3) minimum variance pair weighting; (4) unbiased estimation of the selection function when magnitudes are discrete; and (5) analytic computation of angular integrals in background pair counts.

ALMA Correlator Real-Time Data Processor

NASA Astrophysics Data System (ADS)

Pisano, J.; Amestica, R.; Perez, J.

2005-10-01

The design of a real-time Linux application utilizing Real-Time Application Interface (RTAI) to process real-time data from the radio astronomy correlator for the Atacama Large Millimeter Array (ALMA) is described. The correlator is a custom-built digital signal processor which computes the cross-correlation function of two digitized signal streams. ALMA will have 64 antennas with 2080 signal streams each with a sample rate of 4 giga-samples per second. The correlator's aggregate data output will be 1 gigabyte per second. The software is defined by hard deadlines with high input and processing data rates, while requiring interfaces to non real-time external computers. The designed computer system - the Correlator Data Processor or CDP, consists of a cluster of 17 SMP computers, 16 of which are compute nodes plus a master controller node all running real-time Linux kernels. Each compute node uses an RTAI kernel module to interface to a 32-bit parallel interface which accepts raw data at 64 megabytes per second in 1 megabyte chunks every 16 milliseconds. These data are transferred to tasks running on multiple CPUs in hard real-time using RTAI's LXRT facility to perform quantization corrections, data windowing, FFTs, and phase corrections for a processing rate of approximately 1 GFLOPS. Highly accurate timing signals are distributed to all seventeen computer nodes in order to synchronize them to other time-dependent devices in the observatory array. RTAI kernel tasks interface to the timing signals providing sub-millisecond timing resolution. The CDP interfaces, via the master node, to other computer systems on an external intra-net for command and control, data storage, and further data (image) processing. The master node accesses these external systems utilizing ALMA Common Software (ACS), a CORBA-based client-server software infrastructure providing logging, monitoring, data delivery, and intra-computer function invocation. The software is being developed in tandem with the correlator hardware which presents software engineering challenges as the hardware evolves. The current status of this project and future goals are also presented.

Relative velocity change measurement based on seismic noise analysis in exploration geophysics

NASA Astrophysics Data System (ADS)

Corciulo, M.; Roux, P.; Campillo, M.; Dubuq, D.

2011-12-01

Passive monitoring techniques based on noise cross-correlation analysis are still debated in exploration geophysics even if recent studies showed impressive performance in seismology at larger scale. Time evolution of complex geological structure using noise data includes localization of noise sources and measurement of relative velocity variations. Monitoring relative velocity variations only requires the measurement of phase shifts of seismic noise cross-correlation functions computed for successive time recordings. The existing algorithms, such as the Stretching and the Doublet, classically need great efforts in terms of computation time, making them not practical when continuous dataset on dense arrays are acquired. We present here an innovative technique for passive monitoring based on the measure of the instantaneous phase of noise-correlated signals. The Instantaneous Phase Variation (IPV) technique aims at cumulating the advantages of the Stretching and Doublet methods while proposing a faster measurement of the relative velocity change. The IPV takes advantage of the Hilbert transform to compute in the time domain the phase difference between two noise correlation functions. The relative velocity variation is measured through the slope of the linear regression of the phase difference curve as a function of correlation time. The large amount of noise correlation functions, classically available at exploration scale on dense arrays, allows for a statistical analysis that further improves the precision of the estimation of the velocity change. In this work, numerical tests first aim at comparing the IPV performance to the Stretching and Doublet techniques in terms of accuracy, robustness and computation time. Then experimental results are presented using a seismic noise dataset with five days of continuous recording on 397 geophones spread on a ~1 km-squared area.

Elucidation of spin echo small angle neutron scattering correlation functions through model studies.

PubMed

Shew, Chwen-Yang; Chen, Wei-Ren

2012-02-14

Several single-modal Debye correlation functions to approximate part of the overall Debey correlation function of liquids are closely examined for elucidating their behavior in the corresponding spin echo small angle neutron scattering (SESANS) correlation functions. We find that the maximum length scale of a Debye correlation function is identical to that of its SESANS correlation function. For discrete Debye correlation functions, the peak of SESANS correlation function emerges at their first discrete point, whereas for continuous Debye correlation functions with greater width, the peak position shifts to a greater value. In both cases, the intensity and shape of the peak of the SESANS correlation function are determined by the width of the Debye correlation functions. Furthermore, we mimic the intramolecular and intermolecular Debye correlation functions of liquids composed of interacting particles based on a simple model to elucidate their competition in the SESANS correlation function. Our calculations show that the first local minimum of a SESANS correlation function can be negative and positive. By adjusting the spatial distribution of the intermolecular Debye function in the model, the calculated SESANS spectra exhibit the profile consistent with that of hard-sphere and sticky-hard-sphere liquids predicted by more sophisticated liquid state theory and computer simulation. © 2012 American Institute of Physics

Generating series for GUE correlators

NASA Astrophysics Data System (ADS)

Dubrovin, Boris; Yang, Di

2017-11-01

We extend to the Toda lattice hierarchy the approach of Bertola et al. (Phys D Nonlinear Phenom 327:30-57, 2016; IMRN, 2016) to computation of logarithmic derivatives of tau-functions in terms of the so-called matrix resolvents of the corresponding difference Lax operator. As a particular application we obtain explicit generating series for connected GUE correlators. On this basis an efficient recursive procedure for computing the correlators in full genera is developed.

Kinetic theory of coupled oscillators.

PubMed

Hildebrand, Eric J; Buice, Michael A; Chow, Carson C

2007-02-02

We present an approach for the description of fluctuations that are due to finite system size induced correlations in the Kuramoto model of coupled oscillators. We construct a hierarchy for the moments of the density of oscillators that is analogous to the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy in the kinetic theory of plasmas and gases. To calculate the lowest order system size effect, we truncate this hierarchy at second order and solve the resulting closed equations for the two-oscillator correlation function around the incoherent state. We use this correlation function to compute the fluctuations of the order parameter, including the effect of transients, and compare this computation with numerical simulations.

Spatial distribution of nuclei in progressive nucleation: Modeling and application

NASA Astrophysics Data System (ADS)

Tomellini, Massimo

2018-04-01

Phase transformations ruled by non-simultaneous nucleation and growth do not lead to random distribution of nuclei. Since nucleation is only allowed in the untransformed portion of space, positions of nuclei are correlated. In this article an analytical approach is presented for computing pair-correlation function of nuclei in progressive nucleation. This quantity is further employed for characterizing the spatial distribution of nuclei through the nearest neighbor distribution function. The modeling is developed for nucleation in 2D space with power growth law and it is applied to describe electrochemical nucleation where correlation effects are significant. Comparison with both computer simulations and experimental data lends support to the model which gives insights into the transition from Poissonian to correlated nearest neighbor probability density.

When can Empirical Green Functions be computed from Noise Cross-Correlations? Hints from different Geographical and Tectonic environments

NASA Astrophysics Data System (ADS)

Matos, Catarina; Silveira, Graça; Custódio, Susana; Domingues, Ana; Dias, Nuno; Fonseca, João F. B.; Matias, Luís; Krueger, Frank; Carrilho, Fernando

2014-05-01

Noise cross-correlations are now widely used to extract Green functions between station pairs. But, do all the cross-correlations routinely computed produce successful Green Functions? What is the relationship between noise recorded in a couple of stations and the cross-correlation between them? During the last decade, we have been involved in the deployment of several temporary dense broadband (BB) networks within the scope of both national projects and international collaborations. From 2000 to 2002, a pool of 8 BB stations continuously operated in the Azores in the scope of the Memorandum of Understanding COSEA (COordinated Seismic Experiment in the Azores). Thanks to the Project WILAS (West Iberia Lithosphere and Astenosphere Structure, PTDC/CTE-GIX/097946/2008) we temporarily increased the number of BB deployed in mainland Portugal to more than 50 (permanent + temporary) during the period 2010 - 2012. In 2011/12 a temporary pool of 12 seismometers continuously recorded BB data in the Madeira archipelago, as part of the DOCTAR (Deep Ocean Test Array Experiment) project. Project CV-PLUME (Investigation on the geometry and deep signature of the Cape Verde mantle plume, PTDC/CTE-GIN/64330/2006) covered the archipelago of Cape Verde, North Atlantic, with 40 temporary BB stations in 2007/08. Project MOZART (Mozambique African Rift Tomography, PTDC/CTE-GIX/103249/2008), covered Mozambique, East Africa, with 30 temporary BB stations in the period 2011 - 2013. These networks, located in very distinct geographical and tectonic environments, offer an interesting opportunity to study seasonal and spatial variations of noise sources and their impact on Empirical Green functions computed from noise cross-correlation. Seismic noise recorded at different seismic stations is evaluated by computation of the probability density functions of power spectral density (PSD) of continuous data. To assess seasonal variations of ambient noise sources in frequency content, time-series of PSD at different frequency bands have been computed. The influence of the spatial and seasonal variation is evaluated by analysis of the one-day length cross-correlations, stacked with a 30-day moving window and with an overlap of 30 days. To inspect the effects of frequency content variations, 30-day cross-correlograms have also been computed at different frequency bands. This work is supported by project QuakeLoc-PT (PTDC/GEO-FIQ/3522/2012) and a contribution to project AQUAREL (PTDC/CTE-GIX/116819/2010).

PERFORMANCE OF A COMPUTER-BASED ASSESSMENT OF COGNITIVE FUNCTION MEASURES IN TWO COHORTS OF SENIORS

PubMed Central

Espeland, Mark A.; Katula, Jeffrey A.; Rushing, Julia; Kramer, Arthur F.; Jennings, Janine M.; Sink, Kaycee M.; Nadkarni, Neelesh K.; Reid, Kieran F.; Castro, Cynthia M.; Church, Timothy; Kerwin, Diana R.; Williamson, Jeff D.; Marottoli, Richard A.; Rushing, Scott; Marsiske, Michael; Rapp, Stephen R.

2013-01-01

Background Computer-administered assessment of cognitive function is being increasingly incorporated in clinical trials, however its performance in these settings has not been systematically evaluated. Design The Seniors Health and Activity Research Program (SHARP) pilot trial (N=73) developed a computer-based tool for assessing memory performance and executive functioning. The Lifestyle Interventions and Independence for Seniors (LIFE) investigators incorporated this battery in a full scale multicenter clinical trial (N=1635). We describe relationships that test scores have with those from interviewer-administered cognitive function tests and risk factors for cognitive deficits and describe performance measures (completeness, intra-class correlations). Results Computer-based assessments of cognitive function had consistent relationships across the pilot and full scale trial cohorts with interviewer-administered assessments of cognitive function, age, and a measure of physical function. In the LIFE cohort, their external validity was further demonstrated by associations with other risk factors for cognitive dysfunction: education, hypertension, diabetes, and physical function. Acceptable levels of data completeness (>83%) were achieved on all computer-based measures, however rates of missing data were higher among older participants (odds ratio=1.06 for each additional year; p<0.001) and those who reported no current computer use (odds ratio=2.71; p<0.001). Intra-class correlations among clinics were at least as low (ICC≤0.013) as for interviewer measures (ICC≤0.023), reflecting good standardization. All cognitive measures loaded onto the first principal component (global cognitive function), which accounted for 40% of the overall variance. Conclusion Our results support the use of computer-based tools for assessing cognitive function in multicenter clinical trials of older individuals. PMID:23589390

Universal RCFT correlators from the holomorphic bootstrap

NASA Astrophysics Data System (ADS)

Mukhi, Sunil; Muralidhara, Girish

2018-02-01

We elaborate and extend the method of Wronskian differential equations for conformal blocks to compute four-point correlation functions on the plane for classes of primary fields in rational (and possibly more general) conformal field theories. This approach leads to universal differential equations for families of CFT's and provides a very simple re-derivation of the BPZ results for the degenerate fields ϕ 1,2 and ϕ 2,1 in the c < 1 minimal models. We apply this technique to compute correlators for the WZW models corresponding to the Deligne-Cvitanović exceptional series of Lie algebras. The application turns out to be subtle in certain cases where there are multiple decoupled primaries. The power of this approach is demonstrated by applying it to compute four-point functions for the Baby Monster CFT, which does not belong to any minimal series.

Computed tomographic-based quantification of emphysema and correlation to pulmonary function and mechanics.

PubMed

Washko, George R; Criner, Gerald J; Mohsenifar, Zab; Sciurba, Frank C; Sharafkhaneh, Amir; Make, Barry J; Hoffman, Eric A; Reilly, John J

2008-06-01

Computed tomographic based indices of emphysematous lung destruction may highlight differences in disease pathogenesis and further enable the classification of subjects with Chronic Obstructive Pulmonary Disease. While there are multiple techniques that can be utilized for such radiographic analysis, there is very little published information comparing the performance of these methods in a clinical case series. Our objective was to examine several quantitative and semi-quantitative methods for the assessment of the burden of emphysema apparent on computed tomographic scans and compare their ability to predict lung mechanics and function. Automated densitometric analysis was performed on 1094 computed tomographic scans collected upon enrollment into the National Emphysema Treatment Trial. Trained radiologists performed an additional visual grading of emphysema on high resolution CT scans. Full pulmonary function test results were available for correlation, with a subset of subjects having additional measurements of lung static recoil. There was a wide range of emphysematous lung destruction apparent on the CT scans and univariate correlations to measures of lung function were of modest strength. No single method of CT scan analysis clearly outperformed the rest of the group. Quantification of the burden of emphysematous lung destruction apparent on CT scan is a weak predictor of lung function and mechanics in severe COPD with no uniformly superior method found to perform this analysis. The CT based quantification of emphysema may augment pulmonary function testing in the characterization of COPD by providing complementary phenotypic information.

One-dimensional Euclidean matching problem: exact solutions, correlation functions, and universality.

PubMed

Caracciolo, Sergio; Sicuro, Gabriele

2014-10-01

We discuss the equivalence relation between the Euclidean bipartite matching problem on the line and on the circumference and the Brownian bridge process on the same domains. The equivalence allows us to compute the correlation function and the optimal cost of the original combinatorial problem in the thermodynamic limit; moreover, we solve also the minimax problem on the line and on the circumference. The properties of the average cost and correlation functions are discussed.

Mapping the current–current correlation function near a quantum critical point

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

Prodan, Emil, E-mail: prodan@yu.edu; Bellissard, Jean

2016-05-15

The current–current correlation function is a useful concept in the theory of electron transport in homogeneous solids. The finite-temperature conductivity tensor as well as Anderson’s localization length can be computed entirely from this correlation function. Based on the critical behavior of these two physical quantities near the plateau–insulator or plateau–plateau transitions in the integer quantum Hall effect, we derive an asymptotic formula for the current–current correlation function, which enables us to make several theoretical predictions about its generic behavior. For the disordered Hofstadter model, we employ numerical simulations to map the current–current correlation function, obtain its asymptotic form near amore » critical point and confirm the theoretical predictions.« less

Nonequilibrium fluctuations in metaphase spindles: polarized light microscopy, image registration, and correlation functions

NASA Astrophysics Data System (ADS)

Brugués, Jan; Needleman, Daniel J.

2010-02-01

Metaphase spindles are highly dynamic, nonequilibrium, steady-state structures. We study the internal fluctuations of spindles by computing spatio-temporal correlation functions of movies obtained from quantitative polarized light microscopy. These correlation functions are only physically meaningful if corrections are made for the net motion of the spindle. We describe our image registration algorithm in detail and we explore its robustness. Finally, we discuss the expression used for the estimation of the correlation function in terms of the nematic order of the microtubules which make up the spindle. Ultimately, studying the form of these correlation functions will provide a quantitative test of the validity of coarse-grained models of spindle structure inspired from liquid crystal physics.

ESTIMATION OF FUNCTIONALS OF SPARSE COVARIANCE MATRICES.

PubMed

Fan, Jianqing; Rigollet, Philippe; Wang, Weichen

High-dimensional statistical tests often ignore correlations to gain simplicity and stability leading to null distributions that depend on functionals of correlation matrices such as their Frobenius norm and other ℓ r norms. Motivated by the computation of critical values of such tests, we investigate the difficulty of estimation the functionals of sparse correlation matrices. Specifically, we show that simple plug-in procedures based on thresholded estimators of correlation matrices are sparsity-adaptive and minimax optimal over a large class of correlation matrices. Akin to previous results on functional estimation, the minimax rates exhibit an elbow phenomenon. Our results are further illustrated in simulated data as well as an empirical study of data arising in financial econometrics.

ESTIMATION OF FUNCTIONALS OF SPARSE COVARIANCE MATRICES

PubMed Central

Fan, Jianqing; Rigollet, Philippe; Wang, Weichen

2016-01-01

High-dimensional statistical tests often ignore correlations to gain simplicity and stability leading to null distributions that depend on functionals of correlation matrices such as their Frobenius norm and other ℓr norms. Motivated by the computation of critical values of such tests, we investigate the difficulty of estimation the functionals of sparse correlation matrices. Specifically, we show that simple plug-in procedures based on thresholded estimators of correlation matrices are sparsity-adaptive and minimax optimal over a large class of correlation matrices. Akin to previous results on functional estimation, the minimax rates exhibit an elbow phenomenon. Our results are further illustrated in simulated data as well as an empirical study of data arising in financial econometrics. PMID:26806986

A simplified implementation of van der Waals density functionals for first-principles molecular dynamics applications

NASA Astrophysics Data System (ADS)

Wu, Jun; Gygi, François

2012-06-01

We present a simplified implementation of the non-local van der Waals correlation functional introduced by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)] and reformulated by Román-Pérez et al. [Phys. Rev. Lett. 103, 096102 (2009)]. The proposed numerical approach removes the logarithmic singularity of the kernel function. Complete expressions of the self-consistent correlation potential and of the stress tensor are given. Combined with various choices of exchange functionals, five versions of van der Waals density functionals are implemented. Applications to the computation of the interaction energy of the benzene-water complex and to the computation of the equilibrium cell parameters of the benzene crystal are presented. As an example of crystal structure calculation involving a mixture of hydrogen bonding and dispersion interactions, we compute the equilibrium structure of two polymorphs of aspirin (2-acetoxybenzoic acid, C9H8O4) in the P21/c monoclinic structure.

Efficient construction of exchange and correlation potentials by inverting the Kohn-Sham equations.

PubMed

Kananenka, Alexei A; Kohut, Sviataslau V; Gaiduk, Alex P; Ryabinkin, Ilya G; Staroverov, Viktor N

2013-08-21

Given a set of canonical Kohn-Sham orbitals, orbital energies, and an external potential for a many-electron system, one can invert the Kohn-Sham equations in a single step to obtain the corresponding exchange-correlation potential, vXC(r). For orbitals and orbital energies that are solutions of the Kohn-Sham equations with a multiplicative vXC(r) this procedure recovers vXC(r) (in the basis set limit), but for eigenfunctions of a non-multiplicative one-electron operator it produces an orbital-averaged potential. In particular, substitution of Hartree-Fock orbitals and eigenvalues into the Kohn-Sham inversion formula is a fast way to compute the Slater potential. In the same way, we efficiently construct orbital-averaged exchange and correlation potentials for hybrid and kinetic-energy-density-dependent functionals. We also show how the Kohn-Sham inversion approach can be used to compute functional derivatives of explicit density functionals and to approximate functional derivatives of orbital-dependent functionals.

Initial state q q g correlations as a background for the chiral magnetic effect in collision of small systems

DOE PAGES

Kovner, Alex; Lublinsky, Michael; Skokov, Vladimir

2017-11-13

Motivated by understanding the background to chiral magnetic effect in proton-nucleus collisions from first principles, we compute the three particle correlation in the projectile wave function. We extract the correlations between two quarks and one gluon in the framework of the color glass condensate. This is related to the same-charge correlation of the conventional observable for the chiral magnetic effect. We show that there are two different contributions to this correlation function. One contribution is rapidity-independent and as such can be identified with the pedestal; while the other displays rather strong rapidity dependence. The pedestal contribution and the rapidity-dependent contributionmore » at large rapidity separation between the two quarks result in the negative same charge correlations, while at small rapidity separation the second contribution changes sign. We argue that the computed initial state correlations might be partially responsible for the experimentally observed signal in proton-nucleus collisions.« less

Initial state q q g correlations as a background for the chiral magnetic effect in collision of small systems

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

Kovner, Alex; Lublinsky, Michael; Skokov, Vladimir

Motivated by understanding the background to chiral magnetic effect in proton-nucleus collisions from first principles, we compute the three particle correlation in the projectile wave function. We extract the correlations between two quarks and one gluon in the framework of the color glass condensate. This is related to the same-charge correlation of the conventional observable for the chiral magnetic effect. We show that there are two different contributions to this correlation function. One contribution is rapidity-independent and as such can be identified with the pedestal; while the other displays rather strong rapidity dependence. The pedestal contribution and the rapidity-dependent contributionmore » at large rapidity separation between the two quarks result in the negative same charge correlations, while at small rapidity separation the second contribution changes sign. We argue that the computed initial state correlations might be partially responsible for the experimentally observed signal in proton-nucleus collisions.« less

Initial state q q g correlations as a background for the chiral magnetic effect in collision of small systems

NASA Astrophysics Data System (ADS)

Kovner, Alex; Lublinsky, Michael; Skokov, Vladimir

2017-11-01

Motivated by understanding the background to chiral magnetic effect in proton-nucleus collisions from first principles, we compute the three particle correlation in the projectile wave function. We extract the correlations between two quarks and one gluon in the framework of the color glass condensate. This is related to the same-charge correlation of the conventional observable for the chiral magnetic effect. We show that there are two different contributions to this correlation function. One contribution is rapidity-independent and as such can be identified with the pedestal; while the other displays rather strong rapidity dependence. The pedestal contribution and the rapidity-dependent contribution at large rapidity separation between the two quarks result in the negative same charge correlations, while at small rapidity separation the second contribution changes sign. We argue that the computed initial state correlations might be partially responsible for the experimentally observed signal in proton-nucleus collisions.

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

Williams, Brian J.; Marcy, Peter W.

We will investigate the use of derivative information in complex computer model emulation when the correlation function is of the compactly supported Bohman class. To this end, a Gaussian process model similar to that used by Kaufman et al. (2011) is extended to a situation where first partial derivatives in each dimension are calculated at each input site (i.e. using gradients). A simulation study in the ten-dimensional case is conducted to assess the utility of the Bohman correlation function against strictly positive correlation functions when a high degree of sparsity is induced.

Mitigating the impact of the DESI fiber assignment on galaxy clustering

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

Burden, Angela; Padmanabhan, Nikhil; Cahn, Robert N.

2017-03-01

We present a simple strategy to mitigate the impact of an incomplete spectroscopic redshift galaxy sample as a result of fiber assignment and survey tiling. The method has been designed for the Dark Energy Spectroscopic Instrument (DESI) galaxy survey but may have applications beyond this. We propose a modification to the usual correlation function that nulls the almost purely angular modes affected by survey incompleteness due to fiber assignment. Predictions of this modified statistic can be calculated given a model of the two point correlation function. The new statistic can be computed with a slight modification to the data cataloguesmore » input to the standard correlation function code and does not incur any additional computational time. Finally we show that the spherically averaged baryon acoustic oscillation signal is not biased by the new statistic.« less

Optical Implementation Of The Synthetic Discrimination Function

NASA Astrophysics Data System (ADS)

Butler, Steve; Riggins, James

1985-01-01

Computer-generated holograms of geometrical shape and synthetic discriminant function (SDF) matched filters are modeled and produced. The models include ideal correlations and Allebach-Keegan binary holograms. A distinction between Phase-Only-Information and Phase-Only-Material Filters is demonstrated. Signal-to-noise and efficiency measurements were made on the resultant correlation planes.

Penalized weighted least-squares approach for low-dose x-ray computed tomography

NASA Astrophysics Data System (ADS)

Wang, Jing; Li, Tianfang; Lu, Hongbing; Liang, Zhengrong

2006-03-01

The noise of low-dose computed tomography (CT) sinogram follows approximately a Gaussian distribution with nonlinear dependence between the sample mean and variance. The noise is statistically uncorrelated among detector bins at any view angle. However the correlation coefficient matrix of data signal indicates a strong signal correlation among neighboring views. Based on above observations, Karhunen-Loeve (KL) transform can be used to de-correlate the signal among the neighboring views. In each KL component, a penalized weighted least-squares (PWLS) objective function can be constructed and optimal sinogram can be estimated by minimizing the objective function, followed by filtered backprojection (FBP) for CT image reconstruction. In this work, we compared the KL-PWLS method with an iterative image reconstruction algorithm, which uses the Gauss-Seidel iterative calculation to minimize the PWLS objective function in image domain. We also compared the KL-PWLS with an iterative sinogram smoothing algorithm, which uses the iterated conditional mode calculation to minimize the PWLS objective function in sinogram space, followed by FBP for image reconstruction. Phantom experiments show a comparable performance of these three PWLS methods in suppressing the noise-induced artifacts and preserving resolution in reconstructed images. Computer simulation concurs with the phantom experiments in terms of noise-resolution tradeoff and detectability in low contrast environment. The KL-PWLS noise reduction may have the advantage in computation for low-dose CT imaging, especially for dynamic high-resolution studies.

On the role of structure-dynamic relationship in determining the excess entropy of mixing and chemical ordering in binary square-well liquid alloys

NASA Astrophysics Data System (ADS)

Lalneihpuii, R.; Shrivastava, Ruchi; Mishra, Raj Kumar

2018-05-01

Using statistical mechanical model with square-well (SW) interatomic potential within the frame work of mean spherical approximation, we determine the composition dependent microscopic correlation functions, interdiffusion coefficients, surface tension and chemical ordering in Ag-Cu melts. Further Dzugutov universal scaling law of normalized diffusion is verified with SW potential in binary mixtures. We find that the excess entropy scaling law is valid for SW binary melts. The partial and total structure factors in the attractive and repulsive regions of the interacting potential are evaluated and then Fourier transformed to get partial and total radial distribution functions. A good agreement between theoretical and experimental values for total structure factor and the reduced radial distribution function are observed, which consolidates our model calculations. The well-known Bhatia-Thornton correlation functions are also computed for Ag-Cu melts. The concentration-concentration correlations in the long wavelength limit in liquid Ag-Cu alloys have been analytically derived through the long wavelength limit of partial correlation functions and apply it to demonstrate the chemical ordering and interdiffusion coefficients in binary liquid alloys. We also investigate the concentration dependent viscosity coefficients and surface tension using the computed diffusion data in these alloys. Our computed results for structure, transport and surface properties of liquid Ag-Cu alloys obtained with square-well interatomic interaction are fully consistent with their corresponding experimental values.

A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

PubMed

Hirano, Toshiyuki; Sato, Fumitoshi

2014-07-28

We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

Effect of addiction to computer games on physical and mental health of female and male students of guidance school in city of isfahan.

PubMed

Zamani, Eshrat; Chashmi, Maliheh; Hedayati, Nasim

2009-01-01

This study aimed to investigate the effects of addiction to computer games on physical and mental health of students. The study population includes all students in the second year of public guidance schools in the city of Isfahan in the educational year of 2009-2010. The sample size includes 564 students selected by multiple steps stratified sampling. Dependent variables include general health in dimensions of physical health, anxiety and sleeplessness and impaired social functioning. Data were collected using General Health Questionnaire (GHQ-28) scale and a questionnaire on addiction to computer games. Pearson's correlation coefficient and structural model were used for data analysis. There was a significant positive correlation between students' computer games addiction and their physical and mental health in dimensions of physical health, anxiety and sleeplessness There was a significant negative relationship between addictions to computer games and impaired social functioning. The results of this study are in agreement with the findings of other studies around the world. As the results show, addiction to computer games affects various dimensions of health and increases physical problems, anxiety and depression, while decreases social functioning disorder.

Effect of Addiction to Computer Games on Physical and Mental Health of Female and Male Students of Guidance School in City of Isfahan

PubMed Central

Zamani, Eshrat; Chashmi, Maliheh; Hedayati, Nasim

2009-01-01

Background: This study aimed to investigate the effects of addiction to computer games on physical and mental health of students. Methods: The study population includes all students in the second year of public guidance schools in the city of Isfahan in the educational year of 2009-2010. The sample size includes 564 students selected by multiple steps stratified sampling. Dependent variables include general health in dimensions of physical health, anxiety and sleeplessness and impaired social functioning. Data were collected using General Health Questionnaire (GHQ-28) scale and a questionnaire on addiction to computer games. Pearson's correlation coefficient and structural model were used for data analysis. Findings: There was a significant positive correlation between students' computer games addiction and their physical and mental health in dimensions of physical health, anxiety and sleeplessness There was a significant negative relationship between addictions to computer games and impaired social functioning. Conclusion: The results of this study are in agreement with the findings of other studies around the world. As the results show, addiction to computer games affects various dimensions of health and increases physical problems, anxiety and depression, while decreases social functioning disorder. PMID:24494091

Correlation between the signal-to-noise ratio improvement factor (KSNR) and clinical image quality for chest imaging with a computed radiography system

NASA Astrophysics Data System (ADS)

Moore, C. S.; Wood, T. J.; Saunderson, J. R.; Beavis, A. W.

2015-12-01

This work assessed the appropriateness of the signal-to-noise ratio improvement factor (KSNR) as a metric for the optimisation of computed radiography (CR) of the chest. The results of a previous study in which four experienced image evaluators graded computer simulated chest images using a visual grading analysis scoring (VGAS) scheme to quantify the benefit of using an anti-scatter grid were used for the clinical image quality measurement (number of simulated patients  =  80). The KSNR was used to calculate the improvement in physical image quality measured in a physical chest phantom. KSNR correlation with VGAS was assessed as a function of chest region (lung, spine and diaphragm/retrodiaphragm), and as a function of x-ray tube voltage in a given chest region. The correlation of the latter was determined by the Pearson correlation coefficient. VGAS and KSNR image quality metrics demonstrated no correlation in the lung region but did show correlation in the spine and diaphragm/retrodiaphragmatic regions. However, there was no correlation as a function of tube voltage in any region; a Pearson correlation coefficient (R) of  -0.93 (p  =  0.015) was found for lung, a coefficient (R) of  -0.95 (p  =  0.46) was found for spine, and a coefficient (R) of  -0.85 (p  =  0.015) was found for diaphragm. All demonstrate strong negative correlations indicating conflicting results, i.e. KSNR increases with tube voltage but VGAS decreases. Medical physicists should use the KSNR metric with caution when assessing any potential improvement in clinical chest image quality when introducing an anti-scatter grid for CR imaging, especially in the lung region. This metric may also be a limited descriptor of clinical chest image quality as a function of tube voltage when a grid is used routinely.

Spectral functions of strongly correlated extended systems via an exact quantum embedding

NASA Astrophysics Data System (ADS)

Booth, George H.; Chan, Garnet Kin-Lic

2015-04-01

Density matrix embedding theory (DMET) [Phys. Rev. Lett. 109, 186404 (2012), 10.1103/PhysRevLett.109.186404], introduced an approach to quantum cluster embedding methods whereby the mapping of strongly correlated bulk problems to an impurity with finite set of bath states was rigorously formulated to exactly reproduce the entanglement of the ground state. The formalism provided similar physics to dynamical mean-field theory at a tiny fraction of the cost but was inherently limited by the construction of a bath designed to reproduce ground-state, static properties. Here, we generalize the concept of quantum embedding to dynamic properties and demonstrate accurate bulk spectral functions at similarly small computational cost. The proposed spectral DMET utilizes the Schmidt decomposition of a response vector, mapping the bulk dynamic correlation functions to that of a quantum impurity cluster coupled to a set of frequency-dependent bath states. The resultant spectral functions are obtained on the real-frequency axis, without bath discretization error, and allows for the construction of arbitrary dynamic correlation functions. We demonstrate the method on the one- (1D) and two-dimensional (2D) Hubbard model, where we obtain zero temperature and thermodynamic limit spectral functions, and show the trivial extension to two-particle Green's functions. This advance therefore extends the scope and applicability of DMET in condensed-matter problems as a computationally tractable route to correlated spectral functions of extended systems and provides a competitive alternative to dynamical mean-field theory for dynamic quantities.

Commercial counterboard for 10 ns software correlator for photon and fluorescence correlation spectroscopy.

PubMed

Molteni, Matteo; Ferri, Fabio

2016-11-01

A 10 ns time resolution, multi-tau software correlator, capable of computing simultaneous autocorrelation (A-A, B-B) and cross (A-B) correlation functions at count rates up to ∼10 MHz, with no data loss, has been developed in LabVIEW and C++ by using the National Instrument timer/counterboard (NI PCIe-6612) and a fast Personal Computer (PC) (Intel Core i7-4790 Processor 3.60 GHz ). The correlator works by using two algorithms: for large lag times (τ ≳ 1 μs), a classical time-mode scheme, based on the measure of the number of pulses per time interval, is used; differently, for τ ≲ 1 μs a photon-mode (PM) scheme is adopted and the correlation function is retrieved from the sequence of the photon arrival times. Single auto- and cross-correlation functions can be processed online in full real time up to count rates of ∼1.8 MHz and ∼1.2 MHz, respectively. Two autocorrelation (A-A, B-B) and a cross correlation (A-B) functions can be simultaneously processed in full real time only up to count rates of ∼750 kHz. At higher count rates, the online processing takes place in a delayed modality, but with no data loss. When tested with simulated correlation data and latex spheres solutions, the overall performances of the correlator appear to be comparable with those of commercial hardware correlators, but with several nontrivial advantages related to its flexibility, low cost, and easy adaptability to future developments of PC and data acquisition technology.

Commercial counterboard for 10 ns software correlator for photon and fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Molteni, Matteo; Ferri, Fabio

2016-11-01

A 10 ns time resolution, multi-tau software correlator, capable of computing simultaneous autocorrelation (A-A, B-B) and cross (A-B) correlation functions at count rates up to ˜10 MHz, with no data loss, has been developed in LabVIEW and C++ by using the National Instrument timer/counterboard (NI PCIe-6612) and a fast Personal Computer (PC) (Intel Core i7-4790 Processor 3.60 GHz ). The correlator works by using two algorithms: for large lag times (τ ≳ 1 μs), a classical time-mode scheme, based on the measure of the number of pulses per time interval, is used; differently, for τ ≲ 1 μs a photon-mode (PM) scheme is adopted and the correlation function is retrieved from the sequence of the photon arrival times. Single auto- and cross-correlation functions can be processed online in full real time up to count rates of ˜1.8 MHz and ˜1.2 MHz, respectively. Two autocorrelation (A-A, B-B) and a cross correlation (A-B) functions can be simultaneously processed in full real time only up to count rates of ˜750 kHz. At higher count rates, the online processing takes place in a delayed modality, but with no data loss. When tested with simulated correlation data and latex spheres solutions, the overall performances of the correlator appear to be comparable with those of commercial hardware correlators, but with several nontrivial advantages related to its flexibility, low cost, and easy adaptability to future developments of PC and data acquisition technology.

Large-angle correlations in the cosmic microwave background

NASA Astrophysics Data System (ADS)

Efstathiou, George; Ma, Yin-Zhe; Hanson, Duncan

2010-10-01

It has been argued recently by Copi et al. 2009 that the lack of large angular correlations of the CMB temperature field provides strong evidence against the standard, statistically isotropic, inflationary Lambda cold dark matter (ΛCDM) cosmology. We compare various estimators of the temperature correlation function showing how they depend on assumptions of statistical isotropy and how they perform on the Wilkinson Microwave Anisotropy Probe (WMAP) 5-yr Internal Linear Combination (ILC) maps with and without a sky cut. We show that the low multipole harmonics that determine the large-scale features of the temperature correlation function can be reconstructed accurately from the data that lie outside the sky cuts. The reconstructions are only weakly dependent on the assumed statistical properties of the temperature field. The temperature correlation functions computed from these reconstructions are in good agreement with those computed from the ILC map over the whole sky. We conclude that the large-scale angular correlation function for our realization of the sky is well determined. A Bayesian analysis of the large-scale correlations is presented, which shows that the data cannot exclude the standard ΛCDM model. We discuss the differences between our results and those of Copi et al. Either there exists a violation of statistical isotropy as claimed by Copi et al., or these authors have overestimated the significance of the discrepancy because of a posteriori choices of estimator, statistic and sky cut.

Function Package for Computing Quantum Resource Measures

NASA Astrophysics Data System (ADS)

Huang, Zhiming

2018-05-01

In this paper, we present a function package for to calculate quantum resource measures and dynamics of open systems. Our package includes common operators and operator lists, frequently-used functions for computing quantum entanglement, quantum correlation, quantum coherence, quantum Fisher information and dynamics in noisy environments. We briefly explain the functions of the package and illustrate how to use the package with several typical examples. We expect that this package is a useful tool for future research and education.

Accuracy of RGD approximation for computing light scattering properties of diffusing and motile bacteria. [Rayleigh-Gans-Debye

NASA Technical Reports Server (NTRS)

Kottarchyk, M.; Chen, S.-H.; Asano, S.

1979-01-01

The study tests the accuracy of the Rayleigh-Gans-Debye (RGD) approximation against a rigorous scattering theory calculation for a simplified model of E. coli (about 1 micron in size) - a solid spheroid. A general procedure is formulated whereby the scattered field amplitude correlation function, for both polarized and depolarized contributions, can be computed for a collection of particles. An explicit formula is presented for the scattered intensity, both polarized and depolarized, for a collection of randomly diffusing or moving particles. Two specific cases for the intermediate scattering functions are considered: diffusing particles and freely moving particles with a Maxwellian speed distribution. The formalism is applied to microorganisms suspended in a liquid medium. Sensitivity studies revealed that for values of the relative index of refraction greater than 1.03, RGD could be in serious error in computing the intensity as well as correlation functions.

Computing sextic centrifugal distortion constants by DFT: A benchmark analysis on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi

2017-05-01

This work presents a benchmark study on the calculation of the sextic centrifugal distortion constants employing cubic force fields computed by means of density functional theory (DFT). For a set of semi-rigid halogenated organic compounds several functionals (B2PLYP, B3LYP, B3PW91, M06, M06-2X, O3LYP, X3LYP, ωB97XD, CAM-B3LYP, LC-ωPBE, PBE0, B97-1 and B97-D) were used for computing the sextic centrifugal distortion constants. The effects related to the size of basis sets and the performances of hybrid approaches, where the harmonic data obtained at higher level of electronic correlation are coupled with cubic force constants yielded by DFT functionals, are presented and discussed. The predicted values were compared to both the available data published in the literature and those obtained by calculations carried out at increasing level of electronic correlation: Hartree-Fock Self Consistent Field (HF-SCF), second order Møller-Plesset perturbation theory (MP2), and coupled-cluster single and double (CCSD) level of theory. Different hybrid approaches, having the cubic force field computed at DFT level of theory coupled to harmonic data computed at increasing level of electronic correlation (up to CCSD level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T)) were considered. The obtained results demonstrate that they can represent reliable and computationally affordable methods to predict sextic centrifugal terms with an accuracy almost comparable to that yielded by the more expensive anharmonic force fields fully computed at MP2 and CCSD levels of theory. In view of their reduced computational cost, these hybrid approaches pave the route to the study of more complex systems.

Computer Simulation for Calculating the Second-Order Correlation Function of Classical and Quantum Light

ERIC Educational Resources Information Center

Facao, M.; Lopes, A.; Silva, A. L.; Silva, P.

2011-01-01

We propose an undergraduate numerical project for simulating the results of the second-order correlation function as obtained by an intensity interference experiment for two kinds of light, namely bunched light with Gaussian or Lorentzian power density spectrum and antibunched light obtained from single-photon sources. While the algorithm for…

From quantum affine groups to the exact dynamical correlation function of the Heisenberg model

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

Bougourzi, A.H.; Couture, M.; Kacir, M.

1997-01-20

The exact form factors of the Heisenberg models XXX and XXZ have been recently computed through the quantum affine symmetry of XXZ model in the thermodynamic limit. The authors use them to derive an exact formula for the contribution of two spinons to the dynamical correlation function of XXX model at zero temperature.

The correlation function for density perturbations in an expanding universe. IV - The evolution of the correlation function. [galaxy distribution

NASA Technical Reports Server (NTRS)

Mcclelland, J.; Silk, J.

1979-01-01

The evolution of the two-point correlation function for the large-scale distribution of galaxies in an expanding universe is studied on the assumption that the perturbation densities lie in a Gaussian distribution centered on any given mass scale. The perturbations are evolved according to the Friedmann equation, and the correlation function for the resulting distribution of perturbations at the present epoch is calculated. It is found that: (1) the computed correlation function gives a satisfactory fit to the observed function in cosmological models with a density parameter (Omega) of approximately unity, provided that a certain free parameter is suitably adjusted; (2) the power-law slope in the nonlinear regime reflects the initial fluctuation spectrum, provided that the density profile of individual perturbations declines more rapidly than the -2.4 power of distance; and (3) both positive and negative contributions to the correlation function are predicted for cosmological models with Omega less than unity.

Automated Quantitative Computed Tomography Versus Visual Computed Tomography Scoring in Idiopathic Pulmonary Fibrosis: Validation Against Pulmonary Function.

PubMed

Jacob, Joseph; Bartholmai, Brian J; Rajagopalan, Srinivasan; Kokosi, Maria; Nair, Arjun; Karwoski, Ronald; Raghunath, Sushravya M; Walsh, Simon L F; Wells, Athol U; Hansell, David M

2016-09-01

The aim of the study was to determine whether a novel computed tomography (CT) postprocessing software technique (CALIPER) is superior to visual CT scoring as judged by functional correlations in idiopathic pulmonary fibrosis (IPF). A total of 283 consecutive patients with IPF had CT parenchymal patterns evaluated quantitatively with CALIPER and by visual scoring. These 2 techniques were evaluated against: forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), diffusing capacity for carbon monoxide (DLco), carbon monoxide transfer coefficient (Kco), and a composite physiological index (CPI), with regard to extent of interstitial lung disease (ILD), extent of emphysema, and pulmonary vascular abnormalities. CALIPER-derived estimates of ILD extent demonstrated stronger univariate correlations than visual scores for most pulmonary function tests (PFTs): (FEV1: CALIPER R=0.29, visual R=0.18; FVC: CALIPER R=0.41, visual R=0.27; DLco: CALIPER R=0.31, visual R=0.35; CPI: CALIPER R=0.48, visual R=0.44). Correlations between CT measures of emphysema extent and PFTs were weak and did not differ significantly between CALIPER and visual scoring. Intriguingly, the pulmonary vessel volume provided similar correlations to total ILD extent scored by CALIPER for FVC, DLco, and CPI (FVC: R=0.45; DLco: R=0.34; CPI: R=0.53). CALIPER was superior to visual scoring as validated by functional correlations with PFTs. The pulmonary vessel volume, a novel CALIPER CT parameter with no visual scoring equivalent, has the potential to be a CT feature in the assessment of patients with IPF and requires further exploration.

On exact correlation functions of chiral ring operators in 2 d N=(2, 2) SCFTs via localization

NASA Astrophysics Data System (ADS)

Chen, Jin

2018-03-01

We study the extremal correlation functions of (twisted) chiral ring operators via superlocalization in N=(2, 2) superconformal field theories (SCFTs) with central charge c ≥ 3, especially for SCFTs with Calabi-Yau geometric phases. We extend the method in arXiv: 1602.05971 with mild modifications, so that it is applicable to disentangle operators mixing on S 2 in nilpotent (twisted) chiral rings of 2 d SCFTs. With the extended algorithm and technique of localization, we compute exactly the extremal correlators in 2 d N=(2, 2) (twisted) chiral rings as non-holomorphic functions of marginal parameters of the theories. Especially in the context of Calabi-Yau geometries, we give an explicit geometric interpretation to our algorithm as the Griffiths transversality with projection on the Hodge bundle over Calabi-Yau complex moduli. We also apply the method to compute extremal correlators in Kähler moduli, or say twisted chiral rings, of several interesting Calabi-Yau manifolds. In the case of complete intersections in toric varieties, we provide an alternative formalism for extremal correlators via localization onto Higgs branch. In addition, as a spinoff we find that, from the extremal correlators of the top element in twisted chiral rings, one can extract chiral correlators in A-twisted topological theories.

Effect of the image resolution on the statistical descriptors of heterogeneous media.

PubMed

Ledesma-Alonso, René; Barbosa, Romeli; Ortegón, Jaime

2018-02-01

The characterization and reconstruction of heterogeneous materials, such as porous media and electrode materials, involve the application of image processing methods to data acquired by scanning electron microscopy or other microscopy techniques. Among them, binarization and decimation are critical in order to compute the correlation functions that characterize the microstructure of the above-mentioned materials. In this study, we present a theoretical analysis of the effects of the image-size reduction, due to the progressive and sequential decimation of the original image. Three different decimation procedures (random, bilinear, and bicubic) were implemented and their consequences on the discrete correlation functions (two-point, line-path, and pore-size distribution) and the coarseness (derived from the local volume fraction) are reported and analyzed. The chosen statistical descriptors (correlation functions and coarseness) are typically employed to characterize and reconstruct heterogeneous materials. A normalization for each of the correlation functions has been performed. When the loss of statistical information has not been significant for a decimated image, its normalized correlation function is forecast by the trend of the original image (reference function). In contrast, when the decimated image does not hold statistical evidence of the original one, the normalized correlation function diverts from the reference function. Moreover, the equally weighted sum of the average of the squared difference, between the discrete correlation functions of the decimated images and the reference functions, leads to a definition of an overall error. During the first stages of the gradual decimation, the error remains relatively small and independent of the decimation procedure. Above a threshold defined by the correlation length of the reference function, the error becomes a function of the number of decimation steps. At this stage, some statistical information is lost and the error becomes dependent on the decimation procedure. These results may help us to restrict the amount of information that one can afford to lose during a decimation process, in order to reduce the computational and memory cost, when one aims to diminish the time consumed by a characterization or reconstruction technique, yet maintaining the statistical quality of the digitized sample.

Effect of the image resolution on the statistical descriptors of heterogeneous media

NASA Astrophysics Data System (ADS)

Ledesma-Alonso, René; Barbosa, Romeli; Ortegón, Jaime

2018-02-01

The characterization and reconstruction of heterogeneous materials, such as porous media and electrode materials, involve the application of image processing methods to data acquired by scanning electron microscopy or other microscopy techniques. Among them, binarization and decimation are critical in order to compute the correlation functions that characterize the microstructure of the above-mentioned materials. In this study, we present a theoretical analysis of the effects of the image-size reduction, due to the progressive and sequential decimation of the original image. Three different decimation procedures (random, bilinear, and bicubic) were implemented and their consequences on the discrete correlation functions (two-point, line-path, and pore-size distribution) and the coarseness (derived from the local volume fraction) are reported and analyzed. The chosen statistical descriptors (correlation functions and coarseness) are typically employed to characterize and reconstruct heterogeneous materials. A normalization for each of the correlation functions has been performed. When the loss of statistical information has not been significant for a decimated image, its normalized correlation function is forecast by the trend of the original image (reference function). In contrast, when the decimated image does not hold statistical evidence of the original one, the normalized correlation function diverts from the reference function. Moreover, the equally weighted sum of the average of the squared difference, between the discrete correlation functions of the decimated images and the reference functions, leads to a definition of an overall error. During the first stages of the gradual decimation, the error remains relatively small and independent of the decimation procedure. Above a threshold defined by the correlation length of the reference function, the error becomes a function of the number of decimation steps. At this stage, some statistical information is lost and the error becomes dependent on the decimation procedure. These results may help us to restrict the amount of information that one can afford to lose during a decimation process, in order to reduce the computational and memory cost, when one aims to diminish the time consumed by a characterization or reconstruction technique, yet maintaining the statistical quality of the digitized sample.

Quantum Monte Carlo for atoms and molecules

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

Barnett, R.N.

1989-11-01

The diffusion quantum Monte Carlo with fixed nodes (QMC) approach has been employed in studying energy-eigenstates for 1--4 electron systems. Previous work employing the diffusion QMC technique yielded energies of high quality for H{sub 2}, LiH, Li{sub 2}, and H{sub 2}O. Here, the range of calculations with this new approach has been extended to include additional first-row atoms and molecules. In addition, improvements in the previously computed fixed-node energies of LiH, Li{sub 2}, and H{sub 2}O have been obtained using more accurate trial functions. All computations were performed within, but are not limited to, the Born-Oppenheimer approximation. In our computations,more » the effects of variation of Monte Carlo parameters on the QMC solution of the Schroedinger equation were studied extensively. These parameters include the time step, renormalization time and nodal structure. These studies have been very useful in determining which choices of such parameters will yield accurate QMC energies most efficiently. Generally, very accurate energies (90--100% of the correlation energy is obtained) have been computed with single-determinant trail functions multiplied by simple correlation functions. Improvements in accuracy should be readily obtained using more complex trial functions.« less

A stochastic-dynamic model for global atmospheric mass field statistics

NASA Technical Reports Server (NTRS)

Ghil, M.; Balgovind, R.; Kalnay-Rivas, E.

1981-01-01

A model that yields the spatial correlation structure of atmospheric mass field forecast errors was developed. The model is governed by the potential vorticity equation forced by random noise. Expansion in spherical harmonics and correlation function was computed analytically using the expansion coefficients. The finite difference equivalent was solved using a fast Poisson solver and the correlation function was computed using stratified sampling of the individual realization of F(omega) and hence of phi(omega). A higher order equation for gamma was derived and solved directly in finite differences by two successive applications of the fast Poisson solver. The methods were compared for accuracy and efficiency and the third method was chosen as clearly superior. The results agree well with the latitude dependence of observed atmospheric correlation data. The value of the parameter c sub o which gives the best fit to the data is close to the value expected from dynamical considerations.

Conformal correlation functions in the Brownian loop soup

NASA Astrophysics Data System (ADS)

Camia, Federico; Gandolfi, Alberto; Kleban, Matthew

2016-01-01

We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point) in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

Fitted Hanbury-Brown Twiss radii versus space-time variances in flow-dominated models

NASA Astrophysics Data System (ADS)

Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

2006-04-01

The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simple Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.

Fitted Hanbury-Brown-Twiss radii versus space-time variances in flow-dominated models

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

Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

2006-04-15

The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown-Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simplemore » Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.« less

Beyond Kohn-Sham Approximation: Hybrid Multistate Wave Function and Density Functional Theory.

PubMed

Gao, Jiali; Grofe, Adam; Ren, Haisheng; Bao, Peng

2016-12-15

A multistate density functional theory (MSDFT) is presented in which the energies and densities for the ground and excited states are treated on the same footing using multiconfigurational approaches. The method can be applied to systems with strong correlation and to correctly describe the dimensionality of the conical intersections between strongly coupled dissociative potential energy surfaces. A dynamic-then-static framework for treating electron correlation is developed to first incorporate dynamic correlation into contracted state functions through block-localized Kohn-Sham density functional theory (KSDFT), followed by diagonalization of the effective Hamiltonian to include static correlation. MSDFT can be regarded as a hybrid of wave function and density functional theory. The method is built on and makes use of the current approximate density functional developed in KSDFT, yet it retains its computational efficiency to treat strongly correlated systems that are problematic for KSDFT but too large for accurate WFT. The results presented in this work show that MSDFT can be applied to photochemical processes involving conical intersections.

Generalized recursion relations for correlators in the gauge-gravity correspondence.

PubMed

Raju, Suvrat

2011-03-04

We show that a generalization of the Britto-Cachazo-Feng-Witten recursion relations gives a new and efficient method of computing correlation functions of the stress tensor or conserved currents in conformal field theories with an (d+1)-dimensional anti-de Sitter space dual, for d≥4, in the limit where the bulk theory is approximated by tree-level Yang-Mills theory or gravity. In supersymmetric theories, additional correlators of operators that live in the same multiplet as a conserved current or stress tensor can be computed by these means.

Quantitative computed tomography of lung parenchyma in patients with emphysema: analysis of higher-density lung regions

NASA Astrophysics Data System (ADS)

Lederman, Dror; Leader, Joseph K.; Zheng, Bin; Sciurba, Frank C.; Tan, Jun; Gur, David

2011-03-01

Quantitative computed tomography (CT) has been widely used to detect and evaluate the presence (or absence) of emphysema applying the density masks at specific thresholds, e.g., -910 or -950 Hounsfield Unit (HU). However, it has also been observed that subjects with similar density-mask based emphysema scores could have varying lung function, possibly indicating differences of disease severity. To assess this possible discrepancy, we investigated whether density distribution of "viable" lung parenchyma regions with pixel values > -910 HU correlates with lung function. A dataset of 38 subjects, who underwent both pulmonary function testing and CT examinations in a COPD SCCOR study, was assembled. After the lung regions depicted on CT images were automatically segmented by a computerized scheme, we systematically divided the lung parenchyma into different density groups (bins) and computed a number of statistical features (i.e., mean, standard deviation (STD), skewness of the pixel value distributions) in these density bins. We then analyzed the correlations between each feature and lung function. The correlation between diffusion lung capacity (DLCO) and STD of pixel values in the bin of -910HU <= PV < -750HU was -0.43, as compared with a correlation of -0.49 obtained between the post-bronchodilator ratio (FEV1/FVC) measured by the forced expiratory volume in 1 second (FEV1) dividing the forced vital capacity (FVC) and the STD of pixel values in the bin of -1024HU <= PV < -910HU. The results showed an association between the distribution of pixel values in "viable" lung parenchyma and lung function, which indicates that similar to the conventional density mask method, the pixel value distribution features in "viable" lung parenchyma areas may also provide clinically useful information to improve assessments of lung disease severity as measured by lung functional tests.

An Analysis of Cryptographically Significant Boolean Functions With High Correlation Immunity by Reconfigurable Computer

DTIC Science & Technology

2010-12-01

with high correlation immunity and then evaluate these functions for other desirable cryptographic features. C. METHOD The only known primary methods...out if not used) # ---------------------------------- # PRIMARY = < primary file 1> < primary file 2> #SECONDARY = <secondary file 1...finding the fuction value for a //set u and for each value of v. end end

The journey from forensic to predictive materials science using density functional theory

DOE PAGES

Schultz, Peter A.

2017-09-12

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.

The journey from forensic to predictive materials science using density functional theory

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

Schultz, Peter A.

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.

An efficient method for hybrid density functional calculation with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Wang, Maoyuan; Liu, Gui-Bin; Guo, Hong; Yao, Yugui

2018-03-01

In first-principles calculations, hybrid functional is often used to improve accuracy from local exchange correlation functionals. A drawback is that evaluating the hybrid functional needs significantly more computing effort. When spin-orbit coupling (SOC) is taken into account, the non-collinear spin structure increases computing effort by at least eight times. As a result, hybrid functional calculations with SOC are intractable in most cases. In this paper, we present an approximate solution to this problem by developing an efficient method based on a mixed linear combination of atomic orbital (LCAO) scheme. We demonstrate the power of this method using several examples and we show that the results compare very well with those of direct hybrid functional calculations with SOC, yet the method only requires a computing effort similar to that without SOC. The presented technique provides a good balance between computing efficiency and accuracy, and it can be extended to magnetic materials.

Hard-spin mean-field theory: A systematic derivation and exact correlations in one dimension

PubMed

Kabakcioglu

2000-04-01

Hard-spin mean-field theory is an improved mean-field approach which has proven to give accurate results, especially for frustrated spin systems, with relatively little computational effort. In this work, the previous phenomenological derivation is supplanted by a systematic and generic derivation that opens the possibility for systematic improvements, especially for the calculation of long-range correlation functions. A first level of improvement suffices to recover the exact long-range values of the correlation functions in one dimension.

Theoretical study of the electric dipole moment function of the ClO molecule

NASA Technical Reports Server (NTRS)

Pettersson, L. G. M.; Langhoff, S. R.; Chong, D. P.

1986-01-01

The potential energy function and electric dipole moment function (EDMF) are computed for ClO X 2Pi using several different techniques to include electron correlation. The EDMF is used to compute Einstein coefficients, vibrational lifetimes, and dipole moments in higher vibrational levels. The band strength of the 1-0 fundamental transition is computed to be 12 + or - 2 per sq cm atm determined from infrared heterodyne spectroscopy. The theoretical methods used include SCF, CASSCF, multireference singles plus doubles configuration interaction (MRCI) and contracted CI, coupled pair functional (CPF), and a modified version of the CPF method. The results obtained using the different methods are critically compared.

Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries.

PubMed

Brorsen, Kurt R; Yang, Yang; Hammes-Schiffer, Sharon

2017-08-03

Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear-electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron-proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron-proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF - . The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pK a 's, optimized geometries, and reaction paths.

Topological electronic liquids: Electronic physics of one dimension beyond the one spatial dimension

NASA Astrophysics Data System (ADS)

Wiegmann, P. B.

1999-06-01

There is a class of electronic liquids in dimensions greater than 1 that shows all essential properties of one-dimensional electronic physics. These are topological liquids-correlated electronic systems with a spectral flow. Compressible topological electronic liquids are superfluids. In this paper we present a study of a conventional model of a topological superfluid in two spatial dimensions. This model is thought to be relevant to a doped Mott insulator. We show how the spectral flow leads to the superfluid hydrodynamics and how the orthogonality catastrophe affects off-diagonal matrix elements. We also compute the major electronic correlation functions. Among them are the spectral function, the pair wave function, and various tunneling amplitudes. To compute correlation functions we develop a method of current algebra-an extension of the bosonization technique of one spatial dimension. In order to emphasize a similarity between electronic liquids in one dimension and topological liquids in dimensions greater than 1, we first review the Fröhlich-Peierls mechanism of ideal conductivity in one dimension and then extend the physics and the methods into two spatial dimensions.

Spatial correlation of the dynamic propensity of a glass-forming liquid

NASA Astrophysics Data System (ADS)

Razul, M. Shajahan G.; Matharoo, Gurpreet S.; Poole, Peter H.

2011-06-01

We present computer simulation results on the dynamic propensity (as defined by Widmer-Cooper et al 2004 Phys. Rev. Lett. 93 135701) in a Kob-Andersen binary Lennard-Jones liquid system consisting of 8788 particles. We compute the spatial correlation function for the dynamic propensity as a function of both the reduced temperature T, and the time scale on which the particle displacements are measured. For T <= 0.6, we find that non-zero correlations occur at the largest length scale accessible in our system. We also show that a cluster-size analysis of particles with extremal values of the dynamic propensity, as well as 3D visualizations, reveal spatially correlated regions that approach the size of our system as T decreases, consistently with the behavior of the spatial correlation function. Next, we define and examine the 'coordination propensity', the isoconfigurational average of the coordination number of the minority B particles around the majority A particles. We show that a significant correlation exists between the spatial fluctuations of the dynamic and coordination propensities. In addition, we find non-zero correlations of the coordination propensity occurring at the largest length scale accessible in our system for all T in the range 0.466 < T < 1.0. We discuss the implications of these results for understanding the length scales of dynamical heterogeneity in glass-forming liquids.

Towards Full-Waveform Ambient Noise Inversion

NASA Astrophysics Data System (ADS)

Sager, K.; Ermert, L. A.; Boehm, C.; Fichtner, A.

2016-12-01

Noise tomography usually works under the assumption that the inter-station ambient noise correlation is equal to a scaled version of the Green function between the two receivers. This assumption, however, is only met under specific conditions, e.g. wavefield diffusivity and equipartitioning, or the isotropic distribution of both mono- and dipolar uncorrelated noise sources. These assumptions are typically not satisfied in the Earth. This inconsistency inhibits the exploitation of the full waveform information contained in noise correlations in order to constrain Earth structure and noise generation. To overcome this limitation, we attempt to develop a method that consistently accounts for the distribution of noise sources, 3D heterogeneous Earth structure and the full seismic wave propagation physics. This is intended to improve the resolution of tomographic images, to refine noise source location, and thereby to contribute to a better understanding of noise generation. We introduce an operator-based formulation for the computation of correlation functions and apply the continuous adjoint method that allows us to compute first and second derivatives of misfit functionals with respect to source distribution and Earth structure efficiently. Based on these developments we design an inversion scheme using a 2D finite-difference code. To enable a joint inversion for noise sources and Earth structure, we investigate the following aspects: The capability of different misfit functionals to image wave speed anomalies and source distribution. Possible source-structure trade-offs, especially to what extent unresolvable structure can be mapped into the inverted noise source distribution and vice versa. In anticipation of real-data applications, we present an extension of the open-source waveform modelling and inversion package Salvus, which allows us to compute correlation functions in 3D media with heterogeneous noise sources at the surface.

Functional correlation approach to operational risk in banking organizations

NASA Astrophysics Data System (ADS)

Kühn, Reimer; Neu, Peter

2003-05-01

A Value-at-Risk-based model is proposed to compute the adequate equity capital necessary to cover potential losses due to operational risks, such as human and system process failures, in banking organizations. Exploring the analogy to a lattice gas model from physics, correlations between sequential failures are modeled by as functionally defined, heterogeneous couplings between mutually supportive processes. In contrast to traditional risk models for market and credit risk, where correlations are described as equal-time-correlations by a covariance matrix, the dynamics of the model shows collective phenomena such as bursts and avalanches of process failures.

Covariance analyses of satellite-derived mesoscale wind fields

NASA Technical Reports Server (NTRS)

Maddox, R. A.; Vonder Haar, T. H.

1979-01-01

Statistical structure functions have been computed independently for nine satellite-derived mesoscale wind fields that were obtained on two different days. Small cumulus clouds were tracked at 5 min intervals, but since these clouds occurred primarily in the warm sectors of midlatitude cyclones the results cannot be considered representative of the circulations within cyclones in general. The field structure varied considerably with time and was especially affected if mesoscale features were observed. The wind fields on the 2 days studied were highly anisotropic with large gradients in structure occurring approximately normal to the mean flow. Structure function calculations for the combined set of satellite winds were used to estimate random error present in the fields. It is concluded for these data that the random error in vector winds derived from cumulus cloud tracking using high-frequency satellite data is less than 1.75 m/s. Spatial correlation functions were also computed for the nine data sets. Normalized correlation functions were considerably different for u and v components and decreased rapidly as data point separation increased for both components. The correlation functions for transverse and longitudinal components decreased less rapidly as data point separation increased.

Microstructural correlates of infant functional development: example of the visual pathways.

