Epitaxial Growth of La1/3_{1/3}Sr2/3_{2/3}FeO3_3 thin films by laser ablation

We report on the synthesis of high quality La$_{1/3}$Sr$_{2/3}$FeO$_3$ (LSFO) thin films using the pulsed laser deposition technique on both SrTiO$_3$ (STO) and LaAlO$_3$ (LAO) substrates (100)-oriented. From X-Ray diffraction (XRD) studies, we find that the films have an out-of-plane lattice parameter around 0.3865nm, almost independent of the substrate (i.e. the nature of the strains). The transport properties reveal that, while LSFO films deposited on STO exhibit an anomaly in the resistivity vs temperature at 180K (corresponding to the charge-ordered transition and associated with a transition from a paramagnetic to an antiferromagnetic state), the films grown on LAO display a very small magnetoresistance behavior and present an hysteresis around 270K under the application of a 4T magnetic field. The changes in transport properties between both substrates are discussed and compared with the corresponding single crystals.Comment: 9 pages, 4 figure

Motif Discovery through Predictive Modeling of Gene Regulation

We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting, to enable feature selection from the high-dimensional search space of candidate binding sequences while avoiding overfitting. At each iteration of the algorithm, MEDUSA builds a motif model whose presence in the promoter region of a gene, coupled with activity of a regulator in an experiment, is predictive of differential expression. In this way, we learn motifs that are functional and predictive of regulatory response rather than motifs that are simply overrepresented in promoter sequences. Moreover, MEDUSA produces a model of the transcriptional control logic that can predict the expression of any gene in the organism, given the sequence of the promoter region of the target gene and the expression state of a set of known or putative transcription factors and signaling molecules. Each motif model is either a $k$-length sequence, a dimer, or a PSSM that is built by agglomerative probabilistic clustering of sequences with similar boosting loss. By applying MEDUSA to a set of environmental stress response expression data in yeast, we learn motifs whose ability to predict differential expression of target genes outperforms motifs from the TRANSFAC dataset and from a previously published candidate set of PSSMs. We also show that MEDUSA retrieves many experimentally confirmed binding sites associated with environmental stress response from the literature.Comment: RECOMB 200

Coulomb correlation and magnetic ordering in double-layered manganites: LaSr2_2Mn2_2O7_7

A detailed study of the electronic structure and magnetic configurations of the 50 % hole-doped double layered manganite LaSr$_2$Mn$_2$O$_7$ is presented. We demonstrate that the on-site Coulomb correlation (U) of Mn d electrons {\it (i)} significantly modifies the electronic structure, magnetic ordering (from FM to AFM), and interlayer exchange interactions, and {\it (ii)} promotes strong anisotropy in electrical transport, reducing the effective hopping parameter along the {\it c} axis for electrically active $e_g$ electrons. This findng is consistent with observations of anisotropic transport -- a property which sets this manganite apart from conventional 3D systems. A half-metallic band structure is predicted with both the LSDA and LSDA+U methods. The experimentally observed A-type AFM ordering in LaSr$_2$Mn$_2$O$_7$ is found to be energetically more favorable with U $\geq$ 7 eV. A simple interpretation of interlayer exchange coupling is given within double and super-exchange mechanisms based on the dependencies on U of the effective exchange parameters and $e_g$ state sub-band widths.Comment: 10 pages, 5 figure

Orbital Structure and Magnetic Ordering in Layered Manganites: Universal Correlation and Its Mechanism

Correlation between orbital structure and magnetic ordering in bilayered manganites is examined. A level separation between the $3d_{3z^2-r^2}$ and $3d_{x^2-y^2}$ orbitals in a Mn ion is calculated in the ionic model for a large number of the compounds. It is found that the relative stability of the orbitals dominates the magnetic transition temperatures as well as the magnetic structures. A mechanism of the correlation between orbital and magnetism is investigated based on the theoretical model with the two $e_g$ orbitals under strong electron correlation.Comment: 4 pages, 4 figure

Solid-phase extraction and purification of membrane proteins using a UV-modified PMMA microfluidic bioaffinity mu SPE device

We present a novel microfluidic solid-phase extraction (??SPE) device for the affinity enrichment of biotinylated membrane proteins from whole cell lysates. The device offers features that address challenges currently associated with the extraction and purification of membrane proteins from whole cell lysates, including the ability to release the enriched membrane protein fraction from the extraction surface so that they are available for downstream processing. The extraction bed was fabricated in PMMA using hot embossing and was comprised of 3600 micropillars. Activation of the PMMA micropillars by UV/O3 treatment permitted generation of surface-confined carboxylic acid groups and the covalent attachment of NeutrAvidin onto the ??SPE device surfaces, which was used to affinity select biotinylated MCF-7 membrane proteins directly from whole cell lysates. The inclusion of a disulfide linker within the biotin moiety permitted release of the isolated membrane proteins via DTT incubation. Very low levels (???20 fmol) of membrane proteins could be isolated and recovered with ???89% efficiency with a bed capacity of 1.7 pmol. Western blotting indicated no traces of cytosolic proteins in the membrane protein fraction as compared to significant contamination using a commercial detergent-based method. We highlight future avenues for enhanced extraction efficiency and increased dynamic range of the ??SPE device using computational simulations of different micropillar geometries to guide future device designs.close2

Charge Ordering and Phase Competition in the Layered Perovskite Lasr2mn2o7

Charge-lattice fluctuations are observed in the layered perovskite manganite LaSr2Mn2O7 by Raman spectroscopy as high as 340 K and with decreasing temperature they become static and form a charge ordered (CO) phase below TCO=210 K. In the static regime, superlattice reflections are observed through neutron and x-ray diffraction with a propagation vector (h+1/4,k-1/4,l). Crystallographic analysis of the CO state demonstrates that the degree of charge and orbital ordering in this manganite is weaker than the charge ordering in three dimensional perovskite manganites. A TN=170K a type-A antiferromagnetism (AF) develops and competes with the charge ordering, that eventually melts below T*=100K. High resolution diffraction measurements suggest that that CO- and AF-states do not coincide within the same region in the material but rather co-exist as separate phases. The transition to type-A antiferromagnetism at lower temperatures is characterized by the competition between these two phases.Comment: 9 pages, 6 figure