1,638 research outputs found
Dzyaloshinskii-Moriya Interaction and Spiral Order in Spin-orbit Coupled Optical Lattices
We show that the recent experimental realization of spin-orbit coupling in
ultracold atomic gases can be used to study different types of spin spiral
order and resulting multiferroic effects. Spin-orbit coupling in optical
lattices can give rise to the Dzyaloshinskii-Moriya (DM) spin interaction which
is essential for spin spiral order. By taking into account spin-orbit coupling
and an external Zeeman field, we derive an effective spin model in the Mott
insulator regime at half filling and demonstrate that the DM interaction in
optical lattices can be made extremely strong with realistic experimental
parameters. The rich finite temperature phase diagrams of the effective spin
models for fermions and bosons are obtained via classical Monte Carlo
simulations.Comment: 7 pages, 5 figure
Topological orbital ladders
We unveil a topological phase of interacting fermions on a two-leg ladder of
unequal parity orbitals, derived from the experimentally realized double-well
lattices by dimension reduction. topological invariant originates simply
from the staggered phases of -orbital quantum tunneling, requiring none of
the previously known mechanisms such as spin-orbit coupling or artificial gauge
field. Another unique feature is that upon crossing over to two dimensions with
coupled ladders, the edge modes from each ladder form a parity-protected flat
band at zero energy, opening the route to strongly correlated states controlled
by interactions. Experimental signatures are found in density correlations and
phase transitions to trivial band and Mott insulators.Comment: 12 pages, 5 figures, Revised title, abstract, and the discussion on
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FindFoci: a focus detection algorithm with automated parameter training that closely matches human assignments, reduces human inconsistencies and increases speed of analysis
Accurate and reproducible quantification of the accumulation of proteins into foci in cells is essential for data interpretation and for biological inferences. To improve reproducibility, much emphasis has been placed on the preparation of samples, but less attention has been given to reporting and standardizing the quantification of foci. The current standard to quantitate foci in open-source software is to manually determine a range of parameters based on the outcome of one or a few representative images and then apply the parameter combination to the analysis of a larger dataset. Here, we demonstrate the power and utility of using machine learning to train a new algorithm (FindFoci) to determine optimal parameters. FindFoci closely matches human assignments and allows rapid automated exploration of parameter space. Thus, individuals can train the algorithm to mirror their own assignments and then automate focus counting using the same parameters across a large number of images. Using the training algorithm to match human assignments of foci, we demonstrate that applying an optimal parameter combination from a single image is not broadly applicable to analysis of other images scored by the same experimenter or by other experimenters. Our analysis thus reveals wide variation in human assignment of foci and their quantification. To overcome this, we developed training on multiple images, which reduces the inconsistency of using a single or a few images to set parameters for focus detection. FindFoci is provided as an open-source plugin for ImageJ
Thermal Properties of Graphene, Carbon Nanotubes and Nanostructured Carbon Materials
Recent years witnessed a rapid growth of interest of scientific and
engineering communities to thermal properties of materials. Carbon allotropes
and derivatives occupy a unique place in terms of their ability to conduct
heat. The room-temperature thermal conductivity of carbon materials span an
extraordinary large range - of over five orders of magnitude - from the lowest
in amorphous carbons to the highest in graphene and carbon nanotubes. I review
thermal and thermoelectric properties of carbon materials focusing on recent
results for graphene, carbon nanotubes and nanostructured carbon materials with
different degrees of disorder. A special attention is given to the unusual size
dependence of heat conduction in two-dimensional crystals and, specifically, in
graphene. I also describe prospects of applications of graphene and carbon
materials for thermal management of electronics.Comment: Review Paper; 37 manuscript pages; 4 figures and 2 boxe
CMR Assessment of endothelial damage and angiogenesis in porcine coronary arteries using gadofosveset