PubMed

Dubois, Jessica; Dehaene-Lambertz, Ghislaine; Soarès, Catherine; Cointepas, Yann; Le Bihan, Denis; Hertz-Pannier, Lucie

2008-02-20

The development of cognitive functions during childhood relies on several neuroanatomical maturation processes. Among these processes is myelination of the white matter pathways, which speeds up electrical conduction. Quantitative indices of such structural processes can be obtained in vivo with diffusion tensor imaging (DTI), but their physiological significance remains uncertain. Here, we investigated the microstructural correlates of early functional development by combining DTI and visual event-related potentials (VEPs) in 15 one- to 4-month-old healthy infants. Interindividual variations of the apparent conduction speed, computed from the latency of the first positive VEP wave (P1), were significantly correlated with the infants' age and DTI indices measured in the optic radiations. This demonstrates that fractional anisotropy and transverse diffusivity are structural markers of functionally efficient myelination. Moreover, these indices computed along the optic radiations showed an early wave of maturation in the anterior region, with the posterior region catching up later in development, which suggests two asynchronous fronts of myelination in both the geniculocortical and corticogeniculate fibers. Thus, in addition to microstructural information, DTI provides noninvasive exquisite information on the functional development of the brain in human infants.

Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions.

PubMed

Calligari, Paolo; Gerolin, Marco; Abergel, Daniel; Polimeno, Antonino

2017-01-10

In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.

A partitioned correlation function interaction approach for describing electron correlation in atoms

NASA Astrophysics Data System (ADS)

Verdebout, S.; Rynkun, P.; Jönsson, P.; Gaigalas, G.; Froese Fischer, C.; Godefroid, M.

2013-04-01

The traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis. For atoms with many closed core shells, or complicated shell structures, a large orbital basis is needed to saturate the different electron correlation effects such as valence, core-valence and correlation within the core shells. The large orbital basis leads to massive configuration state function (CSF) expansions that are difficult to handle, even on large computer systems. We show that it is possible to relax the orthonormality restriction on the orbital basis and break down the originally very large calculations into a series of smaller calculations that can be run in parallel. Each calculation determines a partitioned correlation function (PCF) that accounts for a specific correlation effect. The PCFs are built on optimally localized orbital sets and are added to a zero-order multireference (MR) function to form a total wave function. The expansion coefficients of the PCFs are determined from a low dimensional generalized eigenvalue problem. The interaction and overlap matrices are computed using a biorthonormal transformation technique (Verdebout et al 2010 J. Phys. B: At. Mol. Phys. 43 074017). The new method, called partitioned correlation function interaction (PCFI), converges rapidly with respect to the orbital basis and gives total energies that are lower than the ones from ordinary MCHF and CI calculations. The PCFI method is also very flexible when it comes to targeting different electron correlation effects. Focusing our attention on neutral lithium, we show that by dedicating a PCF to the single excitations from the core, spin- and orbital-polarization effects can be captured very efficiently, leading to highly improved convergence patterns for hyperfine parameters compared with MCHF calculations based on a single orthogonal radial orbital basis. By collecting separately optimized PCFs to correct the MR function, the variational degrees of freedom in the relative mixing coefficients of the CSFs building the PCFs are inhibited. The constraints on the mixing coefficients lead to small off-sets in computed properties such as hyperfine structure, isotope shift and transition rates, with respect to the correct values. By (partially) deconstraining the mixing coefficients one converges to the correct limits and keeps the tremendous advantage of improved convergence rates that comes from the use of several orbital sets. Reducing ultimately each PCF to a single CSF with its own orbital basis leads to a non-orthogonal CI approach. Various perspectives of the new method are given.

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

Evaluation of visual and computer-based CT analysis for the identification of functional patterns of obstruction and restriction in hypersensitivity pneumonitis.

PubMed

Jacob, Joseph; Bartholmai, Brian J; Brun, Anne Laure; Egashira, Ryoko; Rajagopalan, Srinivasan; Karwoski, Ronald; Kouranos, Vasileios; Kokosi, Maria; Hansell, David M; Wells, Athol U

2017-11-01

To determine whether computer-based quantification (CALIPER software) is superior to visual computed tomography (CT) scoring in the identification of CT patterns indicative of restrictive and obstructive functional indices in hypersensitivity pneumonitis (HP). A total of 135 consecutive HP patients had CT parenchymal patterns evaluated quantitatively by both visual scoring and CALIPER. Results were evaluated against: forced vital capacity (FVC), total lung capacity (TLC), diffusing capacity for carbon monoxide (DL CO ) and a composite physiological index (CPI) to identify which CT scoring method better correlated with functional indices. CALIPER-derived scores of total interstitial lung disease extent correlated more strongly than visual scores: FVC (CALIPER R = 0.73, visual R = 0.51); DL CO (CALIPER R = 0.61, visual R = 0.48); and CPI (CALIPER R = 0·70, visual R = 0·55). The CT variable that correlated most strongly with restrictive functional indices was CALIPER pulmonary vessel volume (PVV): FVC R = 0.75, DL CO R = 0.68 and CPI R = 0.76. Ground-glass opacity quantified by CALIPER alone demonstrated strong associations with restrictive functional indices: CALIPER FVC R = 0.65; DL CO R = 0.59; CPI R = 0.64; and visual = not significant. Decreased attenuation lung quantified by CALIPER was a better morphological measure of obstructive lung disease than equivalent visual scores as judged by relationships with TLC (CALIPER R = 0.63 and visual R = 0.12). All results were maintained on multivariate analysis. CALIPER improved on visual scoring in HP as judged by restrictive and obstructive functional correlations. Decreased attenuation regions of the lung quantified by CALIPER demonstrated better linkages to obstructive lung physiology than visually quantified CT scores. A novel CALIPER variable, the PVV, demonstrated the strongest linkages with restrictive functional indices and could represent a new automated index of disease severity in HP. © 2017 Asian Pacific Society of Respirology.

Electron Correlation from the Adiabatic Connection for Multireference Wave Functions

NASA Astrophysics Data System (ADS)

Pernal, Katarzyna

2018-01-01

An adiabatic connection (AC) formula for the electron correlation energy is derived for a broad class of multireference wave functions. The AC expression recovers dynamic correlation energy and assures a balanced treatment of the correlation energy. Coupling the AC formalism with the extended random phase approximation allows one to find the correlation energy only from reference one- and two-electron reduced density matrices. If the generalized valence bond perfect pairing model is employed a simple closed-form expression for the approximate AC formula is obtained. This results in the overall M5 scaling of the computation cost making the method one of the most efficient multireference approaches accounting for dynamic electron correlation also for the strongly correlated systems.

Regression relation for pure quantum states and its implications for efficient computing.

PubMed

Elsayed, Tarek A; Fine, Boris V

2013-02-15

We obtain a modified version of the Onsager regression relation for the expectation values of quantum-mechanical operators in pure quantum states of isolated many-body quantum systems. We use the insights gained from this relation to show that high-temperature time correlation functions in many-body quantum systems can be controllably computed without complete diagonalization of the Hamiltonians, using instead the direct integration of the Schrödinger equation for randomly sampled pure states. This method is also applicable to quantum quenches and other situations describable by time-dependent many-body Hamiltonians. The method implies exponential reduction of the computer memory requirement in comparison with the complete diagonalization. We illustrate the method by numerically computing infinite-temperature correlation functions for translationally invariant Heisenberg chains of up to 29 spins 1/2. Thereby, we also test the spin diffusion hypothesis and find it in a satisfactory agreement with the numerical results. Both the derivation of the modified regression relation and the justification of the computational method are based on the notion of quantum typicality.

The correlation of symptoms, pulmonary function tests and exercise testing with high-resolution computed tomography in patients with idiopathic interstitial pneumonia in a tertiary care hospital in South India.

PubMed

Isaac, Barney Thomas Jesudason; Thangakunam, Balamugesh; Cherian, Rekha A; Christopher, Devasahayam Jesudas

2015-01-01

For the follow-up of patients with idiopathic interstitial pneumonias (IIP), it is unclear which parameters of pulmonary function tests (PFT) and exercise testing would correlate best with high-resolution computed tomography (HRCT).. To find out the correlation of symptom scores, PFTs and exercise testing with HRCT scoring in patients diagnosed as idiopathic interstitial pneumonia. Cross-sectional study done in pulmonary medicine outpatients department of a tertiary care hospital in South India. Consecutive patients who were diagnosed as IIP by a standard algorithm were included into the study. Cough and dyspnea were graded for severity and duration. Pulmonary function tests and exercise testing parameters were noted. HRCT was scored based on an alveolar score, an interstitial score and a total score. The HRCT was correlated with each of the clinical and physiologic parameters. Pearson's/Spearman's correlation coefficient was used for the correlation of symptoms and parameters of ABG, PFT and 6MWT with the HRCT scores. A total of 94 patients were included in the study. Cough and dyspnea severity (r = 0.336 and 0.299), FVC (r = -0.48), TLC (r = -0.439) and DLCO and distance saturation product (DSP) (r = -0.368) and lowest saturation (r = -0.324) had significant correlation with total HRCT score. Among these, DLCO, particularly DLCO corrected % of predicted, correlated best with HRCT score (r = -0.721).. Symptoms, PFT and exercise testing had good correlation with HRCT. DLCO corrected % of predicted correlated best with HRCT.

Temperature dependent structural and dynamical properties of liquid Cu80Si20 binary alloy

NASA Astrophysics Data System (ADS)

Suthar, P. H.; Shah, A. K.; Gajjar, P. N.

2018-05-01

Ashcroft and Langreth binary structure factor have been used to study for pair correlation function and the study of dynamical variable: velocity auto correlation functions, power spectrum and mean square displacement calculated based on the static harmonic well approximation in liquid Cu80Si20 binary alloy at wide temperature range (1140K, 1175K, 1210K, 1250K, 1373K, 1473K.). The effective interaction for the binary alloy is computed by our well established local pseudopotential along with the exchange and correction functions Sarkar et al(S). The negative dip in velocity auto correlation decreases as the various temperature is increases. For power spectrum as temperature increases, the peak of power spectrum shifts toward lower ω. Good agreement with the experiment is observed for the pair correlation functions. Velocity auto correlation showing the transferability of the local pseudopotential used for metallic liquid environment in the case of copper based binary alloys.

Applying standardized uptake values in gallium-67-citrate single-photon emission computed tomography/computed tomography studies and their correlation with blood test results in representative organs.

PubMed

Toriihara, Akira; Daisaki, Hiromitsu; Yamaguchi, Akihiro; Yoshida, Katsuya; Isogai, Jun; Tateishi, Ukihide

2018-05-21

Recently, semiquantitative analysis using standardized uptake value (SUV) has been introduced in bone single-photon emission computed tomography/computed tomography (SPECT/CT). Our purposes were to apply SUV-based semiquantitative analytic method for gallium-67 (Ga)-citrate SPECT/CT and to evaluate correlation between SUV of physiological uptake and blood test results in representative organs. The accuracy of semiquantitative method was validated using an National Electrical Manufacturers Association body phantom study (radioactivity ratio of sphere : background=4 : 1). Thereafter, 59 patients (34 male and 25 female; mean age, 66.9 years) who had undergone Ga-citrate SPECT/CT were retrospectively enrolled in the study. A mean SUV of physiological uptake was calculated for the following organs: the lungs, right atrium, liver, kidneys, spleen, gluteal muscles, and bone marrow. The correlation between physiological uptakes and blood test results was evaluated using Pearson's correlation coefficient. The phantom study revealed only 1% error between theoretical and actual SUVs in the background, suggesting the sufficient accuracy of scatter and attenuation corrections. However, a partial volume effect could not be overlooked, particularly in small spheres with a diameter of less than 28 mm. The highest mean SUV was observed in the liver (range: 0.44-4.64), followed by bone marrow (range: 0.33-3.60), spleen (range: 0.52-2.12), and kidneys (range: 0.42-1.45). There was no significant correlation between hepatic uptake and liver function, renal uptake and renal function, or bone marrow uptake and blood cell count (P>0.05). The physiological uptake in Ga-citrate SPECT/CT can be represented as SUVs, which are not significantly correlated with corresponding blood test results.

Translational, rotational and internal dynamics of amyloid β-peptides (Aβ40 and Aβ42) from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bora, Ram Prasad; Prabhakar, Rajeev

2009-10-01

In this study, diffusion constants [translational (DT) and rotational (DR)], correlation times [rotational (τrot) and internal (τint)], and the intramolecular order parameters (S2) of the Alzheimer amyloid-β peptides Aβ40 and Aβ42 have been calculated from 150 ns molecular dynamics simulations in aqueous solution. The computed parameters have been compared with the experimentally measured values. The calculated DT of 1.61×10-6 cm2/s and 1.43×10-6 cm2/s for Aβ40 and Aβ42, respectively, at 300 K was found to follow the correct trend defined by the Debye-Stokes-Einstein relation that its value should decrease with the increase in the molecular weight. The estimated DR for Aβ40 and Aβ42 at 300 K are 0.085 and 0.071 ns-1, respectively. The rotational (Crot(t)) and internal (Cint(t)) correlation functions of Aβ40 and Aβ42 were observed to decay at nano- and picosecond time scales, respectively. The significantly different time decays of these functions validate the factorization of the total correlation function (Ctot(t)) of Aβ peptides into Crot(t) and Cint(t). At both short and long time scales, the Clore-Szabo model that was used as Cint(t) provided the best behavior of Ctot(t) for both Aβ40 and Aβ42. In addition, an effective rotational correlation time of Aβ40 is also computed at 18 °C and the computed value (2.30 ns) is in close agreement with the experimental value of 2.45 ns. The computed S2 parameters for the central hydrophobic core, the loop region, and C-terminal domains of Aβ40 and Aβ42 are in accord with the previous studies.

Analog computation of auto and cross-correlation functions

NASA Technical Reports Server (NTRS)

1974-01-01

For analysis of the data obtained from the cross beam systems it was deemed desirable to compute the auto- and cross-correlation functions by both digital and analog methods to provide a cross-check of the analysis methods and an indication as to which of the two methods would be most suitable for routine use in the analysis of such data. It is the purpose of this appendix to provide a concise description of the equipment and procedures used for the electronic analog analysis of the cross beam data. A block diagram showing the signal processing and computation set-up used for most of the analog data analysis is provided. The data obtained at the field test sites were recorded on magnetic tape using wide-band FM recording techniques. The data as recorded were band-pass filtered by electronic signal processing in the data acquisition systems.

Speckle-field propagation in 'frozen' turbulence: brightness function approach

NASA Astrophysics Data System (ADS)

Dudorov, Vadim V.; Vorontsov, Mikhail A.; Kolosov, Valeriy V.

2006-08-01

Speckle-field long- and short-exposure spatial correlation characteristics for target-in-the-loop (TIL) laser beam propagation and scattering in atmospheric turbulence are analyzed through the use of two different approaches: the conventional Monte Carlo (MC) technique and the recently developed brightness function (BF) method. Both the MC and the BF methods are applied to analysis of speckle-field characteristics averaged over target surface roughness realizations under conditions of 'frozen' turbulence. This corresponds to TIL applications where speckle-field fluctuations associated with target surface roughness realization updates occur within a time scale that can be significantly shorter than the characteristic atmospheric turbulence time. Computational efficiency and accuracy of both methods are compared on the basis of a known analytical solution for the long-exposure mutual correlation function. It is shown that in the TIL propagation scenarios considered the BF method provides improved accuracy and requires significantly less computational time than the conventional MC technique. For TIL geometry with a Gaussian outgoing beam and Lambertian target surface, both analytical and numerical estimations for the speckle-field long-exposure correlation length are obtained. Short-exposure speckle-field correlation characteristics corresponding to propagation in 'frozen' turbulence are estimated using the BF method. It is shown that atmospheric turbulence-induced static refractive index inhomogeneities do not significantly affect the characteristic correlation length of the speckle field, whereas long-exposure spatial correlation characteristics are strongly dependent on turbulence strength.

Speckle-field propagation in 'frozen' turbulence: brightness function approach.

PubMed

Dudorov, Vadim V; Vorontsov, Mikhail A; Kolosov, Valeriy V

2006-08-01

Speckle-field long- and short-exposure spatial correlation characteristics for target-in-the-loop (TIL) laser beam propagation and scattering in atmospheric turbulence are analyzed through the use of two different approaches: the conventional Monte Carlo (MC) technique and the recently developed brightness function (BF) method. Both the MC and the BF methods are applied to analysis of speckle-field characteristics averaged over target surface roughness realizations under conditions of 'frozen' turbulence. This corresponds to TIL applications where speckle-field fluctuations associated with target surface roughness realization updates occur within a time scale that can be significantly shorter than the characteristic atmospheric turbulence time. Computational efficiency and accuracy of both methods are compared on the basis of a known analytical solution for the long-exposure mutual correlation function. It is shown that in the TIL propagation scenarios considered the BF method provides improved accuracy and requires significantly less computational time than the conventional MC technique. For TIL geometry with a Gaussian outgoing beam and Lambertian target surface, both analytical and numerical estimations for the speckle-field long-exposure correlation length are obtained. Short-exposure speckle-field correlation characteristics corresponding to propagation in 'frozen' turbulence are estimated using the BF method. It is shown that atmospheric turbulence-induced static refractive index inhomogeneities do not significantly affect the characteristic correlation length of the speckle field, whereas long-exposure spatial correlation characteristics are strongly dependent on turbulence strength.

Nonperturbative renormalization-group approach preserving the momentum dependence of correlation functions

NASA Astrophysics Data System (ADS)

Rose, F.; Dupuis, N.

2018-05-01

We present an approximation scheme of the nonperturbative renormalization group that preserves the momentum dependence of correlation functions. This approximation scheme can be seen as a simple improvement of the local potential approximation (LPA) where the derivative terms in the effective action are promoted to arbitrary momentum-dependent functions. As in the LPA, the only field dependence comes from the effective potential, which allows us to solve the renormalization-group equations at a relatively modest numerical cost (as compared, e.g., to the Blaizot-Mendéz-Galain-Wschebor approximation scheme). As an application we consider the two-dimensional quantum O(N ) model at zero temperature. We discuss not only the two-point correlation function but also higher-order correlation functions such as the scalar susceptibility (which allows for an investigation of the "Higgs" amplitude mode) and the conductivity. In particular, we show how, using Padé approximants to perform the analytic continuation i ωn→ω +i 0+ of imaginary frequency correlation functions χ (i ωn) computed numerically from the renormalization-group equations, one can obtain spectral functions in the real-frequency domain.

bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses.

PubMed

Jézéquel, Pascal; Frénel, Jean-Sébastien; Campion, Loïc; Guérin-Charbonnel, Catherine; Gouraud, Wilfried; Ricolleau, Gabriel; Campone, Mario

2013-01-01

We recently developed a user-friendly web-based application called bc-GenExMiner (http://bcgenex.centregauducheau.fr), which offered the possibility to evaluate prognostic informativity of genes in breast cancer by means of a 'prognostic module'. In this study, we develop a new module called 'correlation module', which includes three kinds of gene expression correlation analyses. The first one computes correlation coefficient between 2 or more (up to 10) chosen genes. The second one produces two lists of genes that are most correlated (positively and negatively) to a 'tested' gene. A gene ontology (GO) mining function is also proposed to explore GO 'biological process', 'molecular function' and 'cellular component' terms enrichment for the output lists of most correlated genes. The third one explores gene expression correlation between the 15 telomeric and 15 centromeric genes surrounding a 'tested' gene. These correlation analyses can be performed in different groups of patients: all patients (without any subtyping), in molecular subtypes (basal-like, HER2+, luminal A and luminal B) and according to oestrogen receptor status. Validation tests based on published data showed that these automatized analyses lead to results consistent with studies' conclusions. In brief, this new module has been developed to help basic researchers explore molecular mechanisms of breast cancer. DATABASE URL: http://bcgenex.centregauducheau.fr

Exact correlators on the Wilson loop in N=4 SYM: localization, defect CFT, and integrability

NASA Astrophysics Data System (ADS)

Giombi, Simone; Komatsu, Shota

2018-05-01

We compute a set of correlation functions of operator insertions on the 1 /8 BPS Wilson loop in N=4 SYM by employing supersymmetric localization, OPE and the Gram-Schmidt orthogonalization. These correlators exhibit a simple determinant structure, are position-independent and form a topological subsector, but depend nontrivially on the 't Hooft coupling and the rank of the gauge group. When applied to the 1 /2 BPS circular (or straight) Wilson loop, our results provide an infinite family of exact defect CFT data, including the structure constants of protected defect primaries of arbitrary length inserted on the loop. At strong coupling, we show precise agreement with a direct calculation using perturbation theory around the AdS2 string worldsheet. We also explain the connection of our results to the "generalized Bremsstrahlung functions" previously computed from integrability techniques, reproducing the known results in the planar limit as well as obtaining their finite N generalization. Furthermore, we show that the correlators at large N can be recast as simple integrals of products of polynomials (known as Q-functions) that appear in the Quantum Spectral Curve approach. This suggests an interesting interplay between localization, defect CFT and integrability.

Fast computation of voxel-level brain connectivity maps from resting-state functional MRI using l₁-norm as approximation of Pearson's temporal correlation: proof-of-concept and example vector hardware implementation.

PubMed

Minati, Ludovico; Zacà, Domenico; D'Incerti, Ludovico; Jovicich, Jorge

2014-09-01

An outstanding issue in graph-based analysis of resting-state functional MRI is choice of network nodes. Individual consideration of entire brain voxels may represent a less biased approach than parcellating the cortex according to pre-determined atlases, but entails establishing connectedness for 1(9)-1(11) links, with often prohibitive computational cost. Using a representative Human Connectome Project dataset, we show that, following appropriate time-series normalization, it may be possible to accelerate connectivity determination replacing Pearson correlation with l1-norm. Even though the adjacency matrices derived from correlation coefficients and l1-norms are not identical, their similarity is high. Further, we describe and provide in full an example vector hardware implementation of l1-norm on an array of 4096 zero instruction-set processors. Calculation times <1000 s are attainable, removing the major deterrent to voxel-based resting-sate network mapping and revealing fine-grained node degree heterogeneity. L1-norm should be given consideration as a substitute for correlation in very high-density resting-state functional connectivity analyses. Copyright © 2014 IPEM. Published by Elsevier Ltd. All rights reserved.

Computing thermal Wigner densities with the phase integration method

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

Beutier, J.; Borgis, D.; Vuilleumier, R.

2014-08-28

We discuss how the Phase Integration Method (PIM), recently developed to compute symmetrized time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)], can be adapted to sampling/generating the thermal Wigner density, a key ingredient, for example, in many approximate schemes for simulating quantum time dependent properties. PIM combines a path integral representation of the density with a cumulant expansion to represent the Wigner function in a form calculable via existing Monte Carlo algorithms for sampling noisy probability densities. The method is able to capture highly non-classical effects such as correlation among the momenta andmore » coordinates parts of the density, or correlations among the momenta themselves. By using alternatives to cumulants, it can also indicate the presence of negative parts of the Wigner density. Both properties are demonstrated by comparing PIM results to those of reference quantum calculations on a set of model problems.« less

Computing thermal Wigner densities with the phase integration method.

PubMed

Beutier, J; Borgis, D; Vuilleumier, R; Bonella, S

2014-08-28

We discuss how the Phase Integration Method (PIM), recently developed to compute symmetrized time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)], can be adapted to sampling/generating the thermal Wigner density, a key ingredient, for example, in many approximate schemes for simulating quantum time dependent properties. PIM combines a path integral representation of the density with a cumulant expansion to represent the Wigner function in a form calculable via existing Monte Carlo algorithms for sampling noisy probability densities. The method is able to capture highly non-classical effects such as correlation among the momenta and coordinates parts of the density, or correlations among the momenta themselves. By using alternatives to cumulants, it can also indicate the presence of negative parts of the Wigner density. Both properties are demonstrated by comparing PIM results to those of reference quantum calculations on a set of model problems.

Synthesis of correlation filters: a generalized space-domain approach for improved filter characteristics

NASA Astrophysics Data System (ADS)

Sudharsanan, Subramania I.; Mahalanobis, Abhijit; Sundareshan, Malur K.

1990-12-01

Discrete frequency domain design of Minimum Average Correlation Energy filters for optical pattern recognition introduces an implementational limitation of circular correlation. An alternative methodology which uses space domain computations to overcome this problem is presented. The technique is generalized to construct an improved synthetic discriminant function which satisfies the conflicting requirements of reduced noise variance and sharp correlation peaks to facilitate ease of detection. A quantitative evaluation of the performance characteristics of the new filter is conducted and is shown to compare favorably with the well known Minimum Variance Synthetic Discriminant Function and the space domain Minimum Average Correlation Energy filter, which are special cases of the present design.

An Undergraduate Electrical Engineering Course on Computer Organization.

ERIC Educational Resources Information Center

Commission on Engineering Education, Washington, DC.

Outlined is an undergraduate electrical engineering course on computer organization designed to meet the need for electrical engineers familiar with digital system design. The program includes both hardware and software aspects of digital systems essential to design function and correlates design and organizational aspects of the subject. The…

Computer Aided Training of Cognitive Processing Strategies with Developmentally Handicapped Adults.

ERIC Educational Resources Information Center

Ryba, Kenneth A.; And Others

1985-01-01

Correlational results involving 60 developmentally handicaped adults indicated that a computerized cross-modal memory game had a highly significant relationship with most cognitive and motor coordination measures. Computer aided training was not effective in improving overall cognitive functioning. There was no evidence of cognitive skills being…

Heavy particle signatures in cosmological correlation functions with tensor modes

NASA Astrophysics Data System (ADS)

Saito, Ryo; Kubota, Takahiro

2018-06-01

We explore the possibility to make use of cosmological data to look for signatures of unknown heavy particles whose masses are on the order of the Hubble parameter during the time of inflation. To be more specific we take up the quasi-single field inflation model, in which the isocurvaton σ is supposed to be the heavy particle. We study correlation functions involving both scalar (ζ ) and tensor (γ ) perturbations and search for imprints of the σ-particle effects. We make use of the technique of the effective field theory for inflation to derive the ζ σ and γ ζ σ couplings. With these couplings we compute the effects due to σ to the power spectrum langle ζ ζ rangle and correlations langle γs ζ ζ rangle and langle γs1 γ s2 ζ ζ rangle , where s, s1 and s2 are the polarization indices of gravitons. Numerical analyses of the σ-mass effects to these correlations are presented. It is argued that future precise observations of these correlations could make it possible to measure the σ-mass and the strength of the ζ σ and γ ζ σ couplings. As an extension to the N-graviton case we also compute the correlations langle γ s1 ... γ sN ζ ζ rangle and langle γ s1 ... ... γ s2N ζ ζ rangle and their σ-mass effects. It is suggested that larger N correlation functions are useful to probe larger σ-mass.

Matching-pursuit/split-operator-Fourier-transform computations of thermal correlation functions.

PubMed

Chen, Xin; Wu, Yinghua; Batista, Victor S

2005-02-08

A rigorous and practical methodology for evaluating thermal-equilibrium density matrices, finite-temperature time-dependent expectation values, and time-correlation functions is described. The method involves an extension of the matching-pursuit/split-operator-Fourier-transform method to the solution of the Bloch equation via imaginary-time propagation of the density matrix and the evaluation of Heisenberg time-evolution operators through real-time propagation in dynamically adaptive coherent-state representations.

Correlations for determining thermodynamic properties of hydrogen-helium gas mixtures at temperatures from 7,000 to 35,000 K

NASA Technical Reports Server (NTRS)

Zoby, E. V.; Gnoffo, P. A.; Graves, R. A., Jr.

1976-01-01

Simple relations for determining the enthalpy and temperature of hydrogen-helium gas mixtures were developed for hydrogen volumetric compositions from 1.0 to 0.7. These relations are expressed as a function of pressure and density and are valid for a range of temperatures from 7,000 to 35,000 K and pressures from 0.10 to 3.14 MPa. The proportionality constant and exponents in the correlation equations were determined for each gas composition by applying a linear least squares curve fit to a large number of thermodynamic calculations obtained from a detailed computer code. Although these simple relations yielded thermodynamic properties suitable for many engineering applications, their accuracy was improved significantly by evaluating the proportionality constants at postshock conditions and correlating these values as a function of the gas composition and the product of freestream velocity and shock angle. The resulting equations for the proportionality constants in terms of velocity and gas composition and the corresponding simple realtions for enthalpy and temperature were incorporated into a flow field computational scheme. Comparison was good between the thermodynamic properties determined from these relations and those obtained by using a detailed computer code to determine the properties. Thus, an appreciable savings in computer time was realized with no significant loss in accuracy.

Gradient corrections to the exchange-correlation free energy

DOE PAGES

Sjostrom, Travis; Daligault, Jerome

2014-10-07

We develop the first-order gradient correction to the exchange-correlation free energy of the homogeneous electron gas for use in finite-temperature density functional calculations. Based on this, we propose and implement a simple temperature-dependent extension for functionals beyond the local density approximation. These finite-temperature functionals show improvement over zero-temperature functionals, as compared to path-integral Monte Carlo calculations for deuterium equations of state, and perform without computational cost increase compared to zero-temperature functionals and so should be used for finite-temperature calculations. Furthermore, while the present functionals are valid at all temperatures including zero, non-negligible difference with zero-temperature functionals begins at temperatures abovemore » 10 000 K.« less

Quantitative computed tomography and aerosol morphometry in COPD and alpha1-antitrypsin deficiency.

PubMed

Shaker, S B; Maltbaek, N; Brand, P; Haeussermann, S; Dirksen, A

2005-01-01

Relative area of emphysema below -910 Hounsfield units (RA-910) and 15th percentile density (PD15) are quantitative computed tomography (CT) parameters used in the diagnosis of emphysema. New concepts for noninvasive diagnosis of emphysema are aerosol-derived airway morphometry, which measures effective airspace dimensions (EAD) and aerosol bolus dispersion (ABD). Quantitative CT, ABD and EAD were compared in 20 smokers with chronic obstructive pulmonary disease (COPD) and 22 patients with alpha1-antitrypsin deficiency (AAD) with a similar degree of airway obstruction and reduced diffusion capacity. In both groups, there was a significant correlation between RA-910 and PD15 and pulmonary function tests (PFTs). A significant correlation was also found between EAD, RA-910 and PD15 in the study population as a whole. Upon separation into two groups, the significance disappeared for the smokers with COPD and strengthened for those with AAD, where EAD correlated significantly with RA-910 and PD15. ABD was similar in the two groups and did not correlate with PFT and quantitative CT in either group. In conclusion, based on quantitative computed tomography and aerosol-derived airway morphometry, emphysema was significantly more severe in patients with alpha1-antitrypsin deficiency compared with patients with usual emphysema, despite similar measures of pulmonary function tests.

Quantitative CT analysis of honeycombing area in idiopathic pulmonary fibrosis: Correlations with pulmonary function tests.

PubMed

Nakagawa, Hiroaki; Nagatani, Yukihiro; Takahashi, Masashi; Ogawa, Emiko; Tho, Nguyen Van; Ryujin, Yasushi; Nagao, Taishi; Nakano, Yasutaka

2016-01-01

The 2011 official statement of idiopathic pulmonary fibrosis (IPF) mentions that the extent of honeycombing and the worsening of fibrosis on high-resolution computed tomography (HRCT) in IPF are associated with the increased risk of mortality. However, there are few reports about the quantitative computed tomography (CT) analysis of honeycombing area. In this study, we first proposed a computer-aided method for quantitative CT analysis of honeycombing area in patients with IPF. We then evaluated the correlations between honeycombing area measured by the proposed method with that estimated by radiologists or with parameters of PFTs. Chest HRCTs and pulmonary function tests (PFTs) of 36 IPF patients, who were diagnosed using HRCT alone, were retrospectively evaluated. Two thoracic radiologists independently estimated the honeycombing area as Identified Area (IA) and the percentage of honeycombing area to total lung area as Percent Area (PA) on 3 axial CT slices for each patient. We also developed a computer-aided method to measure the honeycombing area on CT images of those patients. The total honeycombing area as CT honeycombing area (HA) and the percentage of honeycombing area to total lung area as CT %honeycombing area (%HA) were derived from the computer-aided method for each patient. HA derived from three CT slices was significantly correlated with IA (ρ=0.65 for Radiologist 1 and ρ=0.68 for Radiologist 2). %HA derived from three CT slices was also significantly correlated with PA (ρ=0.68 for Radiologist 1 and ρ=0.70 for Radiologist 2). HA and %HA derived from all CT slices were significantly correlated with FVC (%pred.), DLCO (%pred.), and the composite physiologic index (CPI) (HA: ρ=-0.43, ρ=-0.56, ρ=0.63 and %HA: ρ=-0.60, ρ=-0.49, ρ=0.69, respectively). The honeycombing area measured by the proposed computer-aided method was correlated with that estimated by expert radiologists and with parameters of PFTs. This quantitative CT analysis of honeycombing area may be useful and reliable in patients with IPF. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Pulmonary function studies in young healthy Malaysians of Kelantan, Malaysia.

PubMed

Bandyopadhyay, Amit

2011-11-01

Pulmonary function tests have been evolved as clinical tools in diagnosis, management and follow up of respiratory diseases as it provides objective information about the status of an individual's respiratory system. The present study was aimed to evaluate pulmonary function among the male and female young Kelantanese Malaysians of Kota Bharu, Malaysia, and to compare the data with other populations. A total of 128 (64 males, 64 females) non-smoking healthy young subjects were randomly sampled for the study from the Kelantanese students' population of the University Sains Malaysia, Kota Bharu Campus, Kelantan, Malaysia. The study population (20-25 yr age group) had similar socio-economic background. Each subject filled up the ATS (1978) questionnaire to record their personal demographic data, health status and consent to participate in the study. Subjects with any history of pulmonary diseases were excluded from the study. The pulmonary function measurements exhibited significantly higher values among males than the females. FEV 1% did not show any significant inter-group variation probably because the parameter expresses FEV 1 as a percentage of FVC. FVC and FEV 1 exhibited significant correlations with body height and body mass among males whereas in the females exhibited significant correlation with body mass, body weight and also with age. FEV 1% exhibited significant correlation with body height and body mass among males and with body height in females. FEF 25-75% did not show any significant correlation except with body height among females. However, PEFR exhibited significant positive correlation with all the physical parameters except with age among the females. On the basis of the existence of significant correlation between different physical parameters and pulmonary function variables, simple and multiple regression norms have been computed. From the present investigation it can be concluded that Kelantanese Malaysian youths have normal range of pulmonary function in both the sexes and the computed regression norms may be used to predict the pulmonary function values in the studied population.

Pulmonary function studies in young healthy Malaysians of Kelantan, Malaysia

PubMed Central

Bandyopadhyay, Amit

2011-01-01

Background & objectives: Pulmonary function tests have been evolved as clinical tools in diagnosis, management and follow up of respiratory diseases as it provides objective information about the status of an individual's respiratory system. The present study was aimed to evaluate pulmonary function among the male and female young Kelantanese Malaysians of Kota Bharu, Malaysia, and to compare the data with other populations. Methods: A total of 128 (64 males, 64 females) non-smoking healthy young subjects were randomly sampled for the study from the Kelantanese students’ population of the University Sains Malaysia, Kota Bharu Campus, Kelantan, Malaysia. The study population (20-25 yr age group) had similar socio-economic background. Each subject filled up the ATS (1978) questionnaire to record their personal demographic data, health status and consent to participate in the study. Subjects with any history of pulmonary diseases were excluded from the study. Results: The pulmonary function measurements exhibited significantly higher values among males than the females. FEV1% did not show any significant inter-group variation probably because the parameter expresses FEV1 as a percentage of FVC. FVC and FEV1 exhibited significant correlations with body height and body mass among males whereas in the females exhibited significant correlation with body mass, body weight and also with age. FEV1% exhibited significant correlation with body height and body mass among males and with body height in females. FEF25-75% did not show any significant correlation except with body height among females. However, PEFR exhibited significant positive correlation with all the physical parameters except with age among the females. On the basis of the existence of significant correlation between different physical parameters and pulmonary function variables, simple and multiple regression norms have been computed. Interpretation & conclusions: From the present investigation it can be concluded that Kelantanese Malaysian youths have normal range of pulmonary function in both the sexes and the computed regression norms may be used to predict the pulmonary function values in the studied population. PMID:22199104

Blood flow measurement using digital subtraction angiography for assessing hemodialysis access function

NASA Astrophysics Data System (ADS)

Koirala, Nischal; Setser, Randolph M.; Bullen, Jennifer; McLennan, Gordon

2017-03-01

Blood flow rate is a critical parameter for diagnosing dialysis access function during fistulography where a flow rate of 600 ml/min in arteriovenous graft or 400-500 ml/min in arteriovenous fistula is considered the clinical threshold for fully functioning access. In this study, a flow rate computational model for calculating intra-access flow to evaluate dialysis access patency was developed and validated in an in vitro set up using digital subtraction angiography. Flow rates were computed by tracking the bolus through two regions of interest using cross correlation (XCOR) and mean arrival time (MAT) algorithms, and correlated versus an in-line transonic flow meter measurement. The mean difference (mean +/- standard deviation) between XCOR and in-line flow measurements for in vitro setup at 3, 6, 7.5 and 10 frames/s was 118+/-63 37+/-59 31+/-31 and 46+/-57 ml/min respectively while for MAT method it was 86+/-56 57+/-72 35+/-85 and 19+/-129 ml/min respectively. The result of this investigation will be helpful for selecting candidate algorithms while blood flow computational tool is developed for clinical application.

Infinities in Quantum Field Theory and in Classical Computing: Renormalization Program

NASA Astrophysics Data System (ADS)

Manin, Yuri I.

Introduction. The main observable quantities in Quantum Field Theory, correlation functions, are expressed by the celebrated Feynman path integrals. A mathematical definition of them involving a measure and actual integration is still lacking. Instead, it is replaced by a series of ad hoc but highly efficient and suggestive heuristic formulas such as perturbation formalism. The latter interprets such an integral as a formal series of finite-dimensional but divergent integrals, indexed by Feynman graphs, the list of which is determined by the Lagrangian of the theory. Renormalization is a prescription that allows one to systematically "subtract infinities" from these divergent terms producing an asymptotic series for quantum correlation functions. On the other hand, graphs treated as "flowcharts", also form a combinatorial skeleton of the abstract computation theory. Partial recursive functions that according to Church's thesis exhaust the universe of (semi)computable maps are generally not everywhere defined due to potentially infinite searches and loops. In this paper I argue that such infinities can be addressed in the same way as Feynman divergences. More details can be found in [9,10].

Linear-array based full-view high-resolution photoacoustic computed tomography of whole mouse brain functions in vivo

NASA Astrophysics Data System (ADS)

Li, Lei; Zhang, Pengfei; Wang, Lihong V.

2018-02-01

Photoacoustic computed tomography (PACT) is a non-invasive imaging technique offering high contrast, high resolution, and deep penetration in biological tissues. We report a photoacoustic computed tomography (PACT) system equipped with a high frequency linear array for anatomical and functional imaging of the mouse whole brain. The linear array was rotationally scanned in the coronal plane to achieve the full-view coverage. We investigated spontaneous neural activities in the deep brain by monitoring the hemodynamics and observed strong interhemispherical correlations between contralateral regions, both in the cortical layer and in the deep regions.

Classical density functional theory and the phase-field crystal method using a rational function to describe the two-body direct correlation function.

PubMed

Pisutha-Arnond, N; Chan, V W L; Iyer, M; Gavini, V; Thornton, K

2013-01-01

We introduce a new approach to represent a two-body direct correlation function (DCF) in order to alleviate the computational demand of classical density functional theory (CDFT) and enhance the predictive capability of the phase-field crystal (PFC) method. The approach utilizes a rational function fit (RFF) to approximate the two-body DCF in Fourier space. We use the RFF to show that short-wavelength contributions of the two-body DCF play an important role in determining the thermodynamic properties of materials. We further show that using the RFF to empirically parametrize the two-body DCF allows us to obtain the thermodynamic properties of solids and liquids that agree with the results of CDFT simulations with the full two-body DCF without incurring significant computational costs. In addition, the RFF can also be used to improve the representation of the two-body DCF in the PFC method. Last, the RFF allows for a real-space reformulation of the CDFT and PFC method, which enables descriptions of nonperiodic systems and the use of nonuniform and adaptive grids.

Quantitative computed tomography of pulmonary emphysema and ventricular function in chronic obstructive pulmonary disease patients with pulmonary hypertension.

PubMed

Huang, Yu-Sen; Hsu, Hsao-Hsun; Chen, Jo-Yu; Tai, Mei-Hwa; Jaw, Fu-Shan; Chang, Yeun-Chung

2014-01-01

This study strived to evaluate the relationship between degree of pulmonary emphysema and cardiac ventricular function in chronic obstructive pulmonary disease (COPD) patients with pulmonary hypertension (PH) using electrocardiographic-gated multidetector computed tomography (CT). Lung transplantation candidates with the diagnosis of COPD and PH were chosen for the study population, and a total of 15 patients were included. The extent of emphysema is defined as the percentage of voxels below -910 Hounsfield units in the lung windows in whole lung CT without intravenous contrast. Heart function parameters were measured by electrocardiographic-gated CT angiography. Linear regression analysis was conducted to examine the associations between percent emphysema and heart function indicators. Significant correlations were found between percent emphysema and right ventricular (RV) measurements, including RV end-diastolic volume (R(2) = 0.340, p = 0.023), RV stroke volume (R(2) = 0.406, p = 0.011), and RV cardiac output (R(2) = 0.382, p = 0.014); the correlations between percent emphysema and left ventricular function indicators were not observed. The study revealed that percent emphysema is correlated with RV dysfunction among COPD patients with PH. Based on our findings, percent emphysema can be considered for use as an indicator to predict the severity of right ventricular dysfunction among COPD patients.

Cyber-Physical Correlations for Infrastructure Resilience: A Game-Theoretic Approach

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

Rao, Nageswara S; He, Fei; Ma, Chris Y. T.

In several critical infrastructures, the cyber and physical parts are correlated so that disruptions to one affect the other and hence the whole system. These correlations may be exploited to strategically launch components attacks, and hence must be accounted for ensuring the infrastructure resilience, specified by its survival probability. We characterize the cyber-physical interactions at two levels: (i) the failure correlation function specifies the conditional survival probability of cyber sub-infrastructure given the physical sub-infrastructure as a function of their marginal probabilities, and (ii) the individual survival probabilities of both sub-infrastructures are characterized by first-order differential conditions. We formulate a resiliencemore » problem for infrastructures composed of discrete components as a game between the provider and attacker, wherein their utility functions consist of an infrastructure survival probability term and a cost term expressed in terms of the number of components attacked and reinforced. We derive Nash Equilibrium conditions and sensitivity functions that highlight the dependence of infrastructure resilience on the cost term, correlation function and sub-infrastructure survival probabilities. These results generalize earlier ones based on linear failure correlation functions and independent component failures. We apply the results to models of cloud computing infrastructures and energy grids.« less

Influence of super-horizon modes on correlation functions during inflation

NASA Astrophysics Data System (ADS)

Deutsch, Anne-Sylvie

2018-05-01

Coupling between sub- and super-Hubble modes can affect the locally observed statistics of our universe. In the context of Quasi-Single Field Inflation, we can compute correlation functions and derive the influence of those unobservable modes on observed correlation functions as well as on the inferred cosmological parameters. We study how different classes of diagrams affect the bispectrum in the squeezed limit; in particular, while contact-like diagrams leave the scaling between the long and short modes unchanged, exchange-like diagrams do modify the shape of the bispectrum. We show that the mass of the hidden sector field can hence be biased by an unavoidable cosmic variance that can reach a 1-σ uncertainty of Script O(10%) for a weakly non-Gaussian universe. Finally, we go beyond the bispectrum and show how couplings between unobservable and observable modes can affect generic correlation functions with arbitrary order non-derivative self-interactions.

Gluon amplitudes as 2 d conformal correlators

NASA Astrophysics Data System (ADS)

Pasterski, Sabrina; Shao, Shu-Heng; Strominger, Andrew

2017-10-01

Recently, spin-one wave functions in four dimensions that are conformal primaries of the Lorentz group S L (2 ,C ) were constructed. We compute low-point, tree-level gluon scattering amplitudes in the space of these conformal primary wave functions. The answers have the same conformal covariance as correlators of spin-one primaries in a 2 d CFT. The Britto-Cachazo-Feng-Witten (BCFW) recursion relation between three- and four-point gluon amplitudes is recast into this conformal basis.

Recurrence formulas for fully exponentially correlated four-body wave functions

NASA Astrophysics Data System (ADS)

Harris, Frank E.

2009-03-01

Formulas are presented for the recursive generation of four-body integrals in which the integrand consists of arbitrary integer powers (≥-1) of all the interparticle distances rij , multiplied by an exponential containing an arbitrary linear combination of all the rij . These integrals are generalizations of those encountered using Hylleraas basis functions and include all that are needed to make energy computations on the Li atom and other four-body systems with a fully exponentially correlated Slater-type basis of arbitrary quantum numbers. The only quantities needed to start the recursion are the basic four-body integral first evaluated by Fromm and Hill plus some easily evaluated three-body “boundary” integrals. The computational labor in constructing integral sets for practical computations is less than when the integrals are generated using explicit formulas obtained by differentiating the basic integral with respect to its parameters. Computations are facilitated by using a symbolic algebra program (MAPLE) to compute array index pointers and present syntactically correct FORTRAN source code as output; in this way it is possible to obtain error-free high-speed evaluations with minimal effort. The work can be checked by verifying sum rules the integrals must satisfy.

Kubo formulas for the shear and bulk viscosity relaxation times and the scalar field theory shear τπ calculation

NASA Astrophysics Data System (ADS)

Czajka, Alina; Jeon, Sangyong

2017-06-01

In this paper we provide a quantum field theoretical study on the shear and bulk relaxation times. First, we find Kubo formulas for the shear and the bulk relaxation times, respectively. They are found by examining response functions of the stress-energy tensor. We use general properties of correlation functions and the gravitational Ward identity to parametrize analytical structures of the Green functions describing both sound and diffusion mode. We find that the hydrodynamic limits of the real parts of the respective energy-momentum tensor correlation functions provide us with the method of computing both the shear and bulk viscosity relaxation times. Next, we calculate the shear viscosity relaxation time using the diagrammatic approach in the Keldysh basis for the massless λ ϕ4 theory. We derive a respective integral equation which enables us to compute η τπ and then we extract the shear relaxation time. The relaxation time is shown to be inversely related to the thermal width as it should be.

Detection of seizures from small samples using nonlinear dynamic system theory.

PubMed

Yaylali, I; Koçak, H; Jayakar, P

1996-07-01

The electroencephalogram (EEG), like many other biological phenomena, is quite likely governed by nonlinear dynamics. Certain characteristics of the underlying dynamics have recently been quantified by computing the correlation dimensions (D2) of EEG time series data. In this paper, D2 of the unbiased autocovariance function of the scalp EEG data was used to detect electrographic seizure activity. Digital EEG data were acquired at a sampling rate of 200 Hz per channel and organized in continuous frames (duration 2.56 s, 512 data points). To increase the reliability of D2 computations with short duration data, raw EEG data were initially simplified using unbiased autocovariance analysis to highlight the periodic activity that is present during seizures. The D2 computation was then performed from the unbiased autocovariance function of each channel using the Grassberger-Procaccia method with Theiler's box-assisted correlation algorithm. Even with short duration data, this preprocessing proved to be computationally robust and displayed no significant sensitivity to implementation details such as the choices of embedding dimension and box size. The system successfully identified various types of seizures in clinical studies.

Compensated Crystal Assemblies for Type-II Entangled Photon Generation in Quantum Cluster States

DTIC Science & Technology

2010-03-01

in quantum computational architectures that operate by principles entirely distinct from any based on classical physics. In contrast with other...of the SPDC spectral function, to enable applications in regions that have not been accessible with other methods. Quantum Information and Computation ...Eliminating frequency and space-time correlations in multi-photon states, PRA 64, 063815, 2001 [2]A. Zeilinger et.al. Experimental One-way computing

Multicomponent density functional theory embedding formulation.

PubMed

Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

2016-07-28

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.

Multicomponent density functional theory embedding formulation

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

Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density ismore » separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF{sup −} molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.« less

First Principles Study of Chemically Functionalized Graphene

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Vasiliev, Igor

2015-03-01

The electronic, structural and vibrational properties of carbon nanomaterials can be affected by chemical functionalization. We applied ab initio computational methods based on density functional theory to study the covalent functionalization of graphene with benzyne, carboxyl groups and tetracyanoethylene oxide (TCNEO). Our calculations were carried out using the SIESTA and Quantum-ESPRESSO electronic structure codes combined with the local density and generalized gradient approximations for the exchange correlation functional and norm-conserving Troullier-Martins pseudopotentials. The simulated Raman and infrared spectra of graphene functionalized with carboxyl groups and TCNEO were consistent with the available experimental results. The computed vibrational spectra of graphene functionalized with carboxyl groups showed that the presence of point defects near the functionalization site affects the Raman and infrared spectroscopic signatures of functionalized graphene. Supported by NSF CHE-1112388.

Multifractal analysis of information processing in hippocampal neural ensembles during working memory under Δ9-tetrahydrocannabinol administration

PubMed Central

Fetterhoff, Dustin; Opris, Ioan; Simpson, Sean L.; Deadwyler, Sam A.; Hampson, Robert E.; Kraft, Robert A.

2014-01-01

Background Multifractal analysis quantifies the time-scale-invariant properties in data by describing the structure of variability over time. By applying this analysis to hippocampal interspike interval sequences recorded during performance of a working memory task, a measure of long-range temporal correlations and multifractal dynamics can reveal single neuron correlates of information processing. New method Wavelet leaders-based multifractal analysis (WLMA) was applied to hippocampal interspike intervals recorded during a working memory task. WLMA can be used to identify neurons likely to exhibit information processing relevant to operation of brain–computer interfaces and nonlinear neuronal models. Results Neurons involved in memory processing (“Functional Cell Types” or FCTs) showed a greater degree of multifractal firing properties than neurons without task-relevant firing characteristics. In addition, previously unidentified FCTs were revealed because multifractal analysis suggested further functional classification. The cannabinoid-type 1 receptor partial agonist, tetrahydrocannabinol (THC), selectively reduced multifractal dynamics in FCT neurons compared to non-FCT neurons. Comparison with existing methods WLMA is an objective tool for quantifying the memory-correlated complexity represented by FCTs that reveals additional information compared to classification of FCTs using traditional z-scores to identify neuronal correlates of behavioral events. Conclusion z-Score-based FCT classification provides limited information about the dynamical range of neuronal activity characterized by WLMA. Increased complexity, as measured with multifractal analysis, may be a marker of functional involvement in memory processing. The level of multifractal attributes can be used to differentially emphasize neural signals to improve computational models and algorithms underlying brain–computer interfaces. PMID:25086297

Creating a Computer Adaptive Test Version of the Late-Life Function & Disability Instrument

PubMed Central

Jette, Alan M.; Haley, Stephen M.; Ni, Pengsheng; Olarsch, Sippy; Moed, Richard

2009-01-01

Background This study applied Item Response Theory (IRT) and Computer Adaptive Test (CAT) methodologies to develop a prototype function and disability assessment instrument for use in aging research. Herein, we report on the development of the CAT version of the Late-Life Function & Disability instrument (Late-Life FDI) and evaluate its psychometric properties. Methods We employed confirmatory factor analysis, IRT methods, validation, and computer simulation analyses of data collected from 671 older adults residing in residential care facilities. We compared accuracy, precision, and sensitivity to change of scores from CAT versions of two Late-Life FDI scales with scores from the fixed-form instrument. Score estimates from the prototype CAT versus the original instrument were compared in a sample of 40 older adults. Results Distinct function and disability domains were identified within the Late-Life FDI item bank and used to construct two prototype CAT scales. Using retrospective data, scores from computer simulations of the prototype CAT scales were highly correlated with scores from the original instrument. The results of computer simulation, accuracy, precision, and sensitivity to change of the CATs closely approximated those of the fixed-form scales, especially for the 10- or 15-item CAT versions. In the prospective study each CAT was administered in less than 3 minutes and CAT scores were highly correlated with scores generated from the original instrument. Conclusions CAT scores of the Late-Life FDI were highly comparable to those obtained from the full-length instrument with a small loss in accuracy, precision, and sensitivity to change. PMID:19038841

Man-Computer Interactive Data Access System (McIDAS). Continued development of McIDAS and operation in the GARP Atlantic tropical experiment

NASA Technical Reports Server (NTRS)

Suomi, V. E.

1975-01-01

The complete output of the Synchronous Meteorological Satellite was recorded on one inch magnetic tape. A quality control subsystem tests cloud track vectors against four sets of criteria: (1) rejection if best match occurs on correlation boundary; (2) rejection if major correlation peak is not distinct and significantly greater than secondary peak; (3) rejection if correlation is not persistent; and (4) rejection if acceleration is too great. A cloud height program determines cloud optical thickness from visible data and computer infrared emissivity. From infrared data and temperature profile, cloud height is determined. A functional description and electronic schematics of equipment are given.

Game-Theoretic strategies for systems of components using product-form utilities

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

Rao, Nageswara S; Ma, Cheng-Yu; Hausken, K.

Many critical infrastructures are composed of multiple systems of components which are correlated so that disruptions to one may propagate to others. We consider such infrastructures with correlations characterized in two ways: (i) an aggregate failure correlation function specifies the conditional failure probability of the infrastructure given the failure of an individual system, and (ii) a pairwise correlation function between two systems specifies the failure probability of one system given the failure of the other. We formulate a game for ensuring the resilience of the infrastructure, wherein the utility functions of the provider and attacker are products of an infrastructuremore » survival probability term and a cost term, both expressed in terms of the numbers of system components attacked and reinforced. The survival probabilities of individual systems satisfy first-order differential conditions that lead to simple Nash Equilibrium conditions. We then derive sensitivity functions that highlight the dependence of infrastructure resilience on the cost terms, correlation functions, and individual system survival probabilities. We apply these results to simplified models of distributed cloud computing and energy grid infrastructures.« less

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package.

PubMed

Womack, James C; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-28

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package

NASA Astrophysics Data System (ADS)

Womack, James C.; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-01

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Soft Functionals for Hard Matter

NASA Astrophysics Data System (ADS)

Cooper, Valentino R.; Yuk, Simuck F.; Krogel, Jaron T.

Theory and computation are critical to the materials discovery process. While density functional theory (DFT) has become the standard for predicting materials properties, it is often plagued by inaccuracies in the underlying exchange-correlation functionals. Using high-throughput DFT calculations we explore the accuracy of various exchange-correlation functionals for modeling the structural and thermodynamic properties of a wide range of complex oxides. In particular, we examine the feasibility of using the nonlocal van der Waals density correlation functional with C09 exchange (C09x), which was designed for sparsely packed soft matter, for investigating the properties of hard matter like bulk oxides. Preliminary results show unprecedented performance for some prototypical bulk ferroelectrics, which can be correlated with similarities between C09x and PBEsol. This effort lays the groundwork for understanding how these soft functionals can be employed as general purpose functionals for studying a wide range of materials where strong internal bonds and nonlocal interactions coexist. Research was sponsored by the US DOE, Office of Science, BES, MSED and Early Career Research Programs and used resources at NERSC.

Density functional theory for d- and f-electron materials and compounds

DOE PAGES

Mattson, Ann E.; Wills, John M.

2016-02-12

Here, the fundamental requirements for a computationally tractable Density Functional Theory-based method for relativistic f- and (nonrelativistic) d-electron materials and compounds are presented. The need for basing the Kohn–Sham equations on the Dirac equation is discussed. The full Dirac scheme needs exchange-correlation functionals in terms of four-currents, but ordinary functionals, using charge density and spin-magnetization, can be used in an approximate Dirac treatment. The construction of a functional that includes the additional confinement physics needed for these materials is illustrated using the subsystem-functional scheme. If future studies show that a full Dirac, four-current based, exchange-correlation functional is needed, the subsystemmore » functional scheme is one of the few schemes that can still be used for constructing functional approximations.« less

correlcalc: Two-point correlation function from redshift surveys

NASA Astrophysics Data System (ADS)

Rohin, Yeluripati

2017-11-01

correlcalc calculates two-point correlation function (2pCF) of galaxies/quasars using redshift surveys. It can be used for any assumed geometry or Cosmology model. Using BallTree algorithms to reduce the computational effort for large datasets, it is a parallelised code suitable for running on clusters as well as personal computers. It takes redshift (z), Right Ascension (RA) and Declination (DEC) data of galaxies and random catalogs as inputs in form of ascii or fits files. If random catalog is not provided, it generates one of desired size based on the input redshift distribution and mangle polygon file (in .ply format) describing the survey geometry. It also calculates different realisations of (3D) anisotropic 2pCF. Optionally it makes healpix maps of the survey providing visualization.

Functional inverted Wishart for Bayesian multivariate spatial modeling with application to regional climatology model data.

PubMed

Duan, L L; Szczesniak, R D; Wang, X

2017-11-01

Modern environmental and climatological studies produce multiple outcomes at high spatial resolutions. Multivariate spatial modeling is an established means to quantify cross-correlation among outcomes. However, existing models typically suffer from poor computational efficiency and lack the flexibility to simultaneously estimate auto- and cross-covariance structures. In this article, we undertake a novel construction of covariance by utilizing spectral convolution and by imposing an inverted Wishart prior on the cross-correlation structure. The cross-correlation structure with this functional inverted Wishart prior flexibly accommodates not only positive but also weak or negative associations among outcomes while preserving spatial resolution. Furthermore, the proposed model is computationally efficient and produces easily interpretable results, including the individual autocovariances and full cross-correlation matrices, as well as a partial cross-correlation matrix reflecting the outcome correlation after excluding the effects caused by spatial convolution. The model is examined using simulated data sets under different scenarios. It is also applied to the data from the North American Regional Climate Change Assessment Program, examining long-term associations between surface outcomes for air temperature, pressure, humidity, and radiation, on the land area of the North American West Coast. Results and predictive performance are compared with findings from approaches using convolution only or coregionalization.

Functional inverted Wishart for Bayesian multivariate spatial modeling with application to regional climatology model data

PubMed Central

Duan, L. L.; Szczesniak, R. D.; Wang, X.

2018-01-01

Modern environmental and climatological studies produce multiple outcomes at high spatial resolutions. Multivariate spatial modeling is an established means to quantify cross-correlation among outcomes. However, existing models typically suffer from poor computational efficiency and lack the flexibility to simultaneously estimate auto- and cross-covariance structures. In this article, we undertake a novel construction of covariance by utilizing spectral convolution and by imposing an inverted Wishart prior on the cross-correlation structure. The cross-correlation structure with this functional inverted Wishart prior flexibly accommodates not only positive but also weak or negative associations among outcomes while preserving spatial resolution. Furthermore, the proposed model is computationally efficient and produces easily interpretable results, including the individual autocovariances and full cross-correlation matrices, as well as a partial cross-correlation matrix reflecting the outcome correlation after excluding the effects caused by spatial convolution. The model is examined using simulated data sets under different scenarios. It is also applied to the data from the North American Regional Climate Change Assessment Program, examining long-term associations between surface outcomes for air temperature, pressure, humidity, and radiation, on the land area of the North American West Coast. Results and predictive performance are compared with findings from approaches using convolution only or coregionalization. PMID:29576735

Handling of computational in vitro/in vivo correlation problems by Microsoft Excel II. Distribution functions and moments.

PubMed

Langenbucher, Frieder

2003-01-01

MS Excel is a useful tool to handle in vitro/in vivo correlation (IVIVC) distribution functions, with emphasis on the Weibull and the biexponential distribution, which are most useful for the presentation of cumulative profiles, e.g. release in vitro or urinary excretion in vivo, and differential profiles such as the plasma response in vivo. The discussion includes moments (AUC and mean) as summarizing statistics, and data-fitting algorithms for parameter estimation.

Program for the analysis of time series. [by means of fast Fourier transform algorithm

NASA Technical Reports Server (NTRS)

Brown, T. J.; Brown, C. G.; Hardin, J. C.

1974-01-01

A digital computer program for the Fourier analysis of discrete time data is described. The program was designed to handle multiple channels of digitized data on general purpose computer systems. It is written, primarily, in a version of FORTRAN 2 currently in use on CDC 6000 series computers. Some small portions are written in CDC COMPASS, an assembler level code. However, functional descriptions of these portions are provided so that the program may be adapted for use on any facility possessing a FORTRAN compiler and random-access capability. Properly formatted digital data are windowed and analyzed by means of a fast Fourier transform algorithm to generate the following functions: (1) auto and/or cross power spectra, (2) autocorrelations and/or cross correlations, (3) Fourier coefficients, (4) coherence functions, (5) transfer functions, and (6) histograms.

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice–Ramsperger–Kassel theory

PubMed Central

Bao, Junwei Lucas; Zhang, Xin

2016-01-01

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C2F4), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice–Ramsperger–Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements. PMID:27834727

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory.

PubMed

Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

2016-11-29

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C 2 F 4 ), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice-Ramsperger-Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements.

Integrable dissipative exclusion process: Correlation functions and physical properties

NASA Astrophysics Data System (ADS)

Crampe, N.; Ragoucy, E.; Rittenberg, V.; Vanicat, M.

2016-09-01

We study a one-parameter generalization of the symmetric simple exclusion process on a one-dimensional lattice. In addition to the usual dynamics (where particles can hop with equal rates to the left or to the right with an exclusion constraint), annihilation and creation of pairs can occur. The system is driven out of equilibrium by two reservoirs at the boundaries. In this setting the model is still integrable: it is related to the open XXZ spin chain through a gauge transformation. This allows us to compute the full spectrum of the Markov matrix using Bethe equations. We also show that the stationary state can be expressed in a matrix product form permitting to compute the multipoints correlation functions as well as the mean value of the lattice and the creation-annihilation currents. Finally, the variance of the lattice current is computed for a finite-size system. In the thermodynamic limit, it matches the value obtained from the associated macroscopic fluctuation theory.

EXACT DISTRIBUTIONS OF INTRACLASS CORRELATION AND CRONBACH'S ALPHA WITH GAUSSIAN DATA AND GENERAL COVARIANCE.

