Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.Comment: 15 page

Microheated substrates for patterning cells and controlling development

Here, we seek to control cellular development by devising a means through which cells can be subjected to a microheated environment in standard culture conditions. Numerous techniques have been devised for controlling cellular function and development via manipulation of surface environmental cues at the micro- and nanoscale. It is well understood that temperature plays a significant role in the rate of cellular activities, migratory behavior (thermotaxis), and in some cases, protein expression. Yet, the effects and possible utilization of micrometer-scale temperature fields in cell cultures have not been explored. Toward this end, two types of thermally isolated microheated substrates were designed and fabricated, one with standard backside etching beneath a dielectric film and another with a combination of surface and bulk micromachining and backside etching. The substrates were characterized with infrared microscopy, finite element modeling, scanning electron microscopy, stylus profilometry, and electrothermal calibrations. Neuron culture studies were conducted on these substrates to 1) examine the feasibility of using a microheated environment to achieve patterned cell growth and 2) selectively accelerate neural development on regions less than 100$mu m$wide. Results show that attached neurons, grown on microheated regions set at 37$~^circ C$, extended processes substantially faster than those incubated at 25$~^circ C$on the same substrate. Further, unattached neurons were positioned precisely along the length of the heater filament (operating at 45$~^circ C$) using free convection currents. These preliminary findings indicate that microheated substrates may be used to direct cellular development spatially in a practical manner.$hfillhbox[1414]

Critical Susceptibility Exponent Measured from Fe/W(110) Bilayers

The critical phase transition in ferromagnetic ultrathin Fe/W(110) films has been studied using the magnetic ac susceptibility. A statistically objective, unconstrained fitting of the susceptibility is used to extract values for the critical exponent (gamma), the critical temperature Tc, the critical amplitude (chi_o) and the range of temperature that exhibits power-law behaviour. A fitting algorithm was used to simultaneously minimize the statistical variance of a power law fit to individual experimental measurements of chi(T). This avoids systematic errors and generates objective fitting results. An ensemble of 25 measurements on many different films are analyzed. Those which permit an extended fitting range in reduced temperature lower than approximately .00475 give an average value gamma=1.76+-0.01. Bilayer films give a weighted average value of gamma = 1.75+-0.02. These results are in agreement with the -dimensional Ising exponent gamma= 7/4. Measurements that do not exhibit power-law scaling as close to Tc (especially films of thickness 1.75ML) show a value of gamma higher than the Ising value. Several possibilities are considered to account for this behaviour.Comment: -Submitted to Phys. Rev. B -Revtex4 Format -6 postscript figure

Image tag completion by local learning

The problem of tag completion is to learn the missing tags of an image. In this paper, we propose to learn a tag scoring vector for each image by local linear learning. A local linear function is used in the neighborhood of each image to predict the tag scoring vectors of its neighboring images. We construct a unified objective function for the learning of both tag scoring vectors and local linear function parame- ters. In the objective, we impose the learned tag scoring vectors to be consistent with the known associations to the tags of each image, and also minimize the prediction error of each local linear function, while reducing the complexity of each local function. The objective function is optimized by an alternate optimization strategy and gradient descent methods in an iterative algorithm. We compare the proposed algorithm against different state-of-the-art tag completion methods, and the results show its advantages

