Nanoscale periodicity in stripe-forming systems at high temperature: Au/W(110)

We observe using low-energy electron microscopy the self-assembly of monolayer-thick stripes of Au on W(110) near the transition temperature between stripes and the non-patterned (homogeneous) phase. We demonstrate that the amplitude of this Au stripe phase decreases with increasing temperature and vanishes at the order-disorder transition (ODT). The wavelength varies much more slowly with temperature and coverage than theories of stress-domain patterns with sharp phase boundaries would predict, and maintains a finite value of about 100 nm at the ODT. We argue that such nanometer-scale stripes should often appear near the ODT.Comment: 5 page

A machine learning pipeline for discriminant pathways identification

Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a machine learning solution for molecular profiling with a recent network comparison method. The pipeline can identify changes occurring between specific sub-modules of networks built in a case-control biomarker study, discriminating key groups of genes whose interactions are modified by an underlying condition. The proposal is independent from the classification algorithm used. Three applications on genomewide data are presented regarding children susceptibility to air pollution and two neurodegenerative diseases: Parkinson's and Alzheimer's. Availability: Details about the software used for the experiments discussed in this paper are provided in the Appendix

Single cell phenotyping reveals heterogeneity among haematopoietic stem cells following infection.

The haematopoietic stem cell (HSC) niche provides essential micro-environmental cues for the production and maintenance of HSCs within the bone marrow. During inflammation, haematopoietic dynamics are perturbed, but it is not known whether changes to the HSC-niche interaction occur as a result. We visualise HSCs directly in vivo, enabling detailed analysis of the 3D niche dynamics and migration patterns in murine bone marrow following Trichinella spiralis infection. Spatial statistical analysis of these HSC trajectories reveals two distinct modes of HSC behaviour: (i) a pattern of revisiting previously explored space, and (ii) a pattern of exploring new space. Whereas HSCs from control donors predominantly follow pattern (i), those from infected mice adopt both strategies. Using detailed computational analyses of cell migration tracks and life-history theory, we show that the increased motility of HSCs following infection can, perhaps counterintuitively, enable mice to cope better in deteriorating HSC-niche micro-environments following infection

Generating confidence intervals on biological networks

<p>Abstract</p> <p>Background</p> <p>In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network may introduce dependencies among the nodes and it will in general be necessary to account for these dependencies in the statistical analysis. To this end we require some form of Null model of the network: generally rewired replicates of the network are generated which preserve only the degree (number of interactions) of each node. We show that this can fail to capture important features of network structure, and may result in unrealistic significance levels, when potentially confounding additional information is available.</p> <p>Methods</p> <p>We present a new network resampling Null model which takes into account the degree sequence as well as available biological annotations. Using gene ontology information as an illustration we show how this information can be accounted for in the resampling approach, and the impact such information has on the assessment of statistical significance of correlations and motif-abundances in the <it>Saccharomyces cerevisiae </it>protein interaction network. An algorithm, GOcardShuffle, is introduced to allow for the efficient construction of an improved Null model for network data.</p> <p>Results</p> <p>We use the protein interaction network of <it>S. cerevisiae</it>; correlations between the evolutionary rates and expression levels of interacting proteins and their statistical significance were assessed for Null models which condition on different aspects of the available data. The novel GOcardShuffle approach results in a Null model for annotated network data which appears better to describe the properties of real biological networks.</p> <p>Conclusion</p> <p>An improved statistical approach for the statistical analysis of biological network data, which conditions on the available biological information, leads to qualitatively different results compared to approaches which ignore such annotations. In particular we demonstrate the effects of the biological organization of the network can be sufficient to explain the observed similarity of interacting proteins.</p

On the Decomposition of Clifford Algebras of Arbitrary Bilinear Form

Clifford algebras are naturally associated with quadratic forms. These algebras are Z_2-graded by construction. However, only a Z_n-gradation induced by a choice of a basis, or even better, by a Chevalley vector space isomorphism Cl(V) \bigwedge V and an ordering, guarantees a multi-vector decomposition into scalars, vectors, tensors, and so on, mandatory in physics. We show that the Chevalley isomorphism theorem cannot be generalized to algebras if the Z_n-grading or other structures are added, e.g., a linear form. We work with pairs consisting of a Clifford algebra and a linear form or a Z_n-grading which we now call 'Clifford algebras of multi-vectors' or 'quantum Clifford algebras'. It turns out, that in this sense, all multi-vector Clifford algebras of the same quadratic but different bilinear forms are non-isomorphic. The usefulness of such algebras in quantum field theory and superconductivity was shown elsewhere. Allowing for arbitrary bilinear forms however spoils their diagonalizability which has a considerable effect on the tensor decomposition of the Clifford algebras governed by the periodicity theorems, including the Atiyah-Bott-Shapiro mod 8 periodicity. We consider real algebras Cl_{p,q} which can be decomposed in the symmetric case into a tensor product Cl_{p-1,q-1} \otimes Cl_{1,1}. The general case used in quantum field theory lacks this feature. Theories with non-symmetric bilinear forms are however needed in the analysis of multi-particle states in interacting theories. A connection to q-deformed structures through nontrivial vacuum states in quantum theories is outlined.Comment: 25 pages, 1 figure, LaTeX, {Paper presented at the 5th International Conference on Clifford Algebras and their Applications in Mathematical Physics, Ixtapa, Mexico, June 27 - July 4, 199