PubMed

Kistner, Emily O; Muller, Keith E

2004-09-01

Intraclass correlation and Cronbach's alpha are widely used to describe reliability of tests and measurements. Even with Gaussian data, exact distributions are known only for compound symmetric covariance (equal variances and equal correlations). Recently, large sample Gaussian approximations were derived for the distribution functions. New exact results allow calculating the exact distribution function and other properties of intraclass correlation and Cronbach's alpha, for Gaussian data with any covariance pattern, not just compound symmetry. Probabilities are computed in terms of the distribution function of a weighted sum of independent chi-square random variables. New F approximations for the distribution functions of intraclass correlation and Cronbach's alpha are much simpler and faster to compute than the exact forms. Assuming the covariance matrix is known, the approximations typically provide sufficient accuracy, even with as few as ten observations. Either the exact or approximate distributions may be used to create confidence intervals around an estimate of reliability. Monte Carlo simulations led to a number of conclusions. Correctly assuming that the covariance matrix is compound symmetric leads to accurate confidence intervals, as was expected from previously known results. However, assuming and estimating a general covariance matrix produces somewhat optimistically narrow confidence intervals with 10 observations. Increasing sample size to 100 gives essentially unbiased coverage. Incorrectly assuming compound symmetry leads to pessimistically large confidence intervals, with pessimism increasing with sample size. In contrast, incorrectly assuming general covariance introduces only a modest optimistic bias in small samples. Hence the new methods seem preferable for creating confidence intervals, except when compound symmetry definitely holds.

Equilibrium properties and phase diagram of two-dimensional Yukawa systems

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

Hartmann, P.; Donko, Z.; Kutasi, K.

Properties of two-dimensional strongly coupled Yukawa systems are explored through molecular dynamics simulations. An effective coupling coefficient {gamma}{sup *} for the liquid phase is introduced on the basis of the constancy of the first peak amplitude of the pair-correlation functions. Thermodynamic quantities are calculated from the pair-correlation function. The solid-liquid transition of the system is investigated through the analysis of the bond-angular order parameter. The static structure function satisfies consistency relation, attesting to the reliability of the computational method. The response is shown to be governed by the correlational part of the inverse compressibility. An analysis of the velocity autocorrelationmore » demonstrates that this latter also exhibits a universal behavior.« less

High-resolution correlation

NASA Astrophysics Data System (ADS)

Nelson, D. J.

2007-09-01

In the basic correlation process a sequence of time-lag-indexed correlation coefficients are computed as the inner or dot product of segments of two signals. The time-lag(s) for which the magnitude of the correlation coefficient sequence is maximized is the estimated relative time delay of the two signals. For discrete sampled signals, the delay estimated in this manner is quantized with the same relative accuracy as the clock used in sampling the signals. In addition, the correlation coefficients are real if the input signals are real. There have been many methods proposed to estimate signal delay to more accuracy than the sample interval of the digitizer clock, with some success. These methods include interpolation of the correlation coefficients, estimation of the signal delay from the group delay function, and beam forming techniques, such as the MUSIC algorithm. For spectral estimation, techniques based on phase differentiation have been popular, but these techniques have apparently not been applied to the correlation problem . We propose a phase based delay estimation method (PBDEM) based on the phase of the correlation function that provides a significant improvement of the accuracy of time delay estimation. In the process, the standard correlation function is first calculated. A time lag error function is then calculated from the correlation phase and is used to interpolate the correlation function. The signal delay is shown to be accurately estimated as the zero crossing of the correlation phase near the index of the peak correlation magnitude. This process is nearly as fast as the conventional correlation function on which it is based. For real valued signals, a simple modification is provided, which results in the same correlation accuracy as is obtained for complex valued signals.

Estimating Function Approaches for Spatial Point Processes

NASA Astrophysics Data System (ADS)

Deng, Chong

Spatial point pattern data consist of locations of events that are often of interest in biological and ecological studies. Such data are commonly viewed as a realization from a stochastic process called spatial point process. To fit a parametric spatial point process model to such data, likelihood-based methods have been widely studied. However, while maximum likelihood estimation is often too computationally intensive for Cox and cluster processes, pairwise likelihood methods such as composite likelihood, Palm likelihood usually suffer from the loss of information due to the ignorance of correlation among pairs. For many types of correlated data other than spatial point processes, when likelihood-based approaches are not desirable, estimating functions have been widely used for model fitting. In this dissertation, we explore the estimating function approaches for fitting spatial point process models. These approaches, which are based on the asymptotic optimal estimating function theories, can be used to incorporate the correlation among data and yield more efficient estimators. We conducted a series of studies to demonstrate that these estmating function approaches are good alternatives to balance the trade-off between computation complexity and estimating efficiency. First, we propose a new estimating procedure that improves the efficiency of pairwise composite likelihood method in estimating clustering parameters. Our approach combines estimating functions derived from pairwise composite likeli-hood estimation and estimating functions that account for correlations among the pairwise contributions. Our method can be used to fit a variety of parametric spatial point process models and can yield more efficient estimators for the clustering parameters than pairwise composite likelihood estimation. We demonstrate its efficacy through a simulation study and an application to the longleaf pine data. Second, we further explore the quasi-likelihood approach on fitting second-order intensity function of spatial point processes. However, the original second-order quasi-likelihood is barely feasible due to the intense computation and high memory requirement needed to solve a large linear system. Motivated by the existence of geometric regular patterns in the stationary point processes, we find a lower dimension representation of the optimal weight function and propose a reduced second-order quasi-likelihood approach. Through a simulation study, we show that the proposed method not only demonstrates superior performance in fitting the clustering parameter but also merits in the relaxation of the constraint of the tuning parameter, H. Third, we studied the quasi-likelihood type estimating funciton that is optimal in a certain class of first-order estimating functions for estimating the regression parameter in spatial point process models. Then, by using a novel spectral representation, we construct an implementation that is computationally much more efficient and can be applied to more general setup than the original quasi-likelihood method.

A new technique to determine the correlation between the QT interval and heart-rate for control and SIDS babies

NASA Technical Reports Server (NTRS)

Sadeh, D.; Shannon, D. C.; Abboud, S.; Akselrod, S.; Cohen, R. J.

1987-01-01

The ability of the autonomic nervous system to alter the QT interval in response to heart rate changes is essential to cardiovascular control. An accurate way to determine the relation between QT intervals and their corresponding RR intervals is described. A computer algorithm measures the RR intervals using digital filtering and cross-correlating the QRS sections of consecutive waveforms. The QT intervals is calculated by choosing a section of, the ECG that includes the T wave and cross-correlating it with all the consecutive T waves. At least 4000 pairs of QT-RR intervals are computed for each subject and a best fit correlation function determines the relations between the QT and RR intervals. This technique enables to establish a precise correlation between RR and QT in order to distinguish between control and SIDS babies.

Coupled Cluster Method with Single and Double Excitations Tailored by Matrix Product State Wave Functions.

PubMed

Veis, Libor; Antalík, Andrej; Brabec, Jiří; Neese, Frank; Legeza, Örs; Pittner, Jiří

2016-10-03

In the past decade, the quantum chemical version of the density matrix renormalization group (DMRG) method has established itself as the method of choice for calculations of strongly correlated molecular systems. Despite its favorable scaling, it is in practice not suitable for computations of dynamic correlation. We present a novel method for accurate "post-DMRG" treatment of dynamic correlation based on the tailored coupled cluster (CC) theory in which the DMRG method is responsible for the proper description of nondynamic correlation, whereas dynamic correlation is incorporated through the framework of the CC theory. We illustrate the potential of this method on prominent multireference systems, in particular, N 2 and Cr 2 molecules and also oxo-Mn(Salen), for which we have performed the first post-DMRG computations in order to shed light on the energy ordering of the lowest spin states.

Functional connectivity and structural covariance between regions of interest can be measured more accurately using multivariate distance correlation.

PubMed

Geerligs, Linda; Cam-Can; Henson, Richard N

2016-07-15

Studies of brain-wide functional connectivity or structural covariance typically use measures like the Pearson correlation coefficient, applied to data that have been averaged across voxels within regions of interest (ROIs). However, averaging across voxels may result in biased connectivity estimates when there is inhomogeneity within those ROIs, e.g., sub-regions that exhibit different patterns of functional connectivity or structural covariance. Here, we propose a new measure based on "distance correlation"; a test of multivariate dependence of high dimensional vectors, which allows for both linear and non-linear dependencies. We used simulations to show how distance correlation out-performs Pearson correlation in the face of inhomogeneous ROIs. To evaluate this new measure on real data, we use resting-state fMRI scans and T1 structural scans from 2 sessions on each of 214 participants from the Cambridge Centre for Ageing & Neuroscience (Cam-CAN) project. Pearson correlation and distance correlation showed similar average connectivity patterns, for both functional connectivity and structural covariance. Nevertheless, distance correlation was shown to be 1) more reliable across sessions, 2) more similar across participants, and 3) more robust to different sets of ROIs. Moreover, we found that the similarity between functional connectivity and structural covariance estimates was higher for distance correlation compared to Pearson correlation. We also explored the relative effects of different preprocessing options and motion artefacts on functional connectivity. Because distance correlation is easy to implement and fast to compute, it is a promising alternative to Pearson correlations for investigating ROI-based brain-wide connectivity patterns, for functional as well as structural data. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Quantitative evaluation of cross correlation between two finite-length time series with applications to single-molecule FRET.

PubMed

Hanson, Jeffery A; Yang, Haw

2008-11-06

The statistical properties of the cross correlation between two time series has been studied. An analytical expression for the cross correlation function's variance has been derived. On the basis of these results, a statistically robust method has been proposed to detect the existence and determine the direction of cross correlation between two time series. The proposed method has been characterized by computer simulations. Applications to single-molecule fluorescence spectroscopy are discussed. The results may also find immediate applications in fluorescence correlation spectroscopy (FCS) and its variants.

Brownian thermal noise in functional optical surfaces

NASA Astrophysics Data System (ADS)

Kroker, S.; Dickmann, J.; Rojas Hurtado, C. B.; Heinert, D.; Nawrodt, R.; Levin, Y.; Vyatchanin, S. P.

2017-07-01

We present a formalism to compute Brownian thermal noise in functional optical surfaces such as grating reflectors, photonic crystal slabs, or complex metamaterials. Such computations are based on a specific readout variable, typically a surface integral of a dielectric interface displacement weighed by a form factor. This paper shows how to relate this form factor to Maxwell's stress tensor computed on all interfaces of the moving surface. As an example, we examine Brownian thermal noise in monolithic T-shaped grating reflectors. The previous computations by Heinert et al. [Phys. Rev. D 88, 042001 (2013), 10.1103/PhysRevD.88.042001] utilizing a simplified readout form factor produced estimates of thermal noise that are tens of percent higher than those of the exact analysis in the present paper. The relation between the form factor and Maxwell's stress tensor implies a close correlation between the optical properties of functional optical surfaces and thermal noise.

SD-CAS: Spin Dynamics by Computer Algebra System.

PubMed

Filip, Xenia; Filip, Claudiu

2010-11-01

A computer algebra tool for describing the Liouville-space quantum evolution of nuclear 1/2-spins is introduced and implemented within a computational framework named Spin Dynamics by Computer Algebra System (SD-CAS). A distinctive feature compared with numerical and previous computer algebra approaches to solving spin dynamics problems results from the fact that no matrix representation for spin operators is used in SD-CAS, which determines a full symbolic character to the performed computations. Spin correlations are stored in SD-CAS as four-entry nested lists of which size increases linearly with the number of spins into the system and are easily mapped into analytical expressions in terms of spin operator products. For the so defined SD-CAS spin correlations a set of specialized functions and procedures is introduced that are essential for implementing basic spin algebra operations, such as the spin operator products, commutators, and scalar products. They provide results in an abstract algebraic form: specific procedures to quantitatively evaluate such symbolic expressions with respect to the involved spin interaction parameters and experimental conditions are also discussed. Although the main focus in the present work is on laying the foundation for spin dynamics symbolic computation in NMR based on a non-matrix formalism, practical aspects are also considered throughout the theoretical development process. In particular, specific SD-CAS routines have been implemented using the YACAS computer algebra package (http://yacas.sourceforge.net), and their functionality was demonstrated on a few illustrative examples. Copyright © 2010 Elsevier Inc. All rights reserved.

Utility of Quantitative Parameters from Single-Photon Emission Computed Tomography/Computed Tomography in Patients with Destructive Thyroiditis.

PubMed

Kim, Ji-Young; Kim, Ji Hyun; Moon, Jae Hoon; Kim, Kyoung Min; Oh, Tae Jung; Lee, Dong-Hwa; So, Young; Lee, Won Woo

2018-01-01

Quantitative parameters from Tc-99m pertechnetate single-photon emission computed tomography/computed tomography (SPECT/CT) are emerging as novel diagnostic markers for functional thyroid diseases. We intended to assess the utility of SPECT/CT parameters in patients with destructive thyroiditis. Thirty-five destructive thyroiditis patients (7 males and 28 females; mean age, 47.3 ± 13.0 years) and 20 euthyroid patients (6 males and 14 females; mean age, 45.0 ± 14.8 years) who underwent Tc-99m pertechnetate quantitative SPECT/CT were retrospectively enrolled. Quantitative parameters from the SPECT/CT (%uptake, standardized uptake value [SUV], thyroid volume, and functional thyroid mass [SUVmean × thyroid volume]) and thyroid hormone levels were investigated to assess correlations and predict the prognosis for destructive thyroiditis. The occurrence of hypothyroidism was the outcome for prognosis. All the SPECT/CT quantitative parameters were significantly lower in the 35 destructive thyroiditis patients compared to the 20 euthyroid patients using the same SPECT/CT scanner and protocol ( p < 0.001 for all parameters). T3 and free T4 did not correlate with any SPECT/CT parameters, but thyroid-stimulating hormone (TSH) significantly correlated with %uptake ( p = 0.004), SUVmean ( p < 0.001), SUVmax ( p = 0.002), and functional thyroid mass ( p < 0.001). Of the 35 destructive thyroiditis patients, 16 progressed to hypothyroidism. On univariate and multivariate analyses, only T3 levels were associated with the later occurrence of hypothyroidism ( p = 0.002, exp(β) = 1.022, 95% confidence interval: 1.008 - 1.035). Novel quantitative SPECT/CT parameters could discriminate patients with destructive thyroiditis from euthyroid patients, suggesting the robustness of the quantitative SPECT/CT approach. However, disease progression of destructive thyroiditis could not be predicted using the parameters, as these only correlated with TSH, but not with T3, the sole predictor of the later occurrence of hypothyroidism.

Utility of Quantitative Parameters from Single-Photon Emission Computed Tomography/Computed Tomography in Patients with Destructive Thyroiditis

PubMed Central

Kim, Ji-Young; Kim, Ji Hyun; Moon, Jae Hoon; Kim, Kyoung Min; Oh, Tae Jung; Lee, Dong-Hwa; So, Young

2018-01-01

Objective Quantitative parameters from Tc-99m pertechnetate single-photon emission computed tomography/computed tomography (SPECT/CT) are emerging as novel diagnostic markers for functional thyroid diseases. We intended to assess the utility of SPECT/CT parameters in patients with destructive thyroiditis. Materials and Methods Thirty-five destructive thyroiditis patients (7 males and 28 females; mean age, 47.3 ± 13.0 years) and 20 euthyroid patients (6 males and 14 females; mean age, 45.0 ± 14.8 years) who underwent Tc-99m pertechnetate quantitative SPECT/CT were retrospectively enrolled. Quantitative parameters from the SPECT/CT (%uptake, standardized uptake value [SUV], thyroid volume, and functional thyroid mass [SUVmean × thyroid volume]) and thyroid hormone levels were investigated to assess correlations and predict the prognosis for destructive thyroiditis. The occurrence of hypothyroidism was the outcome for prognosis. Results All the SPECT/CT quantitative parameters were significantly lower in the 35 destructive thyroiditis patients compared to the 20 euthyroid patients using the same SPECT/CT scanner and protocol (p < 0.001 for all parameters). T3 and free T4 did not correlate with any SPECT/CT parameters, but thyroid-stimulating hormone (TSH) significantly correlated with %uptake (p = 0.004), SUVmean (p < 0.001), SUVmax (p = 0.002), and functional thyroid mass (p < 0.001). Of the 35 destructive thyroiditis patients, 16 progressed to hypothyroidism. On univariate and multivariate analyses, only T3 levels were associated with the later occurrence of hypothyroidism (p = 0.002, exp(β) = 1.022, 95% confidence interval: 1.008 – 1.035). Conclusion Novel quantitative SPECT/CT parameters could discriminate patients with destructive thyroiditis from euthyroid patients, suggesting the robustness of the quantitative SPECT/CT approach. However, disease progression of destructive thyroiditis could not be predicted using the parameters, as these only correlated with TSH, but not with T3, the sole predictor of the later occurrence of hypothyroidism. PMID:29713225

Inter-hemispheric functional connectivity disruption in children with prenatal alcohol exposure

PubMed Central

Wozniak, Jeffrey R.; Mueller, Bryon A.; Muetzel, Ryan L.; Bell, Christopher J.; Hoecker, Heather L.; Nelson, Miranda L.; Chang, Pi-Nian; Lim, Kelvin O.

2010-01-01

Background MRI studies, including recent diffusion tensor imaging (DTI) studies, have shown corpus callosum abnormalities in children prenatally exposed to alcohol, especially in the posterior regions. These abnormalities appear across the range of Fetal Alcohol Spectrum Disorders (FASD). Several studies have demonstrated cognitive correlates of callosal abnormalities in FASD including deficits in visual-motor skill, verbal learning, and executive functioning. The goal of this study was to determine if inter-hemispheric structural connectivity abnormalities in FASD are associated with disrupted inter-hemispheric functional connectivity and disrupted cognition. Methods Twenty-one children with FASD and 23 matched controls underwent a six minute resting-state functional MRI scan as well as anatomical imaging and DTI. Using a semiautomated method, we parsed the corpus callosum and delineated seven inter-hemispheric white matter tracts with DTI tractography. Cortical regions of interest (ROIs) at the distal ends of these tracts were identified. Right-left correlations in resting fMRI signal were computed for these sets of ROIs and group comparisons were done. Correlations with facial dysmorphology, cognition, and DTI measures were computed. Results A significant group difference in inter-hemispheric functional connectivity was seen in a posterior set of ROIs, the para-central region. Children with FASD had functional connectivity that was 12% lower than controls in this region. Sub-group analyses were not possible due to small sample size, but the data suggest that there were effects across the FASD spectrum. No significant association with facial dysmorphology was found. Para-central functional connectivity was significantly correlated with DTI mean diffusivity, a measure of microstructural integrity, in posterior callosal tracts in controls but not in FASD. Significant correlations were seen between these structural and functional measures and Wechsler perceptual reasoning ability. Conclusions Inter-hemispheric functional connectivity disturbances were observed in children with FASD relative to controls. The disruption was measured in medial parietal regions (para-central) that are connected by posterior callosal fiber projections. We have previously shown microstructural abnormalities in these same posterior callosal regions and the current study suggests a possible relationship between the two. These measures have clinical relevance as they are associated with cognitive functioning. PMID:21303384

Image classification at low light levels

NASA Astrophysics Data System (ADS)

Wernick, Miles N.; Morris, G. Michael

1986-12-01

An imaging photon-counting detector is used to achieve automatic sorting of two image classes. The classification decision is formed on the basis of the cross correlation between a photon-limited input image and a reference function stored in computer memory. Expressions for the statistical parameters of the low-light-level correlation signal are given and are verified experimentally. To obtain a correlation-based system for two-class sorting, it is necessary to construct a reference function that produces useful information for class discrimination. An expression for such a reference function is derived using maximum-likelihood decision theory. Theoretically predicted results are used to compare on the basis of performance the maximum-likelihood reference function with Fukunaga-Koontz basis vectors and average filters. For each method, good class discrimination is found to result in milliseconds from a sparse sampling of the input image.

A real-time moment-tensor inversion system (GRiD-MT-3D) using 3-D Green's functions

NASA Astrophysics Data System (ADS)

Nagao, A.; Furumura, T.; Tsuruoka, H.

2016-12-01

We developed a real-time moment-tensor inversion system using 3-D Green's functions (GRiD-MT-3D) by improving the current system (GRiD-MT; Tsuruoka et al., 2009), which uses 1-D Green's functions for longer periods than 20 s. Our moment-tensor inversion is applied to the real-time monitoring of earthquakes occurring beneath Kanto basin area. The basin, which is constituted of thick sediment layers, lies on the complex subduction of the Philippine-Sea Plate and the Pacific Plate that can significantly affect the seismic wave propagation. We compute 3-D Green's functions using finite-difference-method (FDM) simulations considering a 3-D velocity model, which is based on the Japan Integrated Velocity Structure Model (Koketsu et al., 2012), that includes crust, mantle, and subducting plates. The 3-D FDM simulations are computed over a volume of 468 km by 432 km by 120 km in the EW, NS, and depth directions, respectively, that is discretized into 0.25 km grids. Considering that the minimum S wave velocity of the sedimentary layer is 0.5 km/s, simulations can compute seismograms up to 0.5 Hz. We calculate Green's functions between 24,700 sources, which are distributed every 0.1° in the horizontal direction and every 9 km in depth direction, and 13 F-net stations. To compute this large number of Green's functions, we used the EIC parallel computer of ERI. The reciprocity theory, which switches the source and station positions, is used to reduce total computation costs. It took 156 hours to compute all the Green's functions. Results show that at long-periods (T>15 s), only small differences are observed between the 3-D and 1-D Green's functions as indicated by high correlation coefficients of 0.9 between the waveforms. However, at shorter periods (T<10 s), the differences become larger and the correlation coefficients drop to 0.5. The effect of the 3-D heterogeneous structure especially affects the Green's functions for the ray paths that across complex geological structures, such as the sedimentary basin or the subducting plates. After incorporation of the 3-D Green's functions in the GRiD-MT-3D system, we compare the results to the former GRiD-MT system to demonstrate the effectiveness of the new system in terms of variance reduction and accuracy of the moment-tensor estimation for much smaller events than the current one.

Novel density functional methodology for the computation of accurate electronic and thermodynamic properties of molecular systems and improved long-range behavior

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

Kafafi, S.A.

1998-12-10

A novel general purpose density functional methodology for the computation of accurate electronic and thermodynamic properties of molecules and improved long-range behavior is reported. Assuming the separability of the exchange (E{sub x}) and correlation (E{sub c}) contributions to the total exchange-correlation energy functional (E{sub xc}), the E{sub x} term consists of a hybrid mixture of 37.5% Hartree-Fock exchange and the appropriate local spin density exchange using the adiabatic connection formula. He demonstrated that E{sub x} and its corresponding potential V{sub x} [=dE{sub x}/d{rho}(r)] have the proper asymptotic limits at r = 0 and r {r_arrow} {infinity}, E{sub c} consists ofmore » the Vosko, Wilk, and Nusair formula for the free-electron gas correlation energy and a generalized gradient approximation term with one adjustable parameter. V{sub c} [=dE{sub c}/d{rho}(r)] was shown to obey the r {r_arrow} {infinity} limit of the corresponding potential derived from exact atomic exchange-correlation computations; namely, V{sub c} is proportional to r{sup {minus}4}. Most importantly, he demonstrated that, at r values where dispersion forces are operating, V{sub c} is proportional to 1/r{sup n} (n = 4, 6, 8, {hor_ellipsis}). The reported method was denoted by K2-BVWN because it used two adjustable parameters in its formulation. The K2-BVWN scheme scales as N{sup 3}, where N is the number of basis functions, compared to {approximately}N{sup 7} for Gaussian-2 (G2) ab initio theory and related methods, {approximately}N{sup 5} for Barone`s mPW1,3PW, and {approximately}N{sup 4} for Becke`s three-parameter density functional approaches. The G2 data set complemented by the reported molecular systems investigated in this work was recommended as a critical test for evaluating novel ab initio and density functional methodologies. The K2-BVWN method has been implemented in the Gaussian series of programs.« less

Combined Ventilation and Perfusion Imaging Correlates With the Dosimetric Parameters of Radiation Pneumonitis in Radiation Therapy Planning for Lung Cancer

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

Kimura, Tomoki, E-mail: tkkimura@hiroshima-u.ac.jp; Doi, Yoshiko; Nakashima, Takeo

2015-11-15

Purpose: The purpose of this study was to prospectively investigate clinical correlations between dosimetric parameters associated with radiation pneumonitis (RP) and functional lung imaging. Methods and Materials: Functional lung imaging was performed using four-dimensional computed tomography (4D-CT) for ventilation imaging, single-photon emission computed tomography (SPECT) for perfusion imaging, or both (V/Q-matched region). Using 4D-CT, ventilation imaging was derived from a low attenuation area according to CT numbers below different thresholds (vent-860 and -910). Perfusion imaging at the 10th, 30th, 50th, and 70th percentile perfusion levels (F10-F70) were defined as the top 10%, 30%, 50%, and 70% hyperperfused normal lung, respectively.more » All imaging data were incorporated into a 3D planning system to evaluate correlations between RP dosimetric parameters (where fV20 is the percentage of functional lung volume irradiated with >20 Gy, or fMLD, the mean dose administered to functional lung) and the percentage of functional lung volume. Radiation pneumonitis was evaluated using Common Terminology Criteria for Adverse Events version 4.0. Statistical significance was defined as a P value of <.05. Results: Sixty patients who underwent curative radiation therapy were enrolled (48 patients for non-small cell lung cancer, and 12 patients for small cell lung cancer). Grades 1, 2, and ≥3 RP were observed in 16, 44, and 6 patients, respectively. Significant correlations were observed between the percentage of functional lung volume and fV20 (r=0.4475 in vent-860 and 0.3508 in F30) or fMLD (r=0.4701 in vent-860 and 0.3128 in F30) in patients with grade ≥2 RP. F30∩vent-860 results exhibited stronger correlations with fV20 and fMLD in patients with grade ≥2 (r=0.5509 in fV20 and 0.5320 in fMLD) and grade ≥3 RP (r=0.8770 in fV20 and 0.8518 in fMLD). Conclusions: RP dosimetric parameters correlated significantly with functional lung imaging.« less

SU-E-J-120: Comparing 4D CT Computed Ventilation to Lung Function Measured with Hyperpolarized Xenon-129 MRI

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

Neal, B; Chen, Q

2015-06-15

Purpose: To correlate ventilation parameters computed from 4D CT to ventilation, profusion, and gas exchange measured with hyperpolarized Xenon-129 MRI for a set of lung cancer patients. Methods: Hyperpolarized Xe-129 MRI lung scans were acquired for lung cancer patients, before and after radiation therapy, measuring ventilation, perfusion, and gas exchange. In the standard clinical workflow, these patients also received 4D CT scans before treatment. Ventilation was computed from 4D CT using deformable image registration (DIR). All phases of the 4D CT scan were registered using a B-spline deformable registration. Ventilation at the voxel level was then computed for each phasemore » based on a Jacobian volume expansion metric, yielding phase sorted ventilation images. Ventilation based upon 4D CT and Xe-129 MRI were co-registered, allowing qualitative visual comparison and qualitative comparison via the Pearson correlation coefficient. Results: Analysis shows a weak correlation between hyperpolarized Xe-129 MRI and 4D CT DIR ventilation, with a Pearson correlation coefficient of 0.17 to 0.22. Further work will refine the DIR parameters to optimize the correlation. The weak correlation could be due to the limitations of 4D CT, registration algorithms, or the Xe-129 MRI imaging. Continued development will refine parameters to optimize correlation. Conclusion: Current analysis yields a minimal correlation between 4D CT DIR and Xe-129 MRI ventilation. Funding provided by the 2014 George Amorino Pilot Grant in Radiation Oncology at the University of Virginia.« less

Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling

PubMed Central

Gallion, Jonathan; Koire, Amanda; Katsonis, Panagiotis; Schoenegge, Anne‐Marie; Bouvier, Michel

2017-01-01

Abstract Computational prediction yields efficient and scalable initial assessments of how variants of unknown significance may affect human health. However, when discrepancies between these predictions and direct experimental measurements of functional impact arise, inaccurate computational predictions are frequently assumed as the source. Here, we present a methodological analysis indicating that shortcomings in both computational and biological data can contribute to these disagreements. We demonstrate that incomplete assaying of multifunctional proteins can affect the strength of correlations between prediction and experiments; a variant's full impact on function is better quantified by considering multiple assays that probe an ensemble of protein functions. Additionally, many variants predictions are sensitive to protein alignment construction and can be customized to maximize relevance of predictions to a specific experimental question. We conclude that inconsistencies between computation and experiment can often be attributed to the fact that they do not test identical hypotheses. Aligning the design of the computational input with the design of the experimental output will require cooperation between computational and biological scientists, but will also lead to improved estimations of computational prediction accuracy and a better understanding of the genotype–phenotype relationship. PMID:28230923

Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling.

PubMed

Gallion, Jonathan; Koire, Amanda; Katsonis, Panagiotis; Schoenegge, Anne-Marie; Bouvier, Michel; Lichtarge, Olivier

2017-05-01

Computational prediction yields efficient and scalable initial assessments of how variants of unknown significance may affect human health. However, when discrepancies between these predictions and direct experimental measurements of functional impact arise, inaccurate computational predictions are frequently assumed as the source. Here, we present a methodological analysis indicating that shortcomings in both computational and biological data can contribute to these disagreements. We demonstrate that incomplete assaying of multifunctional proteins can affect the strength of correlations between prediction and experiments; a variant's full impact on function is better quantified by considering multiple assays that probe an ensemble of protein functions. Additionally, many variants predictions are sensitive to protein alignment construction and can be customized to maximize relevance of predictions to a specific experimental question. We conclude that inconsistencies between computation and experiment can often be attributed to the fact that they do not test identical hypotheses. Aligning the design of the computational input with the design of the experimental output will require cooperation between computational and biological scientists, but will also lead to improved estimations of computational prediction accuracy and a better understanding of the genotype-phenotype relationship. © 2017 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Correlation of pulmonary function and usual interstitial pneumonia computed tomography patterns in idiopathic pulmonary fibrosis.

PubMed

Arcadu, Antonella; Byrne, Suzanne C; Pirina, Pietro; Hartman, Thomas E; Bartholmai, Brian J; Moua, Teng

2017-08-01

Little is known about presenting 'inconsistent' or 'possible' usual interstitial pneumonia (UIP) computed tomography (CT) patterns advancing to 'consistent' UIP as disease progresses in idiopathic pulmonary fibrosis (IPF). We hypothesized that if 'consistent' UIP represented more advanced disease, such a pattern on presentation should also correlate with more severe pulmonary function test (PFT) abnormalities. Consecutive IPF patients (2005-2013) diagnosed by international criteria with baseline PFT and CT were included. Presenting CTs were assessed by three expert radiologists for consensus UIP pattern ('consistent', 'possible', and 'inconsistent'). Approximation of individual and combined interstitial abnormalities was also performed with correlation of interstitial abnormalities and UIP CT pattern made with PFT findings and survival. Three-hundred and fifty patients (70% male) were included with a mean age of 68.3 years. Mean percent predicted forced vital capacity (FVC%) and diffusion capacity (DLCO%) was 64% and 45.5% respectively. Older age and male gender correlated more with 'consistent' UIP CT pattern. FVC% was not associated with any UIP pattern but did correlate with total volume of radiologist assessed interstitial abnormalities. DLCO% was lower in those with 'consistent' UIP pattern. A 'consistent' UIP CT pattern was also not independently predictive of survival after correction for age, gender, FVC%, and DLCO%. PFT findings appear to correlate with extent of radiologic disease but not specific morphologic patterns. Whether such UIP patterns represent different stages of disease severity or radiologic progression is not supported by coinciding pulmonary function decline. Copyright © 2017 Elsevier Ltd. All rights reserved.

Studying flow close to an interface by total internal reflection fluorescence cross-correlation spectroscopy: Quantitative data analysis

NASA Astrophysics Data System (ADS)

Schmitz, R.; Yordanov, S.; Butt, H. J.; Koynov, K.; Dünweg, B.

2011-12-01

Total internal reflection fluorescence cross-correlation spectroscopy (TIR-FCCS) has recently [S. Yordanov , Optics ExpressOPEXFF1094-408710.1364/OE.17.021149 17, 21149 (2009)] been established as an experimental method to probe hydrodynamic flows near surfaces, on length scales of tens of nanometers. Its main advantage is that fluorescence occurs only for tracer particles close to the surface, thus resulting in high sensitivity. However, the measured correlation functions provide only rather indirect information about the flow parameters of interest, such as the shear rate and the slip length. In the present paper, we show how to combine detailed and fairly realistic theoretical modeling of the phenomena by Brownian dynamics simulations with accurate measurements of the correlation functions, in order to establish a quantitative method to retrieve the flow properties from the experiments. First, Brownian dynamics is used to sample highly accurate correlation functions for a fixed set of model parameters. Second, these parameters are varied systematically by means of an importance-sampling Monte Carlo procedure in order to fit the experiments. This provides the optimum parameter values together with their statistical error bars. The approach is well suited for massively parallel computers, which allows us to do the data analysis within moderate computing times. The method is applied to flow near a hydrophilic surface, where the slip length is observed to be smaller than 10nm, and, within the limitations of the experiments and the model, indistinguishable from zero.

An estimate for the thermal photon rate from lattice QCD

NASA Astrophysics Data System (ADS)

Brandt, Bastian B.; Francis, Anthony; Harris, Tim; Meyer, Harvey B.; Steinberg, Aman

2018-03-01

We estimate the production rate of photons by the quark-gluon plasma in lattice QCD. We propose a new correlation function which provides better control over the systematic uncertainty in estimating the photon production rate at photon momenta in the range πT/2 to 2πT. The relevant Euclidean vector current correlation functions are computed with Nf = 2 Wilson clover fermions in the chirally-symmetric phase. In order to estimate the photon rate, an ill-posed problem for the vector-channel spectral function must be regularized. We use both a direct model for the spectral function and a modelindependent estimate from the Backus-Gilbert method to give an estimate for the photon rate.

Temporal cross-correlation asymmetry and departure from equilibrium in a bistable chemical system.

PubMed

Bianca, C; Lemarchand, A

2014-06-14

This paper aims at determining sustained reaction fluxes in a nonlinear chemical system driven in a nonequilibrium steady state. The method relies on the computation of cross-correlation functions for the internal fluctuations of chemical species concentrations. By employing Langevin-type equations, we derive approximate analytical formulas for the cross-correlation functions associated with nonlinear dynamics. Kinetic Monte Carlo simulations of the chemical master equation are performed in order to check the validity of the Langevin equations for a bistable chemical system. The two approaches are found in excellent agreement, except for critical parameter values where the bifurcation between monostability and bistability occurs. From the theoretical point of view, the results imply that the behavior of cross-correlation functions cannot be exploited to measure sustained reaction fluxes in a specific nonlinear system without the prior knowledge of the associated chemical mechanism and the rate constants.

Random-Phase Approximation Methods

NASA Astrophysics Data System (ADS)

Chen, Guo P.; Voora, Vamsee K.; Agee, Matthew M.; Balasubramani, Sree Ganesh; Furche, Filipp

2017-05-01

Random-phase approximation (RPA) methods are rapidly emerging as cost-effective validation tools for semilocal density functional computations. We present the theoretical background of RPA in an intuitive rather than formal fashion, focusing on the physical picture of screening and simple diagrammatic analysis. A new decomposition of the RPA correlation energy into plasmonic modes leads to an appealing visualization of electron correlation in terms of charge density fluctuations. Recent developments in the areas of beyond-RPA methods, RPA correlation potentials, and efficient algorithms for RPA energy and property calculations are reviewed. The ability of RPA to approximately capture static correlation in molecules is quantified by an analysis of RPA natural occupation numbers. We illustrate the use of RPA methods in applications to small-gap systems such as open-shell d- and f-element compounds, radicals, and weakly bound complexes, where semilocal density functional results exhibit strong functional dependence.

Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids.

PubMed

Holmes, Sean T; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2015-11-10

Calculations of the principal components of magnetic-shielding tensors in crystalline solids require the inclusion of the effects of lattice structure on the local electronic environment to obtain significant agreement with experimental NMR measurements. We assess periodic (GIPAW) and GIAO/symmetry-adapted cluster (SAC) models for computing magnetic-shielding tensors by calculations on a test set containing 72 insulating molecular solids, with a total of 393 principal components of chemical-shift tensors from 13C, 15N, 19F, and 31P sites. When clusters are carefully designed to represent the local solid-state environment and when periodic calculations include sufficient variability, both methods predict magnetic-shielding tensors that agree well with experimental chemical-shift values, demonstrating the correspondence of the two computational techniques. At the basis-set limit, we find that the small differences in the computed values have no statistical significance for three of the four nuclides considered. Subsequently, we explore the effects of additional DFT methods available only with the GIAO/cluster approach, particularly the use of hybrid-GGA functionals, meta-GGA functionals, and hybrid meta-GGA functionals that demonstrate improved agreement in calculations on symmetry-adapted clusters. We demonstrate that meta-GGA functionals improve computed NMR parameters over those obtained by GGA functionals in all cases, and that hybrid functionals improve computed results over the respective pure DFT functional for all nuclides except 15N.

Theoretical Study of the Electric Dipole Moment Function of the CIO Molecule

NASA Technical Reports Server (NTRS)

Pettersson, Lars G. M.; Langhoff, Stephen R.; Chong, Delano P.

1986-01-01

The potential energy function and electric dipole moment function (EDMF) are computed for CIO Chi(sup 2)Pi using several different techniques to include electron correlation. The EDMF is used to compute Einstein coefficients, vibrational lifetimes, and dipole moments in higher vibrational levels. Remaining questions concerning the position of the maximum of the EDMF may be resolved through experimental measurement of dipole moments of higher vibrational levels. The band strength of the 1-0 fundamental transition is computed to be 12 +/- 2 /sq cm atm in good agreement with three experimental values, but larger than a recent value of 5 /sq cm atm determined from infrared heterodyne spectroscopy. The theoretical methods used include SCF, CASSCF, multireference singles plus doubles configuration interaction (MRCI) and contracted CI, coupled pair functional (CPF), and a modified version of the CPF method. The results obtained using the different methods are critically compared.

Voronoi Tessellation for reducing the processing time of correlation functions

NASA Astrophysics Data System (ADS)

Cárdenas-Montes, Miguel; Sevilla-Noarbe, Ignacio

2018-01-01

The increase of data volume in Cosmology is motivating the search of new solutions for solving the difficulties associated with the large processing time and precision of calculations. This is specially true in the case of several relevant statistics of the galaxy distribution of the Large Scale Structure of the Universe, namely the two and three point angular correlation functions. For these, the processing time has critically grown with the increase of the size of the data sample. Beyond parallel implementations to overcome the barrier of processing time, space partitioning algorithms are necessary to reduce the computational load. These can delimit the elements involved in the correlation function estimation to those that can potentially contribute to the final result. In this work, Voronoi Tessellation is used to reduce the processing time of the two-point and three-point angular correlation functions. The results of this proof-of-concept show a significant reduction of the processing time when preprocessing the galaxy positions with Voronoi Tessellation.

Noncommutative Wilson lines in higher-spin theory and correlation functions of conserved currents for free conformal fields

NASA Astrophysics Data System (ADS)

Bonezzi, Roberto; Boulanger, Nicolas; De Filippi, David; Sundell, Per

2017-11-01

We first prove that, in Vasiliev’s theory, the zero-form charges studied in Sezgin E and Sundell P 2011 (arXiv:1103.2360 [hep-th]) and Colombo N and Sundell P 20 (arXiv:1208.3880 [hep-th]) are twisted open Wilson lines in the noncommutative Z space. This is shown by mapping Vasiliev’s higher-spin model on noncommutative Yang-Mills theory. We then prove that, prior to Bose-symmetrising, the cyclically-symmetric higher-spin invariants given by the leading order of these n-point zero-form charges are equal to corresponding cyclically-invariant building blocks of n-point correlation functions of bilinear operators in free conformal field theories (CFT) in three dimensions. On the higher spin gravity side, our computation reproduces the results of Didenko V and Skvortsov E 2013 J. High Energy Phys. JHEP04(2013)158 using an alternative method amenable to the computation of subleading corrections obtained by perturbation theory in normal order. On the free CFT side, our proof involves the explicit computation of the separate cyclic building blocks of the correlation functions of n conserved currents in arbitrary dimension d>2 using polarization vectors, which is an original result. It is shown to agree, for d=3 , with the results obtained in Gelfond O A and Vasiliev M A 2013 Nucl. Phys. B 876 871-917 in various dimensions and where polarization spinors were used.

What a Decade of Experiments Reveals about Factors that Influence the Sense of Presence

DTIC Science & Technology

2006-03-01

Function HRV heart rate variability IBM International Business Machines Corporation ICAT International Conference on Artificial Intelligence and...Questionnaire. Person-related meas.: Social anxiety , age, gender, computer use. Task-related measures: Social anxiety assessment of partner. Performance...co-presence. (4) Computer use had a significant positive correlation with co-presence. (5) Participant’s social anxiety had a significant

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

Lobar analysis of collapsibility indices to assess functional lung volumes in COPD patients.

PubMed

Kitano, Mariko; Iwano, Shingo; Hashimoto, Naozumi; Matsuo, Keiji; Hasegawa, Yoshinori; Naganawa, Shinji

2014-01-01

We investigated correlations between lung volume collapsibility indices and pulmonary function test (PFT) results and assessed lobar differences in chronic obstructive pulmonary disease (COPD) patients, using paired inspiratory and expiratory three dimensional (3D) computed tomography (CT) images. We retrospectively assessed 28 COPD patients who underwent paired inspiratory and expiratory CT and PFT exams on the same day. A computer-aided diagnostic system calculated total lobar volume and emphysematous lobar volume (ELV). Normal lobar volume (NLV) was determined by subtracting ELV from total lobar volume, both for inspiratory phase (NLVI) and for expiratory phase (NLVE). We also determined lobar collapsibility indices: NLV collapsibility ratio (NLVCR) (%)=(1-NLVE/NLVI)×100%. Associations between lobar volumes and PFT results, and collapsibility indices and PFT results were determined by Pearson correlation analysis. NLVCR values were significantly correlated with PFT results. Forced expiratory volume in 1 second, measured as percent of predicted results (FEV1%P) was significantly correlated with NLVCR values for the lower lobes (P<0.01), whereas this correlation was not significant for the upper lobes (P=0.05). FEV1%P results were also moderately correlated with inspiratory, expiratory ELV (ELVI,E) for the lower lobes (P<0.05). In contrast, the ratio of the diffusion capacity for carbon monoxide to alveolar gas volume, measured as percent of predicted (DLCO/VA%P) results were strongly correlated with ELVI for the upper lobes (P<0.001), whereas this correlation with NLVCR values was weaker for upper lobes (P<0.01) and was not significant for the lower lobes (P=0.26). FEV1%P results were correlated with NLV collapsibility indices for lower lobes, whereas DLCO/VA%P results were correlated with NLV collapsibility indices and ELV for upper lobes. Thus, evaluating lobar NLV collapsibility might be useful for estimating pulmonary function in COPD patients.

The large-scale three-point correlation function of the SDSS BOSS DR12 CMASS galaxies

NASA Astrophysics Data System (ADS)

Slepian, Zachary; Eisenstein, Daniel J.; Beutler, Florian; Chuang, Chia-Hsun; Cuesta, Antonio J.; Ge, Jian; Gil-Marín, Héctor; Ho, Shirley; Kitaura, Francisco-Shu; McBride, Cameron K.; Nichol, Robert C.; Percival, Will J.; Rodríguez-Torres, Sergio; Ross, Ashley J.; Scoccimarro, Román; Seo, Hee-Jong; Tinker, Jeremy; Tojeiro, Rita; Vargas-Magaña, Mariana

2017-06-01

We report a measurement of the large-scale three-point correlation function of galaxies using the largest data set for this purpose to date, 777 202 luminous red galaxies in the Sloan Digital Sky Survey Baryon Acoustic Oscillation Spectroscopic Survey (SDSS BOSS) DR12 CMASS sample. This work exploits the novel algorithm of Slepian & Eisenstein to compute the multipole moments of the 3PCF in O(N^2) time, with N the number of galaxies. Leading-order perturbation theory models the data well in a compressed basis where one triangle side is integrated out. We also present an accurate and computationally efficient means of estimating the covariance matrix. With these techniques, the redshift-space linear and non-linear bias are measured, with 2.6 per cent precision on the former if σ8 is fixed. The data also indicate a 2.8σ preference for the BAO, confirming the presence of BAO in the three-point function.

An Efficient Local Correlation Matrix Decomposition Approach for the Localization Implementation of Ensemble-Based Assimilation Methods

NASA Astrophysics Data System (ADS)

Zhang, Hongqin; Tian, Xiangjun

2018-04-01

Ensemble-based data assimilation methods often use the so-called localization scheme to improve the representation of the ensemble background error covariance (Be). Extensive research has been undertaken to reduce the computational cost of these methods by using the localized ensemble samples to localize Be by means of a direct decomposition of the local correlation matrix C. However, the computational costs of the direct decomposition of the local correlation matrix C are still extremely high due to its high dimension. In this paper, we propose an efficient local correlation matrix decomposition approach based on the concept of alternating directions. This approach is intended to avoid direct decomposition of the correlation matrix. Instead, we first decompose the correlation matrix into 1-D correlation matrices in the three coordinate directions, then construct their empirical orthogonal function decomposition at low resolution. This procedure is followed by the 1-D spline interpolation process to transform the above decompositions to the high-resolution grid. Finally, an efficient correlation matrix decomposition is achieved by computing the very similar Kronecker product. We conducted a series of comparison experiments to illustrate the validity and accuracy of the proposed local correlation matrix decomposition approach. The effectiveness of the proposed correlation matrix decomposition approach and its efficient localization implementation of the nonlinear least-squares four-dimensional variational assimilation are further demonstrated by several groups of numerical experiments based on the Advanced Research Weather Research and Forecasting model.

Wave Propagation in Non-Stationary Statistical Mantle Models at the Global Scale

NASA Astrophysics Data System (ADS)

Meschede, M.; Romanowicz, B. A.

2014-12-01

We study the effect of statistically distributed heterogeneities that are smaller than the resolution of current tomographic models on seismic waves that propagate through the Earth's mantle at teleseismic distances. Current global tomographic models are missing small-scale structure as evidenced by the failure of even accurate numerical synthetics to explain enhanced coda in observed body and surface waveforms. One way to characterize small scale heterogeneity is to construct random models and confront observed coda waveforms with predictions from these models. Statistical studies of the coda typically rely on models with simplified isotropic and stationary correlation functions in Cartesian geometries. We show how to construct more complex random models for the mantle that can account for arbitrary non-stationary and anisotropic correlation functions as well as for complex geometries. Although this method is computationally heavy, model characteristics such as translational, cylindrical or spherical symmetries can be used to greatly reduce the complexity such that this method becomes practical. With this approach, we can create 3D models of the full spherical Earth that can be radially anisotropic, i.e. with different horizontal and radial correlation functions, and radially non-stationary, i.e. with radially varying model power and correlation functions. Both of these features are crucial for a statistical description of the mantle in which structure depends to first order on the spherical geometry of the Earth. We combine different random model realizations of S velocity with current global tomographic models that are robust at long wavelengths (e.g. Meschede and Romanowicz, 2014, GJI submitted), and compute the effects of these hybrid models on the wavefield with a spectral element code (SPECFEM3D_GLOBE). We finally analyze the resulting coda waves for our model selection and compare our computations with observations. Based on these observations, we make predictions about the strength of unresolved small-scale structure and extrinsic attenuation.

A Short Note on the Scaling Function Constant Problem in the Two-Dimensional Ising Model

NASA Astrophysics Data System (ADS)

Bothner, Thomas

2018-02-01

We provide a simple derivation of the constant factor in the short-distance asymptotics of the tau-function associated with the 2-point function of the two-dimensional Ising model. This factor was first computed by Tracy (Commun Math Phys 142:297-311, 1991) via an exponential series expansion of the correlation function. Further simplifications in the analysis are due to Tracy and Widom (Commun Math Phys 190:697-721, 1998) using Fredholm determinant representations of the correlation function and Wiener-Hopf approximation results for the underlying resolvent operator. Our method relies on an action integral representation of the tau-function and asymptotic results for the underlying Painlevé-III transcendent from McCoy et al. (J Math Phys 18:1058-1092, 1977).

Chamber dimensions and functional assessment with coronary computed tomographic angiography as compared to echocardiography using American Society of Echocardiography guidelines

PubMed Central

Rose, Michael; Rubal, Bernard; Hulten, Edward; Slim, Jennifer N; Steel, Kevin; Furgerson, James L; Villines, Todd C

2014-01-01

Background: The correlation between normal cardiac chamber linear dimensions measured during retrospective coronary computed tomographic angiography as compared to transthoracic echocardiography using the American Society of Echocardiography guidelines is not well established. Methods: We performed a review from January 2005 to July 2011 to identify subjects with retrospective electrocardiogram-gated coronary computed tomographic angiography scans for chest pain and transthoracic echocardiography with normal cardiac structures performed within 90 days. Dimensions were manually calculated in both imaging modalities in accordance with the American Society of Echocardiography published guidelines. Left ventricular ejection fraction was calculated on echocardiography manually using the Simpson’s formula and by coronary computed tomographic angiography using the end-systolic and end-diastolic volumes. Results: We reviewed 532 studies, rejected 412 and had 120 cases for review with a median time between studies of 7 days (interquartile range (IQR25,75) = 0–22 days) with no correlation between the measurements made by coronary computed tomographic angiography and transthoracic echocardiography using Bland–Altman analysis. We generated coronary computed tomographic angiography cardiac dimension reference ranges for both genders for our population. Conclusion: Our findings represent a step towards generating cardiac chamber dimensions’ reference ranges for coronary computed tomographic angiography as compared to transthoracic echocardiography in patients with normal cardiac morphology and function using the American Society of Echocardiography guideline measurements that are commonly used by cardiologists. PMID:26770706

Ab Initio Optimized Effective Potentials for Real Molecules in Optical Cavities: Photon Contributions to the Molecular Ground State

PubMed Central

2018-01-01

We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density-functional theory (QEDFT).1−5 Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical cavities and described in full real space. While the first example is a two-dimensional system and allows to benchmark the employed approximations, the latter two examples demonstrate that the correlated electron-photon interaction appreciably distorts the ground-state electronic structure of a real molecule. By using this scheme, we not only construct typical electronic observables, such as the electronic ground-state density, but also illustrate how photon observables, such as the photon number, and mixed electron-photon observables, for example, electron–photon correlation functions, become accessible in a density-functional theory (DFT) framework. This work constitutes the first three-dimensional ab initio calculation within the new QEDFT formalism and thus opens up a new computational route for the ab initio study of correlated electron–photon systems in quantum cavities. PMID:29594185

Application of Cross-Correlation Greens Function Along With FDTD for Fast Computation of Envelope Correlation Coefficient Over Wideband for MIMO Antennas

NASA Astrophysics Data System (ADS)

Sarkar, Debdeep; Srivastava, Kumar Vaibhav

2017-02-01

In this paper, the concept of cross-correlation Green's functions (CGF) is used in conjunction with the finite difference time domain (FDTD) technique for calculation of envelope correlation coefficient (ECC) of any arbitrary MIMO antenna system over wide frequency band. Both frequency-domain (FD) and time-domain (TD) post-processing techniques are proposed for possible application with this FDTD-CGF scheme. The FDTD-CGF time-domain (FDTD-CGF-TD) scheme utilizes time-domain signal processing methods and exhibits significant reduction in ECC computation time as compared to the FDTD-CGF frequency domain (FDTD-CGF-FD) scheme, for high frequency-resolution requirements. The proposed FDTD-CGF based schemes can be applied for accurate and fast prediction of wideband ECC response, instead of the conventional scattering parameter based techniques which have several limitations. Numerical examples of the proposed FDTD-CGF techniques are provided for two-element MIMO systems involving thin-wire half-wavelength dipoles in parallel side-by-side as well as orthogonal arrangements. The results obtained from the FDTD-CGF techniques are compared with results from commercial electromagnetic solver Ansys HFSS, to verify the validity of proposed approach.

Application of abstract harmonic analysis to the high-speed recognition of images

NASA Technical Reports Server (NTRS)

Usikov, D. A.

1979-01-01

Methods are constructed for rapidly computing correlation functions using the theory of abstract harmonic analysis. The theory developed includes as a particular case the familiar Fourier transform method for a correlation function which makes it possible to find images which are independent of their translation in the plane. Two examples of the application of the general theory described are the search for images, independent of their rotation and scale, and the search for images which are independent of their translations and rotations in the plane.

A Parallel Approach in Computing Correlation Immunity up to Six Variables

DTIC Science & Technology

2015-03-10

their nonlinearity is divisible by 4. Let CI(n, k) (respectively, BCI (n, k)) be the number of exact order k correlation im- mune, (respectively...further balanced) n-variable Boolean functions. The notations CI(n, k, d), BCI (n, k, d) restricts the previous count to degree d Boolean functions...Theorem 3. The following are true: (i) BCI (n, n, 0) = 0, CI(n, n, 0) = 2, CI(n, k, 1) = BCI (n, k, 1) = 2 ( n k+1 ) , 0 ≤ k ≤ n− 1. (ii) BCI (n, n− 2) = 2

Locating Microseism Sources Using Spurious Arrivals in Intercontinental Noise Correlations

NASA Astrophysics Data System (ADS)

Retailleau, Lise; Boué, Pierre; Stehly, Laurent; Campillo, Michel

2017-10-01

The accuracy of Green's functions retrieved from seismic noise correlations in the microseism frequency band is limited by the uneven distribution of microseism sources at the surface of the Earth. As a result, correlation functions are often biased as compared to the expected Green's functions, and they can include spurious arrivals. These spurious arrivals are seismic arrivals that are visible on the correlation and do not belong to the theoretical impulse response. In this article, we propose to use Rayleigh wave spurious arrivals detected on correlation functions computed between European and United States seismic stations to locate microseism sources in the Atlantic Ocean. We perform a slant stack on a time distance gather of correlations obtained from an array of stations that comprises a regional deployment and a distant station. The arrival times and the apparent slowness of the spurious arrivals lead to the location of their source, which is obtained through a grid search procedure. We discuss improvements in the location through this methodology as compared to classical back projection of microseism energy. This method is interesting because it only requires an array and a distant station on each side of an ocean, conditions that can be met relatively easily.

Optimized effective potential method and application to static RPA correlation

NASA Astrophysics Data System (ADS)

Fukazawa, Taro; Akai, Hisazumi

2015-03-01

The optimized effective potential (OEP) method is a promising technique for calculating the ground state properties of a system within the density functional theory. However, it is not widely used as its computational cost is rather high and, also, some ambiguity remains in the theoretical framework. In order to overcome these problems, we first introduced a method that accelerates the OEP scheme in a static RPA-level correlation functional. Second, the Krieger-Li-Iafrate (KLI) approximation is exploited to solve the OEP equation. Although seemingly too crude, this approximation did not reduce the accuracy of the description of the magnetic transition metals (Fe, Co, and Ni) examined here, the magnetic properties of which are rather sensitive to correlation effects. Finally, we reformulated the OEP method to render it applicable to the direct RPA correlation functional and other, more precise, functionals. Emphasis is placed on the following three points of the discussion: (i) level-crossing at the Fermi surface is taken into account; (ii) eigenvalue variations in a Kohn-Sham functional are correctly treated; and (iii) the resultant OEP equation is different from those reported to date.

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.

PubMed

Ritchie, David W; Kozakov, Dima; Vajda, Sandor

2008-09-01

Predicting how proteins interact at the molecular level is a computationally intensive task. Many protein docking algorithms begin by using fast Fourier transform (FFT) correlation techniques to find putative rigid body docking orientations. Most such approaches use 3D Cartesian grids and are therefore limited to computing three dimensional (3D) translational correlations. However, translational FFTs can speed up the calculation in only three of the six rigid body degrees of freedom, and they cannot easily incorporate prior knowledge about a complex to focus and hence further accelerate the calculation. Furthemore, several groups have developed multi-term interaction potentials and others use multi-copy approaches to simulate protein flexibility, which both add to the computational cost of FFT-based docking algorithms. Hence there is a need to develop more powerful and more versatile FFT docking techniques. This article presents a closed-form 6D spherical polar Fourier correlation expression from which arbitrary multi-dimensional multi-property multi-resolution FFT correlations may be generated. The approach is demonstrated by calculating 1D, 3D and 5D rotational correlations of 3D shape and electrostatic expansions up to polynomial order L=30 on a 2 GB personal computer. As expected, 3D correlations are found to be considerably faster than 1D correlations but, surprisingly, 5D correlations are often slower than 3D correlations. Nonetheless, we show that 5D correlations will be advantageous when calculating multi-term knowledge-based interaction potentials. When docking the 84 complexes of the Protein Docking Benchmark, blind 3D shape plus electrostatic correlations take around 30 minutes on a contemporary personal computer and find acceptable solutions within the top 20 in 16 cases. Applying a simple angular constraint to focus the calculation around the receptor binding site produces acceptable solutions within the top 20 in 28 cases. Further constraining the search to the ligand binding site gives up to 48 solutions within the top 20, with calculation times of just a few minutes per complex. Hence the approach described provides a practical and fast tool for rigid body protein-protein docking, especially when prior knowledge about one or both binding sites is available.

Describing a Strongly Correlated Model System with Density Functional Theory.

PubMed

Kong, Jing; Proynov, Emil; Yu, Jianguo; Pachter, Ruth

2017-07-06

The linear chain of hydrogen atoms, a basic prototype for the transition from a metal to Mott insulator, is studied with a recent density functional theory model functional for nondynamic and strong correlation. The computed cohesive energy curve for the transition agrees well with accurate literature results. The variation of the electronic structure in this transition is characterized with a density functional descriptor that yields the atomic population of effectively localized electrons. These new methods are also applied to the study of the Peierls dimerization of the stretched even-spaced Mott insulator to a chain of H 2 molecules, a different insulator. The transitions among the two insulating states and the metallic state of the hydrogen chain system are depicted in a semiquantitative phase diagram. Overall, we demonstrate the capability of studying strongly correlated materials with a mean-field model at the fundamental level, in contrast to the general pessimistic view on such a feasibility.

Exploring biorthonormal transformations of pair-correlation functions in atomic structure variational calculations

NASA Astrophysics Data System (ADS)

Verdebout, S.; Jönsson, P.; Gaigalas, G.; Godefroid, M.; Froese Fischer, C.

2010-04-01

Multiconfiguration expansions frequently target valence correlation and correlation between valence electrons and the outermost core electrons. Correlation within the core is often neglected. A large orbital basis is needed to saturate both the valence and core-valence correlation effects. This in turn leads to huge numbers of configuration state functions (CSFs), many of which are unimportant. To avoid the problems inherent to the use of a single common orthonormal orbital basis for all correlation effects in the multiconfiguration Hartree-Fock (MCHF) method, we propose to optimize independent MCHF pair-correlation functions (PCFs), bringing their own orthonormal one-electron basis. Each PCF is generated by allowing single- and double-excitations from a multireference (MR) function. This computational scheme has the advantage of using targeted and optimally localized orbital sets for each PCF. These pair-correlation functions are coupled together and with each component of the MR space through a low dimension generalized eigenvalue problem. Nonorthogonal orbital sets being involved, the interaction and overlap matrices are built using biorthonormal transformation of the coupled basis sets followed by a counter-transformation of the PCF expansions. Applied to the ground state of beryllium, the new method gives total energies that are lower than the ones from traditional complete active space (CAS)-MCHF calculations using large orbital active sets. It is fair to say that we now have the possibility to account for, in a balanced way, correlation deep down in the atomic core in variational calculations.

Exact finite volume expectation values of \\overline{Ψ}Ψ in the massive Thirring model from light-cone lattice correlators

NASA Astrophysics Data System (ADS)

Hegedűs, Árpád

2018-03-01

In this paper, using the light-cone lattice regularization, we compute the finite volume expectation values of the composite operator \\overline{Ψ}Ψ between pure fermion states in the Massive Thirring Model. In the light-cone regularized picture, this expectation value is related to 2-point functions of lattice spin operators being located at neighboring sites of the lattice. The operator \\overline{Ψ}Ψ is proportional to the trace of the stress-energy tensor. This is why the continuum finite volume expectation values can be computed also from the set of non-linear integral equations (NLIE) governing the finite volume spectrum of the theory. Our results for the expectation values coming from the computation of lattice correlators agree with those of the NLIE computations. Previous conjectures for the LeClair-Mussardo-type series representation of the expectation values are also checked.

A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms

PubMed Central

Cumming, Bruce G.

2016-01-01

In order to extract retinal disparity from a visual scene, the brain must match corresponding points in the left and right retinae. This computationally demanding task is known as the stereo correspondence problem. The initial stage of the solution to the correspondence problem is generally thought to consist of a correlation-based computation. However, recent work by Doi et al suggests that human observers can see depth in a class of stimuli where the mean binocular correlation is 0 (half-matched random dot stereograms). Half-matched random dot stereograms are made up of an equal number of correlated and anticorrelated dots, and the binocular energy model—a well-known model of V1 binocular complex cells—fails to signal disparity here. This has led to the proposition that a second, match-based computation must be extracting disparity in these stimuli. Here we show that a straightforward modification to the binocular energy model—adding a point output nonlinearity—is by itself sufficient to produce cells that are disparity-tuned to half-matched random dot stereograms. We then show that a simple decision model using this single mechanism can reproduce psychometric functions generated by human observers, including reduced performance to large disparities and rapidly updating dot patterns. The model makes predictions about how performance should change with dot size in half-matched stereograms and temporal alternation in correlation, which we test in human observers. We conclude that a single correlation-based computation, based directly on already-known properties of V1 neurons, can account for the literature on mixed correlation random dot stereograms. PMID:27196696

Instantaneous phase estimation to measure weak velocity variations: application to noise correlation on seismic data at the exploration scale

NASA Astrophysics Data System (ADS)

Corciulo, M.; Roux, P.; Campillo, M.; Dubucq, D.

