Elisha Moses

Curvature of co-links uncovers hidden thematic layers in the World Wide Web

Beyond the information stored in pages of the World Wide Web, novel types of “meta-information” are created when pages connect to each other. Such meta-information is a collective effect of independent agents writing and linking pages, hidden from the casual user. Accessing it and understanding the interrelation between connectivity and content in the World Wide Web is a challenging problem [Botafogo, R. A. & Shneiderman, B. (1991) in Proceedings of Hypertext (Assoc. Comput. Mach., New York), pp. 63–77 and Albert, R. & Barabási, A.-L. (2002) Rev. Mod. Phys. 74, 47–97]. We demonstrate here how thematic relationships can be located precisely by looking only at the graph of hyperlinks, gleaning content and context from the Web without having to read what is in the pages. We begin by noting that reciprocal links (co-links) between pages signal a mutual recognition of authors and then focus on triangles containing such links, because triangles indicate a transitive relation. The importance of triangles is quantified by the clustering coefficient [Watts, D. J. & Strogatz, S. H. (1999) Nature (London) 393, 440–442], which we interpret as a curvature [Bridson, M. R. & Haefliger, A. (1999) Metric Spaces of Non-Positive Curvature (Springer, Berlin)]. This curvature defines a World Wide Web landscape whose connected regions of high curvature characterize a common topic. We show experimentally that reciprocity and curvature, when combined, accurately capture this meta-information for a wide variety of topics. As an example of future directions we analyze the neural network of Caenorhabditis elegans, using the same methods.

Multiphoton plasmon-resonance microscopy

A novel method for detection of noble-metal nanoparticles by their nonlinear optical properties is presented and applied for specific labeling of cellular organelles. When illuminated by laser light in resonance with their plasmon frequency these nanoparticles generate an enhanced multiphoton signal. This enhanced signal is measured to obtain a depth-resolved image in a laser scanning microscope setup. Plasmon-resonance images of both live and fixed cells, showing specific labeling of cellular organelles and membranes, either by two-photon autofluorescence or by third-harmonic generation, are presented.

Coherent structures in turbulent convection, an experimental study

We present results from a visualization experiment in Rayleigh-Benard convection in water at high Rayleigh number. We distinguish three kinds of coherent structures in the flow: waves along the boundary layers, plumes, and spiraling swirls. The waves originate from the interaction of plumes with the boundary layers. The spiraling swirls appear to be the result of a shear instability of the viscous boundary layer. We describe the “life cycle” of these structures in the cell, and when we focus on the waves and characterize them quantitatively using local temperature measurements.

Dynamic excitations in membranes induced by optical tweezers.

We present the phenomenology of transformations in lipid bilayers that are excited by laser tweezers. A variety of dynamic instabilities and shape transformations are observed, including the pearling instability, expulsion of vesicles, and more exotic ones, such as the formation of passages. Our physical picture of the laser-membrane interaction is based on the generation of tension in the bilayer and loss of surface area. Although tension is the origin of the pearling instability, it does not suffice to explain expulsion of vesicles, where we observe opening of giant pores and creeping motion of bilayers. We present a quantitative theoretical framework to understand most of the observed phenomenology. The main hypothesis is that lipid is pulled into the optical trap by the familiar dielectric effect, is disrupted, and finally is repackaged into an optically unresolvable suspension of colloidal particles. This suspension, in turn, can produce osmotic pressure and depletion forces, driving the observed transformations.

An experimental study of laminar plumes

We present an experimental study of the scaling laws for the front (or cap) of an isolated, laminar starting plume. The scaling relations are formulated and measured experimentally over a range of power, fluids, and heaters. The results are that the cap rises at constant velocity, grows diffusively in width, and its temperature depends inversely on height. This extends analytic results by Batchelor (1954) for the column (stem) below the front. The source size determines initial conditions for the cap, but does not affect it in the far field. The shape of the front is fitted by a model of potential flow. The interaction between plume caps is complex, but with simple underlying dynamics. We conjecture that some of our conclusions can be applied to a distribution of plumes, as in soft turbulent convection.

