New Geometric Algorithms for Fully Connected Staged Self-Assembly

We consider staged self-assembly systems, in which square-shaped tiles can be added to bins in several stages. Within these bins, the tiles may connect to each other, depending on the glue types of their edges. Previous work by Demaine et al. showed that a relatively small number of tile types suffices to produce arbitrary shapes in this model. However, these constructions were only based on a spanning tree of the geometric shape, so they did not produce full connectivity of the underlying grid graph in the case of shapes with holes; designing fully connected assemblies with a polylogarithmic number of stages was left as a major open problem. We resolve this challenge by presenting new systems for staged assembly that produce fully connected polyominoes in O(log^2 n) stages, for various scale factors and temperature {\tau} = 2 as well as {\tau} = 1. Our constructions work even for shapes with holes and uses only a constant number of glues and tiles. Moreover, the underlying approach is more geometric in nature, implying that it promised to be more feasible for shapes with compact geometric description.Comment: 21 pages, 14 figures; full version of conference paper in DNA2

The Bw4 public epitope of HLA-B molecules confers reactivity with natural killer cell clones that express NKB1, a putative HLA receptor.

Although inhibition of natural killer (NK) cell-mediated lysis by the class I HLA molecules of target cells is an established phenomenon, knowledge of the features of class I molecules which induce this effect remains rudimentary. Using class I alleles HLA-B*1502 and B*1513 which differ only at residues 77-83 which define the Bw4 and Bw6 serological epitopes, we tested the hypothesis that the presence of the Bw4 epitope on class I molecules determines recognition by NKB1+ NK cells. HLA-B*1513 possesses the Bw4 epitope, whereas B*1502 has the Bw6 epitope. Lysis by NKB1+ NK cell clones of transfected target cells expressing B*1513 as the only HLA-A, -B, or -C molecule was inhibited, whereas killing of transfectants expressing B*1502 was not. Addition of an an anti-NKB1 monoclonal antibody reconstituted lysis of the targets expressing B*1513, but did not affect killing of targets bearing B*1502. The inhibitory effect of B*1513 could be similarly prevented by the addition of an anti-class I monoclonal antibody. These results show that the presence of the Bw4 epitope influences recognition of HLA-B molecules by NK cells that express NKB1, and suggest that the NKB1 molecule may act as a receptor for Bw4+ HLA-B alleles. Sequences outside of the Bw4 region must also affect recognition by NKB1+ NK cells, because lysis of transfectants expressing HLA-A*2403 or A*2501, which possess the Bw4 epitope but are in other ways substantially different from HLA-B molecules, was not increased by addition of the anti-NKB1 antibody. Asparagine 86, the single site of N-linked glycosylation on class I molecules, is in close proximity to the Bw4/Bw6 region. The glycosylation site of the Bw4-positive molecule B*5801 was mutated, and the mutant molecules tested for inhibition of NKB1+ NK cells. Inhibition that could be reversed by addition of the anti-NKB1 monoclonal antibody was observed, showing the presence of the carbohydrate moiety is not essential for class I recognition by NKB1+ NK cell clones

The limit order book on different time scales

Financial markets can be described on several time scales. We use data from the limit order book of the London Stock Exchange (LSE) to compare how the fluctuation dominated microstructure crosses over to a more systematic global behavior.Comment: 11 pages, 7 figures, 2 tables, to appear in Proc. SPIE, Fluctuations and Noise 2007, Florenc

Origin and dynamics of vortex rings in drop splashing

A vortex is a flow phenomenon that is very commonly observed in nature. More than a century, a vortex ring that forms during drop splashing has caught the attention of many scientists due to its importance in understanding fluid mixing and mass transport processes. However, the origin of the vortices and their dynamics remain unclear, mostly due to the lack of appropriate visualization methods. Here, with ultrafast X-ray phase-contrast imaging, we show that the formation of vortex rings originates from the energy transfer by capillary waves generated at the moment of the drop impact. Interestingly, we find a row of vortex rings along the drop wall, as demonstrated by a phase diagram established here, with different power-law dependencies of the angular velocities on the Reynolds number. These results provide important insight that allows understanding and modelling any type of vortex rings in nature, beyond just vortex rings during drop splashing.111314Ysciescopu

The anomalous U(1) global symmetry and flavors from an SU(5) x SU(5)′' GUT in Z12−IZ_{12-I} orbifold compactification

In string compactifications, frequently there appears the anomalous U(1) gauge symmetry which belonged to E8$\times$E8 of the heterotic string. This anomalous U(1) gauge boson obtains mass at the compactification scale, just below $10^{18\,}$GeV, by absorbing one pseudoscalar (corresponding to the model-independent axion) from the second rank anti-symmetric tensor field $B_{MN}$. Below the compactification scale, there results a global symmetry U(1)$_{\rm anom}$ whose charge $Q_{\rm anom}$ is the original gauge U(1) charge. This is the most natural global symmetry, realizing the "invisible" axion. This global symmetry U(1)$_{\rm anom}$ is suitable for a flavor symmetry. In the simplest compactification model with the flipped SU(5) grand unification, we calculate all the low energy parameters in terms of the vacuum expectation values of the standard model singlets.Comment: 18 pages, 4 figur