Surface reconstruction induced geometries of Si clusters

We discuss a generalization of the surface reconstruction arguments for the structure of intermediate size Si clusters, which leads to model geometries for the sizes 33, 39 (two isomers), 45 (two isomers), 49 (two isomers), 57 and 61 (two isomers). The common feature in all these models is a structure that closely resembles the most stable reconstruction of Si surfaces, surrounding a core of bulk-like tetrahedrally bonded atoms. We investigate the energetics and the electronic structure of these models through first-principles density functional theory calculations. These models may be useful in understanding experimental results on the reactivity of Si clusters and their shape as inferred from mobility measurements.Comment: 9 figures (available from the author upon request) Submitted to Phys. Rev.

Anisotropic optical response of the diamond (111)-2x1 surface

The optical properties of the 2$\times$1 reconstruction of the diamond (111) surface are investigated. The electronic structure and optical properties of the surface are studied using a microscopic tight-binding approach. We calculate the dielectric response describing the surface region and investigate the origin of the electronic transitions involving surface and bulk states. A large anisotropy in the surface dielectric response appears as a consequence of the asymmetric reconstruction on the surface plane, which gives rise to the zigzag Pandey chains. The results are presented in terms of the reflectance anisotropy and electron energy loss spectra. While our results are in good agreement with available experimental data, additional experiments are proposed in order to unambiguously determine the surface electronic structure of this interesting surface.Comment: REVTEX manuscript with 6 postscript figures, all included in uu file. Also available at http://www.phy.ohiou.edu/~ulloa/ulloa.html Submitted to Phys. Rev.

Decay of isolated surface features driven by the Gibbs-Thomson effect in analytic model and simulation

A theory based on the thermodynamic Gibbs-Thomson relation is presented which provides the framework for understanding the time evolution of isolated nanoscale features (i.e., islands and pits) on surfaces. Two limiting cases are predicted, in which either diffusion or interface transfer is the limiting process. These cases correspond to similar regimes considered in previous works addressing the Ostwald ripening of ensembles of features. A third possible limiting case is noted for the special geometry of "stacked" islands. In these limiting cases, isolated features are predicted to decay in size with a power law scaling in time: A is proportional to (t0-t)^n, where A is the area of the feature, t0 is the time at which the feature disappears, and n=2/3 or 1. The constant of proportionality is related to parameters describing both the kinetic and equilibrium properties of the surface. A continuous time Monte Carlo simulation is used to test the application of this theory to generic surfaces with atomic scale features. A new method is described to obtain macroscopic kinetic parameters describing interfaces in such simulations. Simulation and analytic theory are compared directly, using measurements of the simulation to determine the constants of the analytic theory. Agreement between the two is very good over a range of surface parameters, suggesting that the analytic theory properly captures the necessary physics. It is anticipated that the simulation will be useful in modeling complex surface geometries often seen in experiments on physical surfaces, for which application of the analytic model is not straightforward.Comment: RevTeX (with .bbl file), 25 pages, 7 figures from 9 Postscript files embedded using epsf. Submitted to Phys. Rev. B A few minor changes made on 9/24/9

Search for Yukawa Production of a Light Neutral Higgs Boson at LEP

Within a Two-Higgs-Doublet Model (2HDM) a search for a light Higgs boson in the mass range of 4-12 GeV has been performed in the Yukawa process e+e- -> b bbar A/h -> b bbar tau+tau-, using the data collected by the OPAL detector at LEP between 1992 and 1995 in e+e- collisions at about 91 GeV centre-of-mass energy. A likelihood selection is applied to separate background and signal. The number of observed events is in good agreement with the expected background. Within a CP-conserving 2HDM type II model the cross-section for Yukawa production depends on xiAd = |tan beta| and xihd = |sin alpha/cos beta| for the production of the CP-odd A and the CP-even h, respectively, where tan beta is the ratio of the vacuum expectation values of the Higgs doublets and alpha is the mixing angle between the neutral CP-even Higgs bosons. From our data 95% C.L. upper limits are derived for xiAd within the range of 8.5 to 13.6 and for xihd between 8.2 to 13.7, depending on the mass of the Higgs boson, assuming a branching fraction into tau+tau- of 100%. An interpretation of the limits within a 2HDM type II model with Standard Model particle content is given. These results impose constraints on several models that have been proposed to explain the recent BNL measurement of the muon anomalous magnetic moment.Comment: 24 pages, 9 figures, Submitted to Euro. Phys. J.