Strain-induced partially flat band, helical snake states, and interface superconductivity in topological crystalline insulators

Topological crystalline insulators in IV-VI compounds host novel topological surface states consisting of multi-valley massless Dirac fermions at low energy. Here we show that strain generically acts as an effective gauge field on these Dirac fermions and creates pseudo-Landau orbitals without breaking time-reversal symmetry. We predict the realization of this phenomenon in IV-VI semiconductor heterostructures, due to a naturally occurring misfit dislocation array at the interface that produces a periodically varying strain field. Remarkably, the zero-energy Landau orbitals form a flat band in the vicinity of the Dirac point, and coexist with a network of snake states at higher energy. We propose that the high density of states of this flat band gives rise to interface superconductivity observed in IV-VI semiconductor multilayers at unusually high temperatures, with non-BCS behavior. Our work demonstrates a new route to altering macroscopic electronic properties to achieve a partially flat band, and paves the way for realizing novel correlated states of matter.Comment: Accepted by Nature Physic

Unsupervised Bayesian linear unmixing of gene expression microarrays

Background: This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Results: Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. Conclusions: The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor

Absence of a Zero Temperature Vortex Solid Phase in Strongly Disordered Superconducting Bi Films

We present low temperature measurements of the resistance in magnetic field of superconducting ultrathin amorphous Bi films with normal state sheet resistances, $R_N$, near the resistance quantum, $R_Q={\hbar\over {e^2}}$. For $R_N<R_Q$, the tails of the resistive transitions show the thermally activated flux flow signature characteristic of defect motion in a vortex solid with a finite correlation length. When $R_N$ exceeds $R_Q$, the tails become non-activated. We conclude that in films where $R_N>R_Q$ there is no vortex solid and, hence, no zero resistance state in magnetic field. We describe how disorder induced quantum and/or mesoscopic fluctuations can eliminate the vortex solid and also discuss implications for the magnetic-field-tuned superconductor-insulator transition.Comment: REVTEX, 4 pages, 3 figure

Flat bands as a route to high-temperature superconductivity in graphite

Superconductivity is traditionally viewed as a low-temperature phenomenon. Within the BCS theory this is understood to result from the fact that the pairing of electrons takes place only close to the usually two-dimensional Fermi surface residing at a finite chemical potential. Because of this, the critical temperature is exponentially suppressed compared to the microscopic energy scales. On the other hand, pairing electrons around a dispersionless (flat) energy band leads to very strong superconductivity, with a mean-field critical temperature linearly proportional to the microscopic coupling constant. The prize to be paid is that flat bands can generally be generated only on surfaces and interfaces, where high-temperature superconductivity would show up. The flat-band character and the low dimensionality also mean that despite the high critical temperature such a superconducting state would be subject to strong fluctuations. Here we discuss the topological and non-topological flat bands discussed in different systems, and show that graphite is a good candidate for showing high-temperature flat-band interface superconductivity.Comment: Submitted as a chapter to the book on "Basic Physics of functionalized Graphite", 21 pages, 12 figure

Dynamics of Flux Creep in Underdoped Single Crystals of Y_1-xPr_xBa_2Cu_3O_7-d

Transport as well as magnetic relaxation properties of the mixed state were studied on strongly underdoped Y_1-xPr_xBa_2Cu_3O_7-d crystals. We observed two correlated phenomena - a coupling transition and a transition to quantum creep. The distribution of transport current below the coupling transition is highly nonuniform, which facilitates quantum creep. We speculate that in the mixed state below the coupling transition, where dissipation is nonohmic, the current distribution may be unstable with respect to self-channeling resulting in the formation of very thin current-carrying layers.Comment: 11 pages, 9 figures, Submitted to Phys. Rev.

Candidate Screening of the TRPC3 Gene in Cerebellar Ataxia

The hereditary cerebellar ataxias are a diverse group of neurodegenerative disorders primarily characterised by loss of balance and coordination due to dysfunction of the cerebellum and its associated pathways. Although many genetic mutations causing inherited cerebellar ataxia have been identified, a significant percentage of patients remain whose cause is unknown. The transient receptor potential (TRP) family member TRPC3 is a non-selective cation channel linked to key signalling pathways that are affected in cerebellar ataxia. Furthermore, genetic mouse models of TRPC3 dysfunction display cerebellar ataxia, making the TRPC3 gene an excellent candidate for screening ataxic patients with unknown genetic aetiology. Here, we report a genetic screen for TRPC3 mutations in a cohort of 98 patients with genetically undefined late-onset cerebellar ataxia and further ten patients with undefined episodic ataxia. We identified a number of variants but no causative mutations in TRPC3. Our findings suggest that mutations in TRPC3 do not significantly contribute to the cause of late-onset and episodic human cerebellar ataxias

The composition of the protosolar disk and the formation conditions for comets

Conditions in the protosolar nebula have left their mark in the composition of cometary volatiles, thought to be some of the most pristine material in the solar system. Cometary compositions represent the end point of processing that began in the parent molecular cloud core and continued through the collapse of that core to form the protosun and the solar nebula, and finally during the evolution of the solar nebula itself as the cometary bodies were accreting. Disentangling the effects of the various epochs on the final composition of a comet is complicated. But comets are not the only source of information about the solar nebula. Protostellar disks around young stars similar to the protosun provide a way of investigating the evolution of disks similar to the solar nebula while they are in the process of evolving to form their own solar systems. In this way we can learn about the physical and chemical conditions under which comets formed, and about the types of dynamical processing that shaped the solar system we see today. This paper summarizes some recent contributions to our understanding of both cometary volatiles and the composition, structure and evolution of protostellar disks.Comment: To appear in Space Science Reviews. The final publication is available at Springer via http://dx.doi.org/10.1007/s11214-015-0167-