Formulation and performance of variational integrators for rotating bodies

Variational integrators are obtained for two mechanical systems whose configuration spaces are, respectively, the rotation group and the unit sphere. In the first case, an integration algorithm is presented for Euler’s equations of the free rigid body, following the ideas of Marsden et al. (Nonlinearity 12:1647–1662, 1999). In the second example, a variational time integrator is formulated for the rigid dumbbell. Both methods are formulated directly on their nonlinear configuration spaces, without using Lagrange multipliers. They are one-step, second order methods which show exact conservation of a discrete angular momentum which is identified in each case. Numerical examples illustrate their properties and compare them with existing integrators of the literature

Predator-Induced Vertical Behavior of a Ctenophore

Although many studies have focused on Mnemiopsis leidyi predation, little is known about the role of this ctenophore as prey when abundant in native and invaded pelagic systems. We examined the response of the ctenophore M. leidyi to the predatory ctenophore Beroe ovata in an experiment in which the two species could potentially sense each other while being physically separated. On average, M. leidyi responded to the predator’s presence by increasing variability in swimming speeds and by lowering their vertical distribution. Such behavior may help explain field records of vertical migration, as well as stratified and near-bottom distributions of M. leidyi

Critical current of YBa2Cu3O7-delta low-angle grain boundaries

Transport critical current measurements have been performed on 5degrees [001]-tilt thin film YBa2Cu3O7-delta single grain boundaries with the magnetic field rotated in the plane of the film, phi. The variation of the critical current has been determined as a function of the angle between the magnetic field and the grain boundary plane. In applied fields above 1 T the critical current j(c) is found to be strongly suppressed only when the magnetic field is within an angle phi(k) of the grain boundary. Outside this angular range the behavior of the artificial grain boundary is dominated by the critical current of the grains. We show that the phi dependence of j(c) in the suppressed region is well described by a flux cutting model.EPSR

Effect of varying material anisotropy on critical current anisotropy in vicinal YBa2Cu3O7-delta thin films

The high $T_{c}$ cuprate superconductors are noted for their anisotropic layered structure, certain of these materials indeed tend toward the limit of a Lawrence-Doniach superconductor. However, YBa$_2$Cu$_3$O$_{7-\delta}$ has a smaller anisotropy than would be expected from its interlayer spacing. This is due to the cuprate chains in the structure. To investigate the influence of the chain oxygen on transport properties critical current versus applied field angle measurements were performed on fully oxygenated and de-oxygenated YBa$_2$Cu$_3$O$_{7-\delta}$ thin films and optimally oxygenated Y$_{0.75}$Ca$_{0.2}$Ba$_2$Cu$_3$O$_{7-\delta}$ thin films. The films were grown on 10$^{\circ}$ mis-cut SrTiO$_3$ substrates to enable the intrinsic vortex channelling effect to be observed. The form of the vortex channelling minimum observed in field angle dependent critical current studies on the films was seen to depend on film oxygenation. The vortex channelling effect is dependent on a angular dependent cross-over to a string-pancake flux line lattice. The results obtained appear to be consistent with the prediction of Blatter et al. [Rev. Mod. Phys., 66 (4): 1125 (1994)] that increased superconducting anisotropy leads to the kinked string-pancake lattice existing over a smaller angular range.EPSR

Regional variations in ex-vivo diffusion tensor anisotropy are associated with cardiomyocyte remodeling in rats after left ventricular pressure overload

Background Pressure overload left ventricular (LV) hypertrophy is characterized by increased cardiomyocyte width and ventricle wall thickness, however the regional variation of this remodeling is unclear. Cardiovascular magnetic resonance (CMR) diffusion tensor imaging (DTI) may provide a non-invasive, comprehensive, and geometrically accurate method to detect regional differences in structural remodeling in hypertrophy. We hypothesized that DTI parameters, such as fractional and planar anisotropy, would reflect myocyte remodeling due to pressure overload in a regionally-dependent manner. Methods We investigated the regional distributions of myocyte remodeling in rats with or without transverse aortic constriction (TAC) via direct measurement of myocyte dimensions with confocal imaging of thick tissue sections, and correlated myocyte cross-sectional area and other geometric features with parameters of diffusivity from ex-vivo DTI in the same regions of the same hearts. Results We observed regional differences in several parameters from DTI between TAC hearts and SHAM controls. Consistent with previous studies, helix angles from DTI correlated strongly with those measured directly from histological sections (p < 0.001, R2 = 0.71). There was a transmural gradient in myocyte cross-sectional area in SHAM hearts that was diminished in the TAC group. We also found several regions of significantly altered DTI parameters in TAC LV compared to SHAM, especially in myocyte sheet angle dispersion and planar anisotropy. Among others, these parameters correlated significantly with directly measured myocyte aspect ratios. Conclusions These results show that structural remodeling in pressure overload LV hypertrophy is regionally heterogeneous, especially transmurally, with a greater degree of remodeling in the sub-endocardium compared to the sub-epicardium. Additionally, several parameters derived from DTI correlated significantly with measurements of myocyte geometry from direct measurement in histological sections. We suggest that DTI may provide a non-invasive, comprehensive method to detect regional structural myocyte LV remodeling during disease