Multidimensional scaling reveals a color dimension unique to 'color-deficient' observers

Normal color vision depends on the relative rates at which photons are absorbed in three types of retinal cone:short-wave (S), middle-wave (M) and long-wave (L) cones, maximally sensitive near 430, 530 and 560nm, respectively. But 6% of men exhibit an X-linked variant form of color vision called deuteranomaly [1]. Their color vision is thought to depend on S cones and two forms of long-wave cone (L, L′) [2,3]. The two types of L cone contain photopigments that are maximally sensitive near 560nm, but their spectral sensitivities are different enough that the ratio of their activations gives a useful chromatic signal

Finite Size Analysis of the Structure Factors in the Antiferromagnetic XXZ Model

We perform a finite size analysis of the longitudinal and transverse structure factors $S_j(p,\gamma,N),j=1,3$ in the groundstate of the spin-$\frac{1}{2}$ XXZ model. Comparison with the exact results of Tonegawa for the XX model yields excellent agreement. Comparison with the conjecture of M\"uller, Thomas, Puga and Beck reveals discrepancies in the momentum dependence of the longitudinal structure factors.Comment: 9 pages RevTex 3.0 and 17 figures as uuencoded fil

A New Phase of Matter: Quark-Gluon Plasma Beyond the Hagedorn Critical Temperature

I retrace the developments from Hagedorn's concept of a limiting temperature for hadronic matter to the discovery and characterization of the quark-gluon plasma as a new state of matter. My recollections begin with the transformation more than 30 years ago of Hagedorn's original concept into its modern interpretation as the "critical" temperature separating the hadron gas and quark-gluon plasma phases of strongly interacting matter. This was followed by the realization that the QCD phase transformation could be studied experimentally in high-energy nuclear collisions. I describe here my personal effort to help develop the strangeness experimental signatures of quark and gluon deconfinement and recall how the experimental program proceeded soon to investigate this idea, at first at the SPS, then at RHIC, and finally at LHC. As it is often the case, the experiment finds more than theory predicts, and I highlight the discovery of the "perfectly" liquid quark-gluon plasma at RHIC. I conclude with an outline of future opportunities, especially the search for a critical point in the QCD phase diagram.Comment: To appear in {\em Melting Hadrons, Boiling Quarks} by Rolf Hagedorn and Johan Rafelski (editor), Springer Publishers, 2015 (open access

Multiple sequence alignment based on set covers

We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches

Generalized Species Sampling Priors with Latent Beta reinforcements

Many popular Bayesian nonparametric priors can be characterized in terms of exchangeable species sampling sequences. However, in some applications, exchangeability may not be appropriate. We introduce a {novel and probabilistically coherent family of non-exchangeable species sampling sequences characterized by a tractable predictive probability function with weights driven by a sequence of independent Beta random variables. We compare their theoretical clustering properties with those of the Dirichlet Process and the two parameters Poisson-Dirichlet process. The proposed construction provides a complete characterization of the joint process, differently from existing work. We then propose the use of such process as prior distribution in a hierarchical Bayes modeling framework, and we describe a Markov Chain Monte Carlo sampler for posterior inference. We evaluate the performance of the prior and the robustness of the resulting inference in a simulation study, providing a comparison with popular Dirichlet Processes mixtures and Hidden Markov Models. Finally, we develop an application to the detection of chromosomal aberrations in breast cancer by leveraging array CGH data.Comment: For correspondence purposes, Edoardo M. Airoldi's email is [email protected]; Federico Bassetti's email is [email protected]; Michele Guindani's email is [email protected] ; Fabrizo Leisen's email is [email protected]. To appear in the Journal of the American Statistical Associatio

A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

Matrix theory of gravitation

A new classical theory of gravitation within the framework of general relativity is presented. It is based on a matrix formulation of four-dimensional Riemann-spaces and uses no artificial fields or adjustable parameters. The geometrical stress-energy tensor is derived from a matrix-trace Lagrangian, which is not equivalent to the curvature scalar R. To enable a direct comparison with the Einstein-theory a tetrad formalism is utilized, which shows similarities to teleparallel gravitation theories, but uses complex tetrads. Matrix theory might solve a 27-year-old, fundamental problem of those theories (sec. 4.1). For the standard test cases (PPN scheme, Schwarzschild-solution) no differences to the Einstein-theory are found. However, the matrix theory exhibits novel, interesting vacuum solutions.Comment: 24 page

Parametrically Excited Surface Waves: Two-Frequency Forcing, Normal Form Symmetries, and Pattern Selection

Motivated by experimental observations of exotic standing wave patterns in the two-frequency Faraday experiment, we investigate the role of normal form symmetries in the pattern selection problem. With forcing frequency components in ratio m/n, where m and n are co-prime integers, there is the possibility that both harmonic and subharmonic waves may lose stability simultaneously, each with a different wavenumber. We focus on this situation and compare the case where the harmonic waves have a longer wavelength than the subharmonic waves with the case where the harmonic waves have a shorter wavelength. We show that in the former case a normal form transformation can be used to remove all quadratic terms from the amplitude equations governing the relevant resonant triad interactions. Thus the role of resonant triads in the pattern selection problem is greatly diminished in this situation. We verify our general results within the example of one-dimensional surface wave solutions of the Zhang-Vinals model of the two-frequency Faraday problem. In one-dimension, a 1:2 spatial resonance takes the place of a resonant triad in our investigation. We find that when the bifurcating modes are in this spatial resonance, it dramatically effects the bifurcation to subharmonic waves in the case of forcing frequencies are in ratio 1/2; this is consistent with the results of Zhang and Vinals. In sharp contrast, we find that when the forcing frequencies are in ratio 2/3, the bifurcation to (sub)harmonic waves is insensitive to the presence of another spatially-resonant bifurcating mode.Comment: 22 pages, 6 figures, late

Modelling the electric field applied to a tokamak

The vector potential for the Ohmic heating coil system of a tokamak is obtained in semi-analytical form. Comparison is made to the potential of a simple, finite solenoid. In the quasi-static limit, the time rate of change of the potential determines the induced electromotive force through the Maxwell-Lodge effect. Discussion of the gauge constraint is included.Comment: 13 pages, 7 figures, final versio

Dynamical structure factor of the anisotropic Heisenberg chain in a transverse field

We consider the anisotropic Heisenberg spin-1/2 chain in a transverse magnetic field at zero temperature. We first determine all components of the dynamical structure factor by combining exact results with a mean-field approximation recently proposed by Dmitriev {\it et al}., JETP 95, 538 (2002). We then turn to the small anisotropy limit, in which we use field theory methods to obtain exact results. We discuss the relevance of our results to Neutron scattering experiments on the 1D Heisenberg chain compound ${\rm Cs_2CoCl_4}$.Comment: 13 pages, 14 figure