Solar Magnetic Carpet I: Simulation of Synthetic Magnetograms

This paper describes a new 2D model for the photospheric evolution of the magnetic carpet. It is the first in a series of papers working towards constructing a realistic 3D non-potential model for the interaction of small-scale solar magnetic fields. In the model, the basic evolution of the magnetic elements is governed by a supergranular flow profile. In addition, magnetic elements may evolve through the processes of emergence, cancellation, coalescence and fragmentation. Model parameters for the emergence of bipoles are based upon the results of observational studies. Using this model, several simulations are considered, where the range of flux with which bipoles may emerge is varied. In all cases the model quickly reaches a steady state where the rates of emergence and cancellation balance. Analysis of the resulting magnetic field shows that we reproduce observed quantities such as the flux distribution, mean field, cancellation rates, photospheric recycle time and a magnetic network. As expected, the simulation matches observations more closely when a larger, and consequently more realistic, range of emerging flux values is allowed (4e16 - 1e19 Mx). The model best reproduces the current observed properties of the magnetic carpet when we take the minimum absolute flux for emerging bipoles to be 4e16 Mx. In future, this 2D model will be used as an evolving photospheric boundary condition for 3D non-potential modeling.Comment: 33 pages, 16 figures, 5 gif movies included: movies may be viewed at http://www-solar.mcs.st-and.ac.uk/~karen/movies_paper1

Probing neutral top-pion via a flavor-changing process γγ→tcˉΠt0\gamma\gamma\to t\bar{c}\Pi_{t}^{0}

In the framework of topcolor-assisted-technicolor model(TC2), we study a flavor-changing neutral top-pion production process $\gamma\gamma\to t\bar{c}\Pi_{t}^{0}$. The study shows that there exists a resonance effect which can enhance the cross section up to a few fb even tens fb. For a yearly luminosity 100 $fb^{-1}$ at future linear colliders, there might be hundreds even thousands events to be produced. On the other hand, the background of such flavor-changing process is very clean due to the GIM mechanism in SM . With such sufficient events and clean background, neutral toppion could be detected at future linear colliders with high center of energy and luminosity. Our study provides a possible way to test TC2 model.Comment: 10 pages, 4 figures,has been accepted by Phys.Rev.

The productions of the top-pions and top-Higgs associated with the charm quark at the hadron colliders

In the topcolor-assistant technicolor (TC2) model, the typical physical particles, top-pions and top-Higgs, are predicted and the existence of these particles could be regarded as the robust evidence of the model. These particles are accessible at the Tevatron and LHC, and furthermore the flavor-changing(FC) feature of the TC2 model can provide us a unique chance to probe them. In this paper, we study some interesting FC production processes of top-pions and top-Higgs at the Tevatron and LHC, i.e., $c\Pi_{t}^{-}$ and $c\Pi_{t}^{0}(h_{t}^{0})$ productions. We find that the light charged top-pions are not favorable by the Tevatron experiments and the Tevatron has a little capability to probe neutral top-pion and top-Higgs via these FC production processes. At the LHC, however, the cross section can reach the level of $10\sim 100$ pb for $c\Pi_t^-$ production and $10\sim 100$ fb for $c\Pi_t^0(h_t^0)$ production. So one can expect that enough signals could be produced at the LHC experiments. Furthermore, the SM background should be clean due to the FC feature of the processes and the FC decay modes $\Pi_t^-\to b\bar{c}, \Pi_t^0(h_t^0)\to t\bar{c}$ can provide us the typical signal to detect the top-pions and top-Higgs. Therefore, it is hopeful to find the signal of top-pions and top-Higgs with the running of the LHC via these FC processes.Comment: 12 pages, 6 figure

High performance Beowulf computer for lattice QCD

We describe the construction of a high performance parallel computer composed of PC components, as well as the performance test in lattice QCD.Comment: Lattice 2001 (Algorithms and Machines) 3 page

Quantum secure communication scheme with W state

Recently, Cao et al. proposed a new quantum secure direct communication scheme using W state. In their scheme, the error rate introduced by an eavesdropper who takes intercept-resend attack, is only 8.3%. Actually, their scheme is just a quantum key distribution scheme because the communication parties first create a shared key and then encrypt the secret message using one-time pad. We then present a quantum secure communication scheme using three-qubit W state. In our scheme, the error rate is raised to 25% and it is not necessary for the present scheme to use alternative measurement or Bell basis measurement. We also show our scheme is unconditionally secure.Comment: Comments are welcom