2010-12-01

Passive imaging from noise cross-correlation is a consolidated analysis applied at continental and regional scale whereas its use at local scale for seismic exploration purposes is still uncertain. The development of passive imaging by cross-correlation analysis is based on the extraction of the Green’s function from seismic noise data. In a completely random field in time and space, the cross-correlation permits to retrieve the complete Green’s function whatever the complexity of the medium. At the exploration scale and at frequency above 2 Hz, the noise sources are not ideally distributed around the stations which strongly affect the extraction of the direct arrivals from the noise cross-correlation process. In order to overcome this problem, the coda waves extracted from noise correlation could be useful. Coda waves describe long and scattered paths sampling the medium in different ways such that they become sensitive to weak velocity variations without being dependent on the noise source distribution. Indeed, scatters in the medium behave as a set of secondary noise sources which randomize the spatial distribution of noise sources contributing to the coda waves in the correlation process. We developed a new technique to measure weak velocity changes based on the computation of the local phase variations (instantaneous phase variation or IPV) of the cross-correlated signals. This newly-developed technique takes advantage from the doublet and stretching techniques classically used to monitor weak velocity variation from coda waves. We apply IPV to data acquired in Northern America (Canada) on a 1-km side square seismic network laid out by 397 stations. Data used to study temporal variations are cross-correlated signals computed on 10-minutes ambient noise in the frequency band 2-5 Hz. As the data set was acquired over five days, about 660 files are processed to perform a complete temporal analysis for each stations pair. The IPV permits to estimate the phase shift all over the signal length without any assumption on the medium velocity. The instantaneous phase is computed using the Hilbert transform of the signal. For each stations pair, we measure the phase difference between successive correlation functions calculated for 10 minutes of ambient noise. We then fit the instantaneous phase shift using a first-order polynomial function. The measure of the velocity variation corresponds to the slope of this fit. Compared to other techniques, the advantage of IPV is a very fast procedure which efficiently provides the measure of velocity variation on large data sets. Both experimental results and numerical tests on synthetic signals will be presented to assess the reliability of the IPV technique, with comparison to the doublet and stretching methods.

Computer-based quantitative computed tomography image analysis in idiopathic pulmonary fibrosis: A mini review.

PubMed

Ohkubo, Hirotsugu; Nakagawa, Hiroaki; Niimi, Akio

2018-01-01

Idiopathic pulmonary fibrosis (IPF) is the most common type of progressive idiopathic interstitial pneumonia in adults. Many computer-based image analysis methods of chest computed tomography (CT) used in patients with IPF include the mean CT value of the whole lungs, density histogram analysis, density mask technique, and texture classification methods. Most of these methods offer good assessment of pulmonary functions, disease progression, and mortality. Each method has merits that can be used in clinical practice. One of the texture classification methods is reported to be superior to visual CT scoring by radiologist for correlation with pulmonary function and prediction of mortality. In this mini review, we summarize the current literature on computer-based CT image analysis of IPF and discuss its limitations and several future directions. Copyright © 2017 The Japanese Respiratory Society. Published by Elsevier B.V. All rights reserved.

Measurement properties of the Spinal Cord Injury-Functional Index (SCI-FI) short forms.

PubMed

Heinemann, Allen W; Dijkers, Marcel P; Ni, Pengsheng; Tulsky, David S; Jette, Alan

2014-07-01

To evaluate the psychometric properties of the Spinal Cord Injury-Functional Index (SCI-FI) short forms (basic mobility, self-care, fine motor, ambulation, manual wheelchair, and power wheelchair) based on internal consistency; correlations between short forms banks, full item bank forms, and a 10-item computer adaptive test version; magnitude of ceiling and floor effects; and test information functions. Cross-sectional cohort study. Six rehabilitation hospitals in the United States. Individuals with traumatic spinal cord injury (N=855) recruited from 6 national Spinal Cord Injury Model Systems facilities. Not applicable. SCI-FI full item bank, 10-item computer adaptive test, and parallel short form scores. The SCI-FI short forms (with separate versions for individuals with paraplegia and tetraplegia) demonstrate very good internal consistency, group-level reliability, excellent correlations between short forms and scores based on the total item bank, and minimal ceiling and floor effects (except ceiling effects for persons with paraplegia on self-care, fine motor, and power wheelchair ability and floor effects for persons with tetraplegia on self-care, fine motor, and manual wheelchair ability). The test information functions are acceptable across the range of scores where most persons in the sample performed. Clinicians and researchers should consider the SCI-FI short forms when computer adaptive testing is not feasible. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution

NASA Astrophysics Data System (ADS)

Chodera, John D.; Noé, Frank

2010-09-01

Discrete-state Markov (or master equation) models provide a useful simplified representation for characterizing the long-time statistical evolution of biomolecules in a manner that allows direct comparison with experiments as well as the elucidation of mechanistic pathways for an inherently stochastic process. A vital part of meaningful comparison with experiment is the characterization of the statistical uncertainty in the predicted experimental measurement, which may take the form of an equilibrium measurement of some spectroscopic signal, the time-evolution of this signal following a perturbation, or the observation of some statistic (such as the correlation function) of the equilibrium dynamics of a single molecule. Without meaningful error bars (which arise from both approximation and statistical error), there is no way to determine whether the deviations between model and experiment are statistically meaningful. Previous work has demonstrated that a Bayesian method that enforces microscopic reversibility can be used to characterize the statistical component of correlated uncertainties in state-to-state transition probabilities (and functions thereof) for a model inferred from molecular simulation data. Here, we extend this approach to include the uncertainty in observables that are functions of molecular conformation (such as surrogate spectroscopic signals) characterizing each state, permitting the full statistical uncertainty in computed spectroscopic experiments to be assessed. We test the approach in a simple model system to demonstrate that the computed uncertainties provide a useful indicator of statistical variation, and then apply it to the computation of the fluorescence autocorrelation function measured for a dye-labeled peptide previously studied by both experiment and simulation.

Collisional redistribution of radiation. III - The equation of motion for the correlation function and the scattered spectrum

NASA Technical Reports Server (NTRS)

Burnett, K.; Cooper, J.

1980-01-01

Computations were made of the scattering of monochromatic radiation by a degenerate atom in the binary-collision approximation for field strengths whose products of the Rabi frequency for atomic transition and the duration of a strong collision are much less than 1. An expression of motion for the correlation function is derived which does not exclude the region where thermal correlations may be neglected; the equation is valid outside the quantum-regression regime, and has a straightforward solution for practical cases. Solutions for the weak-field linear response regime are presented in terms of generalized absorption and emission profiles which depend on the indices of the atomic multipoles.

Quantum Monte Carlo: Faster, More Reliable, And More Accurate

NASA Astrophysics Data System (ADS)

Anderson, Amos Gerald

2010-06-01

The Schrodinger Equation has been available for about 83 years, but today, we still strain to apply it accurately to molecules of interest. The difficulty is not theoretical in nature, but practical, since we're held back by lack of sufficient computing power. Consequently, effort is applied to find acceptable approximations to facilitate real time solutions. In the meantime, computer technology has begun rapidly advancing and changing the way we think about efficient algorithms. For those who can reorganize their formulas to take advantage of these changes and thereby lift some approximations, incredible new opportunities await. Over the last decade, we've seen the emergence of a new kind of computer processor, the graphics card. Designed to accelerate computer games by optimizing quantity instead of quality in processor, they have become of sufficient quality to be useful to some scientists. In this thesis, we explore the first known use of a graphics card to computational chemistry by rewriting our Quantum Monte Carlo software into the requisite "data parallel" formalism. We find that notwithstanding precision considerations, we are able to speed up our software by about a factor of 6. The success of a Quantum Monte Carlo calculation depends on more than just processing power. It also requires the scientist to carefully design the trial wavefunction used to guide simulated electrons. We have studied the use of Generalized Valence Bond wavefunctions to simply, and yet effectively, captured the essential static correlation in atoms and molecules. Furthermore, we have developed significantly improved two particle correlation functions, designed with both flexibility and simplicity considerations, representing an effective and reliable way to add the necessary dynamic correlation. Lastly, we present our method for stabilizing the statistical nature of the calculation, by manipulating configuration weights, thus facilitating efficient and robust calculations. Our combination of Generalized Valence Bond wavefunctions, improved correlation functions, and stabilized weighting techniques for calculations run on graphics cards, represents a new way for using Quantum Monte Carlo to study arbitrarily sized molecules.

A quenched study of the Schrödinger functional with chirally rotated boundary conditions: Applications

NASA Astrophysics Data System (ADS)

González López, J.; Jansen, K.; Renner, D. B.; Shindler, A.

2013-02-01

In a previous paper (González López, et al., 2013) [1], we have discussed the non-perturbative tuning of the chirally rotated Schrödinger functional (χSF). This tuning is required to eliminate bulk O(a) cutoff effects in physical correlation functions. Using our tuning results obtained in González López et al. (2013) [1] we perform scaling and universality tests analyzing the residual O(a) cutoff effects of several step-scaling functions and we compute renormalization factors at the matching scale. As an example of possible application of the χSF we compute the renormalized strange quark mass using large volume data obtained from Wilson twisted mass fermions at maximal twist.

Image processing via VLSI: A concept paper

NASA Technical Reports Server (NTRS)

Nathan, R.

1982-01-01

Implementing specific image processing algorithms via very large scale integrated systems offers a potent solution to the problem of handling high data rates. Two algorithms stand out as being particularly critical -- geometric map transformation and filtering or correlation. These two functions form the basis for data calibration, registration and mosaicking. VLSI presents itself as an inexpensive ancillary function to be added to almost any general purpose computer and if the geometry and filter algorithms are implemented in VLSI, the processing rate bottleneck would be significantly relieved. A set of image processing functions that limit present systems to deal with future throughput needs, translates these functions to algorithms, implements via VLSI technology and interfaces the hardware to a general purpose digital computer is developed.

Towards full waveform ambient noise inversion

NASA Astrophysics Data System (ADS)

Sager, Korbinian; Ermert, Laura; Boehm, Christian; Fichtner, Andreas

2018-01-01

In this work we investigate fundamentals of a method—referred to as full waveform ambient noise inversion—that improves the resolution of tomographic images by extracting waveform information from interstation correlation functions that cannot be used without knowing the distribution of noise sources. The fundamental idea is to drop the principle of Green function retrieval and to establish correlation functions as self-consistent observables in seismology. This involves the following steps: (1) We introduce an operator-based formulation of the forward problem of computing correlation functions. It is valid for arbitrary distributions of noise sources in both space and frequency, and for any type of medium, including 3-D elastic, heterogeneous and attenuating media. In addition, the formulation allows us to keep the derivations independent of time and frequency domain and it facilitates the application of adjoint techniques, which we use to derive efficient expressions to compute first and also second derivatives. The latter are essential for a resolution analysis that accounts for intra- and interparameter trade-offs. (2) In a forward modelling study we investigate the effect of noise sources and structure on different observables. Traveltimes are hardly affected by heterogeneous noise source distributions. On the other hand, the amplitude asymmetry of correlations is at least to first order insensitive to unmodelled Earth structure. Energy and waveform differences are sensitive to both structure and the distribution of noise sources. (3) We design and implement an appropriate inversion scheme, where the extraction of waveform information is successively increased. We demonstrate that full waveform ambient noise inversion has the potential to go beyond ambient noise tomography based on Green function retrieval and to refine noise source location, which is essential for a better understanding of noise generation. Inherent trade-offs between source and structure are quantified using Hessian-vector products.

Idiopathic Pulmonary Fibrosis: Data-driven Textural Analysis of Extent of Fibrosis at Baseline and 15-Month Follow-up.

PubMed

Humphries, Stephen M; Yagihashi, Kunihiro; Huckleberry, Jason; Rho, Byung-Hak; Schroeder, Joyce D; Strand, Matthew; Schwarz, Marvin I; Flaherty, Kevin R; Kazerooni, Ella A; van Beek, Edwin J R; Lynch, David A

2017-10-01

Purpose To evaluate associations between pulmonary function and both quantitative analysis and visual assessment of thin-section computed tomography (CT) images at baseline and at 15-month follow-up in subjects with idiopathic pulmonary fibrosis (IPF). Materials and Methods This retrospective analysis of preexisting anonymized data, collected prospectively between 2007 and 2013 in a HIPAA-compliant study, was exempt from additional institutional review board approval. The extent of lung fibrosis at baseline inspiratory chest CT in 280 subjects enrolled in the IPF Network was evaluated. Visual analysis was performed by using a semiquantitative scoring system. Computer-based quantitative analysis included CT histogram-based measurements and a data-driven textural analysis (DTA). Follow-up CT images in 72 of these subjects were also analyzed. Univariate comparisons were performed by using Spearman rank correlation. Multivariate and longitudinal analyses were performed by using a linear mixed model approach, in which models were compared by using asymptotic χ 2 tests. Results At baseline, all CT-derived measures showed moderate significant correlation (P < .001) with pulmonary function. At follow-up CT, changes in DTA scores showed significant correlation with changes in both forced vital capacity percentage predicted (ρ = -0.41, P < .001) and diffusing capacity for carbon monoxide percentage predicted (ρ = -0.40, P < .001). Asymptotic χ 2 tests showed that inclusion of DTA score significantly improved fit of both baseline and longitudinal linear mixed models in the prediction of pulmonary function (P < .001 for both). Conclusion When compared with semiquantitative visual assessment and CT histogram-based measurements, DTA score provides additional information that can be used to predict diminished function. Automatic quantification of lung fibrosis at CT yields an index of severity that correlates with visual assessment and functional change in subjects with IPF. © RSNA, 2017.

Discourse Markers in Italian as L2 in Face to Face vs. Computer Mediated Settings

ERIC Educational Resources Information Center

De Marco, Anna; Leone, Paola

2013-01-01

This pilot study aims to highlight a) differences in pragmatic function and distribution of discourse markers (DMs) in computer mediated and face to face (FtF) settings and b) any correlation of DM uses and language competence. The data have been collected by video-recording and analysing three speakers of Italian L2 (language level competence:…

Computing Wigner distributions and time correlation functions using the quantum thermal bath method: application to proton transfer spectroscopy.

PubMed

Basire, Marie; Borgis, Daniel; Vuilleumier, Rodolphe

2013-08-14

Langevin dynamics coupled to a quantum thermal bath (QTB) allows for the inclusion of vibrational quantum effects in molecular dynamics simulations at virtually no additional computer cost. We investigate here the ability of the QTB method to reproduce the quantum Wigner distribution of a variety of model potentials, designed to assess the performances and limits of the method. We further compute the infrared spectrum of a multidimensional model of proton transfer in the gas phase and in solution, using classical trajectories sampled initially from the Wigner distribution. It is shown that for this type of system involving large anharmonicities and strong nonlinear coupling to the environment, the quantum thermal bath is able to sample the Wigner distribution satisfactorily and to account for both zero point energy and tunneling effects. It leads to quantum time correlation functions having the correct short-time behavior, and the correct associated spectral frequencies, but that are slightly too overdamped. This is attributed to the classical propagation approximation rather than the generation of the quantized initial conditions themselves.

nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.

PubMed

Róg, T; Murzyn, K; Hinsen, K; Kneller, G R

2003-04-15

We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques. The quantities that can be calculated by nMoldyn are the mean-square displacement, the velocity autocorrelation function as well as its Fourier transform (the density of states) and its memory function, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function, and several functions specific to neutron scattering: the coherent and incoherent intermediate scattering functions with their Fourier transforms, the memory function of the coherent scattering function, and the elastic incoherent structure factor. The possibility to compute memory function is a new and powerful feature that allows to relate simulation results to theoretical studies. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 657-667, 2003

Integral Equation Study of Molecular Fluids and Liquid Crystals in Two Dimensions

NASA Astrophysics Data System (ADS)

Ward, David Atlee

The Ornstein-Zernike (OZ) equation is solved with a Percus-Yevick (PY) closure for the hard ellipse and hard planar dumbell fluids in two dimensions. The correlation functions, including the orientation correlation function, are expanded in a set of orthogonal functions and the coefficients are solved for using an iterative algorithm developed by Lado. The pressure, compressibility, and orientation coefficients are computed for a variety of densities and molecular elongations. The hard planar dumbell fluid shows no orientational ordering. The PY values for the pressure differ from the corresponding Monte Carlo (MC) values by as much as 8% for the cases studied. The hard ellipse fluid exhibits some orientational ordering. Ordering is much more pronounced for ellipses with an axis ratio larger than 2.0. Pressure values computed for the hard ellipse fluid from the PY theory differ from the corresponding MC values by as much as 11% for the cases studied. As the PY solutions do exhibit a nematic character in the hard ellipse fluid, we find it to be a viable reference system for further studies of the nematic liquid crystal phase, though the isotropic-nematic (I-N) phase transition found by Vieillard-Baron was not observed in the PY solutions. The Maier-Saupe theory was reformulated based on the density functional formalism of Sluckin and Shukla. Using PY data of the hard ellipse as input for the direct correlation function in the isotropic phase, the orientational distribution was calculated. The values obtained showed only extremely weak nematic behavior.

Reversibility of trapped air on chest computed tomography in cystic fibrosis patients.

PubMed

Loeve, Martine; Rosenow, Tim; Gorbunova, Vladlena; Hop, Wim C J; Tiddens, Harm A W M; de Bruijne, Marleen

2015-06-01

To investigate changes in trapped air volume and distribution over time and compare computed tomography (CT) with pulmonary function tests for determining trapped air. Thirty children contributed two CTs and pulmonary function tests over 2 years. Localized changes in trapped air on CT were assessed using image analysis software, by deforming the CT at timepoint 2 to match timepoint 1, and measuring the volume of stable (TAstable), disappeared (TAdisappeared) and new (TAnew) trapped air as a proportion of total lung volume. We used the difference between total lung capacity measured by plethysmography and helium dilution, residual volume to total lung capacity ratio, forced expiratory flow at 75% of vital capacity, and maximum mid-expiratory flow as pulmonary function test markers of trapped air. Statistical analysis included Wilcoxon's signed rank test and Spearman correlation coefficients. Median (range) age at baseline was 11.9 (5-17) years. Median (range) of trapped air was 9.5 (2-33)% at timepoint 1 and 9.0 (0-25)% at timepoint 2 (p=0.49). Median (range) TAstable, TAdisappeared and TAnew were respectively 3.0 (0-12)%, 5.0 (1-22)% and 7.0 (0-20)%. Trapped air on CT correlated statistically significantly with all pulmonary function measures (p<0.01), other than residual volume to total lung capacity ratio (p=0.37). Trapped air on CT did not significantly progress over 2 years, may have a substantial stable component, and is significantly correlated with pulmonary function markers. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes

NASA Astrophysics Data System (ADS)

Wang, Weizhou; Zhang, Yu; Ji, Baoming; Tian, Anmin

2011-06-01

The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal ⋯Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.

Disrupted Structural and Functional Networks and Their Correlation with Alertness in Right Temporal Lobe Epilepsy: A Graph Theory Study.

PubMed

Jiang, Wenyu; Li, Jianping; Chen, Xuemei; Ye, Wei; Zheng, Jinou

2017-01-01

Previous studies have shown that temporal lobe epilepsy (TLE) involves abnormal structural or functional connectivity in specific brain areas. However, limited comprehensive studies have been conducted on TLE associated changes in the topological organization of structural and functional networks. Additionally, epilepsy is associated with impairment in alertness, a fundamental component of attention. In this study, structural networks were constructed using diffusion tensor imaging tractography, and functional networks were obtained from resting-state functional MRI temporal series correlations in 20 right temporal lobe epilepsy (rTLE) patients and 19 healthy controls. Global network properties were computed by graph theoretical analysis, and correlations were assessed between global network properties and alertness. The results from these analyses showed that rTLE patients exhibit abnormal small-world attributes in structural and functional networks. Structural networks shifted toward more regular attributes, but functional networks trended toward more random attributes. After controlling for the influence of the disease duration, negative correlations were found between alertness, small-worldness, and the cluster coefficient. However, alertness did not correlate with either the characteristic path length or global efficiency in rTLE patients. Our findings show that disruptions of the topological construction of brain structural and functional networks as well as small-world property bias are associated with deficits in alertness in rTLE patients. These data suggest that reorganization of brain networks develops as a mechanism to compensate for altered structural and functional brain function during disease progression.

Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

PubMed

Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

2015-05-12

Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.

Time-dependent importance sampling in semiclassical initial value representation calculations for time correlation functions. II. A simplified implementation.

PubMed

Tao, Guohua; Miller, William H

2012-09-28

An efficient time-dependent (TD) Monte Carlo (MC) importance sampling method has recently been developed [G. Tao and W. H. Miller, J. Chem. Phys. 135, 024104 (2011)] for the evaluation of time correlation functions using the semiclassical (SC) initial value representation (IVR) methodology. In this TD-SC-IVR method, the MC sampling uses information from both time-evolved phase points as well as their initial values, and only the "important" trajectories are sampled frequently. Even though the TD-SC-IVR was shown in some benchmark examples to be much more efficient than the traditional time-independent sampling method (which uses only initial conditions), the calculation of the SC prefactor-which is computationally expensive, especially for large systems-is still required for accepted trajectories. In the present work, we present an approximate implementation of the TD-SC-IVR method that is completely prefactor-free; it gives the time correlation function as a classical-like magnitude function multiplied by a phase function. Application of this approach to flux-flux correlation functions (which yield reaction rate constants) for the benchmark H + H(2) system shows very good agreement with exact quantum results. Limitations of the approximate approach are also discussed.

Overcomplete compact representation of two-particle Green's functions

NASA Astrophysics Data System (ADS)

Shinaoka, Hiroshi; Otsuki, Junya; Haule, Kristjan; Wallerberger, Markus; Gull, Emanuel; Yoshimi, Kazuyoshi; Ohzeki, Masayuki

2018-05-01

Two-particle Green's functions and the vertex functions play a critical role in theoretical frameworks for describing strongly correlated electron systems. However, numerical calculations at the two-particle level often suffer from large computation time and massive memory consumption. We derive a general expansion formula for the two-particle Green's functions in terms of an overcomplete representation based on the recently proposed "intermediate representation" basis. The expansion formula is obtained by decomposing the spectral representation of the two-particle Green's function. We demonstrate that the expansion coefficients decay exponentially, while all high-frequency and long-tail structures in the Matsubara-frequency domain are retained. This representation therefore enables efficient treatment of two-particle quantities and opens a route to the application of modern many-body theories to realistic strongly correlated electron systems.

Exact Correlation Functions in S U (2 ) N =2 Superconformal QCD

NASA Astrophysics Data System (ADS)

Baggio, Marco; Niarchos, Vasilis; Papadodimas, Kyriakos

2014-12-01

We report an exact solution of 2- and 3-point functions of chiral primary fields in S U (2 ) N =2 super-Yang-Mills theory coupled to four hypermultiplets. It is shown that these correlation functions are nontrivial functions of the gauge coupling, obeying differential equations which take the form of the semi-infinite Toda chain. We solve these equations recursively in terms of the Zamolodchikov metric that can be determined exactly from supersymmetric localization on the four-sphere. Our results are verified independently in perturbation theory with a Feynman diagram computation up to 2 loops. This is a short version of a companion paper that contains detailed technical remarks, additional material, and aspects of an extension to the S U (N ) gauge group.

Effect of Finite Computational Domain on Turbulence Scaling Law in Both Physical and Spectral Spaces

NASA Technical Reports Server (NTRS)

Hou, Thomas Y.; Wu, Xiao-Hui; Chen, Shiyi; Zhou, Ye

1998-01-01

The well-known translation between the power law of energy spectrum and that of the correlation function or the second order structure function has been widely used in analyzing random data. Here, we show that the translation is valid only in proper scaling regimes. The regimes of valid translation are different for the correlation function and the structure function. Indeed, they do not overlap. Furthermore, in practice, the power laws exist only for a finite range of scales. We show that this finite range makes the translation inexact even in the proper scaling regime. The error depends on the scaling exponent. The current findings are applicable to data analysis in fluid turbulence and other stochastic systems.

Lagrangian velocity and acceleration correlations of large inertial particles in a closed turbulent flow

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

Machicoane, Nathanaël; Volk, Romain

We investigate the response of large inertial particle to turbulent fluctuations in an inhomogeneous and anisotropic flow. We conduct a Lagrangian study using particles both heavier and lighter than the surrounding fluid, and whose diameters are comparable to the flow integral scale. Both velocity and acceleration correlation functions are analyzed to compute the Lagrangian integral time and the acceleration time scale of such particles. The knowledge of how size and density affect these time scales is crucial in understanding particle dynamics and may permit stochastic process modelization using two-time models (for instance, Sawford’s). As particles are tracked over long timesmore » in the quasi-totality of a closed flow, the mean flow influences their behaviour and also biases the velocity time statistics, in particular the velocity correlation functions. By using a method that allows for the computation of turbulent velocity trajectories, we can obtain unbiased Lagrangian integral time. This is particularly useful in accessing the scale separation for such particles and to comparing it to the case of fluid particles in a similar configuration.« less

Real-Space Multiple-Scattering Theory and Its Applications at Exascale

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

Eisenbach, Markus; Wang, Yang

In recent decades, the ab initio methods based on density functional theory (DFT) (Hohenberg and Kohn 1964, Kohn and Sham 1965) have become a widely used tool in computational materials science, which allows theoretical prediction of physical properties of materials from the first principles and theoretical interpretation of new physical phenomena found in experiments. In the framework of DFT, the original problem that requires solving a quantum mechanical equation for a many-electron system is reduced to a one-electron problem that involves an electron moving in an effective field, while the effective field potential is made up of an electrostatic potential,more » also known as Hartree potential, arising from the electronic and ion charge distribution in space and an exchange–correlation potential, which is a function of the electron density and encapsulates the exchange and correlation effects of the many-electron system. Even though the exact functional form of the exchange-correlation potential is formally unknown, a local density approximation (LDA) or a generalized gradient approximation (GGA) is usually applied so that the calculation of the exchange–correlation potential, as well as the exchange–correlation energy, becomes tractable while a required accuracy is retained. Based on DFT, ab initio electronic structure calculations for a material generally involve a self-consistent process that iterates between two computational tasks: (1) solving an one-electron Schrödinger equation, also known as Kohn–Sham equation, to obtain the electron density and, if needed, the magnetic moment density, and (2) solving the Poisson equation to obtain the electrostatic potential corresponding to the electron density and constructing the effective potential by adding the exchange–correlation potential to the electrostatic potential. This self-consistent process proceeds until a convergence criteria is reached.« less

Segmentation of the Speaker's Face Region with Audiovisual Correlation

NASA Astrophysics Data System (ADS)

Liu, Yuyu; Sato, Yoichi

The ability to find the speaker's face region in a video is useful for various applications. In this work, we develop a novel technique to find this region within different time windows, which is robust against the changes of view, scale, and background. The main thrust of our technique is to integrate audiovisual correlation analysis into a video segmentation framework. We analyze the audiovisual correlation locally by computing quadratic mutual information between our audiovisual features. The computation of quadratic mutual information is based on the probability density functions estimated by kernel density estimation with adaptive kernel bandwidth. The results of this audiovisual correlation analysis are incorporated into graph cut-based video segmentation to resolve a globally optimum extraction of the speaker's face region. The setting of any heuristic threshold in this segmentation is avoided by learning the correlation distributions of speaker and background by expectation maximization. Experimental results demonstrate that our method can detect the speaker's face region accurately and robustly for different views, scales, and backgrounds.

Multiscale Models of Melting Arctic Sea Ice

DTIC Science & Technology

2014-09-30

from weakly to highly correlated, or Poissonian toward Wigner -Dyson, as a function of system connectedness. This provides a mechanism for explaining...eluded us. Court Strong found such a method. It creates an optimal fit of a hyperbolic tangent model for the fractal dimension as a function of log A...actual melt pond images, and have made significant advances in the underlying functional and numerical analysis needed for these computations

The AdS/CFT Correspondence: Classical, Quantum, and Thermodynamical Aspects

NASA Astrophysics Data System (ADS)

Young, Donovan

2007-06-01

Certain aspects of the AdS/CFT correspondence are studied in detail. We investigate the one-loop mass shift to certain two-impurity string states in light-cone string field theory on a plane wave background. We find that there exist logarithmic divergences in the sums over intermediate mode numbers which cancel between the cubic Hamiltonian and quartic "contact term". We argue that generically, every order in intermediate state impurities contributes to the mass shift at leading perturbative order. The same mass shift is also computed using an improved 3-string vertex proposed by Dobashi and Yoneya. The result is found to agree with gauge theory at leading order and is close but not quite in agreement at subleading order. We extend the analysis to include discrete light-cone quantization, considering states with up to three units of p+. We study the (apparently) first-order phase transition in the weakly coupled plane-wave matrix model at finite temperature. We analyze the effect of interactions by computing the relevant parts of the effective potential for the Polyakov loop operator to three loop order. We show that the phase transition is indeed of first order. We also compute the 2-loop correction to the Hagedorn temperature. Finally, correlation functions of 1/4 BPS Wilson loops with the infinite family of 1/2 BPS chiral primary operators are computed in N=4 super Yang-Mills theory by summing planar ladder diagrams. The correlation functions are also computed in the strong-coupling limit using string theory; the result is found to agree with the extrapolation of the planar ladders. The result is related to similar correlators of 1/2 BPS loops by a simple re-scaling of the coupling constant, discovered by Drukker for the case of the 1/4 BPS loop VEV.

Nonperturbative quark, gluon, and meson correlators of unquenched QCD

NASA Astrophysics Data System (ADS)

Cyrol, Anton K.; Mitter, Mario; Pawlowski, Jan M.; Strodthoff, Nils

2018-03-01

We present nonperturbative first-principle results for quark, gluon, and meson 1PI correlation functions of two-flavor Landau-gauge QCD in the vacuum. These correlation functions carry the full information about the theory. They are obtained by solving their functional renormalization group equations in a systematic vertex expansion, aiming at apparent convergence. This work represents a crucial prerequisite for quantitative first-principle studies of the QCD phase diagram and the hadron spectrum within this framework. In particular, we have computed the gluon, ghost, quark, and scalar-pseudoscalar meson propagators, as well as gluon, ghost-gluon, quark-gluon, quark, quark-meson, and meson interactions. Our results stress the crucial importance of the quantitatively correct running of different vertices in the semiperturbative regime for describing the phenomena and scales of confinement and spontaneous chiral symmetry breaking without phenomenological input.

Novel Assessment of Interstitial Lung Disease Using the "Computer-Aided Lung Informatics for Pathology Evaluation and Rating" (CALIPER) Software System in Idiopathic Inflammatory Myopathies.

PubMed

Ungprasert, Patompong; Wilton, Katelynn M; Ernste, Floranne C; Kalra, Sanjay; Crowson, Cynthia S; Rajagopalan, Srinivasan; Bartholmai, Brian J

2017-10-01

To evaluate the correlation between measurements from quantitative thoracic high-resolution CT (HRCT) analysis with "Computer-Aided Lung Informatics for Pathology Evaluation and Rating" (CALIPER) software and measurements from pulmonary function tests (PFTs) in patients with idiopathic inflammatory myopathies (IIM)-associated interstitial lung disease (ILD). A cohort of patients with IIM-associated ILD seen at Mayo Clinic was identified from medical record review. Retrospective analysis of HRCT data and PFTs at baseline and 1 year was performed. The abnormalities in HRCT were quantified using CALIPER software. A total of 110 patients were identified. At baseline, total interstitial abnormalities as measured by CALIPER, both by absolute volume and by percentage of total lung volume, had a significant negative correlation with diffusing capacity for carbon monoxide (DLCO), total lung capacity (TLC), and oxygen saturation. Analysis by subtype of interstitial abnormality revealed significant negative correlations between ground glass opacities (GGO) and reticular density (RD) with DLCO and TLC. At one year, changes of total interstitial abnormalities compared with baseline had a significant negative correlation with changes of TLC and oxygen saturation. A negative correlation between changes of total interstitial abnormalities and DLCO was also observed, but it was not statistically significant. Analysis by subtype of interstitial abnormality revealed negative correlations between changes of GGO and RD and changes of DLCO, TLC, and oxygen saturation, but most of the correlations did not achieve statistical significance. CALIPER measurements correlate well with functional measurements in patients with IIM-associated ILD.

Clinical Validation of 4-Dimensional Computed Tomography Ventilation With Pulmonary Function Test Data

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

Brennan, Douglas; Schubert, Leah; Diot, Quentin

Purpose: A new form of functional imaging has been proposed in the form of 4-dimensional computed tomography (4DCT) ventilation. Because 4DCTs are acquired as part of routine care for lung cancer patients, calculating ventilation maps from 4DCTs provides spatial lung function information without added dosimetric or monetary cost to the patient. Before 4DCT-ventilation is implemented it needs to be clinically validated. Pulmonary function tests (PFTs) provide a clinically established way of evaluating lung function. The purpose of our work was to perform a clinical validation by comparing 4DCT-ventilation metrics with PFT data. Methods and Materials: Ninety-eight lung cancer patients withmore » pretreatment 4DCT and PFT data were included in the study. Pulmonary function test metrics used to diagnose obstructive lung disease were recorded: forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity. Four-dimensional CT data sets and spatial registration were used to compute 4DCT-ventilation images using a density change–based and a Jacobian-based model. The ventilation maps were reduced to single metrics intended to reflect the degree of ventilation obstruction. Specifically, we computed the coefficient of variation (SD/mean), ventilation V20 (volume of lung ≤20% ventilation), and correlated the ventilation metrics with PFT data. Regression analysis was used to determine whether 4DCT ventilation data could predict for normal versus abnormal lung function using PFT thresholds. Results: Correlation coefficients comparing 4DCT-ventilation with PFT data ranged from 0.63 to 0.72, with the best agreement between FEV1 and coefficient of variation. Four-dimensional CT ventilation metrics were able to significantly delineate between clinically normal versus abnormal PFT results. Conclusions: Validation of 4DCT ventilation with clinically relevant metrics is essential. We demonstrate good global agreement between PFTs and 4DCT-ventilation, indicating that 4DCT-ventilation provides a reliable assessment of lung function. Four-dimensional CT ventilation enables exciting opportunities to assess lung function and create functional avoidance radiation therapy plans. The present work provides supporting evidence for the integration of 4DCT-ventilation into clinical trials.« less

Critical phenomena in communication/computation networks with various topologies and suboptimal to optimal resource allocation

NASA Astrophysics Data System (ADS)

Cogoni, Marco; Busonera, Giovanni; Anedda, Paolo; Zanetti, Gianluigi

2015-01-01

We generalize previous studies on critical phenomena in communication networks [1,2] by adding computational capabilities to the nodes. In our model, a set of tasks with random origin, destination and computational structure is distributed on a computational network, modeled as a graph. By varying the temperature of a Metropolis Montecarlo, we explore the global latency for an optimal to suboptimal resource assignment at a given time instant. By computing the two-point correlation function for the local overload, we study the behavior of the correlation distance (both for links and nodes) while approaching the congested phase: a transition from peaked to spread g(r) is seen above a critical (Montecarlo) temperature Tc. The average latency trend of the system is predicted by averaging over several network traffic realizations while maintaining a spatially detailed information for each node: a sharp decrease of performance is found over Tc independently of the workload. The globally optimized computational resource allocation and network routing defines a baseline for a future comparison of the transition behavior with respect to existing routing strategies [3,4] for different network topologies.

Reliable semiclassical computations in QCD

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

Dine, Michael; Department of Physics, Stanford University Stanford, California 94305-4060; Festuccia, Guido

We revisit the question of whether or not one can perform reliable semiclassical QCD computations at zero temperature. We study correlation functions with no perturbative contributions, and organize the problem by means of the operator product expansion, establishing a precise criterion for the validity of a semiclassical calculation. For N{sub f}>N, a systematic computation is possible; for N{sub f}

Defense strategies for cloud computing multi-site server infrastructures

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

Rao, Nageswara S.; Ma, Chris Y. T.; He, Fei

We consider cloud computing server infrastructures for big data applications, which consist of multiple server sites connected over a wide-area network. The sites house a number of servers, network elements and local-area connections, and the wide-area network plays a critical, asymmetric role of providing vital connectivity between them. We model this infrastructure as a system of systems, wherein the sites and wide-area network are represented by their cyber and physical components. These components can be disabled by cyber and physical attacks, and also can be protected against them using component reinforcements. The effects of attacks propagate within the systems, andmore » also beyond them via the wide-area network.We characterize these effects using correlations at two levels using: (a) aggregate failure correlation function that specifies the infrastructure failure probability given the failure of an individual site or network, and (b) first-order differential conditions on system survival probabilities that characterize the component-level correlations within individual systems. We formulate a game between an attacker and a provider using utility functions composed of survival probability and cost terms. At Nash Equilibrium, we derive expressions for the expected capacity of the infrastructure given by the number of operational servers connected to the network for sum-form, product-form and composite utility functions.« less

A computer model of molecular arrangement in a n-paraffinic liquid

NASA Astrophysics Data System (ADS)

Vacatello, Michele; Avitabile, Gustavo; Corradini, Paolo; Tuzi, Angela

1980-07-01

A computer model of a bulk liquid polymer was built to investigate the problem of local order. The model is made of C30 n-alkane molecules; it is not a lattice model, but it allows for a continuous variability of torsion angles and interchain distances, subject to realistic intra- and intermolecular potentials. Experimental x-ray scattering curves and radial distribution functions are well reproduced. Calculated properties like end-to-end distances, distribution of torsion angles, radial distribution functions, and chain direction correlation parameters, all indicate a random coil conformation and no tendency to form bundles of parallel chains.

Computational Nuclear Physics and Post Hartree-Fock Methods

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

Lietz, Justin; Sam, Novario; Hjorth-Jensen, M.

We present a computational approach to infinite nuclear matter employing Hartree-Fock theory, many-body perturbation theory and coupled cluster theory. These lectures are closely linked with those of chapters 9, 10 and 11 and serve as input for the correlation functions employed in Monte Carlo calculations in chapter 9, the in-medium similarity renormalization group theory of dense fermionic systems of chapter 10 and the Green's function approach in chapter 11. We provide extensive code examples and benchmark calculations, allowing thereby an eventual reader to start writing her/his own codes. We start with an object-oriented serial code and end with discussions onmore » strategies for porting the code to present and planned high-performance computing facilities.« less

Statistics of time delay and scattering correlation functions in chaotic systems. I. Random matrix theory

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

Novaes, Marcel

2015-06-15

We consider the statistics of time delay in a chaotic cavity having M open channels, in the absence of time-reversal invariance. In the random matrix theory approach, we compute the average value of polynomial functions of the time delay matrix Q = − iħS{sup †}dS/dE, where S is the scattering matrix. Our results do not assume M to be large. In a companion paper, we develop a semiclassical approximation to S-matrix correlation functions, from which the statistics of Q can also be derived. Together, these papers contribute to establishing the conjectured equivalence between the random matrix and the semiclassical approaches.

Quantification of uncertainty in first-principles predicted mechanical properties of solids: Application to solid ion conductors

NASA Astrophysics Data System (ADS)

Ahmad, Zeeshan; Viswanathan, Venkatasubramanian

2016-08-01

Computationally-guided material discovery is being increasingly employed using a descriptor-based screening through the calculation of a few properties of interest. A precise understanding of the uncertainty associated with first-principles density functional theory calculated property values is important for the success of descriptor-based screening. The Bayesian error estimation approach has been built in to several recently developed exchange-correlation functionals, which allows an estimate of the uncertainty associated with properties related to the ground state energy, for example, adsorption energies. Here, we propose a robust and computationally efficient method for quantifying uncertainty in mechanical properties, which depend on the derivatives of the energy. The procedure involves calculating energies around the equilibrium cell volume with different strains and fitting the obtained energies to the corresponding energy-strain relationship. At each strain, we use instead of a single energy, an ensemble of energies, giving us an ensemble of fits and thereby, an ensemble of mechanical properties associated with each fit, whose spread can be used to quantify its uncertainty. The generation of ensemble of energies is only a post-processing step involving a perturbation of parameters of the exchange-correlation functional and solving for the energy non-self-consistently. The proposed method is computationally efficient and provides a more robust uncertainty estimate compared to the approach of self-consistent calculations employing several different exchange-correlation functionals. We demonstrate the method by calculating the uncertainty bounds for several materials belonging to different classes and having different structures using the developed method. We show that the calculated uncertainty bounds the property values obtained using three different GGA functionals: PBE, PBEsol, and RPBE. Finally, we apply the approach to calculate the uncertainty associated with the DFT-calculated elastic properties of solid state Li-ion and Na-ion conductors.

Extended screened exchange functional derived from transcorrelated density functional theory.

PubMed

Umezawa, Naoto

2017-09-14

We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, H TC , is introduced by a similarity transformation of a many-body Hamiltonian, H, with respect to a complex function F: H TC =1FHF. It is proved that an expectation value of H TC for a normalized single Slater determinant, D n , corresponds to the total energy: E[n] = ⟨Ψ n |H|Ψ n ⟩/⟨Ψ n |Ψ n ⟩ = ⟨D n |H TC |D n ⟩ under the two assumptions: (1) The electron density nr associated with a trial wave function Ψ n = D n F is v-representable and (2) Ψ n and D n give rise to the same electron density nr. This formulation, therefore, provides an alternative expression of the total energy that is useful for the development of novel correlation energy functionals. By substituting a specific function for F, we successfully derived a model correlation energy functional, which resembles the functional form of the screened exchange method. The proposed functional, named the extended screened exchange (ESX) functional, is described within two-body integrals and is parametrized for a numerically exact correlation energy of the homogeneous electron gas. The ESX functional does not contain any ingredients of (semi-)local functionals and thus is totally free from self-interactions. The computational cost for solving the self-consistent-field equation is comparable to that of the Hartree-Fock method. We apply the ESX functional to electronic structure calculations for a solid silicon, H - ion, and small atoms. The results demonstrate that the TC-DFT formulation is promising for the systematic improvement of the correlation energy functional.

A Practical Computational Method for the Anisotropic Redshift-Space 3-Point Correlation Function

NASA Astrophysics Data System (ADS)

Slepian, Zachary; Eisenstein, Daniel J.

2018-04-01

We present an algorithm enabling computation of the anisotropic redshift-space galaxy 3-point correlation function (3PCF) scaling as N2, with N the number of galaxies. Our previous work showed how to compute the isotropic 3PCF with this scaling by expanding the radially-binned density field around each galaxy in the survey into spherical harmonics and combining these coefficients to form multipole moments. The N2 scaling occurred because this approach never explicitly required the relative angle between a galaxy pair about the primary galaxy. Here we generalize this work, demonstrating that in the presence of azimuthally-symmetric anisotropy produced by redshift-space distortions (RSD) the 3PCF can be described by two triangle side lengths, two independent total angular momenta, and a spin. This basis for the anisotropic 3PCF allows its computation with negligible additional work over the isotropic 3PCF. We also present the covariance matrix of the anisotropic 3PCF measured in this basis. Our algorithm tracks the full 5-D redshift-space 3PCF, uses an accurate line of sight to each triplet, is exact in angle, and easily handles edge correction. It will enable use of the anisotropic large-scale 3PCF as a probe of RSD in current and upcoming large-scale redshift surveys.

Chaotic Bohmian trajectories for stationary states

NASA Astrophysics Data System (ADS)

Cesa, Alexandre; Martin, John; Struyve, Ward

2016-09-01

In Bohmian mechanics, the nodes of the wave function play an important role in the generation of chaos. However, so far, most of the attention has been on moving nodes; little is known about the possibility of chaos in the case of stationary nodes. We address this question by considering stationary states, which provide the simplest examples of wave functions with stationary nodes. We provide examples of stationary wave functions for which there is chaos, as demonstrated by numerical computations, for one particle moving in three spatial dimensions and for two and three entangled particles in two dimensions. Our conclusion is that the motion of the nodes is not necessary for the generation of chaos. What is important is the overall complexity of the wave function. That is, if the wave function, or rather its phase, has a complex spatial variation, it will lead to complex Bohmian trajectories and hence to chaos. Another aspect of our work concerns the average Lyapunov exponent, which quantifies the overall amount of chaos. Since it is very hard to evaluate the average Lyapunov exponent analytically, which is often computed numerically, it is useful to have simple quantities that agree well with the average Lyapunov exponent. We investigate possible correlations with quantities such as the participation ratio and different measures of entanglement, for different systems and different families of stationary wave functions. We find that these quantities often tend to correlate to the amount of chaos. However, the correlation is not perfect, because, in particular, these measures do not depend on the form of the basis states used to expand the wave function, while the amount of chaos does.

Generalized nonequilibrium vertex correction method in coherent medium theory for quantum transport simulation of disordered nanoelectronics

NASA Astrophysics Data System (ADS)

Yan, Jiawei; Ke, Youqi

2016-07-01

Electron transport properties of nanoelectronics can be significantly influenced by the inevitable and randomly distributed impurities/defects. For theoretical simulation of disordered nanoscale electronics, one is interested in both the configurationally averaged transport property and its statistical fluctuation that tells device-to-device variability induced by disorder. However, due to the lack of an effective method to do disorder averaging under the nonequilibrium condition, the important effects of disorders on electron transport remain largely unexplored or poorly understood. In this work, we report a general formalism of Green's function based nonequilibrium effective medium theory to calculate the disordered nanoelectronics. In this method, based on a generalized coherent potential approximation for the Keldysh nonequilibrium Green's function, we developed a generalized nonequilibrium vertex correction method to calculate the average of a two-Keldysh-Green's-function correlator. We obtain nine nonequilibrium vertex correction terms, as a complete family, to express the average of any two-Green's-function correlator and find they can be solved by a set of linear equations. As an important result, the averaged nonequilibrium density matrix, averaged current, disorder-induced current fluctuation, and averaged shot noise, which involve different two-Green's-function correlators, can all be derived and computed in an effective and unified way. To test the general applicability of this method, we applied it to compute the transmission coefficient and its fluctuation with a square-lattice tight-binding model and compared with the exact results and other previously proposed approximations. Our results show very good agreement with the exact results for a wide range of disorder concentrations and energies. In addition, to incorporate with density functional theory to realize first-principles quantum transport simulation, we have also derived a general form of conditionally averaged nonequilibrium Green's function for multicomponent disorders.

Spectral fingerprints of large-scale neuronal interactions.

PubMed

Siegel, Markus; Donner, Tobias H; Engel, Andreas K

2012-01-11

Cognition results from interactions among functionally specialized but widely distributed brain regions; however, neuroscience has so far largely focused on characterizing the function of individual brain regions and neurons therein. Here we discuss recent studies that have instead investigated the interactions between brain regions during cognitive processes by assessing correlations between neuronal oscillations in different regions of the primate cerebral cortex. These studies have opened a new window onto the large-scale circuit mechanisms underlying sensorimotor decision-making and top-down attention. We propose that frequency-specific neuronal correlations in large-scale cortical networks may be 'fingerprints' of canonical neuronal computations underlying cognitive processes.

Analytical fitting model for rough-surface BRDF.

PubMed

Renhorn, Ingmar G E; Boreman, Glenn D

2008-08-18

A physics-based model is developed for rough surface BRDF, taking into account angles of incidence and scattering, effective index, surface autocovariance, and correlation length. Shadowing is introduced on surface correlation length and reflectance. Separate terms are included for surface scatter, bulk scatter and retroreflection. Using the FindFit function in Mathematica, the functional form is fitted to BRDF measurements over a wide range of incident angles. The model has fourteen fitting parameters; once these are fixed, the model accurately describes scattering data over two orders of magnitude in BRDF without further adjustment. The resulting analytical model is convenient for numerical computations.

Conformal field theories from deformations of theories with Wn symmetry

NASA Astrophysics Data System (ADS)

Babaro, Juan Pablo; Giribet, Gaston; Ranjbar, Arash

2016-10-01

We construct a set of nonrational conformal field theories that consist of deformations of Toda field theory for s l (n ). In addition to preserving conformal invariance, the theories may still exhibit a remnant infinite-dimensional affine symmetry. The case n =3 is used to illustrate this phenomenon, together with further deformations that yield enhanced Kac-Moody symmetry algebras. For generic n we compute N -point correlation functions on the Riemann sphere and show that these can be expressed in terms of s l (n ) Toda field theory ((N -2 )n +2 ) -point correlation functions.

Explicitly-correlated Gaussian geminals in electronic structure calculations

NASA Astrophysics Data System (ADS)

Szalewicz, Krzysztof; Jeziorski, Bogumił

2010-11-01

Explicitly correlated functions have been used since 1929, but initially only for two-electron systems. In 1960, Boys and Singer showed that if the correlating factor is of Gaussian form, many-electron integrals can be computed for general molecules. The capability of explicitly correlated Gaussian (ECG) functions to accurately describe many-electron atoms and molecules was demonstrated only in the early 1980s when Monkhorst, Zabolitzky and the present authors cast the many-body perturbation theory (MBPT) and coupled cluster (CC) equations as a system of integro-differential equations and developed techniques of solving these equations with two-electron ECG functions (Gaussian-type geminals, GTG). This work brought a new accuracy standard to MBPT/CC calculations. In 1985, Kutzelnigg suggested that the linear r 12 correlating factor can also be employed if n-electron integrals, n > 2, are factorised with the resolution of identity. Later, this factor was replaced by more general functions f (r 12), most often by ? , usually represented as linear combinations of Gaussian functions which makes the resulting approach (called F12) a special case of the original GTG expansion. The current state-of-art is that, for few-electron molecules, ECGs provide more accurate results than any other basis available, but for larger systems the F12 approach is the method of choice, giving significant improvements over orbital calculations.

Composite space charge density functions for the calculation of gamma sensitivity of self-powered neutron detectors, using Warren's model

NASA Astrophysics Data System (ADS)

Mahant, A. K.; Rao, P. S.; Misra, S. C.

1994-07-01

In the calculational model developed by Warren and Shah for the computation of the gamma sensitivity ( Sγ) it has been observed that the computed Sγ value is quite sensitive to the space charge distribution function assumed for the insulator region and the energy of the gamma photons. The Sγ of SPNDs with Pt, Co and V emitters (manufactured by Thermocoax, France) has been measured at 60Co photon energy and a good correlation between the measured and computed values has been obtained using a composite space charge density function (CSCD), the details of which are presented in this paper. The arguments are extended for evaluating the Sγ values of several SPNDs for which Warren and Shah reported the measured values for a prompt fission gamma spectrum obtained in a swimming pool reactor. These results are also discussed.

Communication: An exact bound on the bridge function in integral equation theories.

PubMed

Kast, Stefan M; Tomazic, Daniel

2012-11-07

We show that the formal solution of the general closure relation occurring in Ornstein-Zernike-type integral equation theories in terms of the Lambert W function leads to an exact relation between the bridge function and correlation functions, most notably to an inequality that bounds possible bridge values. The analytical results are illustrated on the example of the Lennard-Jones fluid for which the exact bridge function is known from computer simulations under various conditions. The inequality has consequences for the development of bridge function models and rationalizes numerical convergence issues.

2pBAb5. Validation of three-dimensional strain tracking by volumetric ultrasound image correlation in a pubovisceral muscle model

PubMed Central

Nagle, Anna S.; Nageswaren, Ashok R.; Haridas, Balakrishna; Mast, T. D.

2014-01-01

Little is understood about the biomechanical changes leading to pelvic floor disorders such as stress urinary incontinence. In order to measure regional biomechanical properties of the pelvic floor muscles in vivo, a three dimensional (3D) strain tracking technique employing correlation of volumetric ultrasound images has been implemented. In this technique, local 3D displacements are determined as a function of applied stress and then converted to strain maps. To validate this approach, an in vitro model of the pubovisceral muscle, with a hemispherical indenter emulating the downward stress caused by intra-abdominal pressure, was constructed. Volumetric B-scan images were recorded as a function of indenter displacement while muscle strain was measured independently by a sonomicrometry system (Sonometrics). Local strains were computed by ultrasound image correlation and compared with sonomicrometry-measured strains to assess strain tracking accuracy. Image correlation by maximizing an exponential likelihood function was found more reliable than the Pearson correlation coefficient. Strain accuracy was dependent on sizes of the subvolumes used for image correlation, relative to characteristic speckle length scales of the images. Decorrelation of echo signals was mapped as a function of indenter displacement and local tissue orientation. Strain measurement accuracy was weakly related to local echo decorrelation. PMID:24900165

Exact diagonalization library for quantum electron models

NASA Astrophysics Data System (ADS)

Iskakov, Sergei; Danilov, Michael

2018-04-01

We present an exact diagonalization C++ template library (EDLib) for solving quantum electron models, including the single-band finite Hubbard cluster and the multi-orbital impurity Anderson model. The observables that can be computed using EDLib are single particle Green's functions and spin-spin correlation functions. This code provides three different types of Hamiltonian matrix storage that can be chosen based on the model.

A systematic way for the cost reduction of density fitting methods

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

Kállay, Mihály, E-mail: kallay@mail.bme.hu

2014-12-28

We present a simple approach for the reduction of the size of auxiliary basis sets used in methods exploiting the density fitting (resolution of identity) approximation for electron repulsion integrals. Starting out of the singular value decomposition of three-center two-electron integrals, new auxiliary functions are constructed as linear combinations of the original fitting functions. The new functions, which we term natural auxiliary functions (NAFs), are analogous to the natural orbitals widely used for the cost reduction of correlation methods. The use of the NAF basis enables the systematic truncation of the fitting basis, and thereby potentially the reduction of themore » computational expenses of the methods, though the scaling with the system size is not altered. The performance of the new approach has been tested for several quantum chemical methods. It is demonstrated that the most pronounced gain in computational efficiency can be expected for iterative models which scale quadratically with the size of the fitting basis set, such as the direct random phase approximation. The approach also has the promise of accelerating local correlation methods, for which the processing of three-center Coulomb integrals is a bottleneck.« less

Enabling Computational Nanotechnology through JavaGenes in a Cycle Scavenging Environment

NASA Technical Reports Server (NTRS)

Globus, Al; Menon, Madhu; Srivastava, Deepak; Biegel, Bryan A. (Technical Monitor)

2002-01-01

A genetic algorithm procedure is developed and implemented for fitting parameters for many-body inter-atomic force field functions for simulating nanotechnology atomistic applications using portable Java on cycle-scavenged heterogeneous workstations. Given a physics based analytic functional form for the force field, correlated parameters in a multi-dimensional environment are typically chosen to fit properties given either by experiments and/or by higher accuracy quantum mechanical simulations. The implementation automates this tedious procedure using an evolutionary computing algorithm operating on hundreds of cycle-scavenged computers. As a proof of concept, we demonstrate the procedure for evaluating the Stillinger-Weber (S-W) potential by (a) reproducing the published parameters for Si using S-W energies in the fitness function, and (b) evolving a "new" set of parameters using semi-empirical tightbinding energies in the fitness function. The "new" parameters are significantly better suited for Si cluster energies and forces as compared to even the published S-W potential.

Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients.

PubMed

Łazarski, Roman; Burow, Asbjörn Manfred; Grajciar, Lukáš; Sierka, Marek

2016-10-30

A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn-Sham density functional theory using Gaussian-type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange-correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn-Sham matrix formation. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Spectral determinants for twist field correlators

NASA Astrophysics Data System (ADS)

Belitsky, A. V.

2018-04-01

Twist fields were introduced a few decades ago as a quantum counterpart to classical kink configurations and disorder variables in low dimensional field theories. In recent years they received a new incarnation within the framework of geometric entropy and strong coupling limit of four-dimensional scattering amplitudes. In this paper, we study their two-point correlation functions in a free massless scalar theory, namely, twist-twist and twist-antitwist correlators. In spite of the simplicity of the model in question, the properties of the latter are far from being trivial. The problem is reduced, within the formalism of the path integral, to the study of spectral determinants on surfaces with conical points, which are then computed exactly making use of the zeta function regularization. We also provide an insight into twist correlators for a massive complex scalar by means of the Lifshitz-Krein trace formula.

Stochastic reconstructions of spectral functions: Application to lattice QCD

NASA Astrophysics Data System (ADS)

Ding, H.-T.; Kaczmarek, O.; Mukherjee, Swagato; Ohno, H.; Shu, H.-T.

2018-05-01

We present a detailed study of the applications of two stochastic approaches, stochastic optimization method (SOM) and stochastic analytical inference (SAI), to extract spectral functions from Euclidean correlation functions. SOM has the advantage that it does not require prior information. On the other hand, SAI is a more generalized method based on Bayesian inference. Under mean field approximation SAI reduces to the often-used maximum entropy method (MEM) and for a specific choice of the prior SAI becomes equivalent to SOM. To test the applicability of these two stochastic methods to lattice QCD, firstly, we apply these methods to various reasonably chosen model correlation functions and present detailed comparisons of the reconstructed spectral functions obtained from SOM, SAI and MEM. Next, we present similar studies for charmonia correlation functions obtained from lattice QCD computations using clover-improved Wilson fermions on large, fine, isotropic lattices at 0.75 and 1.5 Tc, Tc being the deconfinement transition temperature of a pure gluon plasma. We find that SAI and SOM give consistent results to MEM at these two temperatures.

Efficiently accounting for ion correlations in electrokinetic nanofluidic devices using density functional theory.

PubMed

Gillespie, Dirk; Khair, Aditya S; Bardhan, Jaydeep P; Pennathur, Sumita

2011-07-15

The electrokinetic behavior of nanofluidic devices is dominated by the electrical double layers at the device walls. Therefore, accurate, predictive models of double layers are essential for device design and optimization. In this paper, we demonstrate that density functional theory (DFT) of electrolytes is an accurate and computationally efficient method for computing finite ion size effects and the resulting ion-ion correlations that are neglected in classical double layer theories such as Poisson-Boltzmann. Because DFT is derived from liquid-theory thermodynamic principles, it is ideal for nanofluidic systems with small spatial dimensions, high surface charge densities, high ion concentrations, and/or large ions. Ion-ion correlations are expected to be important in these regimes, leading to nonlinear phenomena such as charge inversion, wherein more counterions adsorb at the wall than is necessary to neutralize its surface charge, leading to a second layer of co-ions. We show that DFT, unlike other theories that do not include ion-ion correlations, can predict charge inversion and other nonlinear phenomena that lead to qualitatively different current densities and ion velocities for both pressure-driven and electro-osmotic flows. We therefore propose that DFT can be a valuable modeling and design tool for nanofluidic devices as they become smaller and more highly charged. Copyright © 2011 Elsevier Inc. All rights reserved.

Paradoxical Expectation: Oscillatory Brain Activity Reveals Social Interaction Impairment in Schizophrenia.

PubMed

Billeke, Pablo; Armijo, Alejandra; Castillo, Daniel; López, Tamara; Zamorano, Francisco; Cosmelli, Diego; Aboitiz, Francisco

2015-09-15

People with schizophrenia show social impairments that are related to functional outcomes. We tested the hypothesis that social interaction impairments in people with schizophrenia are related to alterations in the predictions of others' behavior and explored their underlying neurobiological mechanisms. Electroencephalography was performed in 20 patients with schizophrenia and 25 well-matched control subjects. Participants played as proposers in the repeated version of the Ultimatum Game believing that they were playing with another human or with a computer. The power of oscillatory brain activity was obtained by means of the wavelet transform. We performed a trial-by-trial correlation between the oscillatory activity and the risk of the offer. Control subjects adapted their offers when playing with computers and tended to maintain their offers when playing with humans, as such revealing learning and bargaining strategies, respectively. People with schizophrenia presented the opposite pattern of behavior in both games. During the anticipation of others' responses, the power of alpha oscillations correlated with the risk of the offers made, in a different way in both games. Patients with schizophrenia presented a greater correlation in computer games than in human games; control subjects showed the opposite pattern. The alpha activity correlated with positive symptoms. Our results reveal an alteration in social interaction in patients with schizophrenia that is related to oscillatory brain activity, suggesting maladjustment of expectation when patients face social and nonsocial agents. This alteration is related to psychotic symptoms and could guide further therapies for improving social functioning in patients with schizophrenia. Copyright © 2015 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Increasing the applicability of density functional theory. IV. Consequences of ionization-potential improved exchange-correlation potentials.

PubMed

Verma, Prakash; Bartlett, Rodney J

2014-05-14

This paper's objective is to create a "consistent" mean-field based Kohn-Sham (KS) density functional theory (DFT) meaning the functional should not only provide good total energy properties, but also the corresponding KS eigenvalues should be accurate approximations to the vertical ionization potentials (VIPs) of the molecule, as the latter condition attests to the viability of the exchange-correlation potential (VXC). None of the prominently used DFT approaches show these properties: the optimized effective potential VXC based ab initio dft does. A local, range-separated hybrid potential cam-QTP-00 is introduced as the basis for a "consistent" KS DFT approach. The computed VIPs as the negative of KS eigenvalue have a mean absolute error of 0.8 eV for an extensive set of molecule's electron ionizations, including the core. Barrier heights, equilibrium geometries, and magnetic properties obtained from the potential are in good agreement with experiment. A similar accuracy with less computational efforts can be achieved by using a non-variational global hybrid variant of the QTP-00 approach.

Computer-assisted stereotactic neurological surgery: pre-planning and on-site real-time operating control and simulation system

NASA Astrophysics Data System (ADS)

Zamorano, Lucia J.; Jiang, Charlie Z. W.

1993-09-01

In this decade the concept and development of computer assisted stereotactic neurological surgery has improved dramatically. First, the computer network replaced the tape as the data transportation media. Second, newer systems include multi-modality image correlation and frameless stereotactics as an integral part of their functionality, and offer extensive assistance to the neurosurgeon from the preplanning stages to and throughout the operation itself. These are very important changes, and have spurred the development of many interesting techniques. Successful systems include the ISG and NSPS-3.0.

Visualization of synchronization of the uterine contraction signals: running cross-correlation and wavelet running cross-correlation methods.

PubMed

Oczeretko, Edward; Swiatecka, Jolanta; Kitlas, Agnieszka; Laudanski, Tadeusz; Pierzynski, Piotr

2006-01-01

In physiological research, we often study multivariate data sets, containing two or more simultaneously recorded time series. The aim of this paper is to present the cross-correlation and the wavelet cross-correlation methods to assess synchronization between contractions in different topographic regions of the uterus. From a medical point of view, it is important to identify time delays between contractions, which may be of potential diagnostic significance in various pathologies. The cross-correlation was computed in a moving window with a width corresponding to approximately two or three contractions. As a result, the running cross-correlation function was obtained. The propagation% parameter assessed from this function allows quantitative description of synchronization in bivariate time series. In general, the uterine contraction signals are very complicated. Wavelet transforms provide insight into the structure of the time series at various frequencies (scales). To show the changes of the propagation% parameter along scales, a wavelet running cross-correlation was used. At first, the continuous wavelet transforms as the uterine contraction signals were received and afterwards, a running cross-correlation analysis was conducted for each pair of transformed time series. The findings show that running functions are very useful in the analysis of uterine contractions.