<p>Abstract</p> <p>Background</p> <p>Endothelial damage and angiogenesis are essential for atherosclerotic plaque development and destabilization. We sought to examine whether contrast enhanced cardiovascular magnetic resonance (CMR) using gadofosveset could show endothelial damage and neovessel formation in balloon injured porcine coronary arteries.</p> <p>Methods and Results</p> <p>Data were obtained from seven pigs that all underwent balloon injury of the left anterior descending coronary artery (LAD) to induce endothelial damage and angiogenesis. Between one - 12 days (average four) after balloon injury, in vivo and ex vivo T1-weighted coronary CMR was performed after intravenous injection of gadofosveset. Post contrast, CMR showed contrast enhancement of the coronary arteries with a selective and time-dependent average expansion of the injured LAD segment area of 45% (p = 0.04; CI<sub>95 </sub>= [15%-75%]), indicating local extravasation of gadofosveset. Vascular and perivascular extravasation of albumin (marker of endothelial leakiness) and gadofosveset was demonstrated with agreement between Evans blue staining and ex vivo CMR contrast enhancement (p = 0.026). Coronary MRI contrast enhancement and local microvessel density determined by microscopic examination correlated (ρ = 0.82, p < 0.001).</p> <p>Conclusion</p> <p>Contrast enhanced coronary CMR with gadofosveset can detect experimentally induced endothelial damage and angiogenesis in the porcine coronary artery wall.</p
Accurate Prediction of Protein Structural Class
Because of the increasing gap between the data from sequencing and structural genomics, the accurate prediction of the structural class of a protein domain solely from the primary sequence has remained a challenging problem in structural biology. Traditional sequence-based predictors generally select several sequence features and then feed them directly into a classification program to identify the structural class. The current best sequence-based predictor achieved an overall accuracy of 74.1% when tested on a widely used, non-homologous benchmark dataset 25PDB. In the present work, we built a multiple linear regression (MLR) model to convert the 440-dimensional (440D) sequence feature vector extracted from the Position Specific Scoring Matrix (PSSM) of a protein domain to a 4-dimensinal (4D) structural feature vector, which could then be used to predict the four major structural classes. We performed 10-fold cross-validation and jackknife tests of the method on a large non-homologous dataset containing 8,244 domains distributed among the four major classes. The performance of our approach outperformed all of the existing sequence-based methods and had an overall accuracy of 83.1%, which is even higher than the results of those predicted secondary structure-based methods
Application of amino acid occurrence for discriminating different folding types of globular proteins
<p>Abstract</p> <p>Background</p> <p>Predicting the three-dimensional structure of a protein from its amino acid sequence is a long-standing goal in computational/molecular biology. The discrimination of different structural classes and folding types are intermediate steps in protein structure prediction.</p> <p>Results</p> <p>In this work, we have proposed a method based on linear discriminant analysis (LDA) for discriminating 30 different folding types of globular proteins using amino acid occurrence. Our method was tested with a non-redundant set of 1612 proteins and it discriminated them with the accuracy of 38%, which is comparable to or better than other methods in the literature. A web server has been developed for discriminating the folding type of a query protein from its amino acid sequence and it is available at http://granular.com/PROLDA/.</p> <p>Conclusion</p> <p>Amino acid occurrence has been successfully used to discriminate different folding types of globular proteins. The discrimination accuracy obtained with amino acid occurrence is better than that obtained with amino acid composition and/or amino acid properties. In addition, the method is very fast to obtain the results.</p
Graphene Photonics and Optoelectronics
The richness of optical and electronic properties of graphene attracts
enormous interest. Graphene has high mobility and optical transparency, in
addition to flexibility, robustness and environmental stability. So far, the
main focus has been on fundamental physics and electronic devices. However, we
believe its true potential to be in photonics and optoelectronics, where the
combination of its unique optical and electronic properties can be fully
exploited, even in the absence of a bandgap, and the linear dispersion of the
Dirac electrons enables ultra-wide-band tunability. The rise of graphene in
photonics and optoelectronics is shown by several recent results, ranging from
solar cells and light emitting devices, to touch screens, photodetectors and
ultrafast lasers. Here we review the state of the art in this emerging field.Comment: Review Nature Photonics, in pres
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