FtsK-Dependent Dimer Resolution on Multiple Chromosomes in the Pathogen Vibrio cholerae

Unlike most bacteria, Vibrio cholerae harbors two distinct, nonhomologous circular chromosomes (chromosome I and II). Many features of chromosome II are plasmid-like, which raised questions concerning its chromosomal nature. Plasmid replication and segregation are generally not coordinated with the bacterial cell cycle, further calling into question the mechanisms ensuring the synchronous management of chromosome I and II. Maintenance of circular replicons requires the resolution of dimers created by homologous recombination events. In Escherichia coli, chromosome dimers are resolved by the addition of a crossover at a specific site, dif, by two tyrosine recombinases, XerC and XerD. The process is coordinated with cell division through the activity of a DNA translocase, FtsK. Many E. coli plasmids also use XerCD for dimer resolution. However, the process is FtsK-independent. The two chromosomes of the V. cholerae N16961 strain carry divergent dimer resolution sites, dif1 and dif2. Here, we show that V. cholerae FtsK controls the addition of a crossover at dif1 and dif2 by a common pair of Xer recombinases. In addition, we show that specific DNA motifs dictate its orientation of translocation, the distribution of these motifs on chromosome I and chromosome II supporting the idea that FtsK translocation serves to bring together the resolution sites carried by a dimer at the time of cell division. Taken together, these results suggest that the same FtsK-dependent mechanism coordinates dimer resolution with cell division for each of the two V. cholerae chromosomes. Chromosome II dimer resolution thus stands as a bona fide chromosomal process

Automated Analysis of Chest Radiographs for Cystic Fibrosis Scoring

We present a framework to analyze chest radiographs for cystic fibro-sis using machine learning methods. We compare the representational power of deep learning features with traditional texture features. Specifically, we respec-tively employ VGG-16 based deep learning features, Tamura and Gabor filter based textural features to represent the cystic fibrosis images. We demonstrate that VGG-16 features perform best, with a maximum agreement of 82%. In ad-dition, due to limited dimensionality, Tamura features for unsegmented images achieve no more than 50% agreement; however, after segmentation, the accuracy of Tamura can reach 78%. In combination with using the deep learning features, we also compare back propagation neural network and sparse coding classifiers to the typical SVM classifier with polynomial kernel function. The result shows that neural network and sparse coding classifiers outperform SVM in most cases. Only with insufficient training samples does SVM demonstrate higher accuracy

C–O–H–S fluids and granitic magma : how S partitions and modifies CO2 concentrations of fluid-saturated felsic melt at 200 MPa

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Contributions to Mineralogy and Petrology 162 (2011): 849-865, doi:10.1007/s00410-011-0628-1.Hydrothermal volatile-solubility and partitioning experiments were conducted with fluid-saturated haplogranitic melt, H2O, CO2, and S in an internally heated pressure vessel at 900°C and 200 MPa; three additional experiments were conducted with iron-bearing melt. The run-product glasses were analyzed by electron microprobe, FTIR, and SIMS; and they contain ≤ 0.12 wt% S, ≤ 0.097 wt.% CO2, and ≤ 6.4 wt.% H2O. Apparent values of log ƒO2 for the experiments at run conditions were computed from the [(S6+)/(S6++S2-)] ratio of the glasses, and they range from NNO-0.4 to NNO+1.4. The C-O-H-S fluid compositions at run conditions were computed by mass balance, and they contained 22-99 mol% H2O, 0-78 mol% CO2, 0-12 mol% S, and < 3 wt% alkalis. Eight S-free experiments were conducted to determine the H2O and CO2 concentrations of melt and fluid compositions and to compare them with prior experimental results for C-O-H fluid-saturated rhyolite melt, and the agreement is excellent. Sulfur partitions very strongly in favor of fluid in all experiments, and the presence of S modifies the fluid compositions, and hence, the CO2 solubilities in coexisting felsic melt. The square of the mole fraction of H2O in melt increases in a linear fashion, from 0.05-0.25, with the H2O concentration of the fluid. The mole fraction of CO2 in melt increases linearly, from 0.0003-0.0045, with the CO2 concentration of C-O-H-S fluids. Interestingly, the CO2 concentration in melts, involving relatively reduced runs (log ƒO2 ≤ NNO+0.3) that contain 2.5-7 mol% S in the fluid, decreases significantly with increasing S in the system. This response to the changing fluid composition causes the H2O and CO2 solubility curve for C-O-H-S fluid-saturated haplogranitic melts at 200 MPa to shift to values near that modeled for C-O-H fluid-saturated, S-free rhyolite melt at 150 MPa. The concentration of S in haplogranitic melt increases in a linear fashion with increasing S in C-O-H-S fluids, but these data show significant dispersion that likely reflects the strong influence of ƒO2 on S speciation in melt and fluid. Importantly, the partitioning of S between fluid and melt does not vary with the (H2O/H2O+CO2) ratio of the fluid. The fluid-melt partition coefficients for H2O, CO2, and S and the atomic (C/S) ratios of the run-product fluids are virtually identical to thermodynamic constraints on volatile partitioning and the H, S, and C contents of pre-eruptive magmatic fluids and volcanic gases for subduction-related magmatic systems thus confirming our experiments are relevant to natural eruptive systems.This research was supported in part by National Science Foundation awards EAR 0308866 and EAR-0836741 to J.D.W