161 research outputs found
Mean flow and spiral defect chaos in Rayleigh-Benard convection
We describe a numerical procedure to construct a modified velocity field that
does not have any mean flow. Using this procedure, we present two results.
Firstly, we show that, in the absence of mean flow, spiral defect chaos
collapses to a stationary pattern comprising textures of stripes with angular
bends. The quenched patterns are characterized by mean wavenumbers that
approach those uniquely selected by focus-type singularities, which, in the
absence of mean flow, lie at the zig-zag instability boundary. The quenched
patterns also have larger correlation lengths and are comprised of rolls with
less curvature. Secondly, we describe how mean flow can contribute to the
commonly observed phenomenon of rolls terminating perpendicularly into lateral
walls. We show that, in the absence of mean flow, rolls begin to terminate into
lateral walls at an oblique angle. This obliqueness increases with Rayleigh
number.Comment: 14 pages, 19 figure
Pattern Formation and Dynamics in Rayleigh-B\'{e}nard Convection: Numerical Simulations of Experimentally Realistic Geometries
Rayleigh-B\'{e}nard convection is studied and quantitative comparisons are
made, where possible, between theory and experiment by performing numerical
simulations of the Boussinesq equations for a variety of experimentally
realistic situations. Rectangular and cylindrical geometries of varying aspect
ratios for experimental boundary conditions, including fins and spatial ramps
in plate separation, are examined with particular attention paid to the role of
the mean flow. A small cylindrical convection layer bounded laterally either by
a rigid wall, fin, or a ramp is investigated and our results suggest that the
mean flow plays an important role in the observed wavenumber. Analytical
results are developed quantifying the mean flow sources, generated by amplitude
gradients, and its effect on the pattern wavenumber for a large-aspect-ratio
cylinder with a ramped boundary. Numerical results are found to agree well with
these analytical predictions. We gain further insight into the role of mean
flow in pattern dynamics by employing a novel method of quenching the mean flow
numerically. Simulations of a spiral defect chaos state where the mean flow is
suddenly quenched is found to remove the time dependence, increase the
wavenumber and make the pattern more angular in nature.Comment: 9 pages, 10 figure
Numerical study of pattern formation following a convective instability in non-Boussinesq fluids
We present a numerical study of a model of pattern formation following a
convective instability in a non-Boussinesq fluid. It is shown that many of the
features observed in convection experiments conducted on gas can be
reproduced by using a generalized two-dimensional Swift-Hohenberg equation. The
formation of hexagonal patterns, rolls and spirals is studied, as well as the
transitions and competition among them. We also study nucleation and growth of
hexagonal patterns and find that the front velocity in this two dimensional
model is consistent with the prediction of marginal stability theory for one
dimensional fronts.Comment: 9 pages, report FSU-SCRI-92-6
Microextensive Chaos of a Spatially Extended System
By analyzing chaotic states of the one-dimensional Kuramoto-Sivashinsky
equation for system sizes L in the range 79 <= L <= 93, we show that the
Lyapunov fractal dimension D scales microextensively, increasing linearly with
L even for increments Delta{L} that are small compared to the average cell size
of 9 and to various correlation lengths. This suggests that a spatially
homogeneous chaotic system does not have to increase its size by some
characteristic amount to increase its dynamical complexity, nor is the increase
in dimension related to the increase in the number of linearly unstable modes.Comment: 5 pages including 4 figures. Submitted to PR
Efficient Algorithm on a Non-staggered Mesh for Simulating Rayleigh-Benard Convection in a Box
An efficient semi-implicit second-order-accurate finite-difference method is
described for studying incompressible Rayleigh-Benard convection in a box, with
sidewalls that are periodic, thermally insulated, or thermally conducting.
Operator-splitting and a projection method reduce the algorithm at each time
step to the solution of four Helmholtz equations and one Poisson equation, and
these are are solved by fast direct methods. The method is numerically stable
even though all field values are placed on a single non-staggered mesh
commensurate with the boundaries. The efficiency and accuracy of the method are
characterized for several representative convection problems.Comment: REVTeX, 30 pages, 5 figure
External Fluctuations in a Pattern-Forming Instability
The effect of external fluctuations on the formation of spatial patterns is
analysed by means of a stochastic Swift-Hohenberg model with multiplicative
space-correlated noise. Numerical simulations in two dimensions show a shift of
the bifurcation point controlled by the intensity of the multiplicative noise.
This shift takes place in the ordering direction (i.e. produces patterns), but
its magnitude decreases with that of the noise correlation length. Analytical
arguments are presented to explain these facts.Comment: 11 pages, Revtex, 10 Postscript figures added with psfig style
(included). To appear in Physical Review
Generation of maximum spin entanglement induced by cavity field in quantum-dot systems
Equivalent-neighbor interactions of the conduction-band electron spins of
quantum dots in the model of Imamoglu et al. [Phys. Rev. Lett. 83, 4204 (1999)]
are analyzed. Analytical solution and its Schmidt decomposition are found and
applied to evaluate how much the initially excited dots can be entangled to the
remaining dots if all of them are initially disentangled. It is demonstrated
that the perfect maximally entangled states (MES) can only be generated in the
systems of up to 6 dots with a single dot initially excited. It is also shown
that highly entangled states, approximating the MES with a good accuracy, can
still be generated in systems of odd number of dots with almost half of them
being excited. A sudden decrease of entanglement is observed by increasing the
total number of dots in a system with a fixed number of excitations.Comment: 6 pages, 7 figures, to appear in Phys. Rev.
