Edge excitations and topological order in rotating Bose gas

The edge excitations and related topological orders of correlated states of a fast rotating Bose gas are studied. Using exact diagonalization of small systems, we compute the energies and number of edge excitations, as well as the boson occupancy near the edge for various states. The chiral Luttinger-liquid theory of Wen is found to be a good description of the edges of the bosonic Laughlin and other states identified as members of the principal Jain sequence for bosons. However, we find that in a harmonic trap the edge of the state identified as the Moore-Read (Pfaffian) state shows a number of anomalies. An experimental way of detecting these correlated states is also discussed.

Self-similarity of complex networks and hidden metric spaces

We demonstrate that the self-similarity of some scale-free networks with respect to a simple degree-thresholding renormalization scheme finds a natural interpretation in the assumption that network nodes exist in hidden metric spaces. Clustering, i.e., cycles of length three, plays a crucial role in this framework as a topological reflection of the triangle inequality in the hidden geometry. We prove that a class of hidden variable models with underlying metric spaces are able to accurately reproduce the self-similarity properties that we measured in the real networks. Our findings indicate that hidden geometries underlying these real networks are a plausible explanation for their observed topologies and, in particular, for their self-similarity with respect to the degree-based renormalization.

Class of correlated random networks with hidden variables

We study a class of models of correlated random networks in which vertices are characterized by hidden variables controlling the establishment of edges between pairs of vertices. We find analytical expressions for the main topological properties of these models as a function of the distribution of hidden variables and the probability of connecting vertices. The expressions obtained are checked by means of numerical simulations in a particular example. The general model is extended to describe a practical algorithm to generate random networks with an a priori specified correlation structure. We also present an extension of the class, to map nonequilibrium growing networks to networks with hidden variables that represent the time at which each vertex was introduced in the system.

Topological phases in small quantum Hall samples

Topological order has proven a useful concept to describe quantum phase transitions which are not captured by the Ginzburg-Landau type of symmetry-breaking order. However, lacking a local order parameter, topological order is hard to detect. One way to detect it is via direct observation of anyonic properties of excitations which are usually discussed in the thermodynamic limit, but so far has not been realized in macroscopic quantum Hall samples. Here we consider a system of few interacting bosons subjected to the lowest Landau level by a gauge potential, and theoretically investigate vortex excitations in order to identify topological properties of different ground states. Our investigation demonstrates that even in surprisingly small systems anyonic properties are able to characterize the topological order. In addition, focusing on a system in the Laughlin state, we study the robustness of its anyonic behavior in the presence of tunable finite-range interactions acting as a perturbation. A clear signal of a transition to a different state is reflected by the system's anyonic properties.

Protein oligomers studied by solid-state NMR the case of the full-length nucleoid-associated protein histone-like nucleoid structuring protein

Members of the histone-like nucleoid structuring protein (H-NS) family play roles both as architectural proteins and as modulators of gene expression in Gram-negative bacteria. The H-NS protein participates in modulatory processes that respond to environmental changes in osmolarity, pH, or temperature. H-NS oligomerization is essential for its activity. Structural models of different truncated forms are available. However, high-resolution structural details of full-length H-NS and its DNA-bound state have largely remained elusive. We report on progress in characterizing the biologically active H-NS oligomers with solid-state NMR. We compared uniformly ((13)C,(15)N)-labeled ssNMR preparations of the isolated N-terminal region (H-NS 1-47) and full-length H-NS (H-NS 1-137). In both cases, we obtained ssNMR spectra of good quality and characteristic of well-folded proteins. Analysis of the results of 2D and 3D (13)C-(13)C and (15)N-(13)C correlation experiments conducted at high magnetic field led to assignments of residues located in different topological regions of the free full-length H-NS. These findings confirm that the structure of the N-terminal dimerization domain is conserved in the oligomeric full-length protein. Small changes in the dimerization interface suggested by localized chemical shift variations between solution and solid-state spectra may be relevant for DNA recoginition.