Effective homogeneity of the exchange-correlation and non-interacting kinetic energy functionals under density scaling.

PubMed

Borgoo, Alex; Teale, Andrew M; Tozer, David J

2012-01-21

Correlated electron densities, experimental ionisation potentials, and experimental electron affinities are used to investigate the homogeneity of the exchange-correlation and non-interacting kinetic energy functionals of Kohn-Sham density functional theory under density scaling. Results are presented for atoms and small molecules, paying attention to the influence of the integer discontinuity and the choice of the electron affinity. For the exchange-correlation functional, effective homogeneities are highly system-dependent on either side of the integer discontinuity. By contrast, the average homogeneity-associated with the potential that averages over the discontinuity-is generally close to 4/3 when the discontinuity is computed using positive affinities for systems that do bind an excess electron and negative affinities for those that do not. The proximity to 4/3 becomes increasingly pronounced with increasing atomic number. Evaluating the discontinuity using a zero affinity in systems that do not bind an excess electron instead leads to effective homogeneities on the electron abundant side that are close to 4/3. For the non-interacting kinetic energy functional, the effective homogeneities are less system-dependent and the effect of the integer discontinuity is less pronounced. Average values are uniformly below 5/3. The study provides information that may aid the development of improved exchange-correlation and non-interacting kinetic energy functionals. © 2012 American Institute of Physics

Structure constant of twist-2 light-ray operators in the Regge limit

DOE PAGES

Balitsky, Ian; Kazakov, Vladimir; Sobko, Evgeny

2016-03-11

We compute the correlation function of three twist-2 operators in N = 4 SYM in the leading BFKL approximation at any N c. In this limit, the result is applicable to other gauge theories, including QCD.

An Ultra-Wideband Cross-Correlation Radiometer for Mesoscopic Experiments

NASA Astrophysics Data System (ADS)

Toonen, Ryan; Haselby, Cyrus; Qin, Hua; Eriksson, Mark; Blick, Robert

2007-03-01

We have designed, built and tested a cross-correlation radiometer for detecting statistical order in the quantum fluctuations of mesoscopic experiments at sub-Kelvin temperatures. Our system utilizes a fully analog front-end--operating over the X- and Ku-bands (8 to 18 GHz)--for computing the cross-correlation function. Digital signal processing techniques are used to provide robustness against instrumentation drifts and offsets. The economized version of our instrument can measure, with sufficient correlation efficiency, noise signals having power levels as low as 10 fW. We show that, if desired, we can improve this performance by including cryogenic preamplifiers which boost the signal-to-noise ratio near the signal source. By adding a few extra components, we can measure both the real and imaginary parts of the cross-correlation function--improving the overall signal-to-noise ratio by a factor of sqrt[2]. We demonstrate the utility of our cross-correlator with noise power measurements from a quantum point contact.

Linear and quadratic static response functions and structure functions in Yukawa liquids.

PubMed

Magyar, Péter; Donkó, Zoltán; Kalman, Gabor J; Golden, Kenneth I

2014-08-01

We compute linear and quadratic static density response functions of three-dimensional Yukawa liquids by applying an external perturbation potential in molecular dynamics simulations. The response functions are also obtained from the equilibrium fluctuations (static structure factors) in the system via the fluctuation-dissipation theorems. The good agreement of the quadratic response functions, obtained in the two different ways, confirms the quadratic fluctuation-dissipation theorem. We also find that the three-point structure function may be factorizable into two-point structure functions, leading to a cluster representation of the equilibrium triplet correlation function.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

Bronchiectasis: correlation of high-resolution CT findings with health-related quality of life.

PubMed

Eshed, I; Minski, I; Katz, R; Jones, P W; Priel, I E

2007-02-01

To evaluate the relationship between the severity of bronchiectatic diseases, as evident on high-resolution computed tomography (HRCT) and the patient's quality of life measured using the St George's Respiratory Questionnaire (SGRQ). Forty-six patients (25 women, 21 men, mean age: 63 years) with bronchiectatic disease as evident on recent HRCT examinations were recruited. Each patient completed the SGRQ and underwent respiratory function tests. HRCT findings were blindly and independently scored by two radiologists, using the modified Bhalla scoring system. The relationships between HRCT scores, SGRQ scores and pulmonary function tests were evaluated. The patients' total CT score did not correlate with the SGRQ scores. However, patients with more advanced disease on HRCT, significantly differed in their SGRQ scores from patients with milder bronchiectatic disease. A significant correlation was found between the CT scores for the middle and distal lung zones and the activity, impacts and total SGRQ scores. No correlation was found between CT scores and respiratory function test indices. However, a significant correlation was found between the SGRQ scores and most of the respiratory function test indices. A correlation between the severity of bronchiectatic disease as expressed in HRCT and the health-related quality of life exists in patients with a more severe bronchiectatic disease but not in patients with mild disease. Such correlation depends on the location of the bronchiectasis in the pulmonary tree.

Assessing exchange-correlation functionals for elasticity and thermodynamics of α -ZrW2O8 : A density functional perturbation theory study

NASA Astrophysics Data System (ADS)

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; Gordon, Margaret E.; Bryan, Charles R.

2018-04-01

Elastic and thermodynamic properties of negative thermal expansion (NTE) α -ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ∼ 2 % with PBEsol and ∼ 6 % with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be CP0 = 192.2 and 193.8 J mol-1K-1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.

Temporal correlation functions of concentration fluctuations: an anomalous case.

PubMed

Lubelski, Ariel; Klafter, Joseph

2008-10-09

We calculate, within the framework of the continuous time random walk (CTRW) model, multiparticle temporal correlation functions of concentration fluctuations (CCF) in systems that display anomalous subdiffusion. The subdiffusion stems from the nonstationary nature of the CTRW waiting times, which also lead to aging and ergodicity breaking. Due to aging, a system of diffusing particles tends to slow down as time progresses, and therefore, the temporal correlation functions strongly depend on the initial time of measurement. As a consequence, time averages of the CCF differ from ensemble averages, displaying therefore ergodicity breaking. We provide a simple example that demonstrates the difference between these two averages, a difference that might be amenable to experimental tests. We focus on the case of ensemble averaging and assume that the preparation time of the system coincides with the starting time of the measurement. Our analytical calculations are supported by computer simulations based on the CTRW model.

Redshift space clustering of galaxies and cold dark matter model

NASA Technical Reports Server (NTRS)

Bahcall, Neta A.; Cen, Renyue; Gramann, Mirt

1993-01-01

The distorting effect of peculiar velocities on the power speturm and correlation function of IRAS and optical galaxies is studied. The observed redshift space power spectra and correlation functions of IRAS and optical the galaxies over the entire range of scales are directly compared with the corresponding redshift space distributions using large-scale computer simulations of cold dark matter (CDM) models in order to study the distortion effect of peculiar velocities on the power spectrum and correlation function of the galaxies. It is found that the observed power spectrum of IRAS and optical galaxies is consistent with the spectrum of an Omega = 1 CDM model. The problems that such a model currently faces may be related more to the high value of Omega in the model than to the shape of the spectrum. A low-density CDM model is also investigated and found to be consistent with the data.

Visual computed tomographic scoring of emphysema and its correlation with its diagnostic electrocardiographic sign: the frontal P vector.

PubMed

Chhabra, Lovely; Sareen, Pooja; Gandagule, Amit; Spodick, David H

2012-03-01

Verticalization of the frontal P vector in patients older than 45 years is virtually diagnostic of pulmonary emphysema (sensitivity, 96%; specificity, 87%). We investigated the correlation of P vector and the computed tomographic visual score of emphysema (VSE) in patients with established diagnosis of chronic obstructive pulmonary disease/emphysema. High-resolution computed tomographic scans of 26 patients with emphysema (age, >45 years) were reviewed to assess the type and extent of emphysema using the subjective visual scoring. Electrocardiograms were independently reviewed to determine the frontal P vector. The P vector and VSE were compared for statistical correlation. Both P vector and VSE were also directly compared with the forced expiratory volume at 1 second. The VSE and the orientation of the P vector (ÂP) had an overall significant positive correlation (r = +0.68; P = .0001) in all patients, but the correlation was very strong in patients with predominant lower-lobe emphysema (r = +0.88; P = .0004). Forced expiratory volume at 1 second and ÂP had almost a linear inverse correlation in predominant lower-lobe emphysema (r = -0.92; P < .0001). Orientation of the P vector positively correlates with visually scored emphysema. Both ÂP and VSE are strong reflectors of qualitative lung function in patients with predominant lower-lobe emphysema. A combination of more vertical ÂP and predominant lower-lobe emphysema reflects severe obstructive lung dysfunction. Copyright © 2012 Elsevier Inc. All rights reserved.

Development of surrogate models for the prediction of the flow around an aircraft propeller

NASA Astrophysics Data System (ADS)

Salpigidou, Christina; Misirlis, Dimitris; Vlahostergios, Zinon; Yakinthos, Kyros

2018-05-01

In the present work, the derivation of two surrogate models (SMs) for modelling the flow around a propeller for small aircrafts is presented. Both methodologies use derived functions based on computations with the detailed propeller geometry. The computations were performed using k-ω shear stress transport for modelling turbulence. In the SMs, the modelling of the propeller was performed in a computational domain of disk-like geometry, where source terms were introduced in the momentum equations. In the first SM, the source terms were polynomial functions of swirl and thrust, mainly related to the propeller radius. In the second SM, regression analysis was used to correlate the source terms with the velocity distribution through the propeller. The proposed SMs achieved faster convergence, in relation to the detail model, by providing also results closer to the available operational data. The regression-based model was the most accurate and required less computational time for convergence.

On defense strategies for system of systems using aggregated correlations

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

Rao, Nageswara S.; Imam, Neena; Ma, Chris Y. T.

2017-04-01

We consider a System of Systems (SoS) wherein each system Si, i = 1; 2; ... ;N, is composed of discrete cyber and physical components which can be attacked and reinforced. We characterize the disruptions using aggregate failure correlation functions given by the conditional failure probability of SoS given the failure of an individual system. We formulate the problem of ensuring the survival of SoS as a game between an attacker and a provider, each with a utility function composed of asurvival probability term and a cost term, both expressed in terms of the number of components attacked and reinforced.more » The survival probabilities of systems satisfy simple product-form, first-order differential conditions, which simplify the Nash Equilibrium (NE) conditions. We derive the sensitivity functions that highlight the dependence of SoS survival probability at NE on cost terms, correlation functions, and individual system survival probabilities.We apply these results to a simplified model of distributed cloud computing infrastructure.« less

Communication: The description of strong correlation within self-consistent Green's function second-order perturbation theory

NASA Astrophysics Data System (ADS)

Phillips, Jordan J.; Zgid, Dominika

2014-06-01

We report an implementation of self-consistent Green's function many-body theory within a second-order approximation (GF2) for application with molecular systems. This is done by iterative solution of the Dyson equation expressed in matrix form in an atomic orbital basis, where the Green's function and self-energy are built on the imaginary frequency and imaginary time domain, respectively, and fast Fourier transform is used to efficiently transform these quantities as needed. We apply this method to several archetypical examples of strong correlation, such as a H32 finite lattice that displays a highly multireference electronic ground state even at equilibrium lattice spacing. In all cases, GF2 gives a physically meaningful description of the metal to insulator transition in these systems, without resorting to spin-symmetry breaking. Our results show that self-consistent Green's function many-body theory offers a viable route to describing strong correlations while remaining within a computationally tractable single-particle formalism.

Sampling-Based Stochastic Sensitivity Analysis Using Score Functions for RBDO Problems with Correlated Random Variables

DTIC Science & Technology

2010-08-01

a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. a ...SECURITY CLASSIFICATION OF: This study presents a methodology for computing stochastic sensitivities with respect to the design variables, which are the...Random Variables Report Title ABSTRACT This study presents a methodology for computing stochastic sensitivities with respect to the design variables

Neural and computational processes underlying dynamic changes in self-esteem

PubMed Central

Rutledge, Robb B; Moutoussis, Michael; Dolan, Raymond J

2017-01-01

Self-esteem is shaped by the appraisals we receive from others. Here, we characterize neural and computational mechanisms underlying this form of social influence. We introduce a computational model that captures fluctuations in self-esteem engendered by prediction errors that quantify the difference between expected and received social feedback. Using functional MRI, we show these social prediction errors correlate with activity in ventral striatum/subgenual anterior cingulate cortex, while updates in self-esteem resulting from these errors co-varied with activity in ventromedial prefrontal cortex (vmPFC). We linked computational parameters to psychiatric symptoms using canonical correlation analysis to identify an ‘interpersonal vulnerability’ dimension. Vulnerability modulated the expression of prediction error responses in anterior insula and insula-vmPFC connectivity during self-esteem updates. Our findings indicate that updating of self-evaluative beliefs relies on learning mechanisms akin to those used in learning about others. Enhanced insula-vmPFC connectivity during updating of those beliefs may represent a marker for psychiatric vulnerability. PMID:29061228

Neural and computational processes underlying dynamic changes in self-esteem.

PubMed

Will, Geert-Jan; Rutledge, Robb B; Moutoussis, Michael; Dolan, Raymond J

2017-10-24

Self-esteem is shaped by the appraisals we receive from others. Here, we characterize neural and computational mechanisms underlying this form of social influence. We introduce a computational model that captures fluctuations in self-esteem engendered by prediction errors that quantify the difference between expected and received social feedback. Using functional MRI, we show these social prediction errors correlate with activity in ventral striatum/subgenual anterior cingulate cortex, while updates in self-esteem resulting from these errors co-varied with activity in ventromedial prefrontal cortex (vmPFC). We linked computational parameters to psychiatric symptoms using canonical correlation analysis to identify an 'interpersonal vulnerability' dimension. Vulnerability modulated the expression of prediction error responses in anterior insula and insula-vmPFC connectivity during self-esteem updates. Our findings indicate that updating of self-evaluative beliefs relies on learning mechanisms akin to those used in learning about others. Enhanced insula-vmPFC connectivity during updating of those beliefs may represent a marker for psychiatric vulnerability.

Detection of circuit-board components with an adaptive multiclass correlation filter

NASA Astrophysics Data System (ADS)

Diaz-Ramirez, Victor H.; Kober, Vitaly

2008-08-01

A new method for reliable detection of circuit-board components is proposed. The method is based on an adaptive multiclass composite correlation filter. The filter is designed with the help of an iterative algorithm using complex synthetic discriminant functions. The impulse response of the filter contains information needed to localize and classify geometrically distorted circuit-board components belonging to different classes. Computer simulation results obtained with the proposed method are provided and compared with those of known multiclass correlation based techniques in terms of performance criteria for recognition and classification of objects.

Theoretical Studies of the Kinetics of First-Order Phase Transitions.

NASA Astrophysics Data System (ADS)

Zheng, Qiang

This thesis involves theoretical studies of the kinetics of orderings in three classes of systems. The first class involves problems of phase separation in which the order parameter is conserved, such as occurs in the binary alloy Al-Zn. A theory is developed for the late stages of phase separation in the droplet regime for two -dimensional systems, namely, Ostwald ripening in two dimensions. The theory considers droplet correlations, which was neglected before, by a proper treatment of the screening effect of the correlations. This correlation effect is found that it does not alert the scaling features of phase separation, but significantly changes the shape of droplet-size distribution function. Further experiments and computer simulations are needed before this long-time subject may be closed. A second class of problem involves a study of the finite-size effects on domain growth described by the Allen-Cahn dynamics. Based on a theoretical approach of Ohta, Jasnow, and Kawasaki the explicit scaling functions for the scattering intensity for hypercubes and films are obtained. These results are for the cases in which the order-parameter is not conserved, such as in an order-disorder transition in alloys. These studies will be relevant to the experimental and computer simulation research projects currently being carried out in the United States and Europe. The last class of problems involves orderings in strong correlated systems, namely, the growth of Breath Figures. A special feature of this class of problems is that the coalescence effect. A theoretical model is proposed which can handle the two growth mechanisms, the individual droplet growth and coalescence simultaneously. Under certain approximations, the droplet-size distribution function is obtained analytically, and is in qualitative agreement with computer simulations. Our model also suggests that there may be an interesting relationship between the growth of Breath Figures and a geometric structure (ultrametricity) of general complex systems.

Population coding and decoding in a neural field: a computational study.

PubMed

Wu, Si; Amari, Shun-Ichi; Nakahara, Hiroyuki

2002-05-01

This study uses a neural field model to investigate computational aspects of population coding and decoding when the stimulus is a single variable. A general prototype model for the encoding process is proposed, in which neural responses are correlated, with strength specified by a gaussian function of their difference in preferred stimuli. Based on the model, we study the effect of correlation on the Fisher information, compare the performances of three decoding methods that differ in the amount of encoding information being used, and investigate the implementation of the three methods by using a recurrent network. This study not only rediscovers main results in existing literatures in a unified way, but also reveals important new features, especially when the neural correlation is strong. As the neural correlation of firing becomes larger, the Fisher information decreases drastically. We confirm that as the width of correlation increases, the Fisher information saturates and no longer increases in proportion to the number of neurons. However, we prove that as the width increases further--wider than (sqrt)2 times the effective width of the turning function--the Fisher information increases again, and it increases without limit in proportion to the number of neurons. Furthermore, we clarify the asymptotic efficiency of the maximum likelihood inference (MLI) type of decoding methods for correlated neural signals. It shows that when the correlation covers a nonlocal range of population (excepting the uniform correlation and when the noise is extremely small), the MLI type of method, whose decoding error satisfies the Cauchy-type distribution, is not asymptotically efficient. This implies that the variance is no longer adequate to measure decoding accuracy.

Computer task performance by subjects with Duchenne muscular dystrophy.

PubMed

Malheiros, Silvia Regina Pinheiro; da Silva, Talita Dias; Favero, Francis Meire; de Abreu, Luiz Carlos; Fregni, Felipe; Ribeiro, Denise Cardoso; de Mello Monteiro, Carlos Bandeira

2016-01-01

Two specific objectives were established to quantify computer task performance among people with Duchenne muscular dystrophy (DMD). First, we compared simple computational task performance between subjects with DMD and age-matched typically developing (TD) subjects. Second, we examined correlations between the ability of subjects with DMD to learn the computational task and their motor functionality, age, and initial task performance. The study included 84 individuals (42 with DMD, mean age of 18±5.5 years, and 42 age-matched controls). They executed a computer maze task; all participants performed the acquisition (20 attempts) and retention (five attempts) phases, repeating the same maze. A different maze was used to verify transfer performance (five attempts). The Motor Function Measure Scale was applied, and the results were compared with maze task performance. In the acquisition phase, a significant decrease was found in movement time (MT) between the first and last acquisition block, but only for the DMD group. For the DMD group, MT during transfer was shorter than during the first acquisition block, indicating improvement from the first acquisition block to transfer. In addition, the TD group showed shorter MT than the DMD group across the study. DMD participants improved their performance after practicing a computational task; however, the difference in MT was present in all attempts among DMD and control subjects. Computational task improvement was positively influenced by the initial performance of individuals with DMD. In turn, the initial performance was influenced by their distal functionality but not their age or overall functionality.

Development and Initial Validation of an Instrument to Measure Physicians' Use of, Knowledge about, and Attitudes Toward Computers

PubMed Central

Cork, Randy D.; Detmer, William M.; Friedman, Charles P.

1998-01-01

This paper describes details of four scales of a questionnaire—“Computers in Medical Care”—measuring attributes of computer use, self-reported computer knowledge, computer feature demand, and computer optimism of academic physicians. The reliability (i.e., precision, or degree to which the scale's result is reproducible) and validity (i.e., accuracy, or degree to which the scale actually measures what it is supposed to measure) of each scale were examined by analysis of the responses of 771 full-time academic physicians across four departments at five academic medical centers in the United States. The objectives of this paper were to define the psychometric properties of the scales as the basis for a future demonstration study and, pending the results of further validity studies, to provide the questionnaire and scales to the medical informatics community as a tool for measuring the attitudes of health care providers. Methodology: The dimensionality of each scale and degree of association of each item with the attribute of interest were determined by principal components factor analysis with othogonal varimax rotation. Weakly associated items (factor loading <.40) were deleted. The reliability of each resultant scale was computed using Cronbach's alpha coefficient. Content validity was addressed during scale construction; construct validity was examined through factor analysis and by correlational analyses. Results: Attributes of computer use, computer knowledge, and computer optimism were unidimensional, with the corresponding scales having reliabilities of.79,.91, and.86, respectively. The computer-feature demand attribute differentiated into two dimensions: the first reflecting demand for high-level functionality with reliability of.81 and the second demand for usability with reliability of.69. There were significant positive correlations between computer use, computer knowledge, and computer optimism scale scores and respondents' hands-on computer use, computer training, and self-reported computer sophistication. In addition, items posited on the computer knowledge scale to be more difficult generated significantly lower scores. Conclusion: The four scales of the questionnaire appear to measure with adequate reliability five attributes of academic physicians' attitudes toward computers in medical care: computer use, self-reported computer knowledge, demand for computer functionality, demand for computer usability, and computer optimism. Results of initial validity studies are positive, but further validation of the scales is needed. The URL of a downloadable HTML copy of the questionnaire is provided. PMID:9524349

Surrogate Structures for Computationally Expensive Optimization Problems With CPU-Time Correlated Functions

DTIC Science & Technology

2007-06-01

xc)−∇2g(x̃c)](x− xc). The second transformation is a space mapping function P that handles the change in variable dimensions (see Bandler et al. [11...17(2):188–217, 2004. 11. Bandler, J. W., Q. Cheng, S. Dakroury, A. S. Mohamed, M.H. Bakr, K. Madsen, J. Søndergaard. “ Space Mapping : The State of

On the decay of correlations in Sinai billiards with infinite horizon

NASA Astrophysics Data System (ADS)

Dahlqvist, Per; Artuso, Roberto

1996-02-01

We compute the decay of the autocorrelation function of the observable | vx| in the Sinai billiard and of the observable vx in the associated Lorentz gas with an approximation due to Baladi, Eckmann and Ruelle. We consider the standard configuration where the disk is centered inside a unit square. The asymptotic decay is found to be C( t) ∼ c( R)/ t. An explicit expression is given for the prefactor c( R) as a function of the radius of the scatterer. For the small scatterer case we also present expressions for the preasymptotic regime. Our findings are supported by numerical computations.

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

Giveon, Amit; Kutasov, David

We show that in any two dimensional conformal field theory with (2, 2) super-symmetry one can define a supersymmetric analog of the usual Renyi entropy of a spatial region A. It differs from the Renyi entropy by a universal function (which we compute) of the central charge, Renyi parameter n and the geometric parameters of A. In the limit n → 1 it coincides with the entanglement entropy. Thus, it contains the same information as the Renyi entropy but its computation only involves correlation functions of chiral and anti-chiral operators. We also show that this quantity appears naturally in stringmore » theory on AdS3.« less

Packing of nonoverlapping cubic particles: Computational algorithms and microstructural characteristics

NASA Astrophysics Data System (ADS)

Malmir, Hessam; Sahimi, Muhammad; Tabar, M. Reza Rahimi

2016-12-01

Packing of cubic particles arises in a variety of problems, ranging from biological materials to colloids and the fabrication of new types of porous materials with controlled morphology. The properties of such packings may also be relevant to problems involving suspensions of cubic zeolites, precipitation of salt crystals during CO2 sequestration in rock, and intrusion of fresh water in aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We present a detailed simulation and microstructural characterization of packings of nonoverlapping monodisperse cubic particles, following up on our preliminary results [H. Malmir et al., Sci. Rep. 6, 35024 (2016), 10.1038/srep35024]. A modification of the random sequential addition (RSA) algorithm has been developed to generate such packings, and a variety of microstructural descriptors, including the radial distribution function, the face-normal correlation function, two-point probability and cluster functions, the lineal-path function, the pore-size distribution function, and surface-surface and surface-void correlation functions, have been computed, along with the specific surface and mean chord length of the packings. The results indicate the existence of both spatial and orientational long-range order as the the packing density increases. The maximum packing fraction achievable with the RSA method is about 0.57, which represents the limit for a structure similar to liquid crystals.

Structure and orientational ordering in a fluid of elongated quadrupolar molecules

NASA Astrophysics Data System (ADS)

Singh, Ram Chandra

2013-01-01

A second-order density-functional theory is used to study the effect of quadrupolar interactions on the isotropic-nematic transition in a system of fluids of elongated molecules interacting via the Gay-Berne potential. The direct pair-correlation functions of the coexisting isotropic fluid that enter in the theory as input information are obtained by solving the Ornstein-Zernike equation using the Percus-Yevick integral equation theory in the (reduced) temperature range of 1.6≤T∗≤3.0 for different densities, temperatures and quadrupole moments. Using the harmonic coefficients of the direct pair-correlation functions, isotropic-nematic phase coexistence and thermodynamic parameters have been calculated. The theoretical results have been compared with the available computer simulation results.

Statistics of time delay and scattering correlation functions in chaotic systems. II. Semiclassical approximation

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

Novaes, Marcel

2015-06-15

We consider S-matrix correlation functions for a chaotic cavity having M open channels, in the absence of time-reversal invariance. Relying on a semiclassical approximation, we compute the average over E of the quantities Tr[S{sup †}(E − ϵ) S(E + ϵ)]{sup n}, for general positive integer n. Our result is an infinite series in ϵ, whose coefficients are rational functions of M. From this, we extract moments of the time delay matrix Q = − iħS{sup †}dS/dE and check that the first 8 of them agree with the random matrix theory prediction from our previous paper [M. Novaes, J. Math. Phys.more » 56, 062110 (2015)].« less

Real-time autocorrelator for fluorescence correlation spectroscopy based on graphical-processor-unit architecture: method, implementation, and comparative studies

NASA Astrophysics Data System (ADS)

Laracuente, Nicholas; Grossman, Carl

2013-03-01

We developed an algorithm and software to calculate autocorrelation functions from real-time photon-counting data using the fast, parallel capabilities of graphical processor units (GPUs). Recent developments in hardware and software have allowed for general purpose computing with inexpensive GPU hardware. These devices are more suited for emulating hardware autocorrelators than traditional CPU-based software applications by emphasizing parallel throughput over sequential speed. Incoming data are binned in a standard multi-tau scheme with configurable points-per-bin size and are mapped into a GPU memory pattern to reduce time-expensive memory access. Applications include dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS) experiments. We ran the software on a 64-core graphics pci card in a 3.2 GHz Intel i5 CPU based computer running Linux. FCS measurements were made on Alexa-546 and Texas Red dyes in a standard buffer (PBS). Software correlations were compared to hardware correlator measurements on the same signals. Supported by HHMI and Swarthmore College

A Coupling Function Linking Solar Wind /IMF Variations and Geomagnetic Activity

NASA Astrophysics Data System (ADS)

Lyatsky, W.; Lyatskaya, S.; Tan, A.

2006-12-01

From a theoretical consideration we have obtained expressions for the coupling function linking solar wind and IMF parameters to geomagnetic activity. While deriving these expressions, we took into account (1) a scaling factor due to polar cap expansion while increasing a reconnected magnetic flux in the dayside magnetosphere, and (2) a modified Akasofu function for the reconnected flux for combined IMF Bz and By components. The resulting coupling function may be written as Fa = aVsw B^1/2 sina (q/2), where Vsw is the solar wind speed, B^ is the magnitude of the IMF vector in the Y-Z plane, q is the clock angle between the Z axis and IMF vector in the Y-Z plane, a is a coefficient, and the exponent, a, is derived from the experimental data and equals approximately to 2. The Fa function differs primary by the power of B^ from coupling functions proposed earlier. For testing the obtained coupling function, we used solar wind and interplanetary magnetic field data for four years for maximum and minimum solar activity. We computed 2-D contour plots for correlation coefficients for the dependence of geomagnetic activity indices on solar wind parameters for different coupling functions. The obtained diagrams showed a good correspondence to the theoretic coupling function Fa for a »2. The maximum correlation coefficient for the dependence of the polar cap PC index on the Fa coupling function is significantly higher than that computed for other coupling functions used researchers, for the same time intervals.

Preliminary study on liver function changes after trisectionectomy with versus without prior portal vein embolization.

PubMed

Malinowski, Maciej; Lock, Johan Friso; Seehofer, Daniel; Gebauer, Bernhard; Schulz, Antje; Demirel, Lina; Bednarsch, Jan; Stary, Victoria; Neuhaus, Peter; Stockmann, Martin

2016-09-01

Post-hepatectomy liver failure (PHLF) is the major risk factor for mortality after hepatectomy. Preoperative planning of the future liver remnant volume reduces PHLF rates; however, future liver remnant function (FLR-F) might have an even stronger predictive value. In this preliminary study, we used a new method to calculate FLR-F by the LiMAx test and computer tomography-assisted volumetric-analysis to visualize liver function changes after portal vein embolization (PVE) before extended hepatectomy. The subjects included patients undergoing extended right hepatectomy either directly (NO-PVE group) or after PVE (PVE group). Computed tomography (CT) scan and liver function tests (LiMAx) were done before PVE and preoperatively. FLR-F was calculated and correlated with the postoperative liver function. There were 12 patients in the NO-PVE group and 19 patients in the PVE group. FLR-F and postoperative liver function correlated significantly in both groups (p = 0.036, p = 0.011), although postoperative liver function was slightly overestimated, at 32 and 45 µg/kg/min, in the NO-PVE and PVE groups, respectively. LiMAx value did not change after PVE. Volume-function analysis using LiMAx and CT scan enables us to reliably predict early postoperative liver function. Global enzymatic liver function measured by the LiMAx test did not change after PVE, confirming that liver function distribution in the liver stays constant after PVE. An overestimation of FLR-F is needed to compensate for the intraoperative liver injury that occurs in patients undergoing extended hepatectomy.

Density functional study of double ionization energies

NASA Astrophysics Data System (ADS)

Chong, D. P.

2008-02-01

In this paper, double ionization energies (DIEs) of gas-phase atoms and molecules are calculated by energy difference method with density functional theory. To determine the best functional for double ionization energies, we first study 24 main group atoms in the second, third, and fourth periods. An approximation is used in which the electron density is first obtained from a density functional computation with the exchange-correlation potential Vxc known as statistical average of orbital potentials, after which the energy is computed from that density with 59 different exchange-correlation energy functionals Exc. For the 24 atoms, the two best Exc functional providing DIEs with average absolute deviation (AAD) of only 0.25eV are the Perdew-Burke-Ernzerhof functional modified by Hammer et al. [Phys. Rev. B 59, 6413 (1999)] and one known as the Krieger-Chen-Iafrate-Savin functional modified by Krieger et al. (unpublished). Surprisingly, none of the 20 available hybrid functionals is among the top 15 functionals for the DIEs of the 24 atoms. A similar procedure is then applied to molecules, with opposite results: Only hybrid functionals are among the top 15 functionals for a selection of 29molecules. The best Exc functional for the 29molecules is found to be the Becke 1997 functional modified by Wilson et al. [J. Chem. Phys. 115, 9233 (2001)]. With that functional, the AAD from experiment for DIEs of 29molecules is just under 0.5eV. If the two suspected values for C2H2 and Fe(CO)5 are excluded, the AAD improves to 0.32eV. Many other hybrid functionals perform almost as well.

Left ventricular eccentricity index measured with SPECT myocardial perfusion imaging: An additional parameter of adverse cardiac remodeling.

PubMed

Gimelli, Alessia; Liga, Riccardo; Clemente, Alberto; Marras, Gavino; Kusch, Annette; Marzullo, Paolo

2017-01-12

Single-photon emission computed-tomography (SPECT) allows the quantification of LV eccentricity index (EI), a measure of cardiac remodeling. We sought to evaluate the feasibility of EI measurement with SPECT myocardial perfusion imaging and its interactions with relevant LV functional and structural parameters. Four-hundred and fifty-six patients underwent myocardial perfusion imaging on a Cadmium-Zinc-Telluride (CZT) camera. The summed rest, stress, and difference scores were calculated. From rest images, the LV end-diastolic (EDV) and end-systolic volumes, ejection fraction (EF), and peak filling rate (PFR) were calculated. In every patient, the EI, ranging from 0 (sphere) to 1 (line), was computed using a dedicated software (QGS/QPS; Cedars-Sinai Medical Center). Three-hundred and thirty-eight/456 (74%) patients showed a normal EF (>50%), while 26% had LV systolic dysfunction. The EI was computed from CZT images with excellent reproducibility (interclass correlation coefficient: 0.99, 95% CI 0.98-0.99). More impaired EI values correlated with the presence of a more abnormal LV perfusion (P < .001), function (EF and PFR, P < .001), and structure (EDV, P < .001). On multivariate analysis, higher EDV (P < .001) and depressed EF (P = .014) values were independent predictors of abnormal EI. The evaluation of LV eccentricity is feasible on gated CZT images. Abnormal EI associates with significant cardiac structural and functional abnormalities.

Finite-fault source inversion using adjoint methods in 3D heterogeneous media

NASA Astrophysics Data System (ADS)

Somala, Surendra Nadh; Ampuero, Jean-Paul; Lapusta, Nadia

2018-04-01

Accounting for lateral heterogeneities in the 3D velocity structure of the crust is known to improve earthquake source inversion, compared to results based on 1D velocity models which are routinely assumed to derive finite-fault slip models. The conventional approach to include known 3D heterogeneity in source inversion involves pre-computing 3D Green's functions, which requires a number of 3D wave propagation simulations proportional to the number of stations or to the number of fault cells. The computational cost of such an approach is prohibitive for the dense datasets that could be provided by future earthquake observation systems. Here, we propose an adjoint-based optimization technique to invert for the spatio-temporal evolution of slip velocity. The approach does not require pre-computed Green's functions. The adjoint method provides the gradient of the cost function, which is used to improve the model iteratively employing an iterative gradient-based minimization method. The adjoint approach is shown to be computationally more efficient than the conventional approach based on pre-computed Green's functions in a broad range of situations. We consider data up to 1 Hz from a Haskell source scenario (a steady pulse-like rupture) on a vertical strike-slip fault embedded in an elastic 3D heterogeneous velocity model. The velocity model comprises a uniform background and a 3D stochastic perturbation with the von Karman correlation function. Source inversions based on the 3D velocity model are performed for two different station configurations, a dense and a sparse network with 1 km and 20 km station spacing, respectively. These reference inversions show that our inversion scheme adequately retrieves the rise time when the velocity model is exactly known, and illustrates how dense coverage improves the inference of peak slip velocities. We investigate the effects of uncertainties in the velocity model by performing source inversions based on an incorrect, homogeneous velocity model. We find that, for velocity uncertainties that have standard deviation and correlation length typical of available 3D crustal models, the inverted sources can be severely contaminated by spurious features even if the station density is high. When data from thousand or more receivers is used in source inversions in 3D heterogeneous media, the computational cost of the method proposed in this work is at least two orders of magnitude lower than source inversion based on pre-computed Green's functions.

Finite-fault source inversion using adjoint methods in 3-D heterogeneous media

NASA Astrophysics Data System (ADS)

Somala, Surendra Nadh; Ampuero, Jean-Paul; Lapusta, Nadia

2018-07-01

Accounting for lateral heterogeneities in the 3-D velocity structure of the crust is known to improve earthquake source inversion, compared to results based on 1-D velocity models which are routinely assumed to derive finite-fault slip models. The conventional approach to include known 3-D heterogeneity in source inversion involves pre-computing 3-D Green's functions, which requires a number of 3-D wave propagation simulations proportional to the number of stations or to the number of fault cells. The computational cost of such an approach is prohibitive for the dense data sets that could be provided by future earthquake observation systems. Here, we propose an adjoint-based optimization technique to invert for the spatio-temporal evolution of slip velocity. The approach does not require pre-computed Green's functions. The adjoint method provides the gradient of the cost function, which is used to improve the model iteratively employing an iterative gradient-based minimization method. The adjoint approach is shown to be computationally more efficient than the conventional approach based on pre-computed Green's functions in a broad range of situations. We consider data up to 1 Hz from a Haskell source scenario (a steady pulse-like rupture) on a vertical strike-slip fault embedded in an elastic 3-D heterogeneous velocity model. The velocity model comprises a uniform background and a 3-D stochastic perturbation with the von Karman correlation function. Source inversions based on the 3-D velocity model are performed for two different station configurations, a dense and a sparse network with 1 and 20 km station spacing, respectively. These reference inversions show that our inversion scheme adequately retrieves the rise time when the velocity model is exactly known, and illustrates how dense coverage improves the inference of peak-slip velocities. We investigate the effects of uncertainties in the velocity model by performing source inversions based on an incorrect, homogeneous velocity model. We find that, for velocity uncertainties that have standard deviation and correlation length typical of available 3-D crustal models, the inverted sources can be severely contaminated by spurious features even if the station density is high. When data from thousand or more receivers is used in source inversions in 3-D heterogeneous media, the computational cost of the method proposed in this work is at least two orders of magnitude lower than source inversion based on pre-computed Green's functions.

Content range and precision of a computer adaptive test of upper extremity function for children with cerebral palsy.

PubMed

Montpetit, Kathleen; Haley, Stephen; Bilodeau, Nathalie; Ni, Pengsheng; Tian, Feng; Gorton, George; Mulcahey, M J

2011-02-01

This article reports on the content range and measurement precision of an upper extremity (UE) computer adaptive testing (CAT) platform of physical function in children with cerebral palsy. Upper extremity items representing skills of all abilities were administered to 305 parents. These responses were compared with two traditional standardized measures: Pediatric Outcomes Data Collection Instrument and Functional Independence Measure for Children. The UE CAT correlated strongly with the upper extremity component of these measures and had greater precision when describing individual functional ability. The UE item bank has wider range with items populating the lower end of the ability spectrum. This new UE item bank and CAT have the capability to quickly assess children of all ages and abilities with good precision and, most importantly, with items that are meaningful and appropriate for their age and level of physical function.

Computational methodology to predict satellite system-level effects from impacts of untrackable space debris

NASA Astrophysics Data System (ADS)

Welty, N.; Rudolph, M.; Schäfer, F.; Apeldoorn, J.; Janovsky, R.

2013-07-01

This paper presents a computational methodology to predict the satellite system-level effects resulting from impacts of untrackable space debris particles. This approach seeks to improve on traditional risk assessment practices by looking beyond the structural penetration of the satellite and predicting the physical damage to internal components and the associated functional impairment caused by untrackable debris impacts. The proposed method combines a debris flux model with the Schäfer-Ryan-Lambert ballistic limit equation (BLE), which accounts for the inherent shielding of components positioned behind the spacecraft structure wall. Individual debris particle impact trajectories and component shadowing effects are considered and the failure probabilities of individual satellite components as a function of mission time are calculated. These results are correlated to expected functional impairment using a Boolean logic model of the system functional architecture considering the functional dependencies and redundancies within the system.

Efficient Processing of Data for Locating Lightning Strikes

NASA Technical Reports Server (NTRS)

Medelius, Pedro J.; Starr, Stan

2003-01-01

Two algorithms have been devised to increase the efficiency of processing of data in lightning detection and ranging (LDAR) systems so as to enable the accurate location of lightning strikes in real time. In LDAR, the location of a lightning strike is calculated by solving equations for the differences among the times of arrival (DTOAs) of the lightning signals at multiple antennas as functions of the locations of the antennas and the speed of light. The most difficult part of the problem is computing the DTOAs from digitized versions of the signals received by the various antennas. One way (a time-domain approach) to determine the DTOAs is to compute cross-correlations among variously differentially delayed replicas of the digitized signals and to select, as the DTOAs, those differential delays that yield the maximum correlations. Another way (a frequency-domain approach) to determine the DTOAs involves the computation of cross-correlations among Fourier transforms of variously differentially phased replicas of the digitized signals, along with utilization of the relationship among phase difference, time delay, and frequency.

A Small World of Neuronal Synchrony

PubMed Central

Yu, Shan; Huang, Debin; Singer, Wolf

2008-01-01

A small-world network has been suggested to be an efficient solution for achieving both modular and global processing—a property highly desirable for brain computations. Here, we investigated functional networks of cortical neurons using correlation analysis to identify functional connectivity. To reconstruct the interaction network, we applied the Ising model based on the principle of maximum entropy. This allowed us to assess the interactions by measuring pairwise correlations and to assess the strength of coupling from the degree of synchrony. Visual responses were recorded in visual cortex of anesthetized cats, simultaneously from up to 24 neurons. First, pairwise correlations captured most of the patterns in the population's activity and, therefore, provided a reliable basis for the reconstruction of the interaction networks. Second, and most importantly, the resulting networks had small-world properties; the average path lengths were as short as in simulated random networks, but the clustering coefficients were larger. Neurons differed considerably with respect to the number and strength of interactions, suggesting the existence of “hubs” in the network. Notably, there was no evidence for scale-free properties. These results suggest that cortical networks are optimized for the coexistence of local and global computations: feature detection and feature integration or binding. PMID:18400792

fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets.

PubMed

Madrigal, Pedro

2017-03-01

Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomic science, as it allows both to evaluate reproducibility of biological or technical replicates, and to compare different datasets to identify their potential correlations. Here we present fCCAC, an application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). We show how this method differs from other measures of correlation, and exemplify how it can reveal shared covariance between histone modifications and DNA binding proteins, such as the relationship between the H3K4me3 chromatin mark and its epigenetic writers and readers. An R/Bioconductor package is available at http://bioconductor.org/packages/fCCAC/ . pmb59@cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Designing Waveform Sets with Good Correlation and Stopband Properties for MIMO Radar via the Gradient-Based Method

PubMed Central

Tang, Liang; Zhu, Yongfeng; Fu, Qiang

2017-01-01

Waveform sets with good correlation and/or stopband properties have received extensive attention and been widely used in multiple-input multiple-output (MIMO) radar. In this paper, we aim at designing unimodular waveform sets with good correlation and stopband properties. To formulate the problem, we construct two criteria to measure the correlation and stopband properties and then establish an unconstrained problem in the frequency domain. After deducing the phase gradient and the step size, an efficient gradient-based algorithm with monotonicity is proposed to minimize the objective function directly. For the design problem without considering the correlation weights, we develop a simplified algorithm, which only requires a few fast Fourier transform (FFT) operations and is more efficient. Because both of the algorithms can be implemented via the FFT operations and the Hadamard product, they are computationally efficient and can be used to design waveform sets with a large waveform number and waveform length. Numerical experiments show that the proposed algorithms can provide better performance than the state-of-the-art algorithms in terms of the computational complexity. PMID:28468308

Designing Waveform Sets with Good Correlation and Stopband Properties for MIMO Radar via the Gradient-Based Method.

PubMed

Tang, Liang; Zhu, Yongfeng; Fu, Qiang

2017-05-01

Waveform sets with good correlation and/or stopband properties have received extensive attention and been widely used in multiple-input multiple-output (MIMO) radar. In this paper, we aim at designing unimodular waveform sets with good correlation and stopband properties. To formulate the problem, we construct two criteria to measure the correlation and stopband properties and then establish an unconstrained problem in the frequency domain. After deducing the phase gradient and the step size, an efficient gradient-based algorithm with monotonicity is proposed to minimize the objective function directly. For the design problem without considering the correlation weights, we develop a simplified algorithm, which only requires a few fast Fourier transform (FFT) operations and is more efficient. Because both of the algorithms can be implemented via the FFT operations and the Hadamard product, they are computationally efficient and can be used to design waveform sets with a large waveform number and waveform length. Numerical experiments show that the proposed algorithms can provide better performance than the state-of-the-art algorithms in terms of the computational complexity.

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study

PubMed Central

2016-01-01

Binding free energies of bromodomain inhibitors are calculated with recently formulated approaches, namely ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling). A set of compounds is provided by GlaxoSmithKline, which represents a range of chemical functionality and binding affinities. The predicted binding free energies exhibit a good Spearman correlation of 0.78 with the experimental data from the 3-trajectory ESMACS, and an excellent correlation of 0.92 from the TIES approach where applicable. Given access to suitable high end computing resources and a high degree of automation, we can compute individual binding affinities in a few hours with precisions no greater than 0.2 kcal/mol for TIES, and no larger than 0.34 and 1.71 kcal/mol for the 1- and 3-trajectory ESMACS approaches. PMID:28005370

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

An adiabatic linearized path integral approach for quantum time-correlation functions II: a cumulant expansion method for improving convergence.

PubMed

Causo, Maria Serena; Ciccotti, Giovanni; Bonella, Sara; Vuilleumier, Rodolphe

2006-08-17

Linearized mixed quantum-classical simulations are a promising approach for calculating time-correlation functions. At the moment, however, they suffer from some numerical problems that may compromise their efficiency and reliability in applications to realistic condensed-phase systems. In this paper, we present a method that improves upon the convergence properties of the standard algorithm for linearized calculations by implementing a cumulant expansion of the relevant averages. The effectiveness of the new approach is tested by applying it to the challenging computation of the diffusion of an excess electron in a metal-molten salt solution.

Exact exchange-correlation potentials of singlet two-electron systems

NASA Astrophysics Data System (ADS)

Ryabinkin, Ilya G.; Ospadov, Egor; Staroverov, Viktor N.

2017-10-01

We suggest a non-iterative analytic method for constructing the exchange-correlation potential, v XC ( r ) , of any singlet ground-state two-electron system. The method is based on a convenient formula for v XC ( r ) in terms of quantities determined only by the system's electronic wave function, exact or approximate, and is essentially different from the Kohn-Sham inversion technique. When applied to Gaussian-basis-set wave functions, the method yields finite-basis-set approximations to the corresponding basis-set-limit v XC ( r ) , whereas the Kohn-Sham inversion produces physically inappropriate (oscillatory and divergent) potentials. The effectiveness of the procedure is demonstrated by computing accurate exchange-correlation potentials of several two-electron systems (helium isoelectronic series, H2, H3 + ) using common ab initio methods and Gaussian basis sets.

Screened hybrid density functionals for solid-state chemistry and physics.

PubMed

Janesko, Benjamin G; Henderson, Thomas M; Scuseria, Gustavo E

2009-01-21

Density functional theory incorporating hybrid exchange-correlation functionals has been extraordinarily successful in providing accurate, computationally tractable treatments of molecular properties. However, conventional hybrid functionals can be problematic for solids. Their nonlocal, Hartree-Fock-like exchange term decays slowly and incorporates unphysical features in metals and narrow-bandgap semiconductors. This article provides an overview of our group's work on designing hybrid functionals for solids. We focus on the Heyd-Scuseria-Ernzerhof screened hybrid functional [J. Chem. Phys. 2003, 118, 8207], its applications to the chemistry and physics of solids and surfaces, and our efforts to build upon its successes.

Hybrid density-functional calculations of phonons in LaCoO3

NASA Astrophysics Data System (ADS)

Gryaznov, Denis; Evarestov, Robert A.; Maier, Joachim

2010-12-01

Phonon frequencies at Γ point in nonmagnetic rhombohedral phase of LaCoO3 were calculated using density-functional theory with hybrid exchange correlation functional PBE0. The calculations involved a comparison of results for two types of basis functions commonly used in ab initio calculations, namely, the plane-wave approach and linear combination of atomic orbitals, as implemented in VASP and CRYSTAL computer codes, respectively. A good qualitative, but also within an error margin of less than 30%, a quantitative agreement was observed not only between the two formalisms but also between theoretical and experimental phonon frequency predictions. Moreover, the correlation between the phonon symmetries in cubic and rhombohedral phases is discussed in detail on the basis of group-theoretical analysis. It is concluded that the hybrid PBE0 functional is able to predict correctly the phonon properties in LaCoO3 .

A Method for the Alignment of Heterogeneous Macromolecules from Electron Microscopy

PubMed Central

Shatsky, Maxim; Hall, Richard J.; Brenner, Steven E.; Glaeser, Robert M.

2009-01-01

We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal to noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single particle images. Our method is tested on data from three model structures and one real dataset. PMID:19166941

Robust validation of approximate 1-matrix functionals with few-electron harmonium atoms

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

Cioslowski, Jerzy, E-mail: jerzy@wmf.univ.szczecin.pl; Piris, Mario; Matito, Eduard

2015-12-07

A simple comparison between the exact and approximate correlation components U of the electron-electron repulsion energy of several states of few-electron harmonium atoms with varying confinement strengths provides a stringent validation tool for 1-matrix functionals. The robustness of this tool is clearly demonstrated in a survey of 14 known functionals, which reveals their substandard performance within different electron correlation regimes. Unlike spot-testing that employs dissociation curves of diatomic molecules or more extensive benchmarking against experimental atomization energies of molecules comprising some standard set, the present approach not only uncovers the flaws and patent failures of the functionals but, even moremore » importantly, also allows for pinpointing their root causes. Since the approximate values of U are computed at exact 1-densities, the testing requires minimal programming and thus is particularly suitable for rapid screening of new functionals.« less

Neuronal Correlation Parameter and the Idea of Thermodynamic Entropy of an N-Body Gravitationally Bounded System.

PubMed

Haranas, Ioannis; Gkigkitzis, Ioannis; Kotsireas, Ilias; Austerlitz, Carlos

2017-01-01

Understanding how the brain encodes information and performs computation requires statistical and functional analysis. Given the complexity of the human brain, simple methods that facilitate the interpretation of statistical correlations among different brain regions can be very useful. In this report we introduce a numerical correlation measure that may serve the interpretation of correlational neuronal data, and may assist in the evaluation of different brain states. The description of the dynamical brain system, through a global numerical measure may indicate the presence of an action principle which may facilitate a application of physics principles in the study of the human brain and cognition.

Continuous Fluorescence Microphotolysis and Correlation Spectroscopy Using 4Pi Microscopy

PubMed Central

Arkhipov, Anton; Hüve, Jana; Kahms, Martin; Peters, Reiner; Schulten, Klaus

2007-01-01

Continuous fluorescence microphotolysis (CFM) and fluorescence correlation spectroscopy (FCS) permit measurement of molecular mobility and association reactions in single living cells. CFM and FCS complement each other ideally and can be realized using identical equipment. So far, the spatial resolution of CFM and FCS was restricted by the resolution of the light microscope to the micrometer scale. However, cellular functions generally occur on the nanometer scale. Here, we develop the theoretical and computational framework for CFM and FCS experiments using 4Pi microscopy, which features an axial resolution of ∼100 nm. The framework, taking the actual 4Pi point spread function of the instrument into account, was validated by measurements on model systems, employing 4Pi conditions or normal confocal conditions together with either single- or two-photon excitation. In all cases experimental data could be well fitted by computed curves for expected diffusion coefficients, even when the signal/noise ratio was small due to the small number of fluorophores involved. PMID:17704168

Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

PubMed

Hoy, Erik P; Mazziotti, David A

2015-08-14

Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

Structural γ-ε phase transition in Fe-Mn alloys from a CPA  +  DMFT approach.

PubMed

Belozerov, A S; Poteryaev, A I; Skornyakov, S L; Anisimov, V I

2015-11-25

We present a computational scheme for total energy calculations of disordered alloys with strong electronic correlations. It employs the coherent potential approximation combined with the dynamical mean-field theory and allows one to study the structural transformations. The material-specific Hamiltonians in the Wannier function basis are obtained by density functional theory. The proposed computational scheme is applied to study the γ-ε structural transition in paramagnetic Fe-Mn alloys for Mn content from 10 to 20 at.%. The electronic correlations are found to play a crucial role in this transition. The calculated transition temperature decreases with increasing Mn content and is in good agreement with experiment. We demonstrate that in contrast to the α-γ transition in pure iron, the γ-ε transition in Fe-Mn alloys is driven by a combination of kinetic and Coulomb energies. The latter is found to be responsible for the decrease of the γ-ε transition temperature with Mn content.

The Relationship between Family Functioning and Academic Achievement in Female High School Students of Isfahan, Iran, in 2013-2014.

PubMed

Rezaei-Dehaghani, Abdollah; Keshvari, Mahrokh; Paki, Somayeh

2018-01-01

Nowadays, the most important problem of the educational system is the vast spread of school failure. Therefore, detection of the factors leading to or preventing students' academic achievement is of utmost importance. Family function is considered to be a critical component of academic success. This study aimed to investigate the relationship between family functioning and academic achievement in high school female students in Isfahan. This descriptive correlational study was conducted through random sampling among 237 female high school students in Isfahan during school year 2013-2014. Data were collected by participants' personal characteristics and Bloom family function questionnaires. To analyze the data, descriptive statistics (mean and standard deviation) and inferential statistics (Pearson correlation and linear regression analysis) were adopted and computed using SPSS software. The results showed a significant correlation between family function (except lack of independence) and students' academic achievement ( p < 0.05). Further, among family function dimensions, expressiveness ( β = 0.235, p < 0.001), family socialization ( β = 0.219, p = 0.001), and cohesion ( β = 0.211, p = 0.001) were more reliable predictors of academic achievement. The results of this study showed that students' academic achievement is highly correlated with the performance of their families. Therefore, to improve students' educational status in cultural and educational programs, which are specified for them, family function centered plans should be at the heart of attention.

Clinical utility of computed tomographic lung volumes in patients with chronic obstructive pulmonary disease.

PubMed

Lee, Jae Seung; Lee, Sang-Min; Seo, Joon Beom; Lee, Sei Won; Huh, Jin Won; Oh, Yeon-Mok; Lee, Sang-Do

2014-01-01

Published data concerning the utility of computed tomography (CT)-based lung volumes are limited to correlation with lung function. The aim of this study was to evaluate the clinical utility of the CT expiratory-to-inspiratory lung volume ratio (CT Vratio) by assessing the relationship with clinically relevant outcomes. A total of 75 stable chronic obstructive pulmonary disease (COPD) patients having pulmonary function testing and volumetric CT at full inspiration and expiration were retrospectively evaluated. Inspiratory and expiratory CT lung volumes were measured using in-house software. Correlation of the CT Vratio with patient-centered outcomes, including the modified Medical Research Council (MMRC) dyspnea score, the 6-min walk distance (6MWD), the St. George's Respiratory Questionnaire (SGRQ) score, and multidimensional COPD severity indices, such as the BMI, airflow obstruction, dyspnea, and exercise capacity index (BODE) and age, dyspnea, and airflow obstruction (ADO), were analyzed. The CT Vratio correlated significantly with BMI (r = -0.528, p < 0.001). The CT Vratio was also significantly associated with MMRC dyspnea (r = 0.387, p = 0.001), 6MWD (r = -0.459, p < 0.001), and SGRQ (r = 0.369, p = 0.001) scores. Finally, the CT Vratio had significant correlations with the BODE and ADO multidimensional COPD severity indices (r = 0.605, p < 0.001; r = 0.411, p < 0.001). The CT Vratio had significant correlations with patient-centered outcomes and multidimensional COPD severity indices. © 2013 S. Karger AG, Basel.

Comparison of high pressure transient PVT measurements and model predictions. Part I.

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

Felver, Todd G.; Paradiso, Nicholas Joseph; Evans, Gregory Herbert

2010-07-01

A series of experiments consisting of vessel-to-vessel transfers of pressurized gas using Transient PVT methodology have been conducted to provide a data set for optimizing heat transfer correlations in high pressure flow systems. In rapid expansions such as these, the heat transfer conditions are neither adiabatic nor isothermal. Compressible flow tools exist, such as NETFLOW that can accurately calculate the pressure and other dynamical mechanical properties of such a system as a function of time. However to properly evaluate the mass that has transferred as a function of time these computational tools rely on heat transfer correlations that must bemore » confirmed experimentally. In this work new data sets using helium gas are used to evaluate the accuracy of these correlations for receiver vessel sizes ranging from 0.090 L to 13 L and initial supply pressures ranging from 2 MPa to 40 MPa. The comparisons show that the correlations developed in the 1980s from sparse data sets perform well for the supply vessels but are not accurate for the receivers, particularly at early time during the transfers. This report focuses on the experiments used to obtain high quality data sets that can be used to validate computational models. Part II of this report discusses how these data were used to gain insight into the physics of gas transfer and to improve vessel heat transfer correlations. Network flow modeling and CFD modeling is also discussed.« less

Heat transfer and flow friction correlations for perforated plate matrix heat exchangers

NASA Astrophysics Data System (ADS)

Ratna Raju, L.; Kumar, S. Sunil; Chowdhury, K.; Nandi, T. K.

2017-02-01

Perforated plate matrix heat exchangers (MHE) are constructed of high conductivity perforated plates stacked alternately with low conductivity spacers. They are being increasingly used in many cryogenic applications including Claude cycle or Reversed Brayton cycle cryo-refrigerators and liquefiers. Design of high NTU (number of (heat) transfer unit) cryogenic MHEs requires accurate heat transfer coefficient and flow friction factor. Thermo-hydraulic behaviour of perforated plates strongly depends on the geometrical parameters. Existing correlations, however, are mostly expressed as functions of Reynolds number only. This causes, for a given configuration, significant variations in coefficients from one correlation to the other. In this paper we present heat transfer and flow friction correlations as functions of all geometrical and other controlling variables. A FluentTM based numerical model has been developed for heat transfer and pressure drop studies over a stack of alternately arranged perforated plates and spacers. The model is validated with the data from literature. Generalized correlations are obtained through regression analysis over a large number of computed data.

Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method.

PubMed

Sinha, Debalina; Pavanello, Michele

2015-08-28

The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term the Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.

Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method

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

Sinha, Debalina; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu

2015-08-28

The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term themore » Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.« less

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

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

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; ...

2018-03-15

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

PROMIS PF CAT Outperforms the ODI and SF-36 Physical Function Domain in Spine Patients.

PubMed

Brodke, Darrel S; Goz, Vadim; Voss, Maren W; Lawrence, Brandon D; Spiker, William Ryan; Hung, Man

2017-06-15

The Oswestry Disability Index v2.0 (ODI), SF36 Physical Function Domain (SF-36 PFD), and PROMIS Physical Function CAT v1.2 (PF CAT) questionnaires were prospectively collected from 1607 patients complaining of back or leg pain, visiting a university-based spine clinic. All questionnaires were collected electronically, using a tablet computer. The aim of this study was to compare the psychometric properties of the PROMIS PF CAT with the ODI and SF36 Physical Function Domain in the same patient population. Evidence-based decision-making is improved by using high-quality patient-reported outcomes measures. Prior studies have revealed the shortcomings of the ODI and SF36, commonly used in spine patients. The PROMIS Network has developed measures with excellent psychometric properties. The Physical Function domain, delivered by Computerized Adaptive Testing (PF CAT), performs well in the spine patient population, though to-date direct comparisons with common measures have not been performed. Standard Rasch analysis was performed to directly compare the psychometrics of the PF CAT, ODI, and SF36 PFD. Spearman correlations were computed to examine the correlations of the three instruments. Time required for administration was also recorded. One thousand six hundred seven patients were administered all assessments. The time required to answer all items in the PF CAT, ODI, and SF-36 PFD was 44, 169, and 99 seconds. The ceiling and floor effects were excellent for the PF CAT (0.81%, 3.86%), while the ceiling effects were marginal and floor effects quite poor for the ODI (6.91% and 44.24%) and SF-36 PFD (5.97% and 23.65%). All instruments significantly correlated with each other. The PROMIS PF CAT outperforms the ODI and SF-36 PFD in the spine patient population and is highly correlated. It has better coverage, while taking less time to administer with fewer questions to answer. 2.

Feasibility study of parallel optical correlation-decoding analysis of lightning

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

Descour, M.R.; Sweatt, W.C.; Elliott, G.R.

The optical correlator described in this report is intended to serve as an attention-focusing processor. The objective is to narrowly bracket the range of a parameter value that characterizes the correlator input. The input is a waveform collected by a satellite-borne receiver. In the correlator, this waveform is simultaneously correlated with an ensemble of ionosphere impulse-response functions, each corresponding to a different total-electron-count (TEC) value. We have found that correlation is an effective method of bracketing the range of TEC values likely to be represented by the input waveform. High accuracy in a computational sense is not required of themore » correlator. Binarization of the impulse-response functions and the input waveforms prior to correlation results in a lower correlation-peak-to-background-fluctuation (signal-to-noise) ratio than the peak that is obtained when all waveforms retain their grayscale values. The results presented in this report were obtained by means of an acousto-optic correlator previously developed at SNL as well as by simulation. An optical-processor architecture optimized for 1D correlation of long waveforms characteristic of this application is described. Discussions of correlator components, such as optics, acousto-optic cells, digital micromirror devices, laser diodes, and VCSELs are included.« less

Computation of Ground-State Properties in Molecular Systems: Back-Propagation with Auxiliary-Field Quantum Monte Carlo.

PubMed

Motta, Mario; Zhang, Shiwei

2017-11-14

We address the computation of ground-state properties of chemical systems and realistic materials within the auxiliary-field quantum Monte Carlo method. The phase constraint to control the Fermion phase problem requires the random walks in Slater determinant space to be open-ended with branching. This in turn makes it necessary to use back-propagation (BP) to compute averages and correlation functions of operators that do not commute with the Hamiltonian. Several BP schemes are investigated, and their optimization with respect to the phaseless constraint is considered. We propose a modified BP method for the computation of observables in electronic systems, discuss its numerical stability and computational complexity, and assess its performance by computing ground-state properties in several molecular systems, including small organic molecules.

Associated relaxation time and the correlation function for a tumor cell growth system subjected to color noises

NASA Astrophysics Data System (ADS)

Wang, Can-Jun; Wei, Qun; Mei, Dong-Cheng

2008-03-01

The associated relaxation time T and the normalized correlation function C(s) for a tumor cell growth system subjected to color noises are investigated. Using the Novikov theorem and Fox approach, the steady probability distribution is obtained. Based on them, the expressions of T and C(s) are derived by means of projection operator method, in which the effects of the memory kernels of the correlation function are taken into account. Performing the numerical computations, it is found: (1) With the cross-correlation intensity |λ|, the additive noise intensity α and the multiplicative noise self-correlation time τ increasing, the tumor cell numbers can be restrained; And the cross-correlation time τ, the multiplicative noise intensity D can induce the tumor cell numbers increasing; However, the additive noise self-correlation time τ cannot affect the tumor cell numbers; The relaxation time T is a stochastic resonant phenomenon, and the distribution curves exhibit a single-maximum structure with D increasing. (2) The cross-correlation strength λ weakens the related activity between two states of the tumor cell numbers at different time, and enhances the stability of the tumor cell growth system in the steady state; On the contrast, τ and τ enhance the related activity between two states at different time; However, τ has no effect on the related activity between two states at different time.