An apparatus for imaging liquids, cells, and other wet samples in the scanning electron microscopy

We present a technique of scanning electron microscopy that is adapted to the study of wet samples. The wet environment is protected in a small chamber enclosed by a membrane, which is thin enough for energetic electrons to go through and interact with the sample studied. We detail both the technique and the general mechanisms of signal formation in the imaging of samples through a membrane. We first describe our setup and the properties required for the membrane, the main element in this method. Some simple measurements for its characterization are given, guiding the choice of material and thickness. We then go on to describe the capabilities of the technique in imaging a variety of different samples. We evaluate the accessible contrast and resolution, and the current needed to obtain them. Low contrast samples can be imaged with an improvement in resolution over optical microscopy. High contrast samples like gold markers labeling a biological cell can be imaged with a resolution of the order of 10 nm. The resolution depends on the location of the particle in the sample: the closer to the membrane, the better the resolution. We believe such a result opens up potential applications for routine experiments in biology, and expect this new technique to find numerous applications in domains where liquid samples are investigated such as soft materials science.

Development of input connections in neural cultures

We introduce an approach for the quantitative assessment of the connectivity in neuronal cultures, based on the statistical mechanics of percolation on a graph. This allows us to monitor the development of the culture and to see the emergence of connectivity in the network. The culture becomes fully connected at a time equivalent to the expected time of birth. The spontaneous bursting activity that characterizes cultures develops in parallel with the connectivity. The average number of inputs per neuron can be quantitatively determined in units of m0, the number of activated inputs needed to excite the neuron. For m0 ≃ 15 we find that hippocampal neurons have on average ≈60–120 inputs, whereas cortical neurons have ≈75–150, depending on neuronal density. The ratio of excitatory to inhibitory neurons is determined by using the GABAA antagonist bicuculine. This ratio changes during development and reaches the final value at day 7–8, coinciding with the expected time of the GABA switch. For hippocampal cultures the inhibitory cells comprise ≈30% of the neurons in the culture whereas for cortical cultures they are ≈20%. Such detailed global information on the connectivity of networks in neuronal cultures is at present inaccessible by any electrophysiological or other technique.

Fingering Instability in Combustion

A thin solid (e.g., paper), burning against an oxidizing wind, develops a fingering instability with two decoupled length scales. The spacing between fingers is determined by the Peclet number (ratio between advection and diffusion). The finger width is determined by the degree two dimensionality. Dense fingers develop by recurrent tip splitting. The effect is observed when vertical mass transport (due to gravity) is suppressed. The experimental results quantitatively verify a model based on diffusion limited transport.

Magnetic Stimulation of One-Dimensional Neuronal Cultures

Transcranial magnetic stimulation is a remarkable tool for neuroscience research, with a multitude of diagnostic and therapeutic applications. Surprisingly, application of the same magnetic stimulation directly to neurons that are dissected from the brain and grown in vitro was not reported to activate them to date. Here we report that central nervous system neurons patterned on large enough one-dimensional rings can be magnetically stimulated in vitro. In contrast, two-dimensional cultures with comparable size do not respond to excitation. This happens because the one-dimensional pattern enforces an ordering of the axons along the ring, which is designed to follow the lines of the magnetically induced electric field. A small group of sensitive (i.e., initiating) neurons respond even when the network is disconnected, and are presumed to excite the entire network when it is connected. This implies that morphological and electrophysiological properties of single neurons are crucial for magnetic stimulation. We conjecture that the existence of a select group of neurons with higher sensitivity may occur in the brain in vivo as well, with consequences for transcranial magnetic stimulation.

Pattern selection and transition to turbulence in propagating waves

Abstract We present a study of oscillatory convection in two experimental systems: ethanol-water mixtures in a rectangular container heated from below and a thin layer of nematic liquid crystals under low frequency ac voltage. In both systems the first bifurcation is the transition to travelling waves (TW) with finite wave vector and frequency. We report experimental observations of a sequence of spatial structures and dynamical behaviour of nonlinear TW in a regime of a weak nonlinearity. Most of the rich variety of spatial and dynamical behaviour which we observe in one-dimensional finite geometries has been reproduced by numerical simulations based on a simple model of coupled Ginzburg-Landau equations which considers only the combination of translation and finite geometry. More complicated spatio-temporal behaviour of TW in cells with two-dimensional geometry which initiated by defect nucleation is attributed to the mechanism of modulational instability of TW.