Crystallography on Curved Surfaces

We study static and dynamical properties that distinguish two dimensional crystals constrained to lie on a curved substrate from their flat space counterparts. A generic mechanism of dislocation unbinding in the presence of varying Gaussian curvature is presented in the context of a model surface amenable to full analytical treatment. We find that glide diffusion of isolated dislocations is suppressed by a binding potential of purely geometrical origin. Finally, the energetics and biased diffusion dynamics of point defects such as vacancies and interstitials is explained in terms of their geometric potential.Comment: 12 Pages, 8 Figure

Grain Boundary Scars and Spherical Crystallography

We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the minimum energy configurations of particles with arbitrary repulsive interactions on curved surfaces. Above a critical system size we find that crystals develop distinctive high-angle grain boundaries, or scars, not found in planar crystals. The number of excess defects in a scar is shown to grow linearly with the dimensionless system size. The observed slope is expected to be universal, independent of the microscopic potential.Comment: 4 pages, 3 eps figs (high quality images available from Mark Bowick

Microrheology probes length scale dependent rheology

We exploit the power of microrheology to measure the viscoelasticity of entangled F-actin solutions at different length scales from 1 to 100 mu m over a wide frequency range. We compare the behavior of single probe-particle motion to that of the correlated motion of two particles. By varying the average length of the filaments, we identify fluctuations that dissipate diffusively over the filament length. These provide an important relaxation mechanism of the elasticity between 0.1 and 30 rad/sec

One-Bead Microrheology with Rotating Particles

We lay the theoretical basis for one-bead microrheology with rotating particles, i.e, a method where colloids are used to probe the mechanical properties of viscoelastic media. Based on a two-fluid model, we calculate the compliance and discuss it for two cases. We first assume that the elastic and fluid component exhibit both stick boundary conditions at the particle surface. Then, the compliance fulfills a generalized Stokes law with a complex shear modulus whose validity is only limited by inertial effects, in contrast to translational motion. Secondly, we find that the validity of the Stokes regime is reduced when the elastic network is not coupled to the particleComment: 7 pages, 5 figures, submitted to Europhys. Let

Immunophenotyping without antibodies: New perspectives for lymphoma characterization

Aims: Accurate classification of haematological malignancies is a prerequisite for their correct diagnosis, prognosis and therapy. Clear classification of lymphomas is often hindered by the limited number of available cell surface protein markers that are suitable for immunophenotyping. A systematic and quantitative analysis of cell surface proteins is thus required to identify new protein markers on lymphoma subtypes in an unbiased and discovery-driven approach. Methods: Nine Hodgkin and non-Hodgkin B cell lines of diffuse large cell type and mediastinal type were investigated by cell surface capture (CSC) technology, a mass spectrometry-based method to identify cell surface glycoproteins. Selected proteins are verified by antibody-based methods, including flow cytometry and immunohistochemistry on cell line arrays. Results: A total of 747 predicted transmembrane proteins were identified from all cell lines, including 142 CD (cluster of differentiation) annotated proteins. A group of differentially expressed cell surface glycoproteins between Hodgkin and non-Hodgkin B cell lines was revealed via quantitative CSC technology. In addition to classical and expected CD molecules such as CD20 and CD30, less frequently expressed molecules such as CD2 on Hodgkin lymphoma (HL) cell lines were identified by CSC and verified by immunohistochemistry in cell lines and primary lymphoma tissue. A panel of CSC-identified differentiation glycoprotein candidates is currently under investigation on tissue microarrays (TMAs) from patient sample

Identifizierung VHL-assoziierter Veränderungen im klarzelligen Nierenzellkarzinom: Anwendung von kombinierten Genom- und Expressionsanalysen

Zusammenfassung: Das sporadische Nierenzellkarzinom (NZK) ist ein heterogener solider Tumor, der traditionell basierend auf morphologischen Kriterien in weitere Subtypen unterteilt wird. In den letzten Jahren konnten unter Anwendung molekularer Hochdurchsatzanalysen genetische, transkriptionelle und translationale Alterationen identifiziert werden. Diese Marker eignen sich zum einen für die molekulare Klassifizierung des NZK und haben zum anderen prognostische Wertigkeit. Die isolierte Betrachtung genetischer, transkriptioneller und translationaler Veränderungen verhindert jedoch ein tieferes Verständnis für die komplexen Vorgänge der Karzinogenese. Wir fassen hier aktuelle Forschungsergebnisse zur molekularen Charakterisierung des NZK zusammen und stellen ein systembiologisches Konzept zur Identifizierung neuer Tumormarker vor. Diese könnten zukünftig Einsatz in der Diagnostik und Therapie des sporadischen NZK finde

Microrheology, stress fluctuations and active behavior of living cells

We report the first measurements of the intrinsic strain fluctuations of living cells using a recently-developed tracer correlation technique along with a theoretical framework for interpreting such data in heterogeneous media with non-thermal driving. The fluctuations' spatial and temporal correlations indicate that the cytoskeleton can be treated as a course-grained continuum with power-law rheology, driven by a spatially random stress tensor field. Combined with recent cell rheology results, our data imply that intracellular stress fluctuations have a nearly $1/\omega^2$ power spectrum, as expected for a continuum with a slowly evolving internal prestress.Comment: 4 pages, 2 figures, to appear in Phys. Rev. Let

Probabilistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as samples from weight matrices we derive a unique probability distribution for assignments of sites into clusters. Our algorithm, 'PROCSE' (probabilistic clustering of sequences), uses Monte-Carlo sampling of this distribution to partition and align thousands of short DNA sequences into clusters. The algorithm internally determines the number of clusters from the data, and assigns significance to the resulting clusters. We place theoretical limits on the ability of any algorithm to correctly cluster sequences drawn from weight matrices (WMs) when these WMs are unknown. Our analysis suggests that the set of all putative sites for a single genome (e.g. E. coli) is largely inadequate for clustering. When sites from different genomes are combined and all the homologous sites from the various species are used as a block, clustering becomes feasible. We predict 50-100 new regulons as well as many new members of existing regulons, potentially doubling the number of known regulatory sites in E. coli.Comment: 27 pages including 9 figures and 3 table

Gravity of Monopole and String and Gravitational Constant in 3He-A

We discuss the effective metric produced in superfluid 3He-A by such topological objects as radial disgyration and monopole. In relativistic theories these metrics are similar to that of the local string and global monopole correspondingly. But in 3He-A they have the negative angle deficit, which corresponds to the negative mass of the topological objects. The effective gravitational constant G in superfluid 3He-A, derived from the comparison with relativistic theories, is inversely proportional to the square of the gap amplitude Delta, which plays the part of the Planck energy cut-off. G depends on temperature and increases with T, which corresponds to the vacuum screening of the Newton's constant.Comment: Latex file, 10 pages, no figure

Facet Formation in the Negative Quenched Kardar-Parisi-Zhang Equation

The quenched Kardar-Parisi-Zhang (QKPZ) equation with negative non-linear term shows a first order pinning-depinning (PD) transition as the driving force $F$ is varied. We study the substrate-tilt dependence of the dynamic transition properties in 1+1 dimensions. At the PD transition, the pinned surfaces form a facet with a characteristic slope $s_c$ as long as the substrate-tilt $m$ is less than $s_c$. When $m<s_c$, the transition is discontinuous and the critical value of the driving force $F_c(m)$ is independent of $m$, while the transition is continuous and $F_c(m)$ increases with $m$ when $m>s_c$. We explain these features from a pinning mechanism involving a localized pinning center and the self-organized facet formation.Comment: 4 pages, source TeX file and 7 PS figures are tarred and compressed via uufile