Characterizing genomic alterations in cancer by complementary functional associations | Office of Cancer Genomics

Cancer.gov

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment.

Sarcoidosis: correlation of pulmonary parenchymal pattern at CT with results of pulmonary function tests

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

Bergin, C.J.; Bell, D.Y.; Coblentz, C.L.

1989-06-01

The appearances of the lungs on radiographs and computed tomographic (CT) scans were correlated with degree of uptake on gallium scans and results of pulmonary function tests (PFTs) in 27 patients with sarcoidosis. CT scans were evaluated both qualitatively and quantitatively. Patients were divided into five categories on the basis of the pattern of abnormality at CT: 1 = normal (n = 4); 2 = segmental air-space disease (n = 4); 3 = spherical (alveolar) masslike opacities (n = 4); 4 = multiple, discrete, small nodules (n = 6); and 5 = distortion of parenchymal structures (fibrotic end-stage sarcoidosis) (nmore » = 9). The percentage of the volume judged to be abnormal (CT grade) was correlated with PFT results for each CT and radiographic category. CT grades were also correlated with gallium scanning results and percentage of lymphocytes recovered from bronchoalveolar lavage (BAL). Patients in CT categories 1 and 2 had normal lung function, those in category 3 had mild functional impairment, and those in categories 4 and 5 showed moderate to severe dysfunction. The overall CT grade correlated well with PFT results expressed as a percentage of the predicted value. In five patients, CT scans showed extensive parenchymal disease not seen on radiographs. CT grades did not correlate with the results of gallium scanning or BAL lymphocytes. The authors conclude that patterns of parenchymal sarcoidosis seen at CT correlate with the PFT results and can be used to indicate respiratory impairment.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

The large-scale correlations of multicell densities and profiles: implications for cosmic variance estimates

NASA Astrophysics Data System (ADS)

Codis, Sandrine; Bernardeau, Francis; Pichon, Christophe

2016-08-01

In order to quantify the error budget in the measured probability distribution functions of cell densities, the two-point statistics of cosmic densities in concentric spheres is investigated. Bias functions are introduced as the ratio of their two-point correlation function to the two-point correlation of the underlying dark matter distribution. They describe how cell densities are spatially correlated. They are computed here via the so-called large deviation principle in the quasi-linear regime. Their large-separation limit is presented and successfully compared to simulations for density and density slopes: this regime is shown to be rapidly reached allowing to get sub-percent precision for a wide range of densities and variances. The corresponding asymptotic limit provides an estimate of the cosmic variance of standard concentric cell statistics applied to finite surveys. More generally, no assumption on the separation is required for some specific moments of the two-point statistics, for instance when predicting the generating function of cumulants containing any powers of concentric densities in one location and one power of density at some arbitrary distance from the rest. This exact `one external leg' cumulant generating function is used in particular to probe the rate of convergence of the large-separation approximation.

Comparison of cognitive functioning as measured by the Ruff Figural Fluency Test and the CogState computerized battery within the LifeLines Cohort Study.

PubMed

Kuiper, Jisca S; Oude Voshaar, Richard C; Verhoeven, Floor E A; Zuidema, Sytse U; Smidt, Nynke

2017-05-12

The Ruff Figural Fluency Test (RFFT; a pencil and paper test) and the CogState (a computerized cognitive test battery) are well-validated and suitable tests to evaluate cognitive functioning in large observational studies at the population level. The LifeLines Cohort Study includes the RFFT as baseline measurement and incorporated the CogState as replacement for the RFFT at follow-up. It is unknown how these two tests relate to each other. Therefore, the aim of this study is to examine the correlation between the RFFT and the CogState and the impact of demographic characteristics on this association. A subcohort of the LifeLines Cohort Study, a large population based cohort study, participated in this study. Correlations between the RFFT and six subtasks of the CogState were examined. Subgroup analyses were performed to investigate the influence of age, education, and gender on the results. With sensitivity analyses we investigated the influence of computer experience and (physical) impairments. A total of 509 participants (mean age (SD): 53 years (14.6); range 18-87 years) participated in this study. All correlations between the RFFT and the CogState were statistically significant (except for the correlation between the RFFT error ratio and the CogState One Back Task), ranging from -0.39 to 0.28. Stratifying the analyses for age, education, and gender did not substantially affect our conclusions. Sensitivity analyses showed no substantial influence of level of computer experience or (physical) impairments. Correlations found in the present study were only weak to moderate, indicating that cognitive functioning measured by the RFFT does not measure the same components of cognitive functioning as six subtasks of the CogState. Computerized testing such as the CogState may be very well suited for large cohort studies to assess cognitive functioning in the general population and to identify cognitive changes as early as possible, as it is a less time- and labor intensive tool.

Depth-time interpolation of feature trends extracted from mobile microelectrode data with kernel functions.

PubMed

Wong, Stephen; Hargreaves, Eric L; Baltuch, Gordon H; Jaggi, Jurg L; Danish, Shabbar F

2012-01-01

Microelectrode recording (MER) is necessary for precision localization of target structures such as the subthalamic nucleus during deep brain stimulation (DBS) surgery. Attempts to automate this process have produced quantitative temporal trends (feature activity vs. time) extracted from mobile MER data. Our goal was to evaluate computational methods of generating spatial profiles (feature activity vs. depth) from temporal trends that would decouple automated MER localization from the clinical procedure and enhance functional localization in DBS surgery. We evaluated two methods of interpolation (standard vs. kernel) that generated spatial profiles from temporal trends. We compared interpolated spatial profiles to true spatial profiles that were calculated with depth windows, using correlation coefficient analysis. Excellent approximation of true spatial profiles is achieved by interpolation. Kernel-interpolated spatial profiles produced superior correlation coefficient values at optimal kernel widths (r = 0.932-0.940) compared to standard interpolation (r = 0.891). The choice of kernel function and kernel width resulted in trade-offs in smoothing and resolution. Interpolation of feature activity to create spatial profiles from temporal trends is accurate and can standardize and facilitate MER functional localization of subcortical structures. The methods are computationally efficient, enhancing localization without imposing additional constraints on the MER clinical procedure during DBS surgery. Copyright © 2012 S. Karger AG, Basel.

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

DOE PAGES

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu; ...

2016-06-30

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

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

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Diametrical clustering for identifying anti-correlated gene clusters.

PubMed

Dhillon, Inderjit S; Marcotte, Edward M; Roshan, Usman

2003-09-01

Clustering genes based upon their expression patterns allows us to predict gene function. Most existing clustering algorithms cluster genes together when their expression patterns show high positive correlation. However, it has been observed that genes whose expression patterns are strongly anti-correlated can also be functionally similar. Biologically, this is not unintuitive-genes responding to the same stimuli, regardless of the nature of the response, are more likely to operate in the same pathways. We present a new diametrical clustering algorithm that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i). re-partitioning the genes and (ii). computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a 'diametric' cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method. We present systems whose mRNA expression patterns, and likely their functions, oppose the yeast ribosome and proteosome, along with evidence for the inverse transcriptional regulation of a number of cellular systems.

Cortical thickness and surface area correlates with cognitive dysfunction among first-episode psychosis patients.

PubMed

Haring, L; Müürsepp, A; Mõttus, R; Ilves, P; Koch, K; Uppin, K; Tarnovskaja, J; Maron, E; Zharkovsky, A; Vasar, E; Vasar, V

2016-07-01

In studies using magnetic resonance imaging (MRI), some have reported specific brain structure-function relationships among first-episode psychosis (FEP) patients, but findings are inconsistent. We aimed to localize the brain regions where cortical thickness (CTh) and surface area (cortical area; CA) relate to neurocognition, by performing an MRI on participants and measuring their neurocognitive performance using the Cambridge Neuropsychological Test Automated Battery (CANTAB), in order to investigate any significant differences between FEP patients and control subjects (CS). Exploration of potential correlations between specific cognitive functions and brain structure was performed using CANTAB computer-based neurocognitive testing and a vertex-by-vertex whole-brain MRI analysis of 63 FEP patients and 30 CS. Significant correlations were found between cortical parameters in the frontal, temporal, cingular and occipital brain regions and performance in set-shifting, working memory manipulation, strategy usage and sustained attention tests. These correlations were significantly dissimilar between FEP patients and CS. Significant correlations between CTh and CA with neurocognitive performance were localized in brain areas known to be involved in cognition. The results also suggested a disrupted structure-function relationship in FEP patients compared with CS.

An analysis of scatter decomposition

NASA Technical Reports Server (NTRS)

Nicol, David M.; Saltz, Joel H.

1990-01-01

A formal analysis of a powerful mapping technique known as scatter decomposition is presented. Scatter decomposition divides an irregular computational domain into a large number of equal sized pieces, and distributes them modularly among processors. A probabilistic model of workload in one dimension is used to formally explain why, and when scatter decomposition works. The first result is that if correlation in workload is a convex function of distance, then scattering a more finely decomposed domain yields a lower average processor workload variance. The second result shows that if the workload process is stationary Gaussian and the correlation function decreases linearly in distance until becoming zero and then remains zero, scattering a more finely decomposed domain yields a lower expected maximum processor workload. Finally it is shown that if the correlation function decreases linearly across the entire domain, then among all mappings that assign an equal number of domain pieces to each processor, scatter decomposition minimizes the average processor workload variance. The dependence of these results on the assumption of decreasing correlation is illustrated with situations where a coarser granularity actually achieves better load balance.

Improving the clinical correlation of multiple sclerosis black hole volume change by paired-scan analysis.

PubMed

Tam, Roger C; Traboulsee, Anthony; Riddehough, Andrew; Li, David K B

2012-01-01

The change in T 1-hypointense lesion ("black hole") volume is an important marker of pathological progression in multiple sclerosis (MS). Black hole boundaries often have low contrast and are difficult to determine accurately and most (semi-)automated segmentation methods first compute the T 2-hyperintense lesions, which are a superset of the black holes and are typically more distinct, to form a search space for the T 1w lesions. Two main potential sources of measurement noise in longitudinal black hole volume computation are partial volume and variability in the T 2w lesion segmentation. A paired analysis approach is proposed herein that uses registration to equalize partial volume and lesion mask processing to combine T 2w lesion segmentations across time. The scans of 247 MS patients are used to compare a selected black hole computation method with an enhanced version incorporating paired analysis, using rank correlation to a clinical variable (MS functional composite) as the primary outcome measure. The comparison is done at nine different levels of intensity as a previous study suggests that darker black holes may yield stronger correlations. The results demonstrate that paired analysis can strongly improve longitudinal correlation (from -0.148 to -0.303 in this sample) and may produce segmentations that are more sensitive to clinically relevant changes.

Approximating lens power.

PubMed

Kaye, Stephen B

2009-04-01

To provide a scalar measure of refractive error, based on geometric lens power through principal, orthogonal and oblique meridians, that is not limited to the paraxial and sag height approximations. A function is derived to model sections through the principal meridian of a lens, followed by rotation of the section through orthogonal and oblique meridians. Average focal length is determined using the definition for the average of a function. Average univariate power in the principal meridian (including spherical aberration), can be computed from the average of a function over the angle of incidence as determined by the parameters of the given lens, or adequately computed from an integrated series function. Average power through orthogonal and oblique meridians, can be similarly determined using the derived formulae. The widely used computation for measuring refractive error, the spherical equivalent, introduces non-constant approximations, leading to a systematic bias. The equations proposed provide a good univariate representation of average lens power and are not subject to a systematic bias. They are particularly useful for the analysis of aggregate data, correlating with biological treatment variables and for developing analyses, which require a scalar equivalent representation of refractive power.

Assessment of global and regional left ventricular function using 64-slice multislice computed tomography and 2D echocardiography: a comparison with cardiac magnetic resonance.

PubMed

Annuar, Bin Rapaee; Liew, Chee Khoon; Chin, Sze Piaw; Ong, Tiong Kiam; Seyfarth, M Tobias; Chan, Wei Ling; Fong, Yean Yip; Ang, Choon Kiat; Lin, Naing; Liew, Houng Bang; Sim, Kui Hian

2008-01-01

To compare the assessment of global and regional left ventricular (LV) function using 64-slice multislice computed tomography (MSCT), 2D echocardiography (2DE) and cardiac magnetic resonance (CMR). Thirty-two consecutive patients (mean age, 56.5+/-9.7 years) referred for evaluation of coronary artery using 64-slice MSCT also underwent 2DE and CMR within 48h. The global left ventricular function which include left ventricular ejection fraction (LVEF), left ventricular end diastolic volume (LVdV) and left ventricular end systolic volume (LVsV) were determine using the three modalities. Regional wall motion (RWM) was assessed visually in all three modalities. The CMR served as the gold standard for the comparison between 64-slice MSCT with CMR and 2DE with CMR. Statistical analysis included Pearson correlation coefficient, Bland-Altman plots and kappa-statistics. The 64-slice MSCT agreed well with CMR for assessment of LVEF (r=0.92; p<0.0001), LVdV (r=0.98; p<0.0001) and LVsV (r=0.98; p<0.0001). In comparison with 64-slice MSCT, 2DE showed moderate correlation with CMR for the assessment of LVEF (r=0.84; p<0.0001), LVdV (r=0.83; p<0.0001) and LVsV (r=0.80; p<0.0001). However in RWM analysis, 2DE showed better accuracy than 64-slice MSCT (94.3% versus 82.4%) and closer agreement (kappa=0.89 versus 0.63) with CMR. 64-Slice MSCT correlates strongly with CMR in global LV function however in regional LV function 2DE showed better agreement with CMR than 64-slice MSCT.

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

Parallel algorithm of VLBI software correlator under multiprocessor environment

NASA Astrophysics Data System (ADS)

Zheng, Weimin; Zhang, Dong

2007-11-01

The correlator is the key signal processing equipment of a Very Lone Baseline Interferometry (VLBI) synthetic aperture telescope. It receives the mass data collected by the VLBI observatories and produces the visibility function of the target, which can be used to spacecraft position, baseline length measurement, synthesis imaging, and other scientific applications. VLBI data correlation is a task of data intensive and computation intensive. This paper presents the algorithms of two parallel software correlators under multiprocessor environments. A near real-time correlator for spacecraft tracking adopts the pipelining and thread-parallel technology, and runs on the SMP (Symmetric Multiple Processor) servers. Another high speed prototype correlator using the mixed Pthreads and MPI (Massage Passing Interface) parallel algorithm is realized on a small Beowulf cluster platform. Both correlators have the characteristic of flexible structure, scalability, and with 10-station data correlating abilities.

Fuzzy parametric uncertainty analysis of linear dynamical systems: A surrogate modeling approach

NASA Astrophysics Data System (ADS)

Chowdhury, R.; Adhikari, S.

2012-10-01

Uncertainty propagation engineering systems possess significant computational challenges. This paper explores the possibility of using correlated function expansion based metamodelling approach when uncertain system parameters are modeled using Fuzzy variables. In particular, the application of High-Dimensional Model Representation (HDMR) is proposed for fuzzy finite element analysis of dynamical systems. The HDMR expansion is a set of quantitative model assessment and analysis tools for capturing high-dimensional input-output system behavior based on a hierarchy of functions of increasing dimensions. The input variables may be either finite-dimensional (i.e., a vector of parameters chosen from the Euclidean space RM) or may be infinite-dimensional as in the function space CM[0,1]. The computational effort to determine the expansion functions using the alpha cut method scales polynomially with the number of variables rather than exponentially. This logic is based on the fundamental assumption underlying the HDMR representation that only low-order correlations among the input variables are likely to have significant impacts upon the outputs for most high-dimensional complex systems. The proposed method is integrated with a commercial Finite Element software. Modal analysis of a simplified aircraft wing with Fuzzy parameters has been used to illustrate the generality of the proposed approach. In the numerical examples, triangular membership functions have been used and the results have been validated against direct Monte Carlo simulations.

Reliable but Timesaving: In Search of an Efficient Quantum-chemical Method for the Description of Functional Fullerenes.

PubMed

Reis, H; Rasulev, B; Papadopoulos, M G; Leszczynski, J

2015-01-01

Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C60 and C70 fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans' theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives.

Matching and correlation computations in stereoscopic depth perception.

PubMed

Doi, Takahiro; Tanabe, Seiji; Fujita, Ichiro

2011-03-02

A fundamental task of the visual system is to infer depth by using binocular disparity. To encode binocular disparity, the visual cortex performs two distinct computations: one detects matched patterns in paired images (matching computation); the other constructs the cross-correlation between the images (correlation computation). How the two computations are used in stereoscopic perception is unclear. We dissociated their contributions in near/far discrimination by varying the magnitude of the disparity across separate sessions. For small disparity (0.03°), subjects performed at chance level to a binocularly opposite-contrast (anti-correlated) random-dot stereogram (RDS) but improved their performance with the proportion of contrast-matched (correlated) dots. For large disparity (0.48°), the direction of perceived depth reversed with an anti-correlated RDS relative to that for a correlated one. Neither reversed nor normal depth was perceived when anti-correlation was applied to half of the dots. We explain the decision process as a weighted average of the two computations, with the relative weight of the correlation computation increasing with the disparity magnitude. We conclude that matching computation dominates fine depth perception, while both computations contribute to coarser depth perception. Thus, stereoscopic depth perception recruits different computations depending on the disparity magnitude.

Signatures of van der Waals binding: A coupling-constant scaling analysis

NASA Astrophysics Data System (ADS)

Jiao, Yang; Schröder, Elsebeth; Hyldgaard, Per

2018-02-01

The van der Waals (vdW) density functional (vdW-DF) method [Rep. Prog. Phys. 78, 066501 (2015), 10.1088/0034-4885/78/6/066501] describes dispersion or vdW binding by tracking the effects of an electrodynamic coupling among pairs of electrons and their associated exchange-correlation holes. This is done in a nonlocal-correlation energy term Ecnl, which permits density functional theory calculation in the Kohn-Sham scheme. However, to map the nature of vdW forces in a fully interacting materials system, it is necessary to also account for associated kinetic-correlation energy effects. Here, we present a coupling-constant scaling analysis, which permits us to compute the kinetic-correlation energy Tcnl that is specific to the vdW-DF account of nonlocal correlations. We thus provide a more complete spatially resolved analysis of the electrodynamical-coupling nature of nonlocal-correlation binding, including vdW attraction, in both covalently and noncovalently bonded systems. We find that kinetic-correlation energy effects play a significant role in the account of vdW or dispersion interactions among molecules. Furthermore, our mapping shows that the total nonlocal-correlation binding is concentrated to pockets in the sparse electron distribution located between the material fragments.

Dual-modality imaging of function and physiology

NASA Astrophysics Data System (ADS)

Hasegawa, Bruce H.; Iwata, Koji; Wong, Kenneth H.; Wu, Max C.; Da Silva, Angela; Tang, Hamilton R.; Barber, William C.; Hwang, Andrew B.; Sakdinawat, Anne E.

2002-04-01

Dual-modality imaging is a technique where computed tomography or magnetic resonance imaging is combined with positron emission tomography or single-photon computed tomography to acquire structural and functional images with an integrated system. The data are acquired during a single procedure with the patient on a table viewed by both detectors to facilitate correlation between the structural and function images. The resulting data can be useful for localization for more specific diagnosis of disease. In addition, the anatomical information can be used to compensate the correlated radionuclide data for physical perturbations such as photon attenuation, scatter radiation, and partial volume errors. Thus, dual-modality imaging provides a priori information that can be used to improve both the visual quality and the quantitative accuracy of the radionuclide images. Dual-modality imaging systems also are being developed for biological research that involves small animals. The small-animal dual-modality systems offer advantages for measurements that currently are performed invasively using autoradiography and tissue sampling. By acquiring the required data noninvasively, dual-modality imaging has the potential to allow serial studies in a single animal, to perform measurements with fewer animals, and to improve the statistical quality of the data.

Entanglement entropy between real and virtual particles in ϕ4 quantum field theory

NASA Astrophysics Data System (ADS)

Ardenghi, Juan Sebastián

2015-04-01

The aim of this work is to compute the entanglement entropy of real and virtual particles by rewriting the generating functional of ϕ4 theory as a mean value between states and observables defined through the correlation functions. Then the von Neumann definition of entropy can be applied to these quantum states and in particular, for the partial traces taken over the internal or external degrees of freedom. This procedure can be done for each order in the perturbation expansion showing that the entanglement entropy for real and virtual particles behaves as ln (m0). In particular, entanglement entropy is computed at first order for the correlation function of two external points showing that mutual information is identical to the external entropy and that conditional entropies are negative for all the domain of m0. In turn, from the definition of the quantum states, it is possible to obtain general relations between total traces between different quantum states of a ϕr theory. Finally, discussion about the possibility of taking partial traces over external degrees of freedom is considered, which implies the introduction of some observables that measure space-time points where an interaction occurs.

Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

PubMed

Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

2016-07-12

In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

Separating non-diffuse component from ambient seismic noise cross-correlation in southern California­­

NASA Astrophysics Data System (ADS)

Liu, X.; Beroza, G. C.; Nakata, N.

2017-12-01

Cross-correlation of fully diffuse wavefields provides Green's function between receivers, although the ambient noise field in the real world contains both diffuse and non-diffuse fields. The non-diffuse field potentially degrades the correlation functions. We attempt to blindly separate the diffuse and the non-diffuse components from cross-correlations of ambient seismic noise and analyze the potential bias caused by the non-diffuse components. We compute the 9-component noise cross-correlations for 17 stations in southern California. For the Rayleigh wave components, we assume that the cross-correlation of multiply scattered waves (diffuse component) is independent from the cross-correlation of ocean microseismic quasi-point source responses (non-diffuse component), and the cross-correlation function of ambient seismic data is the sum of both components. Thus we can blindly separate the non-diffuse component due to physical point sources and the more diffuse component due to cross-correlation of multiply scattered noise based on their statistical independence. We also perform beamforming over different frequency bands for the cross-correlations before and after the separation, and we find that the decomposed Rayleigh wave represents more coherent features among all Rayleigh wave polarization cross-correlation components. We show that after separating the non-diffuse component, the Frequency-Time Analysis results are less ambiguous. In addition, we estimate the bias in phase velocity on the raw cross-correlation data due to the non-diffuse component. We also apply this technique to a few borehole stations in Groningen, the Netherlands, to demonstrate its applicability in different instrument/geology settings.

PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees

PubMed Central

Lee, Bongshin; Nachmanson, Lev; Robertson, George; Carlson, Jonathan M.; Heckerman, David

2009-01-01

Summary: Evolutionary biologists are often interested in finding correlations among biological traits across a number of species, as such correlations may lead to testable hypotheses about the underlying function. Because some species are more closely related than others, computing and visualizing these correlations must be done in the context of the evolutionary tree that relates species. In this note, we introduce PhyloDet (short for PhyloDetective), an evolutionary tree visualization tool that enables biologists to visualize multiple traits mapped to the tree. Availability: http://research.microsoft.com/cue/phylodet/ Contact: bongshin@microsoft.com. PMID:19633096

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

Anand, Nikhil; Genest, Vincent X.; Katz, Emanuel

We study 1+1 dimensional Φ 4 theory using the recently proposed method of conformal truncation. Starting in the UV CFT of free field theory, we construct a complete basis of states with definite conformal Casimir, C. We use these states to express the Hamiltonian of the full interacting theory in lightcone quantization. After truncating to states with C≤C max, we numerically diagonalize the Hamiltonian at strong coupling and study the resulting IR dynamics. We compute non-perturbative spectral densities of several local operators, which are equivalent to real-time, infinite-volume correlation functions. These spectral densities, which include the Zamolodchikov C-function along themore » full RG flow, are calculable at any value of the coupling. Near criticality, our numerical results reproduce correlation functions in the 2D Ising model.« less

Quantum coupled mutation finder: predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming.

PubMed

Gültas, Mehmet; Düzgün, Güncel; Herzog, Sebastian; Jäger, Sven Joachim; Meckbach, Cornelia; Wingender, Edgar; Waack, Stephan

2014-04-03

The identification of functionally or structurally important non-conserved residue sites in protein MSAs is an important challenge for understanding the structural basis and molecular mechanism of protein functions. Despite the rich literature on compensatory mutations as well as sequence conservation analysis for the detection of those important residues, previous methods often rely on classical information-theoretic measures. However, these measures usually do not take into account dis/similarities of amino acids which are likely to be crucial for those residues. In this study, we present a new method, the Quantum Coupled Mutation Finder (QCMF) that incorporates significant dis/similar amino acid pair signals in the prediction of functionally or structurally important sites. The result of this study is twofold. First, using the essential sites of two human proteins, namely epidermal growth factor receptor (EGFR) and glucokinase (GCK), we tested the QCMF-method. The QCMF includes two metrics based on quantum Jensen-Shannon divergence to measure both sequence conservation and compensatory mutations. We found that the QCMF reaches an improved performance in identifying essential sites from MSAs of both proteins with a significantly higher Matthews correlation coefficient (MCC) value in comparison to previous methods. Second, using a data set of 153 proteins, we made a pairwise comparison between QCMF and three conventional methods. This comparison study strongly suggests that QCMF complements the conventional methods for the identification of correlated mutations in MSAs. QCMF utilizes the notion of entanglement, which is a major resource of quantum information, to model significant dissimilar and similar amino acid pair signals in the detection of functionally or structurally important sites. Our results suggest that on the one hand QCMF significantly outperforms the previous method, which mainly focuses on dissimilar amino acid signals, to detect essential sites in proteins. On the other hand, it is complementary to the existing methods for the identification of correlated mutations. The method of QCMF is computationally intensive. To ensure a feasible computation time of the QCMF's algorithm, we leveraged Compute Unified Device Architecture (CUDA).The QCMF server is freely accessible at http://qcmf.informatik.uni-goettingen.de/.

Response variance in functional maps: neural darwinism revisited.

PubMed

Takahashi, Hirokazu; Yokota, Ryo; Kanzaki, Ryohei

2013-01-01

The mechanisms by which functional maps and map plasticity contribute to cortical computation remain controversial. Recent studies have revisited the theory of neural Darwinism to interpret the learning-induced map plasticity and neuronal heterogeneity observed in the cortex. Here, we hypothesize that the Darwinian principle provides a substrate to explain the relationship between neuron heterogeneity and cortical functional maps. We demonstrate in the rat auditory cortex that the degree of response variance is closely correlated with the size of its representational area. Further, we show that the response variance within a given population is altered through training. These results suggest that larger representational areas may help to accommodate heterogeneous populations of neurons. Thus, functional maps and map plasticity are likely to play essential roles in Darwinian computation, serving as effective, but not absolutely necessary, structures to generate diverse response properties within a neural population.

Response Variance in Functional Maps: Neural Darwinism Revisited

PubMed Central

Takahashi, Hirokazu; Yokota, Ryo; Kanzaki, Ryohei

2013-01-01

The mechanisms by which functional maps and map plasticity contribute to cortical computation remain controversial. Recent studies have revisited the theory of neural Darwinism to interpret the learning-induced map plasticity and neuronal heterogeneity observed in the cortex. Here, we hypothesize that the Darwinian principle provides a substrate to explain the relationship between neuron heterogeneity and cortical functional maps. We demonstrate in the rat auditory cortex that the degree of response variance is closely correlated with the size of its representational area. Further, we show that the response variance within a given population is altered through training. These results suggest that larger representational areas may help to accommodate heterogeneous populations of neurons. Thus, functional maps and map plasticity are likely to play essential roles in Darwinian computation, serving as effective, but not absolutely necessary, structures to generate diverse response properties within a neural population. PMID:23874733

Supersymmetric Renyi entropy in CFT 2 and AdS 3

DOE PAGES

Giveon, Amit; Kutasov, David

2016-01-01

We show that in any two dimensional conformal field theory with (2, 2) super-symmetry one can define a supersymmetric analog of the usual Renyi entropy of a spatial region A. It differs from the Renyi entropy by a universal function (which we compute) of the central charge, Renyi parameter n and the geometric parameters of A. In the limit n → 1 it coincides with the entanglement entropy. Thus, it contains the same information as the Renyi entropy but its computation only involves correlation functions of chiral and anti-chiral operators. We also show that this quantity appears naturally in stringmore » theory on AdS3.« less

Findings in resting-state fMRI by differences from K-means clustering.

PubMed

Chyzhyk, Darya; Graña, Manuel

2014-01-01

Resting state fMRI has growing number of studies with diverse aims, always centered on some kind of functional connectivity biomarker obtained from correlation regarding seed regions, or by analytical decomposition of the signal towards the localization of the spatial distribution of functional connectivity patterns. In general, studies are computationally costly and very sensitive to noise and preprocessing of data. In this paper we consider clustering by K-means as a exploratory procedure which can provide some results with little computational effort, due to efficient implementations that are readily available. We demonstrate the approach on a dataset of schizophrenia patients, finding differences between patients with and without auditory hallucinations.

Stable isomers and electronic, vibrational, and optical properties of WS2 nano-clusters: A first-principles study

NASA Astrophysics Data System (ADS)

Hafizi, Roohollah; Hashemifar, S. Javad; Alaei, Mojtaba; Jangrouei, MohammadReza; Akbarzadeh, Hadi

2016-12-01

In this paper, we employ an evolutionary algorithm along with the full-potential density functional theory (DFT) computations to perform a comprehensive search for the stable structures of stoichiometric (WS2)n nano-clusters (n = 1 - 9), within three different exchange-correlation functionals. Our results suggest that n = 5 and 8 are possible candidates for the low temperature magic sizes of WS2 nano-clusters while at temperatures above 500 Kelvin, n = 7 exhibits a comparable relative stability with n = 8. The electronic properties and energy gap of the lowest energy isomers were computed within several schemes, including semilocal Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals, hybrid B3LYP functional, many body based DFT+GW approach, ΔSCF method, and time dependent DFT calculations. Vibrational spectra of the lowest lying isomers, computed by the force constant method, are used to address IR spectra and thermal free energy of the clusters. Time dependent density functional calculation in a real time domain is applied to determine the full absorption spectra and optical gap of the lowest energy isomers of the WS2 nano-clusters.

Controller and interface module for the High-Speed Data Acquisition System correlator/accumulator

NASA Technical Reports Server (NTRS)

Brokl, S. S.

1985-01-01

One complex channel of the High-Speed Data Acquisition System (a subsystem used in the Goldstone solar system radar), consisting of two correlator modules and one accumulator module, is operated by the controller and interface module interfaces are provided to the VAX UNIBUS for computer control, monitor, and test of the controller and correlator/accumulator. The correlator and accumulator modules controlled by this module are the key digital signal processing elements of the Goldstone High-Speed Data Acquisition System. This fully programmable unit provides for a wide variety of correlation and filtering functions operating on a three megaword/second data flow. Data flow is to the VAX by way of the I/O port of a FPS 5210 array processor.

Photon scattering cross sections of H2 and He measured with synchrotron radiation

NASA Technical Reports Server (NTRS)

Ice, G. E.

1977-01-01

Total (elastic + inelastic) differential photon scattering cross sections have been measured for H2 gas and He, using an X-ray beam. Absolute measured cross sections agree with theory within the probable errors. Relative cross sections (normalized to theory at large S) agree to better than one percent with theoretical values calculated from wave functions that include the effect of electron-electron Coulomb correlation, but the data deviate significantly from theoretical independent-particle (e.g., Hartree-Fock) results. The ratios of measured absolute He cross sections to those of H2, at any given S, also agree to better than one percent with theoretical He-to-H2 cross-section ratios computed from correlated wave functions. It appears that photon scattering constitutes a very promising tool for probing electron correlation in light atoms and molecules.

Four-electron model for singlet and triplet excitation energy transfers with inclusion of coherence memory, inelastic tunneling and nuclear quantum effects

NASA Astrophysics Data System (ADS)

Suzuki, Yosuke; Ebina, Kuniyoshi; Tanaka, Shigenori

2016-08-01

A computational scheme to describe the coherent dynamics of excitation energy transfer (EET) in molecular systems is proposed on the basis of generalized master equations with memory kernels. This formalism takes into account those physical effects in electron-bath coupling system such as the spin symmetry of excitons, the inelastic electron tunneling and the quantum features of nuclear motions, thus providing a theoretical framework to perform an ab initio description of EET through molecular simulations for evaluating the spectral density and the temporal correlation function of electronic coupling. Some test calculations have then been carried out to investigate the dependence of exciton population dynamics on coherence memory, inelastic tunneling correlation time, magnitude of electronic coupling, quantum correction to temporal correlation function, reorganization energy and energy gap.

Towards a Density Functional Theory Exchange-Correlation Functional able to describe localization/delocalization

NASA Astrophysics Data System (ADS)

Mattsson, Ann E.; Wills, John M.

2013-03-01

The inability to computationally describe the physics governing the properties of actinides and their alloys is the poster child of failure of existing Density Functional Theory exchange-correlation functionals. The intricate competition between localization and delocalization of the electrons, present in these materials, exposes the limitations of functionals only designed to properly describe one or the other situation. We will discuss the manifestation of this competition in real materials and propositions on how to construct a functional able to accurately describe properties of these materials. I addition we will discuss both the importance of using the Dirac equation to describe the relativistic effects in these materials, and the connection to the physics of transition metal oxides. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

A hydrodynamic approach to cosmology - Texture-seeded cold dark matter and hot dark matter cosmogonies

NASA Technical Reports Server (NTRS)

Cen, R. Y.; Ostriker, J. P.; Spergel, D. N.; Turok, N.

1991-01-01

Hydrodynamical simulations of galaxy formation in a texture-seeded cosmology are presented, with attention given to Omega = 1 galaxies dominated by both hot dark matter (HDM) and cold dark matter (CDM). The simulations include both gravitational and hydrodynamical physics with a detailed treatment of collisional and radiative thermal processes, and use a cooling criterion to estimate galaxy formation. Background radiation fields and Zel'dovich-Sunyaev fluctuations are explicitly computed. The derived galaxy mass function is well fitted by the observed Schechter luminosity function for a baryonic M/L of 3 and total M/L of 60 in galaxies. In both HDM and CDM texture scenarios, the 'galaxies' and 'clusters' are significantly more strongly correlated than the dark matter due to physical bias processes. The slope of the correlation function in both cases is consistent with observations. In contrast to Gaussian models, peaks in the dark matter density distributrion are less correlated than average.

T\\overline{T} -deformations, AdS/CFT and correlation functions

NASA Astrophysics Data System (ADS)

Giribet, Gaston

2018-02-01

A solvable irrelevant deformation of AdS3/CFT2 correspondence leading to a theory with Hagedorn spectrum at high energy has been recently proposed. It consists of a single trace deformation of the boundary theory, which is inspired by the recent work on solvable T\\overline{T} deformations of two-dimensional CFTs. Thought of as a worldsheet σ-model, the interpretation of the deformed theory from the bulk viewpoint is that of string theory on a background that interpolates between AdS3 in the IR and a linear dilaton vacuum of little string theory in the UV. The insertion of the operator that realizes the deformation in the correlation functions produces a logarithmic divergence, leading to the renormalization of the primary operators, which thus acquire an anomalous dimension. We compute this anomalous dimension explicitly, and this provides us with a direct way of determining the spectrum of the theory. We discuss this and other features of the correlation functions in presence of the deformation.

Defense strategies for asymmetric networked systems under composite utilities

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

Rao, Nageswara S.; Ma, Chris Y. T.; Hausken, Kjell

We consider an infrastructure of networked systems with discrete components that can be reinforced at certain costs to guard against attacks. The communications network plays a critical, asymmetric role of providing the vital connectivity between the systems. We characterize the correlations within this infrastructure at two levels using (a) aggregate failure correlation function that specifies the infrastructure failure probability giventhe failure of an individual system or network, and (b) first order differential conditions on system survival probabilities that characterize component-level correlations. We formulate an infrastructure survival game between an attacker and a provider, who attacks and reinforces individual components, respectively.more » They use the composite utility functions composed of a survival probability term and a cost term, and the previously studiedsum-form and product-form utility functions are their special cases. At Nash Equilibrium, we derive expressions for individual system survival probabilities and the expected total number of operational components. We apply and discuss these estimates for a simplified model of distributed cloud computing infrastructure« less

A proposed study of multiple scattering through clouds up to 1 THz

NASA Technical Reports Server (NTRS)

Gerace, G. C.; Smith, E. K.

1992-01-01

A rigorous computation of the electromagnetic field scattered from an atmospheric liquid water cloud is proposed. The recent development of a fast recursive algorithm (Chew algorithm) for computing the fields scattered from numerous scatterers now makes a rigorous computation feasible. A method is presented for adapting this algorithm to a general case where there are an extremely large number of scatterers. It is also proposed to extend a new binary PAM channel coding technique (El-Khamy coding) to multiple levels with non-square pulse shapes. The Chew algorithm can be used to compute the transfer function of a cloud channel. Then the transfer function can be used to design an optimum El-Khamy code. In principle, these concepts can be applied directly to the realistic case of a time-varying cloud (adaptive channel coding and adaptive equalization). A brief review is included of some preliminary work on cloud dispersive effects on digital communication signals and on cloud liquid water spectra and correlations.

Dynamic correlation effects in fully differential cross sections for 75-keV proton-impact ionization of helium

NASA Astrophysics Data System (ADS)

Niu, Xiaojie; Sun, Shiyan; Wang, Fujun; Jia, Xiangfu

2017-08-01

The effect of final-state dynamic correlation is investigated for helium single ionization by 75-keV proton impact analyzing fully differential cross sections (FDCS). The final state is represented by a continuum correlated wave (CCW-PT) function which accounts for the interaction between the projectile and the residual target ion (PT interaction). This continuum correlated wave function partially includes the correlation of electron-projectile and electron-target relative motion as coupling terms of the wave equation. The transition matrix is evaluated using the CCW-PT function and the Born initial state. The analytical expression of the transition matrix has been obtained. We have shown that this series is strongly convergent and analyzed the contribution of their different terms to the FDCS within the perturbation method. Illustrative computations are performed in the scattering plane and in the perpendicular plane. Both the correlation effects and the PT interaction are checked by the preset calculations. Our results are compared with absolute experimental data as well as other theoretical models. We have shown that the dynamic correlation plays an important role in the single ionization of atoms by proton impact at intermediate projectile energies, especially at large transverse momentum transfer. While overall agreement between theory and the experimental data is encouraging, detailed agreement is lacking. The need for more theoretical and experimental work is emphasized.

A general statistical test for correlations in a finite-length time series.

PubMed

Hanson, Jeffery A; Yang, Haw

2008-06-07

The statistical properties of the autocorrelation function from a time series composed of independently and identically distributed stochastic variables has been studied. Analytical expressions for the autocorrelation function's variance have been derived. It has been found that two common ways of calculating the autocorrelation, moving-average and Fourier transform, exhibit different uncertainty characteristics. For periodic time series, the Fourier transform method is preferred because it gives smaller uncertainties that are uniform through all time lags. Based on these analytical results, a statistically robust method has been proposed to test the existence of correlations in a time series. The statistical test is verified by computer simulations and an application to single-molecule fluorescence spectroscopy is discussed.

Computing with scale-invariant neural representations

NASA Astrophysics Data System (ADS)

Howard, Marc; Shankar, Karthik

The Weber-Fechner law is perhaps the oldest quantitative relationship in psychology. Consider the problem of the brain representing a function f (x) . Different neurons have receptive fields that support different parts of the range, such that the ith neuron has a receptive field at xi. Weber-Fechner scaling refers to the finding that the width of the receptive field scales with xi as does the difference between the centers of adjacent receptive fields. Weber-Fechner scaling is exponentially resource-conserving. Neurophysiological evidence suggests that neural representations obey Weber-Fechner scaling in the visual system and perhaps other systems as well. We describe an optimality constraint that is solved by Weber-Fechner scaling, providing an information-theoretic rationale for this principle of neural coding. Weber-Fechner scaling can be generated within a mathematical framework using the Laplace transform. Within this framework, simple computations such as translation, correlation and cross-correlation can be accomplished. This framework can in principle be extended to provide a general computational language for brain-inspired cognitive computation on scale-invariant representations. Supported by NSF PHY 1444389 and the BU Initiative for the Physics and Mathematics of Neural Systems,.

Deorbitalization strategies for meta-generalized-gradient-approximation exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Mejia-Rodriguez, Daniel; Trickey, S. B.

2017-11-01

We explore the simplification of widely used meta-generalized-gradient approximation (mGGA) exchange-correlation functionals to the Laplacian level of refinement by use of approximate kinetic-energy density functionals (KEDFs). Such deorbitalization is motivated by the prospect of reducing computational cost while recovering a strictly Kohn-Sham local potential framework (rather than the usual generalized Kohn-Sham treatment of mGGAs). A KEDF that has been rather successful in solid simulations proves to be inadequate for deorbitalization, but we produce other forms which, with parametrization to Kohn-Sham results (not experimental data) on a small training set, yield rather good results on standard molecular test sets when used to deorbitalize the meta-GGA made very simple, Tao-Perdew-Staroverov-Scuseria, and strongly constrained and appropriately normed functionals. We also study the difference between high-fidelity and best-performing deorbitalizations and discuss possible implications for use in ab initio molecular dynamics simulations of complicated condensed phase systems.

Nonperturbative Series Expansion of Green's Functions: The Anatomy of Resonant Inelastic X-Ray Scattering in the Doped Hubbard Model

NASA Astrophysics Data System (ADS)

Lu, Yi; Haverkort, Maurits W.

2017-12-01

We present a nonperturbative, divergence-free series expansion of Green's functions using effective operators. The method is especially suited for computing correlators of complex operators as a series of correlation functions of simpler forms. We apply the method to study low-energy excitations in resonant inelastic x-ray scattering (RIXS) in doped one- and two-dimensional single-band Hubbard models. The RIXS operator is expanded into polynomials of spin, density, and current operators weighted by fundamental x-ray spectral functions. These operators couple to different polarization channels resulting in simple selection rules. The incident photon energy dependent coefficients help to pinpoint main RIXS contributions from different degrees of freedom. We show in particular that, with parameters pertaining to cuprate superconductors, local spin excitation dominates the RIXS spectral weight over a wide doping range in the cross-polarization channel.

Computing the Dynamic Response of a Stratified Elastic Half Space Using Diffuse Field Theory

NASA Astrophysics Data System (ADS)

Sanchez-Sesma, F. J.; Perton, M.; Molina Villegas, J. C.

2015-12-01

The analytical solution for the dynamic response of an elastic half-space for a normal point load at the free surface is due to Lamb (1904). For a tangential force, we have Chaós (1960) formulae. For an arbitrary load at any depth within a stratified elastic half space, the resulting elastic field can be given in the same fashion, by using an integral representation in the radial wavenumber domain. Typically, computations use discrete wave number (DWN) formalism and Fourier analysis allows for solution in space and time domain. Experimentally, these elastic Greeńs functions might be retrieved from ambient vibrations correlations when assuming a diffuse field. In fact, the field could not be totally diffuse and only parts of the Green's functions, associated to surface or body waves, are retrieved. In this communication, we explore the computation of Green functions for a layered media on top of a half-space using a set of equipartitioned elastic plane waves. Our formalism includes body and surface waves (Rayleigh and Love waves). These latter waves correspond to the classical representations in terms of normal modes in the asymptotic case of large separation distance between source and receiver. This approach allows computing Green's functions faster than DWN and separating the surface and body wave contributions in order to better represent Green's function experimentally retrieved.

The Heats of Formation of GaCl3 and its Fragments

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

1998-01-01

The heats of formation of GaC13 and its fragments are computed. The geometries and frequencies are obtained at the B3LYP level. The CCSD(T) approach is used to solve the correlation problem. The effect of Ga 3d correlation is studied, and found to affect the bond energies by up to 1 kcal/mol. Both basis set extrapolation and bond functions are considered as ways to approach the basis set limit. Spin-orbit and scalar relativistic effects are also considered.

Three-Point Correlations in the COBE DMR 2 Year Anisotropy Maps

NASA Technical Reports Server (NTRS)

Hinshaw, G.; Banday, A. J.; Bennett, C. L.; Gorski, K. M.; Kogut, A.

1995-01-01

We compute the three-point temperature correlation function of the COBE Differential Microwave Radiometer (DMR) 2 year sky maps to search for evidence of non-Gaussian temperature fluctuations. We detect three-point correlations in our sky with a substantially higher signal-to-noise ratio than from the first-year data. However, the magnitude of the signal is consistent with the level of cosmic variance expected from Gaussian fluctuations, even when the low-order multipole moments, up to l = 9, are filtered from the data. These results do not strongly constrain most existing models of structure formation, but the absence of intrinsic three-point correlations on large angular scales is an important consistency test for such models.

Statistical Approach To Extraction Of Texture In SAR

NASA Technical Reports Server (NTRS)

Rignot, Eric J.; Kwok, Ronald

1992-01-01

Improved statistical method of extraction of textural features in synthetic-aperture-radar (SAR) images takes account of effects of scheme used to sample raw SAR data, system noise, resolution of radar equipment, and speckle. Treatment of speckle incorporated into overall statistical treatment of speckle, system noise, and natural variations in texture. One computes speckle auto-correlation function from system transfer function that expresses effect of radar aperature and incorporates range and azimuth resolutions.

Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

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

Lutsker, V.; Niehaus, T. A., E-mail: thomas.niehaus@physik.uni-regensburg.de; Aradi, B.

2015-11-14

Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply themore » method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.« less

An open-chain imaginary-time path-integral sampling approach to the calculation of approximate symmetrized quantum time correlation functions.

PubMed

Cendagorta, Joseph R; Bačić, Zlatko; Tuckerman, Mark E

2018-03-14

We introduce a scheme for approximating quantum time correlation functions numerically within the Feynman path integral formulation. Starting with the symmetrized version of the correlation function expressed as a discretized path integral, we introduce a change of integration variables often used in the derivation of trajectory-based semiclassical methods. In particular, we transform to sum and difference variables between forward and backward complex-time propagation paths. Once the transformation is performed, the potential energy is expanded in powers of the difference variables, which allows us to perform the integrals over these variables analytically. The manner in which this procedure is carried out results in an open-chain path integral (in the remaining sum variables) with a modified potential that is evaluated using imaginary-time path-integral sampling rather than requiring the generation of a large ensemble of trajectories. Consequently, any number of path integral sampling schemes can be employed to compute the remaining path integral, including Monte Carlo, path-integral molecular dynamics, or enhanced path-integral molecular dynamics. We believe that this approach constitutes a different perspective in semiclassical-type approximations to quantum time correlation functions. Importantly, we argue that our approximation can be systematically improved within a cumulant expansion formalism. We test this approximation on a set of one-dimensional problems that are commonly used to benchmark approximate quantum dynamical schemes. We show that the method is at least as accurate as the popular ring-polymer molecular dynamics technique and linearized semiclassical initial value representation for correlation functions of linear operators in most of these examples and improves the accuracy of correlation functions of nonlinear operators.

An open-chain imaginary-time path-integral sampling approach to the calculation of approximate symmetrized quantum time correlation functions

NASA Astrophysics Data System (ADS)

Cendagorta, Joseph R.; Bačić, Zlatko; Tuckerman, Mark E.

2018-03-01

We introduce a scheme for approximating quantum time correlation functions numerically within the Feynman path integral formulation. Starting with the symmetrized version of the correlation function expressed as a discretized path integral, we introduce a change of integration variables often used in the derivation of trajectory-based semiclassical methods. In particular, we transform to sum and difference variables between forward and backward complex-time propagation paths. Once the transformation is performed, the potential energy is expanded in powers of the difference variables, which allows us to perform the integrals over these variables analytically. The manner in which this procedure is carried out results in an open-chain path integral (in the remaining sum variables) with a modified potential that is evaluated using imaginary-time path-integral sampling rather than requiring the generation of a large ensemble of trajectories. Consequently, any number of path integral sampling schemes can be employed to compute the remaining path integral, including Monte Carlo, path-integral molecular dynamics, or enhanced path-integral molecular dynamics. We believe that this approach constitutes a different perspective in semiclassical-type approximations to quantum time correlation functions. Importantly, we argue that our approximation can be systematically improved within a cumulant expansion formalism. We test this approximation on a set of one-dimensional problems that are commonly used to benchmark approximate quantum dynamical schemes. We show that the method is at least as accurate as the popular ring-polymer molecular dynamics technique and linearized semiclassical initial value representation for correlation functions of linear operators in most of these examples and improves the accuracy of correlation functions of nonlinear operators.

Percolation analysis for cosmic web with discrete points

NASA Astrophysics Data System (ADS)

Zhang, Jiajun; Cheng, Dalong; Chu, Ming-Chung

2018-01-01

Percolation analysis has long been used to quantify the connectivity of the cosmic web. Most of the previous work is based on density fields on grids. By smoothing into fields, we lose information about galaxy properties like shape or luminosity. The lack of mathematical modeling also limits our understanding for the percolation analysis. To overcome these difficulties, we have studied percolation analysis based on discrete points. Using a friends-of-friends (FoF) algorithm, we generate the S -b b relation, between the fractional mass of the largest connected group (S ) and the FoF linking length (b b ). We propose a new model, the probability cloud cluster expansion theory to relate the S -b b relation with correlation functions. We show that the S -b b relation reflects a combination of all orders of correlation functions. Using N-body simulation, we find that the S -b b relation is robust against redshift distortion and incompleteness in observation. From the Bolshoi simulation, with halo abundance matching (HAM), we have generated a mock galaxy catalog. Good matching of the projected two-point correlation function with observation is confirmed. However, comparing the mock catalog with the latest galaxy catalog from Sloan Digital Sky Survey (SDSS) Data Release (DR)12, we have found significant differences in their S -b b relations. This indicates that the mock galaxy catalog cannot accurately retain higher-order correlation functions than the two-point correlation function, which reveals the limit of the HAM method. As a new measurement, the S -b b relation is applicable to a wide range of data types, fast to compute, and robust against redshift distortion and incompleteness and contains information of all orders of correlation functions.

Towards prediction of correlated material properties using quantum Monte Carlo methods

NASA Astrophysics Data System (ADS)

Wagner, Lucas

Correlated electron systems offer a richness of physics far beyond noninteracting systems. If we would like to pursue the dream of designer correlated materials, or, even to set a more modest goal, to explain in detail the properties and effective physics of known materials, then accurate simulation methods are required. Using modern computational resources, quantum Monte Carlo (QMC) techniques offer a way to directly simulate electron correlations. I will show some recent results on a few extremely challenging materials including the metal-insulator transition of VO2, the ground state of the doped cuprates, and the pressure dependence of magnetic properties in FeSe. By using a relatively simple implementation of QMC, at least some properties of these materials can be described truly from first principles, without any adjustable parameters. Using the QMC platform, we have developed a way of systematically deriving effective lattice models from the simulation. This procedure is particularly attractive for correlated electron systems because the QMC methods treat the one-body and many-body components of the wave function and Hamiltonian on completely equal footing. I will show some examples of using this downfolding technique and the high accuracy of QMC to connect our intuitive ideas about interacting electron systems with high fidelity simulations. The work in this presentation was supported in part by NSF DMR 1206242, the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research, Scientific Discovery through Advanced Computing (SciDAC) program under Award Number FG02-12ER46875, and the Center for Emergent Superconductivity, Department of Energy Frontier Research Center under Grant No. DEAC0298CH1088. Computing resources were provided by a Blue Waters Illinois grant and INCITE PhotSuper and SuperMatSim allocations.

The PROMIS physical function correlates with the QuickDASH in patients with upper extremity illness.

PubMed

Overbeek, Celeste L; Nota, Sjoerd P F T; Jayakumar, Prakash; Hageman, Michiel G; Ring, David

2015-01-01

To assess disability more efficiently with less burden on the patient, the National Institutes of Health has developed the Patient Reported Outcomes Measurement Information System (PROMIS) Physical Function-an instrument based on item response theory and using computer adaptive testing (CAT). Initially, upper and lower extremity disabilities were not separated and we were curious if the PROMIS Physical Function CAT could measure upper extremity disability and the Quick Disability of Arm, Shoulder and Hand (QuickDASH). We aimed to find correlation between the PROMIS Physical Function and the QuickDASH questionnaires in patients with upper extremity illness. Secondarily, we addressed whether the PROMIS Physical Function and QuickDASH correlate with the PROMIS Depression CAT and PROMIS Pain Interference CAT instruments. Finally, we assessed factors associated with QuickDASH and PROMIS Physical Function in multivariable analysis. A cohort of 93 outpatients with upper extremity illnesses completed the QuickDASH and three PROMIS CAT questionnaires: Physical Function, Pain Interference, and Depression. Pain intensity was measured with an 11-point ordinal measure (0-10 numeric rating scale). Correlation between PROMIS Physical Function and the QuickDASH was assessed. Factors that correlated with the PROMIS Physical Function and QuickDASH were assessed in multivariable regression analysis after initial bivariate analysis. There was a moderate correlation between the PROMIS Physical Function and the QuickDASH questionnaire (r=-0.55, p<0.001). Greater disability as measured with the PROMIS and QuickDASH correlated most strongly with PROMIS Depression (r=-0.35, p<0.001 and r=0.34, p<0.001 respectively) and Pain Interference (r=-0.51, p<0.001 and r=0.74, p<0.001 respectively). The factors accounting for the variability in PROMIS scores are comparable to those for the QuickDASH except that the PROMIS Physical Function is influenced by other pain conditions while the QuickDASH is not. The PROMIS Physical Function instrument may be used as an upper extremity disability measure, as it correlates with the QuickDASH questionnaire, and both instruments are influenced most strongly by the degree to which pain interferes with achieving goals. Level III, diagnostic study. See the Instructions for Authors for a complete description of levels of evidence.

Changes in functional brain organization and behavioral correlations after rehabilitative therapy using a brain-computer interface.

PubMed

Young, Brittany M; Nigogosyan, Zack; Walton, Léo M; Song, Jie; Nair, Veena A; Grogan, Scott W; Tyler, Mitchell E; Edwards, Dorothy F; Caldera, Kristin; Sattin, Justin A; Williams, Justin C; Prabhakaran, Vivek

2014-01-01

This study aims to examine the changes in task-related brain activity induced by rehabilitative therapy using brain-computer interface (BCI) technologies and whether these changes are relevant to functional gains achieved through the use of these therapies. Stroke patients with persistent upper-extremity motor deficits received interventional rehabilitation therapy using a closed-loop neurofeedback BCI device (n = 8) or no therapy (n = 6). Behavioral assessments using the Stroke Impact Scale, the Action Research Arm Test (ARAT), and the Nine-Hole Peg Test (9-HPT) as well as task-based fMRI scans were conducted before, during, after, and 1 month after therapy administration or at analogous intervals in the absence of therapy. Laterality Index (LI) values during finger tapping of each hand were calculated for each time point and assessed for correlation with behavioral outcomes. Brain activity during finger tapping of each hand shifted over the course of BCI therapy, but not in the absence of therapy, to greater involvement of the non-lesioned hemisphere (and lesser involvement of the stroke-lesioned hemisphere) as measured by LI. Moreover, changes from baseline LI values during finger tapping of the impaired hand were correlated with gains in both objective and subjective behavioral measures. These findings suggest that the administration of interventional BCI therapy can induce differential changes in brain activity patterns between the lesioned and non-lesioned hemispheres and that these brain changes are associated with changes in specific motor functions.

Structural and vibrational properties of transition-metal oxides from first-principles calculations

NASA Astrophysics Data System (ADS)

Cococcioni, M.; Floris, A.; Himmetoglu, B.

2010-12-01

The calculation of the vibrational spectrum of minerals is of fundamental importance to assess their behavior (e.g. their elastic properties, or possible structural phase transitions) under the high-temperature, high-pressure conditions of the Earth’s interior. The ubiquitous presence of transition metals and the consequent importance of electronic correlations make the study of these materials quite difficult to approach with approximate DFT functionals (as LDA or GGA). The DFT+U, consisting in a Hubbard-modeled correction to the DFT energy functionals, has been successfully used to study the electronic, structural, and magnetic properties of several Fe-bearing minerals. However, the vibrational spectrum of these systems has never been determined entirely (frozen- phonon techniques are overly expensive except for zone-center phonons). In this work we introduce the extension of Density-Functional-Perturbation-Theory to DFT+U, that allows to efficiently compute the phonon spectrum of transition-metal compounds from their correlated ground states. A comparative analysis between the vibrational properties of MnO, FeO, CoO, and NiO (in the undistorted cubic cell) highlights a marked dependence of several features of their phonon spectrum on the occupancy of localized d orbitals and thus, on elec- tronic correlation. The new computational tool is also employed to evaluate the rhombohedral distortion of FeO (particularly abundant in the Earth’s lower mantle) and to assess the stability of its B1 phase in different conditions of pressure and temperature.

Information sensitivity functions to assess parameter information gain and identifiability of dynamical systems.

PubMed

Pant, Sanjay

2018-05-01

A new class of functions, called the 'information sensitivity functions' (ISFs), which quantify the information gain about the parameters through the measurements/observables of a dynamical system are presented. These functions can be easily computed through classical sensitivity functions alone and are based on Bayesian and information-theoretic approaches. While marginal information gain is quantified by decrease in differential entropy, correlations between arbitrary sets of parameters are assessed through mutual information. For individual parameters, these information gains are also presented as marginal posterior variances, and, to assess the effect of correlations, as conditional variances when other parameters are given. The easy to interpret ISFs can be used to (a) identify time intervals or regions in dynamical system behaviour where information about the parameters is concentrated; (b) assess the effect of measurement noise on the information gain for the parameters; (c) assess whether sufficient information in an experimental protocol (input, measurements and their frequency) is available to identify the parameters; (d) assess correlation in the posterior distribution of the parameters to identify the sets of parameters that are likely to be indistinguishable; and (e) assess identifiability problems for particular sets of parameters. © 2018 The Authors.

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

Bouchard, Chris; Chang, Chia Cheng; Kurth, Thorsten

In this paper, the Feynman-Hellmann theorem can be derived from the long Euclidean-time limit of correlation functions determined with functional derivatives of the partition function. Using this insight, we fully develop an improved method for computing matrix elements of external currents utilizing only two-point correlation functions. Our method applies to matrix elements of any external bilinear current, including nonzero momentum transfer, flavor-changing, and two or more current insertion matrix elements. The ability to identify and control all the systematic uncertainties in the analysis of the correlation functions stems from the unique time dependence of the ground-state matrix elements and the fact that all excited states and contact terms are Euclidean-time dependent. We demonstrate the utility of our method with a calculation of the nucleon axial charge using gradient-flowed domain-wall valence quarks on themore » $$N_f=2+1+1$$ MILC highly improved staggered quark ensemble with lattice spacing and pion mass of approximately 0.15 fm and 310 MeV respectively. We show full control over excited-state systematics with the new method and obtain a value of $$g_A = 1.213(26)$$ with a quark-mass-dependent renormalization coefficient.« less

Task-evoked brain functional magnetic susceptibility mapping by independent component analysis (χICA).

PubMed

Chen, Zikuan; Calhoun, Vince D

2016-03-01

Conventionally, independent component analysis (ICA) is performed on an fMRI magnitude dataset to analyze brain functional mapping (AICA). By solving the inverse problem of fMRI, we can reconstruct the brain magnetic susceptibility (χ) functional states. Upon the reconstructed χ dataspace, we propose an ICA-based brain functional χ mapping method (χICA) to extract task-evoked brain functional map. A complex division algorithm is applied to a timeseries of fMRI phase images to extract temporal phase changes (relative to an OFF-state snapshot). A computed inverse MRI (CIMRI) model is used to reconstruct a 4D brain χ response dataset. χICA is implemented by applying a spatial InfoMax ICA algorithm to the reconstructed 4D χ dataspace. With finger-tapping experiments on a 7T system, the χICA-extracted χ-depicted functional map is similar to the SPM-inferred functional χ map by a spatial correlation of 0.67 ± 0.05. In comparison, the AICA-extracted magnitude-depicted map is correlated with the SPM magnitude map by 0.81 ± 0.05. The understanding of the inferiority of χICA to AICA for task-evoked functional map is an ongoing research topic. For task-evoked brain functional mapping, we compare the data-driven ICA method with the task-correlated SPM method. In particular, we compare χICA with AICA for extracting task-correlated timecourses and functional maps. χICA can extract a χ-depicted task-evoked brain functional map from a reconstructed χ dataspace without the knowledge about brain hemodynamic responses. The χICA-extracted brain functional χ map reveals a bidirectional BOLD response pattern that is unavailable (or different) from AICA. Copyright © 2016 Elsevier B.V. All rights reserved.

Remote Measurement of Heat Flux from Power Plant Cooling Lakes

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

Garrett, Alfred J.; Kurzeja, Robert J.; Villa-Aleman, Eliel

2013-06-01

Laboratory experiments have demonstrated a correlation between the rate of heat loss q" from an experimental fluid to the air above and the standard deviation σ of the thermal variability in images of the fluid surface. These experimental results imply that q" can be derived directly from thermal imagery by computing σ. This paper analyses thermal imagery collected over two power plant cooling lakes to determine if the same relationship exists. Turbulent boundary layer theory predicts a linear relationship between q" and σ when both forced (wind driven) and free (buoyancy driven) convection are present. Datasets derived from ground- andmore » helicopter-based imagery collections had correlation coefficients between σ and q" of 0.45 and 0.76, respectively. Values of q" computed from a function of σ and friction velocity u* derived from turbulent boundary layer theory had higher correlations with measured values of q" (0.84 and 0.89). Finally, this research may be applicable to the problem of calculating losses of heat from the ocean to the atmosphere during high-latitude cold-air outbreaks because it does not require the information typically needed to compute sensible, evaporative, and thermal radiation energy losses to the atmosphere.« less

Neuroanatomical correlates of brain-computer interface performance.