Topological phases in small quantum Hall samples

Topological order has proven a useful concept to describe quantum phase transitions which are not captured by the Ginzburg-Landau type of symmetry-breaking order. However, lacking a local order parameter, topological order is hard to detect. One way to detect it is via direct observation of anyonic properties of excitations which are usually discussed in the thermodynamic limit, but so far has not been realized in macroscopic quantum Hall samples. Here we consider a system of few interacting bosons subjected to the lowest Landau level by a gauge potential, and theoretically investigate vortex excitations in order to identify topological properties of different ground states. Our investigation demonstrates that even in surprisingly small systems anyonic properties are able to characterize the topological order. In addition, focusing on a system in the Laughlin state, we study the robustness of its anyonic behavior in the presence of tunable finite-range interactions acting as a perturbation. A clear signal of a transition to a different state is reflected by the system's anyonic properties.

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper webcite.

Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

Clinical usefulness of the Screen for Cognitive Impairment in Psychiatry (SCIP-S) scale in patients with type I bipolar disorder

Background: The relevance of persistent cognitive deficits to the pathogenesis and prognosis of bipolar disorders (BD) is understudied, and its translation into clinical practice has been limited by the absence of brief methods assessing cognitive status in Psychiatry. This investigation assessed the psychometric properties of the Spanish version of the Screen for Cognitive Impairment in Psychiatry (SCIP-S) for the detection of cognitive impairment in BD. Methods: After short training, psychiatrists at 40 outpatient clinics administered the SCIP three times over two weeks to a total of 76 consecutive type I BD admissions. Experienced psychologists also administered a comprehensive battery of standard neuropsychological instruments to clinical sample and 45 healthy control subjects. Results: Feasibility was supported by a brief administration time (approximately 15 minutes) and minimal scoring errors. The reliability of the SCIP was confirmed by good equivalence of forms, acceptable stability (ICC range 0.59 to 0.87) and adequate internal consistency (Chronbach's alpha of 0.74). Construct validity was granted by extraction of a single factor (accounting 52% of the variance), acceptable correlations with conventional neuropsychological instruments, and a clear differentiation between bipolar I and normal samples. Efficiency was also provided by the adequate sensitivity and specificity. Limitations: The sample size is not very large. The SCIP and the neurocognitive battery do not cover all potentially relevant cognitive domains. Also, sensitivity to change remains unexplored. Conclusion: With minimal training, physicians obtained a reliable and valid estimate of cognitive impairment in approximately 15 minutes from an application of the SCIP to type I BD patients.

Clinical usefulness of the Screen for Cognitive Impairment in Psychiatry (SCIP-S) scale in patients with type I bipolar disorder

Background: The relevance of persistent cognitive deficits to the pathogenesis and prognosis of bipolar disorders (BD) is understudied, and its translation into clinical practice has been limited by the absence of brief methods assessing cognitive status in Psychiatry. This investigation assessed the psychometric properties of the Spanish version of the Screen for Cognitive Impairment in Psychiatry (SCIP-S) for the detection of cognitive impairment in BD. Methods: After short training, psychiatrists at 40 outpatient clinics administered the SCIP three times over two weeks to a total of 76 consecutive type I BD admissions. Experienced psychologists also administered a comprehensive battery of standard neuropsychological instruments to clinical sample and 45 healthy control subjects. Results: Feasibility was supported by a brief administration time (approximately 15 minutes) and minimal scoring errors. The reliability of the SCIP was confirmed by good equivalence of forms, acceptable stability (ICC range 0.59 to 0.87) and adequate internal consistency (Chronbach's alpha of 0.74). Construct validity was granted by extraction of a single factor (accounting 52% of the variance), acceptable correlations with conventional neuropsychological instruments, and a clear differentiation between bipolar I and normal samples. Efficiency was also provided by the adequate sensitivity and specificity. Limitations: The sample size is not very large. The SCIP and the neurocognitive battery do not cover all potentially relevant cognitive domains. Also, sensitivity to change remains unexplored. Conclusion: With minimal training, physicians obtained a reliable and valid estimate of cognitive impairment in approximately 15 minutes from an application of the SCIP to type I BD patients.

Mixed Hodge structures and vector bundles on the projective Plane I

We describe an equivalence of categories between the category of mixed Hodge structures and a category of vector bundles on the toric complex projective plane which verify some semistability condition. We then apply this correspondence to define an invariant which generalises the notion of R-split mixed Hodge structure and compute extensions in the category of mixed Hodge structures in terms of extensions of the corresponding vector bundles. We also give a relative version of this correspondence and apply it to define stratifications of the bases of the variations of mixed Hodge structure.