Combining inhomogeneous magnetization transfer and multipoint Dixon acquisition: potential utility and evaluation
Purpose The recently introduced inhomogeneous magnetization transfer (ihMT) method has predominantly been applied for imaging the central nervous system. Future applications of ihMT, such as in peripheral nerves and muscles, will involve imaging in the vicinity of adipose tissues. This work aims to systematically investigate the partial volume effect of fat on the ihMT signal and to propose an efficient fat-separation method that does not interfere with ihMT measurements.Methods First, the influence of fat on ihMT signal was studied using simulations. Next, the ihMT sequence was combined with a multi-echo Dixon acquisition for fat separation. The sequence was tested in 9 healthy volunteers using a 3T human scanner. The ihMT ratio (ihMTR) values were calculated in regions of interest in the brain and the spinal cord using standard acquisition (no fat saturation), water-only, in-phase, and out-of-phase reconstructions. The values obtained were compared with a standard fat suppression method, spectral presaturation with inversion recovery.Results Simulations showed variations in the ihMTR values in the presence of fat, depending on the TEs used. The IhMTR values in the brain and spinal cord derived from the water-only ihMT multi-echo Dixon images were in good agreement with values from the unsuppressed sequence. The ihMT-spectral presaturation with inversion recovery combination resulted in 24%-35% lower ihMTR values compared with the standard non-fat-suppressed acquisition.Conclusion The presence of fat within a voxel affects the ihMTR calculations. The IhMT multi-echo Dixon method does not compromise the observable ihMT effect and can potentially be used to remove fat influence in ihMT.Neuro Imaging Researc
A C6orf10/LOC101929163 locus is associated with age of onset in C9orf72 carriers
The G4C2-repeat expansion in C9orf72 is the most common known cause of amyotrophic lateral sclerosis and frontotemporal dementia. The high phenotypic heterogeneity of C9orf72 patients includes a wide range in age of onset, modifiers of which are largely unknown. Age of onset could be influenced by environmental and genetic factors both of which may trigger DNA methylation changes at CpG sites. We tested the hypothesis that age of onset in C9orf72 patients is associated with some common single nucleotide polymorphisms causing a gain or loss of CpG sites and thus resulting in DNA methylation alterations. Combined analyses of epigenetic and genetic data have the advantage of detecting functional variants with reduced likelihood of false negative results due to excessive correction for multiple testing in genome-wide association studies. First, we estimated the association between age of onset in C9orf72 patients (n = 46) and the DNA methylation levels at all 7603 CpG sites available on the 450 k BeadChip that are mapped to common single nucleotide polymorphisms. This was followed by a genetic association study of the discovery (n = 144) and replication (n = 187) C9orf72 cohorts. We found that age of onset was reproducibly associated with polymorphisms within a 124.7 kb linkage disequilibrium block tagged by top-significant variation, rs9357140, and containing two overlapping genes (LOC101929163 and C6orf10). A meta-analysis of all 331 C9orf72 carriers revealed that every A-allele of rs9357140 reduced hazard by 30% (P = 0.0002); and the median age of onset in AA-carriers was 6 years later than GG-carriers. In addition, we investigated a cohort of C9orf72 negative patients (n = 2634) affected by frontotemporal dementia and/or amyotrophic lateral sclerosis; and also found that the AA-genotype of rs9357140 was associated with a later age of onset (adjusted P = 0.007 for recessive model). Phenotype analyses detected significant association only in the largest subgroup of patients with frontotemporal dementia (n = 2142, adjusted P = 0.01 for recessive model). Gene expression studies of frontal cortex tissues from 25 autopsy cases affected by amyotrophic lateral sclerosis revealed that the G-allele of rs9357140 is associated with increased brain expression of LOC101929163 (a non-coding RNA) and HLA-DRB1 (involved in initiating immune responses), while the A-allele is associated with their reduced expression. Our findings suggest that carriers of the rs9357140 GG-genotype (linked to an earlier age of onset) might be more prone to be in a pro-inflammatory state (e.g. by microglia) than AA-carriers. Further, investigating the functional links within the C6orf10/LOC101929163/HLA-DRB1 pathway will be critical to better define age-dependent pathogenesis of frontotemporal dementia and amyotrophic lateral sclerosis.Ming Zhang, Raffaele Ferrari, Maria Carmela Tartaglia, Julia Keith, Ezequiel I Surace, Uri Wolf ... et al
Improving Genetic Prediction by Leveraging Genetic Correlations Among Human Diseases and Traits
Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7 for height to 47 for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait. © 2018 The Author(s)
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