PubMed

Kasahara, Kazumi; DaSalla, Charles Sayo; Honda, Manabu; Hanakawa, Takashi

2015-04-15

Brain-computer interfaces (BCIs) offer a potential means to replace or restore lost motor function. However, BCI performance varies considerably between users, the reasons for which are poorly understood. Here we investigated the relationship between sensorimotor rhythm (SMR)-based BCI performance and brain structure. Participants were instructed to control a computer cursor using right- and left-hand motor imagery, which primarily modulated their left- and right-hemispheric SMR powers, respectively. Although most participants were able to control the BCI with success rates significantly above chance level even at the first encounter, they also showed substantial inter-individual variability in BCI success rate. Participants also underwent T1-weighted three-dimensional structural magnetic resonance imaging (MRI). The MRI data were subjected to voxel-based morphometry using BCI success rate as an independent variable. We found that BCI performance correlated with gray matter volume of the supplementary motor area, supplementary somatosensory area, and dorsal premotor cortex. We suggest that SMR-based BCI performance is associated with development of non-primary somatosensory and motor areas. Advancing our understanding of BCI performance in relation to its neuroanatomical correlates may lead to better customization of BCIs based on individual brain structure. Copyright © 2015 Elsevier Inc. All rights reserved.

On the performance of large Gaussian basis sets for the computation of total atomization energies

NASA Technical Reports Server (NTRS)

Martin, J. M. L.

1992-01-01

The total atomization energies of a number of molecules have been computed using an augmented coupled-cluster method and (5s4p3d2f1g) and 4s3p2d1f) atomic natural orbital (ANO) basis sets, as well as the correlation consistent valence triple zeta plus polarization (cc-pVTZ) correlation consistent valence quadrupole zeta plus polarization (cc-pVQZ) basis sets. The performance of ANO and correlation consistent basis sets is comparable throughout, although the latter can result in significant CPU time savings. Whereas the inclusion of g functions has significant effects on the computed Sigma D(e) values, chemical accuracy is still not reached for molecules involving multiple bonds. A Gaussian-1 (G) type correction lowers the error, but not much beyond the accuracy of the G1 model itself. Using separate corrections for sigma bonds, pi bonds, and valence pairs brings down the mean absolute error to less than 1 kcal/mol for the spdf basis sets, and about 0.5 kcal/mol for the spdfg basis sets. Some conclusions on the success of the Gaussian-1 and Gaussian-2 models are drawn.

Correlated natural transition orbital framework for low-scaling excitation energy calculations (CorNFLEx).

PubMed

Baudin, Pablo; Kristensen, Kasper

2017-06-07

We present a new framework for calculating coupled cluster (CC) excitation energies at a reduced computational cost. It relies on correlated natural transition orbitals (NTOs), denoted CIS(D')-NTOs, which are obtained by diagonalizing generalized hole and particle density matrices determined from configuration interaction singles (CIS) information and additional terms that represent correlation effects. A transition-specific reduced orbital space is determined based on the eigenvalues of the CIS(D')-NTOs, and a standard CC excitation energy calculation is then performed in that reduced orbital space. The new method is denoted CorNFLEx (Correlated Natural transition orbital Framework for Low-scaling Excitation energy calculations). We calculate second-order approximate CC singles and doubles (CC2) excitation energies for a test set of organic molecules and demonstrate that CorNFLEx yields excitation energies of CC2 quality at a significantly reduced computational cost, even for relatively small systems and delocalized electronic transitions. In order to illustrate the potential of the method for large molecules, we also apply CorNFLEx to calculate CC2 excitation energies for a series of solvated formamide clusters (up to 4836 basis functions).

Syntactic structure building in the anterior temporal lobe during natural story listening.

PubMed

Brennan, Jonathan; Nir, Yuval; Hasson, Uri; Malach, Rafael; Heeger, David J; Pylkkänen, Liina

2012-02-01

The neural basis of syntax is a matter of substantial debate. In particular, the inferior frontal gyrus (IFG), or Broca's area, has been prominently linked to syntactic processing, but the anterior temporal lobe has been reported to be activated instead of IFG when manipulating the presence of syntactic structure. These findings are difficult to reconcile because they rely on different laboratory tasks which tap into distinct computations, and may only indirectly relate to natural sentence processing. Here we assessed neural correlates of syntactic structure building in natural language comprehension, free from artificial task demands. Subjects passively listened to Alice in Wonderland during functional magnetic resonance imaging and we correlated brain activity with a word-by-word measure of the amount syntactic structure analyzed. Syntactic structure building correlated with activity in the left anterior temporal lobe, but there was no evidence for a correlation between syntactic structure building and activity in inferior frontal areas. Our results suggest that the anterior temporal lobe computes syntactic structure under natural conditions. Copyright © 2010 Elsevier Inc. All rights reserved.

Correlation between solar flare productivity and photospheric vector magnetic fields

NASA Astrophysics Data System (ADS)

Cui, Yanmei; Wang, Huaning

2008-11-01

Studying the statistical correlation between the solar flare productivity and photospheric magnetic fields is very important and necessary. It is helpful to set up a practical flare forecast model based on magnetic properties and improve the physical understanding of solar flare eruptions. In the previous study ([Cui, Y.M., Li, R., Zhang, L.Y., He, Y.L., Wang, H.N. Correlation between solar flare productivity and photospheric magnetic field properties 1. Maximum horizontal gradient, length of neutral line, number of singular points. Sol. Phys. 237, 45 59, 2006]; from now on we refer to this paper as ‘Paper I’), three measures of the maximum horizontal gradient, the length of the neutral line, and the number of singular points are computed from 23990 SOHO/MDI longitudinal magnetograms. The statistical relationship between the solar flare productivity and these three measures is well fitted with sigmoid functions. In the current work, the three measures of the length of strong-shear neutral line, total unsigned current, and total unsigned current helicity are computed from 1353 vector magnetograms observed at Huairou Solar Observing Station. The relationship between the solar flare productivity and the current three measures can also be well fitted with sigmoid functions. These results are expected to be beneficial to future operational flare forecasting models.

Computational analysis of microRNA function in heart development.

PubMed

Liu, Ganqiang; Ding, Min; Chen, Jiajia; Huang, Jinyan; Wang, Haiyun; Jing, Qing; Shen, Bairong

2010-09-01

Emerging evidence suggests that specific spatio-temporal microRNA (miRNA) expression is required for heart development. In recent years, hundreds of miRNAs have been discovered. In contrast, functional annotations are available only for a very small fraction of these regulatory molecules. In order to provide a global perspective for the biologists who study the relationship between differentially expressed miRNAs and heart development, we employed computational analysis to uncover the specific cellular processes and biological pathways targeted by miRNAs in mouse heart development. Here, we utilized Gene Ontology (GO) categories, KEGG Pathway, and GeneGo Pathway Maps as a gene functional annotation system for miRNA target enrichment analysis. The target genes of miRNAs were found to be enriched in functional categories and pathway maps in which miRNAs could play important roles during heart development. Meanwhile, we developed miRHrt (http://sysbio.suda.edu.cn/mirhrt/), a database aiming to provide a comprehensive resource of miRNA function in regulating heart development. These computational analysis results effectively illustrated the correlation of differentially expressed miRNAs with cellular functions and heart development. We hope that the identified novel heart development-associated pathways and the database presented here would facilitate further understanding of the roles and mechanisms of miRNAs in heart development.

A meta-analysis of perceptual and cognitive functions involved in useful-field-of-view test performance.

PubMed

Woutersen, Karlijn; Guadron, Leslie; van den Berg, Albert V; Boonstra, F Nienke; Theelen, Thomas; Goossens, Jeroen

2017-12-01

The useful-field-of-view (UFOV) test measures the amount of information someone can extract from a visual scene in one glance. Its scores show relatively strong relationships with everyday activities. The UFOV test consists of three computer tests, suggested to measure processing speed and central vision, divided attention, and selective attention. However, other functions seem to be involved as well. In order to investigate the contribution of these suggested and other perceptual and cognitive functions, we performed a meta-analysis of 116 Pearson's correlation coefficients between UFOV scores and other test scores reported in 18 peer-reviewed articles. We divided these correlations into nine domains: attention, executive functioning, general cognition, memory, spatial ability, visual closure, contrast sensitivity, visual processing speed, and visual acuity. A multivariate mixed-effects model analysis revealed that each domain correlated significantly with each of the UFOV subtest scores. These correlations were stronger for Subtests 2 and 3 than for Subtest 1. Furthermore, some domains were more strongly correlated to the UFOV than others across subtests. We did not find interaction effects between subtest and domain, indicating that none of the UFOV subtests is more selectively sensitive to a particular domain than the others. Thus, none of the three UFOV subtests seem to measure one clear construct. Instead, a range of visual and cognitive functions is involved. Perhaps this is the reason for the UFOV's high ecological validity, as it involves many functions at once, making it harder to compensate if one of them fails.

Neural Correlates of Phrase Quadrature Perception in Harmonic Rhythm: An EEG Study Using a Brain-Computer Interface.

PubMed

Fernández-Soto, Alicia; Martínez-Rodrigo, Arturo; Moncho-Bogani, José; Latorre, José Miguel; Fernández-Caballero, Antonio

2018-06-01

For the sake of establishing the neural correlates of phrase quadrature perception in harmonic rhythm, a musical experiment has been designed to induce music-evoked stimuli related to one important aspect of harmonic rhythm, namely the phrase quadrature. Brain activity is translated to action through electroencephalography (EEG) by using a brain-computer interface. The power spectral value of each EEG channel is estimated to obtain how power variance distributes as a function of frequency. The results of processing the acquired signals are in line with previous studies that use different musical parameters to induce emotions. Indeed, our experiment shows statistical differences in theta and alpha bands between the fulfillment and break of phrase quadrature, an important cue of harmonic rhythm, in two classical sonatas.

The self-consistent calculation of pseudo-molecule energy levels, construction of energy level correlation diagrams and an automated computation system for SCF-X(Alpha)-SW calculations

NASA Technical Reports Server (NTRS)

Schlosser, H.

1981-01-01

The self consistent calculation of the electronic energy levels of noble gas pseudomolecules formed when a metal surface is bombarded by noble gas ions is discussed along with the construction of energy level correlation diagrams as a function of interatomic spacing. The self consistent field x alpha scattered wave (SCF-Xalpha-SW) method is utilized. Preliminary results on the Ne-Mg system are given. An interactive x alpha programming system, implemented on the LeRC IBM 370 computer, is described in detail. This automated system makes use of special PROCDEFS (procedure definitions) to minimize the data to be entered manually at a remote terminal. Listings of the special PROCDEFS and of typical input data are given.

Collective charge excitations and the metal-insulator transition in the square lattice Hubbard-Coulomb model

DOE PAGES

Ulybyshev, Maksim; Winterowd, Christopher; Zafeiropoulos, Savvas

2017-11-09

Here in this article, we discuss the nontrivial collective charge excitations (plasmons) of the extended square lattice Hubbard model. Using a fully nonperturbative approach, we employ the hybrid Monte Carlo algorithm to simulate the system at half-filling. A modified Backus-Gilbert method is introduced to obtain the spectral functions via numerical analytic continuation. We directly compute the single-particle density of states which demonstrates the formation of Hubbard bands in the strongly correlated phase. The momentum-resolved charge susceptibility also is computed on the basis of the Euclidean charge-density-density correlator. In agreement with previous extended dynamical mean-field theory studies, we find that, atmore » high strength of the electron-electron interaction, the plasmon dispersion develops two branches.« less

Collective charge excitations and the metal-insulator transition in the square lattice Hubbard-Coulomb model

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

Ulybyshev, Maksim; Winterowd, Christopher; Zafeiropoulos, Savvas

Here in this article, we discuss the nontrivial collective charge excitations (plasmons) of the extended square lattice Hubbard model. Using a fully nonperturbative approach, we employ the hybrid Monte Carlo algorithm to simulate the system at half-filling. A modified Backus-Gilbert method is introduced to obtain the spectral functions via numerical analytic continuation. We directly compute the single-particle density of states which demonstrates the formation of Hubbard bands in the strongly correlated phase. The momentum-resolved charge susceptibility also is computed on the basis of the Euclidean charge-density-density correlator. In agreement with previous extended dynamical mean-field theory studies, we find that, atmore » high strength of the electron-electron interaction, the plasmon dispersion develops two branches.« less

Three-dimensional computed tomographic volumetry precisely predicts the postoperative pulmonary function.

PubMed

Kobayashi, Keisuke; Saeki, Yusuke; Kitazawa, Shinsuke; Kobayashi, Naohiro; Kikuchi, Shinji; Goto, Yukinobu; Sakai, Mitsuaki; Sato, Yukio

2017-11-01

It is important to accurately predict the patient's postoperative pulmonary function. The aim of this study was to compare the accuracy of predictions of the postoperative residual pulmonary function obtained with three-dimensional computed tomographic (3D-CT) volumetry with that of predictions obtained with the conventional segment-counting method. Fifty-three patients scheduled to undergo lung cancer resection, pulmonary function tests, and computed tomography were enrolled in this study. The postoperative residual pulmonary function was predicted based on the segment-counting and 3D-CT volumetry methods. The predicted postoperative values were compared with the results of postoperative pulmonary function tests. Regarding the linear correlation coefficients between the predicted postoperative values and the measured values, those obtained using the 3D-CT volumetry method tended to be higher than those acquired using the segment-counting method. In addition, the variations between the predicted and measured values were smaller with the 3D-CT volumetry method than with the segment-counting method. These results were more obvious in COPD patients than in non-COPD patients. Our findings suggested that the 3D-CT volumetry was able to predict the residual pulmonary function more accurately than the segment-counting method, especially in patients with COPD. This method might lead to the selection of appropriate candidates for surgery among patients with a marginal pulmonary function.

Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

DOE PAGES

White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William; ...

2017-06-21

The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies.more » Furthermore, the ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

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

White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William

The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies.more » Furthermore, the ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

Partial Correlation-Based Retinotopically Organized Resting-State Functional Connectivity Within and Between Areas of the Visual Cortex Reflects More Than Cortical Distance

PubMed Central

Dawson, Debra Ann; Lam, Jack; Lewis, Lindsay B.; Carbonell, Felix; Mendola, Janine D.

2016-01-01

Abstract Numerous studies have demonstrated functional magnetic resonance imaging (fMRI)-based resting-state functional connectivity (RSFC) between cortical areas. Recent evidence suggests that synchronous fluctuations in blood oxygenation level-dependent fMRI reflect functional organization at a scale finer than that of visual areas. In this study, we investigated whether RSFCs within and between lower visual areas are retinotopically organized and whether retinotopically organized RSFC merely reflects cortical distance. Subjects underwent retinotopic mapping and separately resting-state fMRI. Visual areas V1, V2, and V3, were subdivided into regions of interest (ROIs) according to quadrants and visual field eccentricity. Functional connectivity (FC) was computed based on Pearson's linear correlation (correlation), and Pearson's linear partial correlation (correlation between two time courses after the time courses from all other regions in the network are regressed out). Within a quadrant, within visual areas, all correlation and nearly all partial correlation FC measures showed statistical significance. Consistently in V1, V2, and to a lesser extent in V3, correlation decreased with increasing eccentricity separation. Consistent with previously reported monkey anatomical connectivity, correlation/partial correlation values between regions from adjacent areas (V1-V2 and V2-V3) were higher than those between nonadjacent areas (V1-V3). Within a quadrant, partial correlation showed consistent significance between regions from two different areas with the same or adjacent eccentricities. Pairs of ROIs with similar eccentricity showed higher correlation/partial correlation than pairs distant in eccentricity. Between dorsal and ventral quadrants, partial correlation between common and adjacent eccentricity regions within a visual area showed statistical significance; this extended to more distant eccentricity regions in V1. Within and between quadrants, correlation decreased approximately linearly with increasing distances separating the tested ROIs. Partial correlation showed a more complex dependence on cortical distance: it decreased exponentially with increasing distance within a quadrant, but was best fit by a quadratic function between quadrants. We conclude that RSFCs within and between lower visual areas are retinotopically organized. Correlation-based FC is nonselectively high across lower visual areas, even between regions that do not share direct anatomical connections. The mechanisms likely involve network effects caused by the dense anatomical connectivity within this network and projections from higher visual areas. FC based on partial correlation, which minimizes network effects, follows expectations based on direct anatomical connections in the monkey visual cortex better than correlation. Last, partial correlation-based retinotopically organized RSFC reflects more than cortical distance effects. PMID:26415043

Partial Correlation-Based Retinotopically Organized Resting-State Functional Connectivity Within and Between Areas of the Visual Cortex Reflects More Than Cortical Distance.

PubMed

Dawson, Debra Ann; Lam, Jack; Lewis, Lindsay B; Carbonell, Felix; Mendola, Janine D; Shmuel, Amir

2016-02-01

Numerous studies have demonstrated functional magnetic resonance imaging (fMRI)-based resting-state functional connectivity (RSFC) between cortical areas. Recent evidence suggests that synchronous fluctuations in blood oxygenation level-dependent fMRI reflect functional organization at a scale finer than that of visual areas. In this study, we investigated whether RSFCs within and between lower visual areas are retinotopically organized and whether retinotopically organized RSFC merely reflects cortical distance. Subjects underwent retinotopic mapping and separately resting-state fMRI. Visual areas V1, V2, and V3, were subdivided into regions of interest (ROIs) according to quadrants and visual field eccentricity. Functional connectivity (FC) was computed based on Pearson's linear correlation (correlation), and Pearson's linear partial correlation (correlation between two time courses after the time courses from all other regions in the network are regressed out). Within a quadrant, within visual areas, all correlation and nearly all partial correlation FC measures showed statistical significance. Consistently in V1, V2, and to a lesser extent in V3, correlation decreased with increasing eccentricity separation. Consistent with previously reported monkey anatomical connectivity, correlation/partial correlation values between regions from adjacent areas (V1-V2 and V2-V3) were higher than those between nonadjacent areas (V1-V3). Within a quadrant, partial correlation showed consistent significance between regions from two different areas with the same or adjacent eccentricities. Pairs of ROIs with similar eccentricity showed higher correlation/partial correlation than pairs distant in eccentricity. Between dorsal and ventral quadrants, partial correlation between common and adjacent eccentricity regions within a visual area showed statistical significance; this extended to more distant eccentricity regions in V1. Within and between quadrants, correlation decreased approximately linearly with increasing distances separating the tested ROIs. Partial correlation showed a more complex dependence on cortical distance: it decreased exponentially with increasing distance within a quadrant, but was best fit by a quadratic function between quadrants. We conclude that RSFCs within and between lower visual areas are retinotopically organized. Correlation-based FC is nonselectively high across lower visual areas, even between regions that do not share direct anatomical connections. The mechanisms likely involve network effects caused by the dense anatomical connectivity within this network and projections from higher visual areas. FC based on partial correlation, which minimizes network effects, follows expectations based on direct anatomical connections in the monkey visual cortex better than correlation. Last, partial correlation-based retinotopically organized RSFC reflects more than cortical distance effects.

Performance of Frozen Density Embedding for Modeling Hole Transfer Reactions.

PubMed

Ramos, Pablo; Papadakis, Markos; Pavanello, Michele

2015-06-18

We have carried out a thorough benchmark of the frozen density-embedding (FDE) method for calculating hole transfer couplings. We have considered 10 exchange-correlation functionals, 3 nonadditive kinetic energy functionals, and 3 basis sets. Overall, we conclude that with a 7% mean relative unsigned error, the PBE and PW91 functionals coupled with the PW91k nonadditive kinetic energy functional and a TZP basis set constitute the most stable and accurate levels of theory for hole transfer coupling calculations. The FDE-ET method is found to be an excellent tool for computing diabatic couplings for hole transfer reactions.

Microstructural Quantification, Property Prediction, and Stochastic Reconstruction of Heterogeneous Materials Using Limited X-Ray Tomography Data

NASA Astrophysics Data System (ADS)

Li, Hechao

An accurate knowledge of the complex microstructure of a heterogeneous material is crucial for quantitative structure-property relations establishment and its performance prediction and optimization. X-ray tomography has provided a non-destructive means for microstructure characterization in both 3D and 4D (i.e., structural evolution over time). Traditional reconstruction algorithms like filtered-back-projection (FBP) method or algebraic reconstruction techniques (ART) require huge number of tomographic projections and segmentation process before conducting microstructural quantification. This can be quite time consuming and computationally intensive. In this thesis, a novel procedure is first presented that allows one to directly extract key structural information in forms of spatial correlation functions from limited x-ray tomography data. The key component of the procedure is the computation of a "probability map", which provides the probability of an arbitrary point in the material system belonging to specific phase. The correlation functions of interest are then readily computed from the probability map. Using effective medium theory, accurate predictions of physical properties (e.g., elastic moduli) can be obtained. Secondly, a stochastic optimization procedure that enables one to accurately reconstruct material microstructure from a small number of x-ray tomographic projections (e.g., 20 - 40) is presented. Moreover, a stochastic procedure for multi-modal data fusion is proposed, where both X-ray projections and correlation functions computed from limited 2D optical images are fused to accurately reconstruct complex heterogeneous materials in 3D. This multi-modal reconstruction algorithm is proved to be able to integrate the complementary data to perform an excellent optimization procedure, which indicates its high efficiency in using limited structural information. Finally, the accuracy of the stochastic reconstruction procedure using limited X-ray projection data is ascertained by analyzing the microstructural degeneracy and the roughness of energy landscape associated with different number of projections. Ground-state degeneracy of a microstructure is found to decrease with increasing number of projections, which indicates a higher probability that the reconstructed configurations match the actual microstructure. The roughness of energy landscape can also provide information about the complexity and convergence behavior of the reconstruction for given microstructures and projection number.

Assessment of the Airway Characteristics in Children with Cleft Lip and Palate using Cone Beam Computed Tomography

PubMed Central

Marwah, Nikhil

2016-01-01

ABSTRACT Objective: The aim of our study is to use cone beam computed tomography (CBCT) to assess the dimensional changes in the nasopharyngeal soft-tissue characteristics in children of Indian origin with repaired cleft lip and palate (CLP) and to compare the results with patients with ideal occlusion. Materials and methods: A sample of 20 children (10 girls, 10 boys) with repaired CLP was selected. Cone beam computed tomography scans were taken to measure the nasopharyngeal airway changes in terms of linear measurements and sagittal cross-sectional areas. Error analysis was performed to prevent systematic or random errors. Independent means t-tests and Pearson correlation analysis were used to evaluate sex differences and the correlations among the variables. Results: Nasopharyngeal soft-tissue characteristics were different in the control and the study groups. Subjects with repaired CLP had lesser lower aerial width, lower adenoidal width and lower airway width. The upper airway width was also significantly lesser. The retropalatal and the total airway area were significantly greater in the control group. Conclusion: The narrow pharyngeal airway in patients with CLP might result in functional impairment of breathing in patients. Further investigations are necessary to clarify the relationship between pharyngeal structure and airway function in patients with CLP. How to cite this article: Agarwal A, Marwah N. Assessment of the Airway Characteristics in Children with Cleft Lip and Palate using Cone Beam Computed Tomography. Int J Clin Pediatr Dent 2016;9(1):5-9. PMID:27274147

Density Functional Calculations for Prediction of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings in β-Diketiminate Complexes

PubMed Central

2017-01-01

The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together. PMID:28691111

Correlation of PROMIS Physical Function and Pain CAT Instruments With Oswestry Disability Index and Neck Disability Index in Spine Patients.

PubMed

Papuga, Mark O; Mesfin, Addisu; Molinari, Robert; Rubery, Paul T

2016-07-15

A prospective and retrospective cross-sectional cohort analysis. The aim of this study was to show that Patient-Reported Outcomes Measurement Information System (PROMIS) computer adaptive testing (CAT) assessments for physical function and pain interference can be efficiently collected in a standard office visit and to evaluate these scores with scores from previously validated Oswestry Disability Index (ODI) and Neck Disability Index (NDI) providing evidence of convergent validity for use in patients with spine pathology. Spinal surgery outcomes are highly variable, and substantial debate continues regarding the role and value of spine surgery. The routine collection of patient-based outcomes instruments in spine surgery patients may inform this debate. Traditionally, the inefficiency associated with collecting standard validated instruments has been a barrier to routine use in outpatient clinics. We utilized several CAT instruments available through PROMIS and correlated these with the results obtained using "gold standard" legacy outcomes measurement instruments. All measurements were collected at a routine clinical visit. The ODI and the NDI assessments were used as "gold standard" comparisons for patient-reported outcomes. PROMIS CAT instruments required 4.5 ± 1.8 questions and took 35 ± 16 seconds to complete, compared with ODI/NDI requiring 10 questions and taking 188 ± 85 seconds when administered electronically. Linear regression analysis of retrospective scores involving a primary back complaint revealed moderate to strong correlations between ODI and PROMIS physical function with r values ranging from 0.5846 to 0.8907 depending on the specific assessment and patient subsets examined. Routine collection of physical function outcome measures in clinical practice offers the ability to inform and improve patient care. We have shown that several PROMIS CAT instruments can be efficiently administered during routine clinical visits. The moderate to strong correlations found validate the utility of computer adaptive testing when compared with the gold standard "static" legacy assessments. 4.

RG flow from Φ 4 theory to the 2D Ising model

DOE PAGES

Anand, Nikhil; Genest, Vincent X.; Katz, Emanuel; ...

2017-08-16

We study 1+1 dimensional Φ 4 theory using the recently proposed method of conformal truncation. Starting in the UV CFT of free field theory, we construct a complete basis of states with definite conformal Casimir, C. We use these states to express the Hamiltonian of the full interacting theory in lightcone quantization. After truncating to states with C≤C max, we numerically diagonalize the Hamiltonian at strong coupling and study the resulting IR dynamics. We compute non-perturbative spectral densities of several local operators, which are equivalent to real-time, infinite-volume correlation functions. These spectral densities, which include the Zamolodchikov C-function along themore » full RG flow, are calculable at any value of the coupling. Near criticality, our numerical results reproduce correlation functions in the 2D Ising model.« less

Emergent functions of quantum materials

NASA Astrophysics Data System (ADS)

Tokura, Yoshinori; Kawasaki, Masashi; Nagaosa, Naoto

2017-11-01

Materials can harbour quantum many-body systems, most typically in the form of strongly correlated electrons in solids, that lead to novel and remarkable functions thanks to emergence--collective behaviours that arise from strong interactions among the elements. These include the Mott transition, high-temperature superconductivity, topological superconductivity, colossal magnetoresistance, giant magnetoelectric effect, and topological insulators. These phenomena will probably be crucial for developing the next-generation quantum technologies that will meet the urgent technological demands for achieving a sustainable and safe society. Dissipationless electronics using topological currents and quantum spins, energy harvesting such as photovoltaics and thermoelectrics, and secure quantum computing and communication are the three major fields of applications working towards this goal. Here, we review the basic principles and the current status of the emergent phenomena and functions in materials from the viewpoint of strong correlation and topology.

Rank restriction for the variational calculation of two-electron reduced density matrices of many-electron atoms and molecules

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

Naftchi-Ardebili, Kasra; Hau, Nathania W.; Mazziotti, David A.

2011-11-15

Variational minimization of the ground-state energy as a function of the two-electron reduced density matrix (2-RDM), constrained by necessary N-representability conditions, provides a polynomial-scaling approach to studying strongly correlated molecules without computing the many-electron wave function. Here we introduce a route to enhancing necessary conditions for N representability through rank restriction of the 2-RDM. Rather than adding computationally more expensive N-representability conditions, we directly enhance the accuracy of two-particle (2-positivity) conditions through rank restriction, which removes degrees of freedom in the 2-RDM that are not sufficiently constrained. We select the rank of the particle-hole 2-RDM by deriving the ranks associatedmore » with model wave functions, including both mean-field and antisymmetrized geminal power (AGP) wave functions. Because the 2-positivity conditions are exact for quantum systems with AGP ground states, the rank of the particle-hole 2-RDM from the AGP ansatz provides a minimum for its value in variational 2-RDM calculations of general quantum systems. To implement the rank-restricted conditions, we extend a first-order algorithm for large-scale semidefinite programming. The rank-restricted conditions significantly improve the accuracy of the energies; for example, the percentages of correlation energies recovered for HF, CO, and N{sub 2} improve from 115.2%, 121.7%, and 121.5% without rank restriction to 97.8%, 101.1%, and 100.0% with rank restriction. Similar results are found at both equilibrium and nonequilibrium geometries. While more accurate, the rank-restricted N-representability conditions are less expensive computationally than the full-rank conditions.« less

Novel prediction model of renal function after nephrectomy from automated renal volumetry with preoperative multidetector computed tomography (MDCT).

PubMed

Isotani, Shuji; Shimoyama, Hirofumi; Yokota, Isao; Noma, Yasuhiro; Kitamura, Kousuke; China, Toshiyuki; Saito, Keisuke; Hisasue, Shin-ichi; Ide, Hisamitsu; Muto, Satoru; Yamaguchi, Raizo; Ukimura, Osamu; Gill, Inderbir S; Horie, Shigeo

2015-10-01

The predictive model of postoperative renal function may impact on planning nephrectomy. To develop the novel predictive model using combination of clinical indices with computer volumetry to measure the preserved renal cortex volume (RCV) using multidetector computed tomography (MDCT), and to prospectively validate performance of the model. Total 60 patients undergoing radical nephrectomy from 2011 to 2013 participated, including a development cohort of 39 patients and an external validation cohort of 21 patients. RCV was calculated by voxel count using software (Vincent, FUJIFILM). Renal function before and after radical nephrectomy was assessed via the estimated glomerular filtration rate (eGFR). Factors affecting postoperative eGFR were examined by regression analysis to develop the novel model for predicting postoperative eGFR with a backward elimination method. The predictive model was externally validated and the performance of the model was compared with that of the previously reported models. The postoperative eGFR value was associated with age, preoperative eGFR, preserved renal parenchymal volume (RPV), preserved RCV, % of RPV alteration, and % of RCV alteration (p < 0.01). The significant correlated variables for %eGFR alteration were %RCV preservation (r = 0.58, p < 0.01) and %RPV preservation (r = 0.54, p < 0.01). We developed our regression model as follows: postoperative eGFR = 57.87 - 0.55(age) - 15.01(body surface area) + 0.30(preoperative eGFR) + 52.92(%RCV preservation). Strong correlation was seen between postoperative eGFR and the calculated estimation model (r = 0.83; p < 0.001). The external validation cohort (n = 21) showed our model outperformed previously reported models. Combining MDCT renal volumetry and clinical indices might yield an important tool for predicting postoperative renal function.

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

Azadi, Sam, E-mail: s.azadi@ucl.ac.uk; Cohen, R. E.

We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimalmore » VMC and DMC binding energies of −2.3(4) and −2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is −2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.« less

Alternative separation of exchange and correlation energies in multi-configuration range-separated density-functional theory.

PubMed

Stoyanova, Alexandrina; Teale, Andrew M; Toulouse, Julien; Helgaker, Trygve; Fromager, Emmanuel

2013-10-07

The alternative separation of exchange and correlation energies proposed by Toulouse et al. [Theor. Chem. Acc. 114, 305 (2005)] is explored in the context of multi-configuration range-separated density-functional theory. The new decomposition of the short-range exchange-correlation energy relies on the auxiliary long-range interacting wavefunction rather than the Kohn-Sham (KS) determinant. The advantage, relative to the traditional KS decomposition, is that the wavefunction part of the energy is now computed with the regular (fully interacting) Hamiltonian. One potential drawback is that, because of double counting, the wavefunction used to compute the energy cannot be obtained by minimizing the energy expression with respect to the wavefunction parameters. The problem is overcome by using short-range optimized effective potentials (OEPs). The resulting combination of OEP techniques with wavefunction theory has been investigated in this work, at the Hartree-Fock (HF) and multi-configuration self-consistent-field (MCSCF) levels. In the HF case, an analytical expression for the energy gradient has been derived and implemented. Calculations have been performed within the short-range local density approximation on H2, N2, Li2, and H2O. Significant improvements in binding energies are obtained with the new decomposition of the short-range energy. The importance of optimizing the short-range OEP at the MCSCF level when static correlation becomes significant has also been demonstrated for H2, using a finite-difference gradient. The implementation of the analytical gradient for MCSCF wavefunctions is currently in progress.

Automated Semantic Indices Related to Cognitive Function and Rate of Cognitive Decline

ERIC Educational Resources Information Center

Pakhomov, Serguei V. S.; Hemmy, Laura S.; Lim, Kelvin O.

2012-01-01

The objective of our study is to introduce a fully automated, computational linguistic technique to quantify semantic relations between words generated on a standard semantic verbal fluency test and to determine its cognitive and clinical correlates. Cognitive differences between patients with Alzheimer's disease and mild cognitive impairment are…

The order of three lowest-energy states of the six-electron harmonium at small force constant

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

Strasburger, Krzysztof

2016-06-21

The order of low-energy states of six-electron harmonium is uncertain in the case of strong correlation, which is not a desired situation for the model system being considered for future testing of approximate methods of quantum chemistry. The computational study of these states has been carried out at the frequency parameter ω = 0.01, using the variational method with the basis of symmetry-projected, explicitly correlated Gaussian (ECG) lobe functions. It has revealed that the six-electron harmonium at this confinement strength is an octahedral Wigner molecule, whose order of states is different than in the strong confinement regime and does notmore » agree with the earlier predictions. The results obtained for ω = 0.5 and 10 are consistent with the findings based on the Hund’s rules for the s{sup 2}p{sup 4} electron configuration. Substantial part of the computations has been carried out on the graphical processing units and the efficiency of these devices in calculation of the integrals over ECG functions has been compared with traditional processors.« less

Deterministic alternatives to the full configuration interaction quantum Monte Carlo method for strongly correlated systems

NASA Astrophysics Data System (ADS)

Tubman, Norm; Whaley, Birgitta

The development of exponential scaling methods has seen great progress in tackling larger systems than previously thought possible. One such technique, full configuration interaction quantum Monte Carlo, allows exact diagonalization through stochastically sampling of determinants. The method derives its utility from the information in the matrix elements of the Hamiltonian, together with a stochastic projected wave function, which are used to explore the important parts of Hilbert space. However, a stochastic representation of the wave function is not required to search Hilbert space efficiently and new deterministic approaches have recently been shown to efficiently find the important parts of determinant space. We shall discuss the technique of Adaptive Sampling Configuration Interaction (ASCI) and the related heat-bath Configuration Interaction approach for ground state and excited state simulations. We will present several applications for strongly correlated Hamiltonians. This work was supported through the Scientific Discovery through Advanced Computing (SciDAC) program funded by the U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research and Basic Energy Sciences.

Embedded correlated wavefunction schemes: theory and applications.

PubMed

Libisch, Florian; Huang, Chen; Carter, Emily A

2014-09-16

Conspectus Ab initio modeling of matter has become a pillar of chemical research: with ever-increasing computational power, simulations can be used to accurately predict, for example, chemical reaction rates, electronic and mechanical properties of materials, and dynamical properties of liquids. Many competing quantum mechanical methods have been developed over the years that vary in computational cost, accuracy, and scalability: density functional theory (DFT), the workhorse of solid-state electronic structure calculations, features a good compromise between accuracy and speed. However, approximate exchange-correlation functionals limit DFT's ability to treat certain phenomena or states of matter, such as charge-transfer processes or strongly correlated materials. Furthermore, conventional DFT is purely a ground-state theory: electronic excitations are beyond its scope. Excitations in molecules are routinely calculated using time-dependent DFT linear response; however applications to condensed matter are still limited. By contrast, many-electron wavefunction methods aim for a very accurate treatment of electronic exchange and correlation. Unfortunately, the associated computational cost renders treatment of more than a handful of heavy atoms challenging. On the other side of the accuracy spectrum, parametrized approaches like tight-binding can treat millions of atoms. In view of the different (dis-)advantages of each method, the simulation of complex systems seems to force a compromise: one is limited to the most accurate method that can still handle the problem size. For many interesting problems, however, compromise proves insufficient. A possible solution is to break up the system into manageable subsystems that may be treated by different computational methods. The interaction between subsystems may be handled by an embedding formalism. In this Account, we review embedded correlated wavefunction (CW) approaches and some applications. We first discuss our density functional embedding theory, which is formally exact. We show how to determine the embedding potential, which replaces the interaction between subsystems, at the DFT level. CW calculations are performed using a fixed embedding potential, that is, a non-self-consistent embedding scheme. We demonstrate this embedding theory for two challenging electron transfer phenomena: (1) initial oxidation of an aluminum surface and (2) hot-electron-mediated dissociation of hydrogen molecules on a gold surface. In both cases, the interaction between gas molecules and metal surfaces were treated by sophisticated CW techniques, with the remainder of the extended metal surface being treated by DFT. Our embedding approach overcomes the limitations of conventional Kohn-Sham DFT in describing charge transfer, multiconfigurational character, and excited states. From these embedding simulations, we gained important insights into fundamental processes that are crucial aspects of fuel cell catalysis (i.e., O2 reduction at metal surfaces) and plasmon-mediated photocatalysis by metal nanoparticles. Moreover, our findings agree very well with experimental observations, while offering new views into the chemistry. We finally discuss our recently formulated potential-functional embedding theory that provides a seamless, first-principles way to include back-action onto the environment from the embedded region.

Translation, Validation, and Reliability of the Dutch Late-Life Function and Disability Instrument Computer Adaptive Test.

PubMed

Arensman, Remco M; Pisters, Martijn F; de Man-van Ginkel, Janneke M; Schuurmans, Marieke J; Jette, Alan M; de Bie, Rob A

2016-09-01

Adequate and user-friendly instruments for assessing physical function and disability in older adults are vital for estimating and predicting health care needs in clinical practice. The Late-Life Function and Disability Instrument Computer Adaptive Test (LLFDI-CAT) is a promising instrument for assessing physical function and disability in gerontology research and clinical practice. The aims of this study were: (1) to translate the LLFDI-CAT to the Dutch language and (2) to investigate its validity and reliability in a sample of older adults who spoke Dutch and dwelled in the community. For the assessment of validity of the LLFDI-CAT, a cross-sectional design was used. To assess reliability, measurement of the LLFDI-CAT was repeated in the same sample. The item bank of the LLFDI-CAT was translated with a forward-backward procedure. A sample of 54 older adults completed the LLFDI-CAT, World Health Organization Disability Assessment Schedule 2.0, RAND 36-Item Short-Form Health Survey physical functioning scale (10 items), and 10-Meter Walk Test. The LLFDI-CAT was repeated in 2 to 8 days (mean=4.5 days). Pearson's r and the intraclass correlation coefficient (ICC) (2,1) were calculated to assess validity, group-level reliability, and participant-level reliability. A correlation of .74 for the LLFDI-CAT function scale and the RAND 36-Item Short-Form Health Survey physical functioning scale (10 items) was found. The correlations of the LLFDI-CAT disability scale with the World Health Organization Disability Assessment Schedule 2.0 and the 10-Meter Walk Test were -.57 and -.53, respectively. The ICC (2,1) of the LLFDI-CAT function scale was .84, with a group-level reliability score of .85. The ICC (2,1) of the LLFDI-CAT disability scale was .76, with a group-level reliability score of .81. The high percentage of women in the study and the exclusion of older adults with recent joint replacement or hospitalization limit the generalizability of the results. The Dutch LLFDI-CAT showed strong validity and high reliability when used to assess physical function and disability in older adults dwelling in the community. © 2016 American Physical Therapy Association.

Evaluation of cluster expansions and correlated one-body properties of nuclei

NASA Astrophysics Data System (ADS)

Moustakidis, Ch. C.; Massen, S. E.; Panos, C. P.; Grypeos, M. E.; Antonov, A. N.

2001-07-01

Three different cluster expansions for the evaluation of correlated one-body properties of s-p and s-d shell nuclei are compared. Harmonic oscillator wave functions and Jastrow-type correlations are used, while analytical expressions are obtained for the charge form factor, density distribution, and momentum distribution by truncating the expansions and using a standard Jastrow correlation function f. The harmonic oscillator parameter b and the correlation parameter β have been determined by a least-squares fit to the experimental charge form factors in each case. The information entropy of nuclei in position space (Sr) and momentum space (Sk) according to the three methods are also calculated. It is found that the larger the entropy sum, S=Sr+Sk (the net information content of the system), the smaller the values of χ2. This indicates that maximal S is a criterion of the quality of a given nuclear model, according to the maximum entropy principle. Only two exceptions to this rule, out of many cases examined, were found. Finally an analytic expression for the so-called ``healing'' or ``wound'' integrals is derived with the function f considered, for any state of the relative two-nucleon motion, and their values in certain cases are computed and compared.

Methods for converging correlation energies within the dielectric matrix formalism

NASA Astrophysics Data System (ADS)

Dixit, Anant; Claudot, Julien; Gould, Tim; Lebègue, Sébastien; Rocca, Dario

2018-03-01

Within the dielectric matrix formalism, the random-phase approximation (RPA) and analogous methods that include exchange effects are promising approaches to overcome some of the limitations of traditional density functional theory approximations. The RPA-type methods however have a significantly higher computational cost, and, similarly to correlated quantum-chemical methods, are characterized by a slow basis set convergence. In this work we analyzed two different schemes to converge the correlation energy, one based on a more traditional complete basis set extrapolation and one that converges energy differences by accounting for the size-consistency property. These two approaches have been systematically tested on the A24 test set, for six points on the potential-energy surface of the methane-formaldehyde complex, and for reaction energies involving the breaking and formation of covalent bonds. While both methods converge to similar results at similar rates, the computation of size-consistent energy differences has the advantage of not relying on the choice of a specific extrapolation model.

Unbiased estimators for spatial distribution functions of classical fluids

NASA Astrophysics Data System (ADS)

Adib, Artur B.; Jarzynski, Christopher

2005-01-01

We use a statistical-mechanical identity closely related to the familiar virial theorem, to derive unbiased estimators for spatial distribution functions of classical fluids. In particular, we obtain estimators for both the fluid density ρ(r) in the vicinity of a fixed solute and the pair correlation g(r) of a homogeneous classical fluid. We illustrate the utility of our estimators with numerical examples, which reveal advantages over traditional histogram-based methods of computing such distributions.

PROMIS Physical Function Computer Adaptive Test Compared With Other Upper Extremity Outcome Measures in the Evaluation of Proximal Humerus Fractures in Patients Older Than 60 Years.

PubMed

Morgan, Jordan H; Kallen, Michael A; Okike, Kanu; Lee, Olivia C; Vrahas, Mark S

2015-06-01

To compare the PROMIS Physical Function Computer Adaptive Test (PROMIS PF CAT) to commonly used traditional PF measures for the evaluation of patients with proximal humerus fractures. Prospective. Two Level I trauma centers. Forty-seven patients older than 60 years with displaced proximal humerus fractures treated between 2006 and 2009. Evaluation included completion of the PROMIS PF CAT, the Constant Shoulder Score, the Disabilities of the Arm, Shoulder, and Hand (DASH) and the Short Musculoskeletal Functional Assessment (SMFA). Observed correlations among the administered PF outcome measures. On average, patients responded to 86 outcome-related items for this study: 4 for the PROMIS PF CAT (range: 4-8 items), 6 for the Constant Shoulder Score, 30 for the DASH, and 46 for the SMFA. Time to complete the PROMIS PF CAT (median completion time = 98 seconds) was significantly less than that for the DASH (median completion time = 336 seconds, P < 0.001) and for the SMFA (median completion time = 482 seconds, P < 0.001). PROMIS PF CAT scores correlated statistically significantly and were of moderate-to-high magnitude with all other PF outcome measure scores administered. This study suggests using the PROMIS PF CAT as a sole PF outcome measure can yield an assessment of upper extremity function similar to those provided by traditional PF measures, while substantially reducing patient assessment time.

Computed Tomography Findings of Bronchiectasis in Different Respiratory Phases Correlate with Pulmonary Function Test Data in Adults.

PubMed

do Amaral, Ricardo Holderbaum; Nin, Carlos S; de Souza, Vinicius V S; Alves, Giordano R T; Marchiori, Edson; Irion, Klaus; Meirelles, Gustavo S P; Hochhegger, Bruno

2017-06-01

To investigate bronchiectasis variations in different computed tomography (CT) respiratory phases, and their correlation with pulmonary function test (PFT) data, in adults. Retrospective data analysis from 63 patients with bronchiectasis according to CT criteria selected from the institution database and for whom PFT data were also available. Bronchiectasis diameter was measured on inspiratory and expiratory phases. Its area and matched airway-vessel ratios in both phases were also calculated. Finally, PFT results were compared with radiological measurements. Bronchiectatic airways were larger on inspiration than on expiration (mean cross-sectional area, 69.44 vs. 40.84 mm 2 ; p < 0.05) as were airway-vessel ratios (2.1 vs. 1.4; p < 0.05). Cystic bronchiectasis cases showed the least variation in cross-sectional area (48%). Mean predicted values of forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC) were 81.5 and 77.2%, respectively, in the group in which bronchiectasis could not be identified on expiratory images, and 58.3 and 56.0%, respectively, in the other group (p < 0.05). Variation in bronchiectasis area was associated with poorer lung function (r = 0.32). Bronchiectasis detection, diameter, and area varied significantly according to CT respiratory phase, with non-reducible bronchiectasis showing greater lung function impairment.

Collisional redistribution of radiation. II - The effects of degeneracy on the equations of motion for the density matrix. III - The equation of motion for the correlation function and the scattered spectrum

NASA Technical Reports Server (NTRS)

Burnett, K.; Cooper, J.

1980-01-01

The effect of correlations between an absorber atom and perturbers in the binary-collision approximation are applied to degenerate atomic systems. A generalized absorption profile which specifies the final state of the atom after an absorption event is related to the total intensities of Rayleigh scattering and fluorescence from the atom. It is suggested that additional dynamical information to that obtainable from ordinary absorption experiments is required in order to describe redistributed atomic radiation. The scattering of monochromatic radiation by a degenerate atom is computed in a binary-collision approximation; an equation of motion is derived for the correlation function which is valid outside the quantum-regression regime. Solutions are given for the weak-field conditions in terms of generalized absorption and emission profiles that depend on the indices of the atomic multipoles.

Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets.

PubMed

Xu, Weijun; Lucke, Andrew J; Fairlie, David P

2015-04-01

Accurately predicting relative binding affinities and biological potencies for ligands that interact with proteins remains a significant challenge for computational chemists. Most evaluations of docking and scoring algorithms have focused on enhancing ligand affinity for a protein by optimizing docking poses and enrichment factors during virtual screening. However, there is still relatively limited information on the accuracy of commercially available docking and scoring software programs for correctly predicting binding affinities and biological activities of structurally related inhibitors of different enzyme classes. Presented here is a comparative evaluation of eight molecular docking programs (Autodock Vina, Fitted, FlexX, Fred, Glide, GOLD, LibDock, MolDock) using sixteen docking and scoring functions to predict the rank-order activity of different ligand series for six pharmacologically important protein and enzyme targets (Factor Xa, Cdk2 kinase, Aurora A kinase, COX-2, pla2g2a, β Estrogen receptor). Use of Fitted gave an excellent correlation (Pearson 0.86, Spearman 0.91) between predicted and experimental binding only for Cdk2 kinase inhibitors. FlexX and GOLDScore produced good correlations (Pearson>0.6) for hydrophilic targets such as Factor Xa, Cdk2 kinase and Aurora A kinase. By contrast, pla2g2a and COX-2 emerged as difficult targets for scoring functions to predict ligand activities. Although possessing a high hydrophobicity in its binding site, β Estrogen receptor produced reasonable correlations using LibDock (Pearson 0.75, Spearman 0.68). These findings can assist medicinal chemists to better match scoring functions with ligand-target systems for hit-to-lead optimization using computer-aided drug design approaches. Copyright © 2015 Elsevier Inc. All rights reserved.

Informatic parcellation of the network involved in the computation of subjective value

PubMed Central

Rangel, Antonio

2014-01-01

Understanding how the brain computes value is a basic question in neuroscience. Although individual studies have driven this progress, meta-analyses provide an opportunity to test hypotheses that require large collections of data. We carry out a meta-analysis of a large set of functional magnetic resonance imaging studies of value computation to address several key questions. First, what is the full set of brain areas that reliably correlate with stimulus values when they need to be computed? Second, is this set of areas organized into dissociable functional networks? Third, is a distinct network of regions involved in the computation of stimulus values at decision and outcome? Finally, are different brain areas involved in the computation of stimulus values for different reward modalities? Our results demonstrate the centrality of ventromedial prefrontal cortex (VMPFC), ventral striatum and posterior cingulate cortex (PCC) in the computation of value across tasks, reward modalities and stages of the decision-making process. We also find evidence of distinct subnetworks of co-activation within VMPFC, one involving central VMPFC and dorsal PCC and another involving more anterior VMPFC, left angular gyrus and ventral PCC. Finally, we identify a posterior-to-anterior gradient of value representations corresponding to concrete-to-abstract rewards. PMID:23887811

Functional brain networks associated with eating behaviors in obesity.

PubMed

Park, Bo-Yong; Seo, Jongbum; Park, Hyunjin

2016-03-31

Obesity causes critical health problems including diabetes and hypertension that affect billions of people worldwide. Obesity and eating behaviors are believed to be closely linked but their relationship through brain networks has not been fully explored. We identified functional brain networks associated with obesity and examined how the networks were related to eating behaviors. Resting state functional magnetic resonance imaging (MRI) scans were obtained for 82 participants. Data were from an equal number of people of healthy weight (HW) and non-healthy weight (non-HW). Connectivity matrices were computed with spatial maps derived using a group independent component analysis approach. Brain networks and associated connectivity parameters with significant group-wise differences were identified and correlated with scores on a three-factor eating questionnaire (TFEQ) describing restraint, disinhibition, and hunger eating behaviors. Frontoparietal and cerebellum networks showed group-wise differences between HW and non-HW groups. Frontoparietal network showed a high correlation with TFEQ disinhibition scores. Both frontoparietal and cerebellum networks showed a high correlation with body mass index (BMI) scores. Brain networks with significant group-wise differences between HW and non-HW groups were identified. Parts of the identified networks showed a high correlation with eating behavior scores.

Functional magnetic resonance imaging phase synchronization as a measure of dynamic functional connectivity.

PubMed

Glerean, Enrico; Salmi, Juha; Lahnakoski, Juha M; Jääskeläinen, Iiro P; Sams, Mikko

2012-01-01

Functional brain activity and connectivity have been studied by calculating intersubject and seed-based correlations of hemodynamic data acquired with functional magnetic resonance imaging (fMRI). To inspect temporal dynamics, these correlation measures have been calculated over sliding time windows with necessary restrictions on the length of the temporal window that compromises the temporal resolution. Here, we show that it is possible to increase temporal resolution by using instantaneous phase synchronization (PS) as a measure of dynamic (time-varying) functional connectivity. We applied PS on an fMRI dataset obtained while 12 healthy volunteers watched a feature film. Narrow frequency band (0.04-0.07 Hz) was used in the PS analysis to avoid artifactual results. We defined three metrics for computing time-varying functional connectivity and time-varying intersubject reliability based on estimation of instantaneous PS across the subjects: (1) seed-based PS, (2) intersubject PS, and (3) intersubject seed-based PS. Our findings show that these PS-based metrics yield results consistent with both seed-based correlation and intersubject correlation methods when inspected over the whole time series, but provide an important advantage of maximal single-TR temporal resolution. These metrics can be applied both in studies with complex naturalistic stimuli (e.g., watching a movie or listening to music in the MRI scanner) and more controlled (e.g., event-related or blocked design) paradigms. A MATLAB toolbox FUNPSY ( http://becs.aalto.fi/bml/software.html ) is openly available for using these metrics in fMRI data analysis.

High-Degree Neurons Feed Cortical Computations

PubMed Central

Timme, Nicholas M.; Ito, Shinya; Shimono, Masanori; Yeh, Fang-Chin; Litke, Alan M.; Beggs, John M.

2016-01-01

Recent work has shown that functional connectivity among cortical neurons is highly varied, with a small percentage of neurons having many more connections than others. Also, recent theoretical developments now make it possible to quantify how neurons modify information from the connections they receive. Therefore, it is now possible to investigate how information modification, or computation, depends on the number of connections a neuron receives (in-degree) or sends out (out-degree). To do this, we recorded the simultaneous spiking activity of hundreds of neurons in cortico-hippocampal slice cultures using a high-density 512-electrode array. This preparation and recording method combination produced large numbers of neurons recorded at temporal and spatial resolutions that are not currently available in any in vivo recording system. We utilized transfer entropy (a well-established method for detecting linear and nonlinear interactions in time series) and the partial information decomposition (a powerful, recently developed tool for dissecting multivariate information processing into distinct parts) to quantify computation between neurons where information flows converged. We found that computations did not occur equally in all neurons throughout the networks. Surprisingly, neurons that computed large amounts of information tended to receive connections from high out-degree neurons. However, the in-degree of a neuron was not related to the amount of information it computed. To gain insight into these findings, we developed a simple feedforward network model. We found that a degree-modified Hebbian wiring rule best reproduced the pattern of computation and degree correlation results seen in the real data. Interestingly, this rule also maximized signal propagation in the presence of network-wide correlations, suggesting a mechanism by which cortex could deal with common random background input. These are the first results to show that the extent to which a neuron modifies incoming information streams depends on its topological location in the surrounding functional network. PMID:27159884

C-Speak Aphasia Alternative Communication Program for People with Severe Aphasia: Importance of Executive Functioning and Semantic Knowledge

PubMed Central

Nicholas, Marjorie; Sinotte, Michele P.; Helm-Estabrooks, Nancy

2011-01-01

Learning how to use a computer-based communication system can be challenging for people with severe aphasia even if the system is not word-based. This study explored cognitive and linguistic factors relative to how they affected individual patients’ ability to communicate expressively using C-Speak Aphasia, (CSA), an alternative communication computer program that is primarily picture-based. Ten individuals with severe non-fluent aphasia received at least six months of training with CSA. To assess carryover of training, untrained functional communication tasks (i.e., answering autobiographical questions, describing pictures, making telephone calls, describing a short video, and two writing tasks) were repeatedly probed in two conditions: 1) using CSA in addition to natural forms of communication, and 2) using only natural forms of communication, e.g., speaking, writing, gesturing, drawing. Four of the ten participants communicated more information on selected probe tasks using CSA than they did without the computer. Response to treatment also was examined in relation to baseline measures of non-linguistic executive function skills, pictorial semantic abilities, and auditory comprehension. Only nonlinguistic executive function skills were significantly correlated with treatment response. PMID:21506045

Strategy Plan A Methodology to Predict the Uniformity of Double-Shell Tank Waste Slurries Based on Mixing Pump Operation

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

J.A. Bamberger; L.M. Liljegren; P.S. Lowery

This document presents an analysis of the mechanisms influencing mixing within double-shell slurry tanks. A research program to characterize mixing of slurries within tanks has been proposed. The research program presents a combined experimental and computational approach to produce correlations describing the tank slurry concentration profile (and therefore uniformity) as a function of mixer pump operating conditions. The TEMPEST computer code was used to simulate both a full-scale (prototype) and scaled (model) double-shell waste tank to predict flow patterns resulting from a stationary jet centered in the tank. The simulation results were used to evaluate flow patterns in the tankmore » and to determine whether flow patterns are similar between the full-scale prototype and an existing 1/12-scale model tank. The flow patterns were sufficiently similar to recommend conducting scoping experiments at 1/12-scale. Also, TEMPEST modeled velocity profiles of the near-floor jet were compared to experimental measurements of the near-floor jet with good agreement. Reported values of physical properties of double-shell tank slurries were analyzed to evaluate the range of properties appropriate for conducting scaled experiments. One-twelfth scale scoping experiments are recommended to confirm the prioritization of the dimensionless groups (gravitational settling, Froude, and Reynolds numbers) that affect slurry suspension in the tank. Two of the proposed 1/12-scale test conditions were modeled using the TEMPEST computer code to observe the anticipated flow fields. This information will be used to guide selection of sampling probe locations. Additional computer modeling is being conducted to model a particulate laden, rotating jet centered in the tank. The results of this modeling effort will be compared to the scaled experimental data to quantify the agreement between the code and the 1/12-scale experiment. The scoping experiment results will guide selection of parameters to be varied in the follow-on experiments. Data from the follow-on experiments will be used to develop correlations to describe slurry concentration profile as a function of mixing pump operating conditions. This data will also be used to further evaluate the computer model applications. If the agreement between the experimental data and the code predictions is good, the computer code will be recommended for use to predict slurry uniformity in the tanks under various operating conditions. If the agreement between the code predictions and experimental results is not good, the experimental data correlations will be used to predict slurry uniformity in the tanks within the range of correlation applicability.« less

Water adsorption on a copper formate paddlewheel model of CuBTC: A comparative MP2 and DFT study

NASA Astrophysics Data System (ADS)

Toda, Jordi; Fischer, Michael; Jorge, Miguel; Gomes, José R. B.

2013-11-01

Simultaneous adsorption of two water molecules on open metal sites of the HKUST-1 metal-organic framework (MOF), modeled with a Cu2(HCOO)4 cluster, was studied by means of density functional theory (DFT) and second-order Moller-Plesset (MP2) approaches together with correlation consistent basis sets. Experimental geometries and MP2 energetic data extrapolated to the complete basis set limit were used as benchmarks for testing the accuracy of several different exchange-correlation functionals in the correct description of the water-MOF interaction. M06-L and some LC-DFT methods arise as the most appropriate in terms of the quality of geometrical data, energetic data and computational resources needed.

Correlation between standardized assessment of concussion scores and small-world brain network in mild traumatic brain injury.

PubMed

Yan, Yan; Song, Jian; Xu, Guozheng; Yao, Shun; Cao, Chenglong; Li, Chang; Peng, Guibao; Du, Hao

2017-10-01

This study investigated the characteristics of the small-world brain network architecture of patients with mild traumatic brain injury (MTBI), and a correlation between brain functional connectivity network properties in the resting-state fMRI and Standardized Assessment of Concussion (SAC) parameters. The neurological conditions of 22 MTBI patients and 17 normal control individuals were evaluated according to the SAC. Resting-state fMRI was performed in all subjects 3 and 7days after injury respectively. After preprocessing the fMRI data, cortex functional regions were marked using AAL90 and Dosenbach160 templates. The small-world network parameters and areas under the integral curves were computed in the range of sparsity from 0.01 to 0.5. Independent-sample t-tests were used to compare these parameters between the MTBI and control group. Significantly different parameters were investigated for correlations with SAC scores; those that correlated were chosen for further curve fitting. The clustering coefficient, the communication efficiency across in local networks, and the strength of connectivity were all higher in MTBI patients relative to control individuals. Parameters in 160 brain regions of the MTBI group significantly correlated with total SAC score and score for attention; the network parameters may be a quadratic function of attention scores of SAC and a cubic function of SAC scores. MTBI patients were characterized by elevated communication efficiency across global brain regions, and in local networks, and strength of mean connectivity. These features may be associated with brain function compensation. The network parameters significantly correlated with SAC total and attention scores. Copyright © 2017 Elsevier Ltd. All rights reserved.

What are the ideal properties for functional food peptides with antihypertensive effect? A computational peptidology approach.

PubMed

Zhou, Peng; Yang, Chao; Ren, Yanrong; Wang, Congcong; Tian, Feifei

2013-12-01

Peptides with antihypertensive potency have long been attractive to the medical and food communities. However, serving as food additives, rather than therapeutic agents, peptides should have a good taste. In the present study, we explore the intrinsic relationship between the angiotensin I-converting enzyme (ACE) inhibition and bitterness of short peptides in the framework of computational peptidology, attempting to find out the appropriate properties for functional food peptides with satisfactory bioactivities. As might be expected, quantitative structure-activity relationship modeling reveals a significant positive correlation between the ACE inhibition and bitterness of dipeptides, but this correlation is quite modest for tripeptides and, particularly, tetrapeptides. Moreover, quantum mechanics/molecular mechanics analysis of the structural basis and energetic profile involved in ACE-peptide complexes unravels that peptides of up to 4 amino acids long are sufficient to have efficient binding to ACE, and more additional residues do not bring with substantial enhance in their ACE-binding affinity and, thus, antihypertensive capability. All of above, it is coming together to suggest that the tripeptides and tetrapeptides could be considered as ideal candidates for seeking potential functional food additives with both high antihypertensive activity and low bitterness. Copyright © 2013 Elsevier Ltd. All rights reserved.

Linked-cluster formulation of electron-hole interaction kernel in real-space representation without using unoccupied states.

PubMed

Bayne, Michael G; Scher, Jeremy A; Ellis, Benjamin H; Chakraborty, Arindam

2018-05-21

Electron-hole or quasiparticle representation plays a central role in describing electronic excitations in many-electron systems. For charge-neutral excitation, the electron-hole interaction kernel is the quantity of interest for calculating important excitation properties such as optical gap, optical spectra, electron-hole recombination and electron-hole binding energies. The electron-hole interaction kernel can be formally derived from the density-density correlation function using both Green's function and TDDFT formalism. The accurate determination of the electron-hole interaction kernel remains a significant challenge for precise calculations of optical properties in the GW+BSE formalism. From the TDDFT perspective, the electron-hole interaction kernel has been viewed as a path to systematic development of frequency-dependent exchange-correlation functionals. Traditional approaches, such as MBPT formalism, use unoccupied states (which are defined with respect to Fermi vacuum) to construct the electron-hole interaction kernel. However, the inclusion of unoccupied states has long been recognized as the leading computational bottleneck that limits the application of this approach for larger finite systems. In this work, an alternative derivation that avoids using unoccupied states to construct the electron-hole interaction kernel is presented. The central idea of this approach is to use explicitly correlated geminal functions for treating electron-electron correlation for both ground and excited state wave functions. Using this ansatz, it is derived using both diagrammatic and algebraic techniques that the electron-hole interaction kernel can be expressed only in terms of linked closed-loop diagrams. It is proved that the cancellation of unlinked diagrams is a consequence of linked-cluster theorem in real-space representation. The electron-hole interaction kernel derived in this work was used to calculate excitation energies in many-electron systems and results were found to be in good agreement with the EOM-CCSD and GW+BSE methods. The numerical results highlight the effectiveness of the developed method for overcoming the computational barrier of accurately determining the electron-hole interaction kernel to applications of large finite systems such as quantum dots and nanorods.

Bulk viscosity of the Lennard-Jones fluid for a wide range of states computed by equilibrium molecular dynamics

NASA Astrophysics Data System (ADS)

Hoheisel, C.; Vogelsang, R.; Schoen, M.