Desenvolupament d'hidrogels superficials que contenen motius d'adhesió cel·lular

Projecte de recerca elaborat a partir d’una estada al Departament d’Enginyeria Química del Massachusetts Institute of Technology entre abril i octubre del 2006. S’ha dissenyat i sintetitzat uns nous films polimèrics, amb aplicacions en l’àmbit de l’enginyeria de teixits, utilitzant la tècnica anomenada iCVD (initiated Chemical Vapor Deposition), prèviament desenvolupada pel grup receptor. Es tracta d’uns hidrogels superficials de gruix controlable, que incorporen un monòmer fluorat, el qual s’havia estudiat extensament en el grup d’origen. Aquest monòmer es caracteritza per reaccionar molt fàcilment amb pèptids, de manera que aquests queden units covalentment a la superfície. Diferents estratègies pel desenvolupament d’aquests copolímers han estat avaluades, tant des del punt de vista purament sintètic com de la pròpia aplicació. Les condicions de polimerització han estat optimitzades i els hidrogels s’han caracteritzat químicament per tècniques espectroscòpiques (FTIR, XPS), i físicament per angle de contacte i el·lipsometria. D’aquesta manera, s’ha estudiat la capacitat dels hidrogels d’absorbir aigua i alhora augmentar el seu gruix, depenent de la quantitat d’agent reticulant introduït i de la incorporació del nou monòmer. A continuació, s’han optimitzat les condicions de reacció d’aquestes superfícies amb pèptids que incorporen una molècula fluorescent, la qual permet detectar fàcilment per microscòpia de fluorescència si la reacció ha tingut lloc. Una vegada la plataforma ha estat posada a punt, s’han iniciat assajos cel·lulars tant amb fibroblasts embriònics de ratolí com amb cèl·lules humanes umbilicals. Els resultats preliminars suggereixen una morfologia diferent de les cèl·lules segons si es cultiven sobre films modificats amb pèptids que promouen l’adhesió cel·lular o sobre les seves seqüències permutades no actives. Però, el més interessant és que també s’han observat certes diferències depenent si els films contenen el component hidrogel o no, fet que suggeriria un paper actiu d’aquests noves superfícies en el comportament cel·lular.

The entropy conjecture for partially hyperbolic diffeomorphisms with 1-D center

We prove that if f is a partially hyperbolic diffeomorphism on the compact manifold M with one dimensional center bundle, then the logarithm of the spectral radius of the map induced by f on the real homology groups of M is smaller or equal to the topological entropy of f. This is a particular case of the Shub's entropy conjecture, which claims that the same conclusion should be true for any C1 map on any compact manifold.

Homologia de Lawson i descens

La meva recerca en els tres anys de gaudiment de beca s'ha centrat en l'estudi de teories semitopològiques definides a través d'espais de cicles algebraics, introduïts per Friedlander i Lawson. Hem estudiat propietats de descens d'aquestes teories i hem construït una successió espectral que calcula explícitament la cohomologia mòrfica d'una varietat tòrica. D'altra banda, estem treballant en l'estudi de propietats d'invariància homotòpica per la cohomologia mòrfica, així com en l'estructura algebraica dels grups d'homologia de Lawson.

Adquiridor de dades analògiques

L’empresa TER és una empresa dedicada al disseny i la construcció de projectes electrònics. La necessitat de comprovar el funcionament dels seus dissenys ha motivat a realitzar un projecte capaç de recollir dades significatives de diferents àmbits com pressió, voltatge, intensitat, temperatura etc. En el mercat les dos maneres més freqüents de recollir aquestes dades són per sensors que donen una equivalència d’un paràmetre físic a un rang de voltatge (0 a 10v) o per corrent (4 a 20mA). Aquestes dades seran adquirides i processades periòdicament per un microcontrolador que les emmagatzemarà una a una per posteriorment visualitzar-les en un LCD o en un programa fet per Visual Basic capaç de generar un document que guardi les dades en Excel. Com a conclusions es pot dir que s’han assolit els objectius, tant els personals com els proposats, per tal de tenir un prototip funcional