Viewpoints: A high-performance high-dimensional exploratory data analysis tool

Scientific data sets continue to increase in both size and complexity. In the past, dedicated graphics systems at supercomputing centers were required to visualize large data sets, but as the price of commodity graphics hardware has dropped and its capability has increased, it is now possible, in principle, to view large complex data sets on a single workstation. To do this in practice, an investigator will need software that is written to take advantage of the relevant graphics hardware. The Viewpoints visualization package described herein is an example of such software. Viewpoints is an interactive tool for exploratory visual analysis of large, high-dimensional (multivariate) data. It leverages the capabilities of modern graphics boards (GPUs) to run on a single workstation or laptop. Viewpoints is minimalist: it attempts to do a small set of useful things very well (or at least very quickly) in comparison with similar packages today. Its basic feature set includes linked scatter plots with brushing, dynamic histograms, normalization and outlier detection/removal. Viewpoints was originally designed for astrophysicists, but it has since been used in a variety of fields that range from astronomy, quantum chemistry, fluid dynamics, machine learning, bioinformatics, and finance to information technology server log mining. In this article, we describe the Viewpoints package and show examples of its usage.Comment: 18 pages, 3 figures, PASP in press, this version corresponds more closely to that to be publishe

Atom in a coherently controlled squeezed vacuum

A broadband squeezed vacuum photon field is characterized by a complex squeezing function. We show that by controlling the wavelength dependence of its phase it is possible to change the dynamics of the atomic polarization interacting with the squeezed vacuum. Such a phase modulation effectively produces a finite range temporal interaction kernel between the two quadratures of the atomic polarization yielding the change in the decay rates as well as the appearance of additional oscillation frequencies. We show that decay rates slower than the spontaneous decay rate can be achieved even for a squeezed bath in the classic regime. For linear and quadratic phase modulations the power spectrum of the scattered light exhibits narrowing of the central peak due to the modified decay rates. For strong phase modulations side lobes appear symmetrically around the central peak reflecting additional oscillation frequencies.Comment: 4 pages, 4 figure

Semiclassical treatment of fusion processes in collisions of weakly bound nuclei

We describe a semiclassical treatment of nuclear fusion reactions involving weakly bound nuclei. In this treatment, the complete fusion probabilities are approximated by products of two factors: a tunneling probability and the probability that the system is in its ground state at the strong absorption radius. We investigate the validity of the method in a schematic two-channel application, where the channels in the continuum are represented by a single resonant state. Comparisons with full coupled-channels calculations are performed. The agreement between semiclassical and quantal calculations isquite good, suggesting that the procedure may be extended to more sophisticated discretizations of the continuum.Comment: 11 pages, 5 figure

Rapid, Single-Step Protein Encapsulation via Flash NanoPrecipitation

Flash NanoPrecipitation (FNP) is a rapid method for encapsulating hydrophobic materials in polymer nanoparticles with high loading capacity. Encapsulating biologics such as proteins remains a challenge due to their low hydrophobicity (logP \u3c 6) and current methods require multiple processing steps. In this work, we report rapid, single-step protein encapsulation via FNP using bovine serum albumin (BSA) as a model protein. Nanoparticle formation involves complexation and precipitation of protein with tannic acid and stabilization with a cationic polyelectrolyte. Nanoparticle self-assembly is driven by hydrogen bonding and electrostatic interactions. Using this approach, high encapsulation efficiency (up to ~80%) of protein can be achieved. The resulting nanoparticles are stable at physiological pH and ionic strength. Overall, FNP is a rapid, efficient platform for encapsulating proteins for various applications

Evaluation of discretization procedures for transition elements in adaptive mesh refinement

Three transition interpolation schemes for use in h-or r-refinement have been analyzed in terms of accuracy, implementation ease and extendability. They include blending-function interpolation, displacement averaging, and strain matching at discrete points along the transition edge lines. The results suggest that the choice of matching depends strongly on the element formulations, (viz. displacement or assumed strain, etc.) and mesh refinement criteria employed, and to a lesser extent the choice of computer architecture (serial vs. parallel) and the equation solution procedures. A recommended pairing of some of the elements with the choice factors is suggested

Instantons and radial excitations in attractive Bose-Einstein condensates

Imaginary- and real-time versions of an equation for the condensate density are presented which describe dynamics and decay of any spherical Bose-Einstein condensate (BEC) within the mean field appraoch. We obtain quantized energies of collective finite amplitude radial oscillations and exact numerical instanton solutions which describe quantum tunneling from both the metastable and radially excited states of the BEC of 7Li atoms. The mass parameter for the radial motion is found different from the gaussian value assumed hitherto, but the effect of this difference on decay exponents is small. The collective breathing states form slightly compressed harmonic spectrum, n=4 state lying lower than the second Bogolyubov (small amplitude) mode. The decay of these states, if excited, may simulate a shorter than true lifetime of the metastable state. By scaling arguments, results extend to other attractive BEC-s.Comment: 6 pages, 3 figure

Limitation of energy deposition in classical N body dynamics

Energy transfers in collisions between classical clusters are studied with Classical N Body Dynamics calculations for different entrance channels. It is shown that the energy per particle transferred to thermalised classical clusters does not exceed the energy of the least bound particle in the cluster in its ``ground state''. This limitation is observed during the whole time of the collision, except for the heaviest system.Comment: 13 pages, 15 figures, 1 tabl

Coulomb Drag of Edge Excitations in the Chern-Simons Theory of the Fractional Quantum Hall Effect

Long range Coulomb interaction between the edges of a Hall bar changes the nature of the gapless edge excitations. Instead of independent modes propagating in opposite directions on each edge as expected for a short range interaction one finds elementary excitations living simultaneously on both edges, i.e. composed of correlated density waves propagating in the same direction on opposite edges. We discuss the microscopic features of this Coulomb drag of excitations in the fractional quantum Hall regime within the framework of the bosonic Chern-Simons Landau-Ginzburg theory. The dispersion law of these novel excitations is non linear and depends on the distance between the edges as well as on the current that flows through the sample. The latter dependence indicates a possibility of parametric excitation of these modes. The bulk distributions of the density and currents of the edge excitations differ significantly for short and long range interactions.Comment: 11 pages, REVTEX, 2 uuencoded postscript figure

Interaction and Localization of One-electron Orbitals in an Organic Molecule: Fictitious Parameter Analysis for Multi-physics Simulations

We present a new methodology to analyze complicated multi-physics simulations by introducing a fictitious parameter. Using the method, we study quantum mechanical aspects of an organic molecule in water. The simulation is variationally constructed from the ab initio molecular orbital method and the classical statistical mechanics with the fictitious parameter representing the coupling strength between solute and solvent. We obtain a number of one-electron orbital energies of the solute molecule derived from the Hartree-Fock approximation, and eigenvalue-statistical analysis developed in the study of nonintegrable systems is applied to them. Based on the results, we analyze localization properties of the electronic wavefunctions under the influence of the solvent.Comment: 4 pages, 5 figures, the revised version will appear in J. Phys. Soc. Jpn. Vol.76 (No.1