1987-12-01

Accurate data for the bulk viscosity ηv have been obtained by molecular dynamics calculations. Many thermodynamic states of the Lennard-Jones fluid were considered. The Green-Kubo integrand of ηv is analyzed in terms of partial correlation functions constituting the total one. These partial functions behave rather differently from those found for the shear viscosity or the thermal conductivity. Generally the total autocorrelation function of ηv shows a steeper initial decay and a more pronounced long time form than those of the shear viscosity or the thermal conductivity. For states near transition to solid phases, like the pseudotriple point of argon, the Green-Kubo integrand of ηv has a significantly longer ranged time behavior than that of the shear viscosity. Hence, for the latter states, a systematic error is expected for ηv using equilibrium molecular dynamics for its computation.

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

PubMed Central

2017-01-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac–Coulomb and Dirac–Coulomb–Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved. PMID:28595411

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

NASA Astrophysics Data System (ADS)

Jäger, Benjamin; Bich, Eckard

2017-06-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

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

Oberkampf, William Louis; Tucker, W. Troy; Zhang, Jianzhong

This report summarizes methods to incorporate information (or lack of information) about inter-variable dependence into risk assessments that use Dempster-Shafer theory or probability bounds analysis to address epistemic and aleatory uncertainty. The report reviews techniques for simulating correlated variates for a given correlation measure and dependence model, computation of bounds on distribution functions under a specified dependence model, formulation of parametric and empirical dependence models, and bounding approaches that can be used when information about the intervariable dependence is incomplete. The report also reviews several of the most pervasive and dangerous myths among risk analysts about dependence in probabilistic models.

Surface temperature statistics over Los Angeles - The influence of land use

NASA Technical Reports Server (NTRS)

Dousset, Benedicte

1991-01-01

Surface temperature statistics from 84 NOAA AVHRR (Advanced Very High Resolution Radiometer) satellite images of the Los Angeles basin are interpreted as functions of the corresponding urban land-cover classified from a multispectral SPOT image. Urban heat islands observed in the temperature statistics correlate well with the distribution of industrial and fully built areas. Small cool islands coincide with highly watered parks and golf courses. There is a significant negative correlation between the afternoon surface temperature and a vegetation index computed from the SPOT image.

Caprylate Salts Based on Amines as Volatile Corrosion Inhibitors for Metallic Zinc: Theoretical and Experimental Studies.

PubMed

Valente, Marco A G; Teixeira, Deiver A; Azevedo, David L; Feliciano, Gustavo T; Benedetti, Assis V; Fugivara, Cecílio S

2017-01-01

The interaction of volatile corrosion inhibitors (VCI), caprylate salt derivatives from amines, with zinc metallic surfaces is assessed by density functional theory (DFT) computer simulations, electrochemical impedance (EIS) measurements and humid chamber tests. The results obtained by the different methods were compared, and linear correlations were obtained between theoretical and experimental data. The correlations between experimental and theoretical results showed that the molecular size is the determining factor in the inhibition efficiency. The models used and experimental results indicated that dicyclohexylamine caprylate is the most efficient inhibitor.

Unitary subsector of generalized minimal models

NASA Astrophysics Data System (ADS)

Behan, Connor

2018-05-01

We revisit the line of nonunitary theories that interpolate between the Virasoro minimal models. Numerical bootstrap applications have brought about interest in the four-point function involving the scalar primary of lowest dimension. Using recent progress in harmonic analysis on the conformal group, we prove the conjecture that global conformal blocks in this correlator appear with positive coefficients. We also compute many such coefficients in the simplest mixed correlator system. Finally, we comment on the status of using global conformal blocks to isolate the truly unitary points on this line.

Performance of wind turbines in a turbulent atmosphere

NASA Technical Reports Server (NTRS)

Sundar, R. M.; Sullivan, J. P.

1981-01-01

The effect of atmospheric turbulence on the power fluctuations of large wind turbines was studied. The significance of spatial non-uniformities of the wind is emphasized. The turbulent wind with correlation in time and space is simulated on the computer by Shinozukas method. The wind turbulence is modelled according to the Davenport spectrum with an exponential spatial correlation function. The rotor aerodynamics is modelled by simple blade element theory. Comparison of the spectrum of power output signal between 1-D and 3-D turbulence, shows the significant power fluctuations centered around the blade passage frequency.

Orbital breathing effects in the computation of x-ray d -ion spectra in solids by ab initio wave-function-based methods

DOE PAGES

Bogdanov, Nikolay A.; Bisogni, Valentina; Kraus, Roberto; ...

2016-11-21

In existing theoretical approaches to core-level excitations of transition-metal ions in solids relaxation and polarization effects due to the inner core hole are often ignored or described phenomenologically. Here, we set up an ab initio computational scheme that explicitly accounts for such physics in the calculation of x-ray absorption and resonant inelastic x-ray scattering spectra. Good agreement is found with experimental transition-metal L-edge data for the strongly correlated d 9 cuprate Li 2CuO 2, for which we also determine the absolute scattering intensities. The newly developed methodology opens the way for the investigation of even more complex d n electronicmore » structures of group VI B to VIII B correlated oxide compounds.« less

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.

Nonperturbative finite-temperature Yang-Mills theory

NASA Astrophysics Data System (ADS)

Cyrol, Anton K.; Mitter, Mario; Pawlowski, Jan M.; Strodthoff, Nils

2018-03-01

We present nonperturbative correlation functions in Landau-gauge Yang-Mills theory at finite temperature. The results are obtained from the functional renormalisation group within a self-consistent approximation scheme. In particular, we compute the magnetic and electric components of the gluon propagator, and the three- and four-gluon vertices. We also show the ghost propagator and the ghost-gluon vertex at finite temperature. Our results for the propagators are confronted with lattice simulations and our Debye mass is compared to hard thermal loop perturbation theory.

Some semiclassical structure constants for AdS 4 × CP 3

NASA Astrophysics Data System (ADS)

Ahn, Changrim; Bozhilov, Plamen

2018-02-01

We compute structure constants in three-point functions of three string states in AdS 4× CP 3 in the framework of the semiclassical approach. We consider HHL correlation functions where two of the states are "heavy" string states of finite-size giant magnons carrying one or two angular momenta and the other one corresponds to such "light" states as dilaton operators with non-zero momentum, primary scalar operators, and singlet scalar operators with higher string levels.

Ab-initio study of electronic structure and elastic properties of ZrC

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

Mund, H. S., E-mail: hmoond@gmail.com; Ahuja, B. L.

2016-05-23

The electronic and elastic properties of ZrC have been investigated using the linear combination of atomic orbitals method within the framework of density functional theory. Different exchange-correlation functionals are taken into account within generalized gradient approximation. We have computed energy bands, density of states, elastic constants, bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio, lattice parameters and pressure derivative of the bulk modulus by calculating ground state energy of the rock salt structure type ZrC.

Tuning the redox potential of vitamin K3 derivatives by oxidative functionalization using a Ag(i)/GO catalyst.

PubMed

El-Hout, S I; Suzuki, H; El-Sheikh, S M; Hassan, H M A; Harraz, F A; Ibrahim, I A; El-Sharkawy, E A; Tsujimura, S; Holzinger, M; Nishina, Y

2017-08-03

We propose herein initial results to develop optimum redox mediators by the combination of computational simulation and catalytic functionalization of the core structure of vitamin K 3 . We aim to correlate the calculated energy value of the LUMO of different vitamin K 3 derivatives with their actual redox potential. For this, we optimized the catalytic alkylation of 1,4-naphthoquinones with a designed Ag(i)/GO catalyst and synthesized a series of molecules.

Nonseparable exchange–correlation functional for molecules, including homogeneous catalysis involving transition metals

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

Yu, Haoyu S.; Zhang, Wenjing; Verma, Pragya

2015-01-01

The goal of this work is to develop a gradient approximation to the exchange–correlation functional of Kohn–Sham density functional theory for treating molecular problems with a special emphasis on the prediction of quantities important for homogeneous catalysis and other molecular energetics. Our training and validation of exchange–correlation functionals is organized in terms of databases and subdatabases. The key properties required for homogeneous catalysis are main group bond energies (database MGBE137), transition metal bond energies (database TMBE32), reaction barrier heights (database BH76), and molecular structures (database MS10). We also consider 26 other databases, most of which are subdatabases of a newlymore » extended broad database called Database 2015, which is presented in the present article and in its ESI. Based on the mathematical form of a nonseparable gradient approximation (NGA), as first employed in the N12 functional, we design a new functional by using Database 2015 and by adding smoothness constraints to the optimization of the functional. The resulting functional is called the gradient approximation for molecules, or GAM. The GAM functional gives better results for MGBE137, TMBE32, and BH76 than any available generalized gradient approximation (GGA) or than N12. The GAM functional also gives reasonable results for MS10 with an MUE of 0.018 Å. The GAM functional provides good results both within the training sets and outside the training sets. The convergence tests and the smooth curves of exchange–correlation enhancement factor as a function of the reduced density gradient show that the GAM functional is a smooth functional that should not lead to extra expense or instability in optimizations. NGAs, like GGAs, have the advantage over meta-GGAs and hybrid GGAs of respectively smaller grid-size requirements for integrations and lower costs for extended systems. These computational advantages combined with the relatively high accuracy for all the key properties needed for molecular catalysis make the GAM functional very promising for future applications.« less

Correlation of ultra-low dose chest CT findings with physiologic measures of asbestosis.

PubMed

Manners, David; Wong, Patrick; Murray, Conor; Teh, Joelin; Kwok, Yi Jin; de Klerk, Nick; Alfonso, Helman; Franklin, Peter; Reid, Alison; Musk, A W Bill; Brims, Fraser J H

2017-08-01

The correlation between ultra low dose computed tomography (ULDCT)-detected parenchymal lung changes and pulmonary function abnormalities is not well described. This study aimed to determine the relationship between ULDCT-detected interstitial lung disease (ILD) and measures of pulmonary function in an asbestos-exposed population. Two thoracic radiologists independently categorised prone ULDCT scans from 143 participants for ILD appearances as absent (score 0), probable (1) or definite (2) without knowledge of asbestos exposure or lung function. Pulmonary function measures included spirometry and diffusing capacity to carbon monoxide (DLCO). Participants were 92% male with a median age of 73.0 years. CT dose index volume was between 0.6 and 1.8 mGy. Probable or definite ILD was reported in 63 (44.1%) participants. Inter-observer agreement was good (k = 0.613, p < 0.001). There was a statistically significant correlation between the ILD score and both forced expiratory volume in 1 second (FEV 1 ) and forced vital capacity (FVC) (r = -0.17, p = 0.04 and r = -0.20, p = 0.02). There was a strong correlation between ILD score and DLCO (r = -0.34, p < 0.0001). Changes consistent with ILD on ULDCT correlate well with corresponding reductions in gas transfer, similar to standard CT. In asbestos-exposed populations, ULDCT may be adequate to detect radiological changes consistent with asbestosis. • Interobserver agreement for the ILD score using prone ULDCT is good. • Prone ULDCT appearances of ILD correlate with changes in spirometric observations. • Prone ULDCT appearances of ILD correlate strongly with changes in gas transfer. • Prone ULDCT may provide sufficient radiological evidence to inform the diagnosis of asbestosis.

Computer-Aided Grading of Lymphangioleiomyomatosis (LAM) using HRCT

PubMed Central

Yao, Jianhua; Avila, Nilo; Dwyer, Andrew; Taveira-DaSilva, Angelo M.; Hathaway, Olanda M.; Moss, Joel

2010-01-01

Lymphangioleiomyomatosis (LAM) is a multisystem disorder associated with proliferation of smooth muscle-like cells, which leads to destruction of lung parenchyma. Subjective grading of LAM on HRCT is imprecise and can be arduous especially in cases with severe involvement. We propose a computer-aided evaluation system that grades LAM involvement based on analysis of lung texture patterns. A committee of support vector machines is employed for classification. The system was tested on 36 patients. The computer grade demonstrates good correlation with subjective radiologist grade (R=0.91, p<0.0001) and pulmonary functional tests (R=0.85, p<0.0001). The grade also provides precise progression assessment of disease over time. PMID:21625320

The computational neurobiology of learning and reward.

PubMed

Daw, Nathaniel D; Doya, Kenji

2006-04-01

Following the suggestion that midbrain dopaminergic neurons encode a signal, known as a 'reward prediction error', used by artificial intelligence algorithms for learning to choose advantageous actions, the study of the neural substrates for reward-based learning has been strongly influenced by computational theories. In recent work, such theories have been increasingly integrated into experimental design and analysis. Such hybrid approaches have offered detailed new insights into the function of a number of brain areas, especially the cortex and basal ganglia. In part this is because these approaches enable the study of neural correlates of subjective factors (such as a participant's beliefs about the reward to be received for performing some action) that the computational theories purport to quantify.

Dose-response relationships using brain–computer interface technology impact stroke rehabilitation

PubMed Central

Young, Brittany M.; Nigogosyan, Zack; Walton, Léo M.; Remsik, Alexander; Song, Jie; Nair, Veena A.; Tyler, Mitchell E.; Edwards, Dorothy F.; Caldera, Kristin; Sattin, Justin A.; Williams, Justin C.; Prabhakaran, Vivek

2015-01-01

Brain–computer interfaces (BCIs) are an emerging novel technology for stroke rehabilitation. Little is known about how dose-response relationships for BCI therapies affect brain and behavior changes. We report preliminary results on stroke patients (n = 16, 11 M) with persistent upper extremity motor impairment who received therapy using a BCI system with functional electrical stimulation of the hand and tongue stimulation. We collected MRI scans and behavioral data using the Action Research Arm Test (ARAT), 9-Hole Peg Test (9-HPT), and Stroke Impact Scale (SIS) before, during, and after the therapy period. Using anatomical and functional MRI, we computed Laterality Index (LI) for brain activity in the motor network during impaired hand finger tapping. Changes from baseline LI and behavioral scores were assessed for relationships with dose, intensity, and frequency of BCI therapy. We found that gains in SIS Strength were directly responsive to BCI therapy: therapy dose and intensity correlated positively with increased SIS Strength (p ≤ 0.05), although no direct relationships were identified with ARAT or 9-HPT scores. We found behavioral measures that were not directly sensitive to differences in BCI therapy administration but were associated with concurrent brain changes correlated with BCI therapy administration parameters: therapy dose and intensity showed significant (p ≤ 0.05) or trending (0.05 < p < 0.1) negative correlations with LI changes, while therapy frequency did not affect LI. Reductions in LI were then correlated (p ≤ 0.05) with increased SIS Activities of Daily Living scores and improved 9-HPT performance. Therefore, some behavioral changes may be reflected by brain changes sensitive to differences in BCI therapy administration, while others such as SIS Strength may be directly responsive to BCI therapy administration. Data preliminarily suggest that when using BCI in stroke rehabilitation, therapy frequency may be less important than dose and intensity. PMID:26157378

Development of tight-binding based GW algorithm and its computational implementation for graphene

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

Majidi, Muhammad Aziz; NUSNNI-NanoCore, Department of Physics, National University of Singapore; Singapore Synchrotron Light Source

Graphene has been a hot subject of research in the last decade as it holds a promise for various applications. One interesting issue is whether or not graphene should be classified into a strongly or weakly correlated system, as the optical properties may change upon several factors, such as the substrate, voltage bias, adatoms, etc. As the Coulomb repulsive interactions among electrons can generate the correlation effects that may modify the single-particle spectra (density of states) and the two-particle spectra (optical conductivity) of graphene, we aim to explore such interactions in this study. The understanding of such correlation effects ismore » important because eventually they play an important role in inducing the effective attractive interactions between electrons and holes that bind them into excitons. We do this study theoretically by developing a GW method implemented on the basis of the tight-binding (TB) model Hamiltonian. Unlike the well-known GW method developed within density functional theory (DFT) framework, our TB-based GW implementation may serve as an alternative technique suitable for systems which Hamiltonian is to be constructed through a tight-binding based or similar models. This study includes theoretical formulation of the Green’s function G, the renormalized interaction function W from random phase approximation (RPA), and the corresponding self energy derived from Feynman diagrams, as well as the development of the algorithm to compute those quantities. As an evaluation of the method, we perform calculations of the density of states and the optical conductivity of graphene, and analyze the results.« less

Reduced functional connectivity between V1 and inferior frontal cortex associated with visuomotor performance in autism

PubMed Central

Villalobos, Michele E.; Mizuno, Akiko; Dahl, Branelle C.; Kemmotsu, Nobuko; Müller, Ralph-Axel

2010-01-01

Some recent evidence has suggested abnormalities of the dorsal stream and possibly the mirror neuron system in autism, which may be responsible for impairments of joint attention, imitation, and secondarily for language delays. The current study investigates functional connectivity along the dorsal stream in autism, examining interregional blood oxygenation level dependent (BOLD) signal cross-correlation during visuomotor coordination. Eight high-functioning autistic men and 8 handedness and age-matched controls were included. Visually prompted button presses were performed with the preferred hand. For each subject, functional connectivity was computed in terms of BOLD signal correlation with the mean time series in bilateral visual area 17. Our hypothesis of reduced dorsal stream connectivity in autism was only in part confirmed. Functional connectivity with superior parietal areas was not significantly reduced. However, the autism group showed significantly reduced connectivity with bilateral inferior frontal area 44, which is compatible with the hypothesis of mirror neuron defects in autism. More generally, our findings suggest that dorsal stream connectivity in autism may not be fully functional. PMID:15808991

Reduced functional connectivity between V1 and inferior frontal cortex associated with visuomotor performance in autism.

PubMed

Villalobos, Michele E; Mizuno, Akiko; Dahl, Branelle C; Kemmotsu, Nobuko; Müller, Ralph-Axel

2005-04-15

Some recent evidence has suggested abnormalities of the dorsal stream and possibly the mirror neuron system in autism, which may be responsible for impairments of joint attention, imitation, and secondarily for language delays. The current study investigates functional connectivity along the dorsal stream in autism, examining interregional blood oxygenation level dependent (BOLD) signal cross-correlation during visuomotor coordination. Eight high-functioning autistic men and eight handedness and age-matched controls were included. Visually prompted button presses were performed with the preferred hand. For each subject, functional connectivity was computed in terms of BOLD signal correlation with the mean time series in bilateral visual area 17. Our hypothesis of reduced dorsal stream connectivity in autism was only in part confirmed. Functional connectivity with superior parietal areas was not significantly reduced. However, the autism group showed significantly reduced connectivity with bilateral inferior frontal area 44, which is compatible with the hypothesis of mirror neuron defects in autism. More generally, our findings suggest that dorsal stream connectivity in autism may not be fully functional.

Markers of Vascular Perturbation Correlate with Airway Structural Change in Asthma

PubMed Central

Kruger, Stanley J.; Schiebler, Mark L.; Evans, Michael D.; Sorkness, Ronald L.; Denlinger, Loren C.; Busse, William W.; Jarjour, Nizar N.; Montgomery, Robert R.; Mosher, Deane F.; Fain, Sean B.

2013-01-01

Rationale: Air trapping and ventilation defects on imaging are characteristics of asthma. Airway wall thickening occurs in asthma and is associated with increased bronchial vascularity and vascular permeability. Vascular endothelial cell products have not been explored as a surrogate to mark structural airway changes in asthma. Objectives: Determine whether reporters of vascular endothelial cell perturbation correlate with airway imaging metrics in patients with asthma of varying severity. Methods: Plasma from Severe Asthma Research Program subjects was analyzed by ELISAs for soluble von Willebrand factor mature protein (VWF:Ag) and propeptide (VWFpp), P-selectin, and platelet factor 4. Additional subjects were analyzed over 48 hours after whole-lung antigen challenge. We calculated ventilation defect volume by hyperpolarized helium-3 magnetic resonance imaging and areas of low signal density by multidetector computed tomography (less than −856 Hounsfield units [HU] at functional residual capacity and −950 HU at total lung capacity [TLC]). Measurements and Main Results: VWFpp and VWFpp/Ag ratio correlated with and predicted greater percentage defect volume on hyperpolarized helium-3 magnetic resonance imaging. P-selectin correlated with and predicted greater area of low density on chest multidetector computed tomography less than −950 HU at TLC. Platelet factor 4 did not correlate. Following whole-lung antigen challenge, variation in VWFpp, VWFpp/Ag, and P-selectin among time-points was less than that among subjects, indicating stability and repeatability of the measurements. Conclusions: Plasma VWFpp and P-selectin may be useful as surrogates of functional and structural defects that are evident on imaging. The results raise important questions about why VWFpp and P-selectin are associated specifically with different imaging abnormalities. PMID:23855693

FT-IR, FT-Raman, NMR spectra, density functional computations of the vibrational assignments (for monomer and dimer) and molecular geometry of anticancer drug 7-amino-2-methylchromone

NASA Astrophysics Data System (ADS)

Mariappan, G.; Sundaraganesan, N.

2014-04-01

Vibrational assignments for the 7-amino-2-methylchromone (abbreviated as 7A2MC) molecule using a combination of experimental vibrational spectroscopic measurements and ab initio computational methods are reported. The optimized geometry, intermolecular hydrogen bonding, first order hyperpolarizability and harmonic vibrational wavenumbers of 7A2MC have been investigated with the help of B3LYP density functional theory method. The calculated molecular geometry parameters, the theoretically computed vibrational frequencies for monomer and dimer and relative peak intensities were compared with experimental data. DFT calculations using the B3LYP method and 6-31 + G(d,p) basis set were found to yield results that are very comparable to experimental IR and Raman spectra. Detailed vibrational assignments were performed with DFT calculations and the potential energy distribution (PED) obtained from the Vibrational Energy Distribution Analysis (VEDA) program. Natural Bond Orbital (NBO) study revealed the characteristics of the electronic delocalization of the molecular structure. 13C and 1H NMR spectra have been recorded and 13C and 1H nuclear magnetic resonance chemical shifts of the molecule have been calculated using the gauge independent atomic orbital (GIAO) method. Furthermore, All the possible calculated values are analyzed using correlation coefficients linear fitting equation and are shown strong correlation with the experimental data.

Discontinuity of the exchange-correlation potential and the functional derivative of the noninteracting kinetic energy as the number of electrons crosses integer boundaries in Li, Be, and B.

PubMed

Morrison, Robert C

2015-01-07

Accurate densities were determined from configuration interaction wave functions for atoms and ions of Li, Be, and B with up to four electrons. Exchange-correlation potentials, Vxc(r), and functional derivatives of the noninteracting kinetic energy, δK[ρ]/δρ(r), obtained from these densities were used to examine their discontinuities as the number of electrons N increases across integer boundaries for N = 1, N = 2, and N = 3. These numerical results are consistent with conclusions that the discontinuities are characterized by a jump in the chemical potential while the shape of Vxc(r) varies continuously as an integer boundary is crossed. The discontinuity of the Vxc(r) is positive, depends on the ionization potential, electron affinity, and orbital energy differences, and the discontinuity in δK[ρ]/δρ(r) depends on the difference between the energies of the highest occupied and lowest unoccupied orbitals. The noninteracting kinetic energy and the exchange correlation energy have been computed for integer and noninteger values of N between 1 and 4.

Coulomb branch operators and mirror symmetry in three dimensions

NASA Astrophysics Data System (ADS)

Dedushenko, Mykola; Fan, Yale; Pufu, Silviu S.; Yacoby, Ran

2018-04-01

We develop new techniques for computing exact correlation functions of a class of local operators, including certain monopole operators, in three-dimensional N=4 abelian gauge theories that have superconformal infrared limits. These operators are position-dependent linear combinations of Coulomb branch operators. They form a one-dimensional topological sector that encodes a deformation quantization of the Coulomb branch chiral ring, and their correlation functions completely fix the ( n ≤ 3)-point functions of all half-BPS Coulomb branch operators. Using these results, we provide new derivations of the conformal dimension of half-BPS monopole operators as well as new and detailed tests of mirror symmetry. Our main approach involves supersymmetric localization on a hemisphere HS 3 with half-BPS boundary conditions, where operator insertions within the hemisphere are represented by certain shift operators acting on the HS 3 wavefunction. By gluing a pair of such wavefunctions, we obtain correlators on S 3 with an arbitrary number of operator insertions. Finally, we show that our results can be recovered by dimensionally reducing the Schur index of 4D N=2 theories decorated by BPS 't Hooft-Wilson loops.

A Discrete Probability Function Method for the Equation of Radiative Transfer

NASA Technical Reports Server (NTRS)

Sivathanu, Y. R.; Gore, J. P.

1993-01-01

A discrete probability function (DPF) method for the equation of radiative transfer is derived. The DPF is defined as the integral of the probability density function (PDF) over a discrete interval. The derivation allows the evaluation of the PDF of intensities leaving desired radiation paths including turbulence-radiation interactions without the use of computer intensive stochastic methods. The DPF method has a distinct advantage over conventional PDF methods since the creation of a partial differential equation from the equation of transfer is avoided. Further, convergence of all moments of intensity is guaranteed at the basic level of simulation unlike the stochastic method where the number of realizations for convergence of higher order moments increases rapidly. The DPF method is described for a representative path with approximately integral-length scale-sized spatial discretization. The results show good agreement with measurements in a propylene/air flame except for the effects of intermittency resulting from highly correlated realizations. The method can be extended to the treatment of spatial correlations as described in the Appendix. However, information regarding spatial correlations in turbulent flames is needed prior to the execution of this extension.

Jitter Correction

NASA Technical Reports Server (NTRS)

Waegell, Mordecai J.; Palacios, David M.

2011-01-01

Jitter_Correct.m is a MATLAB function that automatically measures and corrects inter-frame jitter in an image sequence to a user-specified precision. In addition, the algorithm dynamically adjusts the image sample size to increase the accuracy of the measurement. The Jitter_Correct.m function takes an image sequence with unknown frame-to-frame jitter and computes the translations of each frame (column and row, in pixels) relative to a chosen reference frame with sub-pixel accuracy. The translations are measured using a Cross Correlation Fourier transformation method in which the relative phase of the two transformed images is fit to a plane. The measured translations are then used to correct the inter-frame jitter of the image sequence. The function also dynamically expands the image sample size over which the cross-correlation is measured to increase the accuracy of the measurement. This increases the robustness of the measurement to variable magnitudes of inter-frame jitter

Effective equilibrium states in mixtures of active particles driven by colored noise

NASA Astrophysics Data System (ADS)

Wittmann, René; Brader, J. M.; Sharma, A.; Marconi, U. Marini Bettolo

2018-01-01

We consider the steady-state behavior of pairs of active particles having different persistence times and diffusivities. To this purpose we employ the active Ornstein-Uhlenbeck model, where the particles are driven by colored noises with exponential correlation functions whose intensities and correlation times vary from species to species. By extending Fox's theory to many components, we derive by functional calculus an approximate Fokker-Planck equation for the configurational distribution function of the system. After illustrating the predicted distribution in the solvable case of two particles interacting via a harmonic potential, we consider systems of particles repelling through inverse power-law potentials. We compare the analytic predictions to computer simulations for such soft-repulsive interactions in one dimension and show that at linear order in the persistence times the theory is satisfactory. This work provides the toolbox to qualitatively describe many-body phenomena, such as demixing and depletion, by means of effective pair potentials.

Quantum Critical Point revisited by the Dynamical Mean Field Theory

NASA Astrophysics Data System (ADS)

Xu, Wenhu; Kotliar, Gabriel; Tsvelik, Alexei

Dynamical mean field theory is used to study the quantum critical point (QCP) in the doped Hubbard model on a square lattice. The QCP is characterized by a universal scaling form of the self energy and a spin density wave instability at an incommensurate wave vector. The scaling form unifies the low energy kink and the high energy waterfall feature in the spectral function, while the spin dynamics includes both the critical incommensurate and high energy antiferromagnetic paramagnons. We use the frequency dependent four-point correlation function of spin operators to calculate the momentum dependent correction to the electron self energy. Our results reveal a substantial difference with the calculations based on the Spin-Fermion model which indicates that the frequency dependence of the the quasiparitcle-paramagnon vertices is an important factor. The authors are supported by Center for Computational Design of Functional Strongly Correlated Materials and Theoretical Spectroscopy under DOE Grant DE-FOA-0001276.

Design considerations for a real-time ocular counterroll instrument

NASA Technical Reports Server (NTRS)

Hatamian, M.; Anderson, D. J.

1983-01-01

A real-time algorithm for measuring three-dimensional movement of the human eye, especially torsional movement, is presented. As its input, the system uses images of the eyeball taken at video rate. The amount of horizontal and vertical movement is extracted using a pupil tracking technique. The torsional movement is then measured by computing the discrete cross-correlation function between the circular samples of successive images of the iris patterns and searching for the position of the peak of the function. A local least square interpolation around the peak of the cross-correlation function is used to produce nearly unbiased estimates of torsion angle with accuracy of about 3-4 arcmin. Accuracies of better than 0.03 deg are achievable in torsional measurement with SNR higher than 36 dB. Horizontal and vertical rotations of up to + or - 13 deg can occur simultaneously with torsion without introducing any appreciable error in the counterrolling measurement process.

SU-F-J-94: Development of a Plug-in Based Image Analysis Tool for Integration Into Treatment Planning

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

Owen, D; Anderson, C; Mayo, C

Purpose: To extend the functionality of a commercial treatment planning system (TPS) to support (i) direct use of quantitative image-based metrics within treatment plan optimization and (ii) evaluation of dose-functional volume relationships to assist in functional image adaptive radiotherapy. Methods: A script was written that interfaces with a commercial TPS via an Application Programming Interface (API). The script executes a program that performs dose-functional volume analyses. Written in C#, the script reads the dose grid and correlates it with image data on a voxel-by-voxel basis through API extensions that can access registration transforms. A user interface was designed through WinFormsmore » to input parameters and display results. To test the performance of this program, image- and dose-based metrics computed from perfusion SPECT images aligned to the treatment planning CT were generated, validated, and compared. Results: The integration of image analysis information was successfully implemented as a plug-in to a commercial TPS. Perfusion SPECT images were used to validate the calculation and display of image-based metrics as well as dose-intensity metrics and histograms for defined structures on the treatment planning CT. Various biological dose correction models, custom image-based metrics, dose-intensity computations, and dose-intensity histograms were applied to analyze the image-dose profile. Conclusion: It is possible to add image analysis features to commercial TPSs through custom scripting applications. A tool was developed to enable the evaluation of image-intensity-based metrics in the context of functional targeting and avoidance. In addition to providing dose-intensity metrics and histograms that can be easily extracted from a plan database and correlated with outcomes, the system can also be extended to a plug-in optimization system, which can directly use the computed metrics for optimization of post-treatment tumor or normal tissue response models. Supported by NIH - P01 - CA059827.« less

Multimodal investigation of triple network connectivity in patients with 22q11DS and association with executive functions.

PubMed

Padula, Maria C; Schaer, Marie; Scariati, Elisa; Maeder, Johanna; Schneider, Maude; Eliez, Stephan

2017-04-01

Large-scale brain networks play a prominent role in cognitive abilities and their activity is impaired in psychiatric disorders, such as schizophrenia. Patients with 22q11.2 deletion syndrome (22q11DS) are at high risk of developing schizophrenia and present similar cognitive impairments, including executive functions deficits. Thus, 22q11DS represents a model for the study of neural biomarkers associated with schizophrenia. In this study, we investigated structural and functional connectivity within and between the Default Mode (DMN), the Central Executive (CEN), and the Saliency network (SN) in 22q11DS using resting-state fMRI and DTI. Furthermore, we investigated if triple network impairments were related to executive dysfunctions or the presence of psychotic symptoms. Sixty-three patients with 22q11DS and sixty-eighty controls (age 6-33 years) were included in the study. Structural connectivity between main nodes of DMN, CEN, and SN was computed using probabilistic tractography. Functional connectivity was computed as the partial correlation between the time courses extracted from each node. Structural and functional connectivity measures were then correlated to executive functions and psychotic symptom scores. Our results showed mainly reduced structural connectivity within the CEN, DMN, and SN, in patients with 22q11DS compared with controls as well as reduced between-network connectivity. Functional connectivity appeared to be more preserved, with impairments being evident only within the DMN. Structural connectivity impairments were also related to executive dysfunctions. These findings show an association between triple network structural alterations and executive deficits in patients with the microdeletion, suggesting that 22q11DS and schizophrenia share common psychopathological mechanisms. Hum Brain Mapp 38:2177-2189, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Functional brain networks in schizophrenia: a review.

PubMed

Calhoun, Vince D; Eichele, Tom; Pearlson, Godfrey

2009-01-01

Functional magnetic resonance imaging (fMRI) has become a major technique for studying cognitive function and its disruption in mental illness, including schizophrenia. The major proportion of imaging studies focused primarily upon identifying regions which hemodynamic response amplitudes covary with particular stimuli and differentiate between patient and control groups. In addition to such amplitude based comparisons, one can estimate temporal correlations and compute maps of functional connectivity between regions which include the variance associated with event-related responses as well as intrinsic fluctuations of hemodynamic activity. Functional connectivity maps can be computed by correlating all voxels with a seed region when a spatial prior is available. An alternative are multivariate decompositions such as independent component analysis (ICA) which extract multiple components, each of which is a spatially distinct map of voxels with a common time course. Recent work has shown that these networks are pervasive in relaxed resting and during task performance and hence provide robust measures of intact and disturbed brain activity. This in turn bears the prospect of yielding biomarkers for schizophrenia, which can be described both in terms of disrupted local processing as well as altered global connectivity between large-scale networks. In this review we will summarize functional connectivity measures with a focus upon work with ICA and discuss the meaning of intrinsic fluctuations. In addition, examples of how brain networks have been used for classification of disease will be shown. We present work with functional network connectivity, an approach that enables the evaluation of the interplay between multiple networks and how they are affected in disease. We conclude by discussing new variants of ICA for extracting maximally group discriminative networks from data. In summary, it is clear that identification of brain networks and their inter-relationships with fMRI has great potential to improve our understanding of schizophrenia.

On the Feynman-Hellmann theorem in quantum field theory and the calculation of matrix elements

DOE PAGES

Bouchard, Chris; Chang, Chia Cheng; Kurth, Thorsten; ...

2017-07-12

In this paper, the Feynman-Hellmann theorem can be derived from the long Euclidean-time limit of correlation functions determined with functional derivatives of the partition function. Using this insight, we fully develop an improved method for computing matrix elements of external currents utilizing only two-point correlation functions. Our method applies to matrix elements of any external bilinear current, including nonzero momentum transfer, flavor-changing, and two or more current insertion matrix elements. The ability to identify and control all the systematic uncertainties in the analysis of the correlation functions stems from the unique time dependence of the ground-state matrix elements and the fact that all excited states and contact terms are Euclidean-time dependent. We demonstrate the utility of our method with a calculation of the nucleon axial charge using gradient-flowed domain-wall valence quarks on themore » $$N_f=2+1+1$$ MILC highly improved staggered quark ensemble with lattice spacing and pion mass of approximately 0.15 fm and 310 MeV respectively. We show full control over excited-state systematics with the new method and obtain a value of $$g_A = 1.213(26)$$ with a quark-mass-dependent renormalization coefficient.« less

Correlations of Hepatic Hemodynamics, Liver Function, and Fibrosis Markers in Nonalcoholic Fatty Liver Disease: Comparison with Chronic Hepatitis Related to Hepatitis C Virus.

PubMed

Shigefuku, Ryuta; Takahashi, Hideaki; Nakano, Hiroyasu; Watanabe, Tsunamasa; Matsunaga, Kotaro; Matsumoto, Nobuyuki; Kato, Masaki; Morita, Ryo; Michikawa, Yousuke; Tamura, Tomohiro; Hiraishi, Tetsuya; Hattori, Nobuhiro; Noguchi, Yohei; Nakahara, Kazunari; Ikeda, Hiroki; Ishii, Toshiya; Okuse, Chiaki; Sase, Shigeru; Itoh, Fumio; Suzuki, Michihiro

2016-09-14

The progression of chronic liver disease differs by etiology. The aim of this study was to elucidate the difference in disease progression between chronic hepatitis C (CHC) and nonalcoholic fatty liver disease (NAFLD) by means of fibrosis markers, liver function, and hepatic tissue blood flow (TBF). Xenon computed tomography (Xe-CT) was performed in 139 patients with NAFLD and 152 patients with CHC (including liver cirrhosis (LC)). The cutoff values for fibrosis markers were compared between NAFLD and CHC, and correlations between hepatic TBF and liver function tests were examined at each fibrosis stage. The cutoff values for detection of the advanced fibrosis stage were lower in NAFLD than in CHC. Although portal venous TBF (PVTBF) correlated with liver function tests, PVTBF in initial LC caused by nonalcoholic steatohepatitis (NASH-LC) was significantly lower than that in hepatitis C virus (C-LC) (p = 0.014). Conversely, the liver function tests in NASH-LC were higher than those in C-LC (p < 0.05). It is important to recognize the difference between NAFLD and CHC. We concluded that changes in hepatic blood flow occurred during the earliest stage of hepatic fibrosis in patients with NAFLD; therefore, patients with NAFLD need to be followed carefully.

Predictive coupled-cluster isomer orderings for some Si{sub n}C{sub m} (m, n ≤ 12) clusters: A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks

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

Byrd, Jason N., E-mail: byrd.jason@ensco.com; ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940; Lutz, Jesse J., E-mail: jesse.lutz.ctr@afit.edu

The accurate determination of the preferred Si{sub 12}C{sub 12} isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for the opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies, and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC{sub 3} to Si{sub 12}C{sub 12}. It is found that post-MBPT(2) correlation energy plays a significant rolemore » in obtaining converged relative isomer energies, suggesting that predictions using low rung density functional methods will not have adequate accuracy. Utilizing the best composite coupled-cluster energy that is still computationally feasible, entailing a 3-4 SCF and coupled-cluster theory with singles and doubles extrapolation with triple-ζ (T) correlation, the closo Si{sub 12}C{sub 12} isomer is identified to be the preferred isomer in the support of previous calculations [X. F. Duan and L. W. Burggraf, J. Chem. Phys. 142, 034303 (2015)]. Additionally we have investigated more pragmatic approaches to obtaining accurate silicon carbide isomer energies, including the use of frozen natural orbital coupled-cluster theory and several rungs of standard and double-hybrid density functional theory. Frozen natural orbitals as a way to compute post-MBPT(2) correlation energy are found to be an excellent balance between efficiency and accuracy.« less

An accurate global potential energy surface, dipole moment surface, and rovibrational frequencies for NH3

NASA Astrophysics Data System (ADS)

Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

2008-12-01

A global potential energy surface (PES) that includes short and long range terms has been determined for the NH3 molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born-Oppenheimer correction was added. Our best purely ab initio PES, denoted "mixed," is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10300cm-1 above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J =0-2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J =0-6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J =0-2 is 0.023cm-1 and that for each band is always ⩽0.06cm-1. For J =3-5 the rms error is always ⩽0.15cm-1. This agreement means that transition energies computed with our refined PES should be useful in the assignment of new high-resolution NH3 spectra and in correcting mistakes in previous assignments. Ideas for further improvements to our refined PES and for extension to other isotopolog are discussed.

Theoretical Studies of Elementary Hydrocarbon Species and Their Reactions

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

Allen, Wesley D.; Schaefer, Henry F.

The research program supported by this DOE grant carried out both methodological development and computational applications of first-principles theoretical chemistry based on quantum mechanical wavefunctions, as directed toward understanding and harnessing the fundamental chemical physics of combustion. To build and refine the world’s database of thermochemistry, spectroscopy, and chemical kinetics, predictive and definitive computational methods are needed that push the envelope of modern electronic structure theory. The application of such methods has been made to gain comprehensive knowledge of the paradigmatic reaction networks by which the n- and i-propyl, t-butyl, and n-butyl radicals are oxidized by O 2. Numerous ROOmore » and QOOH intermediates in these R + O 2 reaction systems have been characterized along with the interconnecting isomerization transition states and the barriers leading to fragmentation. Other combustion-related intermediates have also been studied, including methylsulfinyl radical, cyclobutylidene, and radicals derived from acetaldehyde and vinyl alcohol. Theoretical advances have been achieved and made available to the scientific community by implementation into PSI4, an open-source electronic structure computer package emphasizing automation, advanced libraries, and interoperability. We have pursued the development of universal explicitly correlated methods applicable to general electronic wavefunctions, as well as a framework that allows multideterminant reference functions to be expressed as a single determinant from quasiparticle operators. Finally, a rigorous analytical tool for correlated wavefunctions has been created to elucidate dispersion interactions, which play essential roles in many areas of chemistry, but whose effects are often masked and enigmatic. Our research decomposes and analyzes the coupled-cluster electron correlation energy in molecular systems as a function of interelectronic distance. Concepts are emerging that can be used to explain the influence of dispersion on the thermochemistry of large hydrocarbons, including fuels important to combustion technologies.« less

Increasing the computational efficient of digital cross correlation by a vectorization method

NASA Astrophysics Data System (ADS)

Chang, Ching-Yuan; Ma, Chien-Ching

2017-08-01

This study presents a vectorization method for use in MATLAB programming aimed at increasing the computational efficiency of digital cross correlation in sound and images, resulting in a speedup of 6.387 and 36.044 times compared with performance values obtained from looped expression. This work bridges the gap between matrix operations and loop iteration, preserving flexibility and efficiency in program testing. This paper uses numerical simulation to verify the speedup of the proposed vectorization method as well as experiments to measure the quantitative transient displacement response subjected to dynamic impact loading. The experiment involved the use of a high speed camera as well as a fiber optic system to measure the transient displacement in a cantilever beam under impact from a steel ball. Experimental measurement data obtained from the two methods are in excellent agreement in both the time and frequency domain, with discrepancies of only 0.68%. Numerical and experiment results demonstrate the efficacy of the proposed vectorization method with regard to computational speed in signal processing and high precision in the correlation algorithm. We also present the source code with which to build MATLAB-executable functions on Windows as well as Linux platforms, and provide a series of examples to demonstrate the application of the proposed vectorization method.

Information properties of morphologically complex words modulate brain activity during word reading

PubMed Central

Hultén, Annika; Lehtonen, Minna; Lagus, Krista; Salmelin, Riitta

2018-01-01

Abstract Neuroimaging studies of the reading process point to functionally distinct stages in word recognition. Yet, current understanding of the operations linked to those various stages is mainly descriptive in nature. Approaches developed in the field of computational linguistics may offer a more quantitative approach for understanding brain dynamics. Our aim was to evaluate whether a statistical model of morphology, with well‐defined computational principles, can capture the neural dynamics of reading, using the concept of surprisal from information theory as the common measure. The Morfessor model, created for unsupervised discovery of morphemes, is based on the minimum description length principle and attempts to find optimal units of representation for complex words. In a word recognition task, we correlated brain responses to word surprisal values derived from Morfessor and from other psycholinguistic variables that have been linked with various levels of linguistic abstraction. The magnetoencephalography data analysis focused on spatially, temporally and functionally distinct components of cortical activation observed in reading tasks. The early occipital and occipito‐temporal responses were correlated with parameters relating to visual complexity and orthographic properties, whereas the later bilateral superior temporal activation was correlated with whole‐word based and morphological models. The results show that the word processing costs estimated by the statistical Morfessor model are relevant for brain dynamics of reading during late processing stages. PMID:29524274

Information properties of morphologically complex words modulate brain activity during word reading.

PubMed

Hakala, Tero; Hultén, Annika; Lehtonen, Minna; Lagus, Krista; Salmelin, Riitta

2018-06-01

Neuroimaging studies of the reading process point to functionally distinct stages in word recognition. Yet, current understanding of the operations linked to those various stages is mainly descriptive in nature. Approaches developed in the field of computational linguistics may offer a more quantitative approach for understanding brain dynamics. Our aim was to evaluate whether a statistical model of morphology, with well-defined computational principles, can capture the neural dynamics of reading, using the concept of surprisal from information theory as the common measure. The Morfessor model, created for unsupervised discovery of morphemes, is based on the minimum description length principle and attempts to find optimal units of representation for complex words. In a word recognition task, we correlated brain responses to word surprisal values derived from Morfessor and from other psycholinguistic variables that have been linked with various levels of linguistic abstraction. The magnetoencephalography data analysis focused on spatially, temporally and functionally distinct components of cortical activation observed in reading tasks. The early occipital and occipito-temporal responses were correlated with parameters relating to visual complexity and orthographic properties, whereas the later bilateral superior temporal activation was correlated with whole-word based and morphological models. The results show that the word processing costs estimated by the statistical Morfessor model are relevant for brain dynamics of reading during late processing stages. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Complex-energy approach to sum rules within nuclear density functional theory

DOE PAGES

Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; ...

2015-04-27

The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish anmore » efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.« less

Computer-assisted photogrammetric mapping systems for geologic studies-A progress report

USGS Publications Warehouse

Pillmore, C.L.; Dueholm, K.S.; Jepsen, H.S.; Schuch, C.H.

1981-01-01

Photogrammetry has played an important role in geologic mapping for many years; however, only recently have attempts been made to automate mapping functions for geology. Computer-assisted photogrammetric mapping systems for geologic studies have been developed and are currently in use in offices of the Geological Survey of Greenland at Copenhagen, Denmark, and the U.S. Geological Survey at Denver, Colorado. Though differing somewhat, the systems are similar in that they integrate Kern PG-2 photogrammetric plotting instruments and small desk-top computers that are programmed to perform special geologic functions and operate flat-bed plotters by means of specially designed hardware and software. A z-drive capability, in which stepping motors control the z-motions of the PG-2 plotters, is an integral part of both systems. This feature enables the computer to automatically position the floating mark on computer-calculated, previously defined geologic planes, such as contacts or the base of coal beds, throughout the stereoscopic model in order to improve the mapping capabilities of the instrument and to aid in correlation and tracing of geologic units. The common goal is to enhance the capabilities of the PG-2 plotter and provide a means by which geologists can make conventional geologic maps more efficiently and explore ways to apply computer technology to geologic studies. ?? 1981.

Phenomenological constraints on A N in p ↑ p → π X from Lorentz invariance relations

DOE PAGES

Gamberg, Leonard; Kang, Zhong-Bo; Pitonyak, Daniel; ...

2017-04-27

Here, we present a new analysis of A N in p ↑ p → πX within the collinear twist-3 factorization formalism. We incorporate recently derived Lorentz invariance relations into our calculation and focus on input from the kinematical twist-3 functions, which are weighted integrals of transverse momentum dependent (TMD) functions. Particularly, we use the latest extractions of the Sivers and Collins functions with TMD evolution to compute certain terms in AN . Consequently, we are able to constrain the remaining contributions from the lesser known dynamical twist-3 correlators.

Intensity-based masking: A tool to improve functional connectivity results of resting-state fMRI.

PubMed

Peer, Michael; Abboud, Sami; Hertz, Uri; Amedi, Amir; Arzy, Shahar

2016-07-01

Seed-based functional connectivity (FC) of resting-state functional MRI data is a widely used methodology, enabling the identification of functional brain networks in health and disease. Based on signal correlations across the brain, FC measures are highly sensitive to noise. A somewhat neglected source of noise is the fMRI signal attenuation found in cortical regions in close vicinity to sinuses and air cavities, mainly in the orbitofrontal, anterior frontal and inferior temporal cortices. BOLD signal recorded at these regions suffers from dropout due to susceptibility artifacts, resulting in an attenuated signal with reduced signal-to-noise ratio in as many as 10% of cortical voxels. Nevertheless, signal attenuation is largely overlooked during FC analysis. Here we first demonstrate that signal attenuation can significantly influence FC measures by introducing false functional correlations and diminishing existing correlations between brain regions. We then propose a method for the detection and removal of the attenuated signal ("intensity-based masking") by fitting a Gaussian-based model to the signal intensity distribution and calculating an intensity threshold tailored per subject. Finally, we apply our method on real-world data, showing that it diminishes false correlations caused by signal dropout, and significantly improves the ability to detect functional networks in single subjects. Furthermore, we show that our method increases inter-subject similarity in FC, enabling reliable distinction of different functional networks. We propose to include the intensity-based masking method as a common practice in the pre-processing of seed-based functional connectivity analysis, and provide software tools for the computation of intensity-based masks on fMRI data. Hum Brain Mapp 37:2407-2418, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Binary collision approximations for the memory function for density fluctuations in equilibrium atomic liquids

NASA Astrophysics Data System (ADS)

Noah, Joyce E.

Time correlation functions of density fluctuations of liquids at equilibrium can be used to relate the microscopic dynamics of a liquid to its macroscopic transport properties. Time correlation functions are especially useful since they can be generated in a variety of ways, from scattering experiments to computer simulation to analytic theory. The kinetic theory of fluctuations in equilibrium liquids is an analytic theory for calculating correlation functions using memory functions. In this work, we use a diagrammatic formulation of the kinetic theory to develop a series of binary collision approximations for the collisional part of the memory function. We define binary collisions as collisions between two distinct density fluctuations whose identities are fixed during the duration of a collsion. R approximations are for the short time part of the memory function, and build upon the work of Ranganathan and Andersen. These approximations have purely repulsive interactions between the fluctuations. The second type of approximation, RA approximations, is for the longer time part of the memory function, where the density fluctuations now interact via repulsive and attractive forces. Although RA approximations are a natural extension of R approximations, they permit two density fluctuations to become trapped in the wells of the interaction potential, leading to long-lived oscillatory behavior, which is unphysical. Therefore we consider S approximations which describe binary particles which experience the random effect of the surroundings while interacting via repulsive or repulsive and attractive interactions. For each of these approximations for the memory function we numerically solve the kinetic equation to generate correlation functions. These results are compared to molecular dynamics results for the correlation functions. Comparing the successes and failures of the different approximations, we conclude that R approximations give more accurate intermediate and long time results while RA and S approximations do particularly well at predicting the short time behavior. Lastly, we also develop a series of non-graphically derived approximations and use an optimization procedure to determine the underlying memory function from the simulation data. These approaches provide valuable information about the memory function that will be used in the development of future kinetic theories.

Non-local boxes and their implementation in Minecraft

NASA Astrophysics Data System (ADS)

Simnacher, Timo Yannick

PR-boxes are binary devices connecting two remote parties satisfying x AND y = a + b mod 2, where x and y denote the binary inputs and a and b are the respective outcomes without signaling. These devices are named after their inventors Sandu Popescu and Daniel Rohrlich and saturate the Clauser-Horne-Shimony-Holt (CHSH) inequality. This Bell-like inequality bounds the correlation that can exist between two remote, non-signaling, classical systems described by local hidden variable theories. Experiments have now convincingly shown that quantum entanglement cannot be explained by local hidden variable theories. Furthermore, the CHSH inequality provides a method to distinguish quantum systems from super-quantum correlations. The correlation between the outputs of the PR-box goes beyond any quantum entanglement. Though PR-boxes would have impressive consequences, as far as we know they are not physically realizable. However, by introducing PR-boxes to Minecraft as part of the redstone system, which simulates the electrical components for binary computing, we can experience the consequences of super-quantum correlations. For instance, Wim van Dam proved that two parties can use a sufficient number of PR-boxes to compute any Boolean function f(x,y) with only one bit of communication.

Plane-wave pseudopotential implementation and performance of SCAN meta-GGA exchange-correlation functional for extended systems

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

2017-06-01

We present the implementation and performance of the strongly constrained and appropriately normed, SCAN, meta-GGA exchange-correlation (XC) approximation in the planewave-pseudopotential (PW-PP) formalism using the Troullier-Martins pseudopotential scheme. We studied its performance by applying the PW-PP implementation to several practical applications of interest in condensed matter sciences: (a) crystalline silicon and germanium, (b) martensitic phase transition energetics of phosphorene, and (c) a single water molecule physisorption on a graphene sheet. Given the much-improved accuracy over the GGA functionals and its relatively low computational cost compared to hybrid XC functionals, the SCAN functional is highly promising for various practical applications of density functional theory calculations for condensed matter systems. At same time, the SCAN meta-GGA functional appears to require more careful attention to numerical details. The meta-GGA functional shows more significant dependence on the fast Fourier transform grid, which is used for evaluating the XC potential in real space in the PW-PP formalism, than other more conventional GGA functionals do. Additionally, using pseudopotentials that are generated at a different/lower level of XC approximation could introduce noticeable errors in calculating some properties such as phase transition energetics.

Clustering Coefficients for Correlation Networks.

PubMed

Masuda, Naoki; Sakaki, Michiko; Ezaki, Takahiro; Watanabe, Takamitsu

2018-01-01

Graph theory is a useful tool for deciphering structural and functional networks of the brain on various spatial and temporal scales. The clustering coefficient quantifies the abundance of connected triangles in a network and is a major descriptive statistics of networks. For example, it finds an application in the assessment of small-worldness of brain networks, which is affected by attentional and cognitive conditions, age, psychiatric disorders and so forth. However, it remains unclear how the clustering coefficient should be measured in a correlation-based network, which is among major representations of brain networks. In the present article, we propose clustering coefficients tailored to correlation matrices. The key idea is to use three-way partial correlation or partial mutual information to measure the strength of the association between the two neighboring nodes of a focal node relative to the amount of pseudo-correlation expected from indirect paths between the nodes. Our method avoids the difficulties of previous applications of clustering coefficient (and other) measures in defining correlational networks, i.e., thresholding on the correlation value, discarding of negative correlation values, the pseudo-correlation problem and full partial correlation matrices whose estimation is computationally difficult. For proof of concept, we apply the proposed clustering coefficient measures to functional magnetic resonance imaging data obtained from healthy participants of various ages and compare them with conventional clustering coefficients. We show that the clustering coefficients decline with the age. The proposed clustering coefficients are more strongly correlated with age than the conventional ones are. We also show that the local variants of the proposed clustering coefficients (i.e., abundance of triangles around a focal node) are useful in characterizing individual nodes. In contrast, the conventional local clustering coefficients were strongly correlated with and therefore may be confounded by the node's connectivity. The proposed methods are expected to help us to understand clustering and lack thereof in correlational brain networks, such as those derived from functional time series and across-participant correlation in neuroanatomical properties.

Clustering Coefficients for Correlation Networks

PubMed Central

Masuda, Naoki; Sakaki, Michiko; Ezaki, Takahiro; Watanabe, Takamitsu

2018-01-01

Graph theory is a useful tool for deciphering structural and functional networks of the brain on various spatial and temporal scales. The clustering coefficient quantifies the abundance of connected triangles in a network and is a major descriptive statistics of networks. For example, it finds an application in the assessment of small-worldness of brain networks, which is affected by attentional and cognitive conditions, age, psychiatric disorders and so forth. However, it remains unclear how the clustering coefficient should be measured in a correlation-based network, which is among major representations of brain networks. In the present article, we propose clustering coefficients tailored to correlation matrices. The key idea is to use three-way partial correlation or partial mutual information to measure the strength of the association between the two neighboring nodes of a focal node relative to the amount of pseudo-correlation expected from indirect paths between the nodes. Our method avoids the difficulties of previous applications of clustering coefficient (and other) measures in defining correlational networks, i.e., thresholding on the correlation value, discarding of negative correlation values, the pseudo-correlation problem and full partial correlation matrices whose estimation is computationally difficult. For proof of concept, we apply the proposed clustering coefficient measures to functional magnetic resonance imaging data obtained from healthy participants of various ages and compare them with conventional clustering coefficients. We show that the clustering coefficients decline with the age. The proposed clustering coefficients are more strongly correlated with age than the conventional ones are. We also show that the local variants of the proposed clustering coefficients (i.e., abundance of triangles around a focal node) are useful in characterizing individual nodes. In contrast, the conventional local clustering coefficients were strongly correlated with and therefore may be confounded by the node's connectivity. The proposed methods are expected to help us to understand clustering and lack thereof in correlational brain networks, such as those derived from functional time series and across-participant correlation in neuroanatomical properties. PMID:29599714

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

Senesi, Andrew; Lee, Byeongdu

Herein, a general method to calculate the scattering functions of polyhedra, including both regular and semi-regular polyhedra, is presented. These calculations may be achieved by breaking a polyhedron into sets of congruent pieces, thereby reducing computation time by taking advantage of Fourier transforms and inversion symmetry. Each piece belonging to a set or subunit can be generated by either rotation or translation. Further, general strategies to compute truncated, concave and stellated polyhedra are provided. Using this method, the asymptotic behaviors of the polyhedral scattering functions are compared with that of a sphere. It is shown that, for a regular polyhedron,more » the form factor oscillation at highqis correlated with the face-to-face distance. In addition, polydispersity affects the Porod constant. The ideas presented herein will be important for the characterization of nanomaterials using small-angle scattering.« less

Respiratory impedance is correlated with airway narrowing in asthma using three-dimensional computed tomography.

PubMed

Karayama, M; Inui, N; Mori, K; Kono, M; Hozumi, H; Suzuki, Y; Furuhashi, K; Hashimoto, D; Enomoto, N; Fujisawa, T; Nakamura, Y; Watanabe, H; Suda, T

2018-03-01

Respiratory impedance comprises the resistance and reactance of the respiratory system and can provide detailed information on respiratory function. However, details of the relationship between impedance and morphological airway changes in asthma are unknown. We aimed to evaluate the correlation between imaging-based airway changes and respiratory impedance in patients with asthma. Respiratory impedance and spirometric data were evaluated in 72 patients with asthma and 29 reference subjects. We measured the intraluminal area (Ai) and wall thickness (WT) of third- to sixth-generation bronchi using three-dimensional computed tomographic analyses, and values were adjusted by body surface area (BSA, Ai/BSA, and WT/the square root (√) of BSA). Asthma patients had significantly increased respiratory impedance, decreased Ai/BSA, and increased WT/√BSA, as was the case in those without airflow limitation as assessed by spirometry. Ai/BSA was inversely correlated with respiratory resistance at 5 Hz (R5) and 20 Hz (R20). R20 had a stronger correlation with Ai/BSA than did R5. Ai/BSA was positively correlated with forced expiratory volume in 1 second/forced vital capacity ratio, percentage predicted forced expiratory volume in 1 second, and percentage predicted mid-expiratory flow. WT/√BSA had no significant correlation with spirometry or respiratory impedance. Respiratory resistance is associated with airway narrowing. © 2018 John Wiley & Sons Ltd.

Neural Correlates of Phrase Rhythm: An EEG Study of Bipartite vs. Rondo Sonata Form.

PubMed

Martínez-Rodrigo, Arturo; Fernández-Sotos, Alicia; Latorre, José Miguel; Moncho-Bogani, José; Fernández-Caballero, Antonio

2017-01-01

This paper introduces the neural correlates of phrase rhythm. In short, phrase rhythm is the rhythmic aspect of phrase construction and the relationships between phrases. For the sake of establishing the neural correlates, a musical experiment has been designed to induce music-evoked stimuli related to phrase rhythm. Brain activity is monitored through electroencephalography (EEG) by using a brain-computer interface. The power spectral value of each EEG channel is estimated to obtain how power variance distributes as a function of frequency. Our experiment shows statistical differences in theta and alpha bands in the phrase rhythm variations of two classical sonatas, one in bipartite form and the other in rondo form.

Neural Correlates of Phrase Rhythm: An EEG Study of Bipartite vs. Rondo Sonata Form

PubMed Central

Martínez-Rodrigo, Arturo; Fernández-Sotos, Alicia; Latorre, José Miguel; Moncho-Bogani, José; Fernández-Caballero, Antonio

2017-01-01

This paper introduces the neural correlates of phrase rhythm. In short, phrase rhythm is the rhythmic aspect of phrase construction and the relationships between phrases. For the sake of establishing the neural correlates, a musical experiment has been designed to induce music-evoked stimuli related to phrase rhythm. Brain activity is monitored through electroencephalography (EEG) by using a brain–computer interface. The power spectral value of each EEG channel is estimated to obtain how power variance distributes as a function of frequency. Our experiment shows statistical differences in theta and alpha bands in the phrase rhythm variations of two classical sonatas, one in bipartite form and the other in rondo form. PMID:28496406

Multiconfiguration Pair-Density Functional Theory.

PubMed

Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura

2014-09-09

We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.

Generalized Jastrow Variational Method for Liquid HELIUM-3-HELIUM-4 Mixtures at T = 0 K.

NASA Astrophysics Data System (ADS)

Mirabbaszadeh, Kavoos

Microscopic theory of dilute liquid { ^3 He}-{^4 He} mixtures is of great interest, because it provides a physical realization of a nearly degenerate weakly interacting Fermion system. An understanding of properties of the mixtures has received considerable attention both theoretically and experimentally over the past thirty years. We present here a variational procedure based on the Jastrow function for the ground state of {^3 He}- {^4 He} mixtures by minimizing the total energy of the mixture using the hypernetted-chain (HNC) approximation and the Percus-Yevick (PY) approximation for the two body correlation functions. Our goal is to compute from first principles the internal energy of the system and the various two body correlation functions at various densities and compare the results with experiment. The Jastrow variational method for the ground state energy of liquid {^4 He} consists of the following ansatz for the wave function Psi_alpha {rm(vec r_{1 alpha},} {vec r_{2alpha},} dots, {vec r_{N _alpha})} = prod _{rm i < j} {rm f_ {alphaalpha}(r_{ij}). } For a {^3 He } system the corresponding ansatz is Psi_beta {rm( vec r_{1beta},} {vec r_{2beta },} dots, {vec r_{N_beta})} = {[prod _{i < j} f_{betabeta }(r_{ij})]} Phi {rm( vec r_{1beta},} {vec r_{2beta },} dots, {vec r_{Nbeta}),} where Phi is a Slater determinant of plane waves for the ground state of the Fermion system. The total energy per particle can be written in the form: E = x_sp{alpha}{2} E_{alphaalpha} + x_sp{beta}{2 }E_{betabeta } + 2x_{alpha} x_{beta}E _{alphabeta}, where E_{alphaalpha} , E_{betabeta} , E_{alphabeta} are unknown parameters to be determined from a microscopic theory. Using the Jastrow wave function Psi for the mixture, a general expression is given for the ground state energy in terms of the two body potential and two and three body correlation functions. The Kirkwood Super-position Approximation (KSA) is used for the three-body correlation functions. The antisymmetry of the wave function for Fermions is incorporated following the procedure given earlier by Lado, Inguva and Smith. This procedure for treating the antisymmetry of the wave function simplifies the equations for the two-body correlation functions considerably. The equations for the correlation functions are solved in the hypernetted-chain approximation. Once the two-particle correlation functions for the mixture ( ^3He-^4He) have been obtained, the energy is minimized with respect to the variational parameters involved in the Jastrow wave function. The binding energy and the optimal correlation functions are then obtained as a function of the concentration of ^3He atoms in the mixture. (Abstract shortened with permission of author.).