Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology

Models have made numerous contributions to evolutionary biology, but misunderstandings persist regarding their purpose. By formally testing the logic of verbal hypotheses, proof-of-concept models clarify thinking, uncover hidden assumptions, and spur new directions of study. thumbnail image credit: modified from the Biodiversity Heritage Librar

Fast Quantum Modular Exponentiation

We present a detailed analysis of the impact on modular exponentiation of architectural features and possible concurrent gate execution. Various arithmetic algorithms are evaluated for execution time, potential concurrency, and space tradeoffs. We find that, to exponentiate an n-bit number, for storage space 100n (twenty times the minimum 5n), we can execute modular exponentiation two hundred to seven hundred times faster than optimized versions of the basic algorithms, depending on architecture, for n=128. Addition on a neighbor-only architecture is limited to O(n) time when non-neighbor architectures can reach O(log n), demonstrating that physical characteristics of a computing device have an important impact on both real-world running time and asymptotic behavior. Our results will help guide experimental implementations of quantum algorithms and devices.Comment: to appear in PRA 71(5); RevTeX, 12 pages, 12 figures; v2 revision is substantial, with new algorithmic variants, much shorter and clearer text, and revised equation formattin

Kepler Presearch Data Conditioning II - A Bayesian Approach to Systematic Error Correction

With the unprecedented photometric precision of the Kepler Spacecraft, significant systematic and stochastic errors on transit signal levels are observable in the Kepler photometric data. These errors, which include discontinuities, outliers, systematic trends and other instrumental signatures, obscure astrophysical signals. The Presearch Data Conditioning (PDC) module of the Kepler data analysis pipeline tries to remove these errors while preserving planet transits and other astrophysically interesting signals. The completely new noise and stellar variability regime observed in Kepler data poses a significant problem to standard cotrending methods such as SYSREM and TFA. Variable stars are often of particular astrophysical interest so the preservation of their signals is of significant importance to the astrophysical community. We present a Bayesian Maximum A Posteriori (MAP) approach where a subset of highly correlated and quiet stars is used to generate a cotrending basis vector set which is in turn used to establish a range of "reasonable" robust fit parameters. These robust fit parameters are then used to generate a Bayesian Prior and a Bayesian Posterior Probability Distribution Function (PDF) which when maximized finds the best fit that simultaneously removes systematic effects while reducing the signal distortion and noise injection which commonly afflicts simple least-squares (LS) fitting. A numerical and empirical approach is taken where the Bayesian Prior PDFs are generated from fits to the light curve distributions themselves.Comment: 43 pages, 21 figures, Submitted for publication in PASP. Also see companion paper "Kepler Presearch Data Conditioning I - Architecture and Algorithms for Error Correction in Kepler Light Curves" by Martin C. Stumpe, et a

Localization, Coulomb interactions and electrical heating in single-wall carbon nanotubes/polymer composites

Low field and high field transport properties of carbon nanotubes/polymer composites are investigated for different tube fractions. Above the percolation threshold f_c=0.33%, transport is due to hopping of localized charge carriers with a localization length xi=10-30 nm. Coulomb interactions associated with a soft gap Delta_CG=2.5 meV are present at low temperature close to f_c. We argue that it originates from the Coulomb charging energy effect which is partly screened by adjacent bundles. The high field conductivity is described within an electrical heating scheme. All the results suggest that using composites close to the percolation threshold may be a way to access intrinsic properties of the nanotubes by experiments at a macroscopic scale.Comment: 4 pages, 5 figures, Submitted to Phys. Rev.

Spitzer Infrared Spectrograph Observations of M, L, and T Dwarfs

We present the first mid-infrared spectra of brown dwarfs, together with observations of a low-mass star. Our targets are the M3.5 dwarf GJ 1001A, the L8 dwarf DENIS-P J0255-4700, and the T1/T6 binary system epsilon Indi Ba/Bb. As expected, the mid-infrared spectral morphology of these objects changes rapidly with spectral class due to the changes in atmospheric chemistry resulting from their differing effective temperatures and atmospheric structures. By taking advantage of the unprecedented sensitivity of the Infrared Spectrograph on the Spitzer Space Telescope we have detected the 7.8 micron methane and 10 micron ammonia bands for the first time in brown dwarf spectra.Comment: 4 pages, 2 figure

Initial Characteristics of Kepler Short Cadence Data

The Kepler Mission offers two options for observations -- either Long Cadence (LC) used for the bulk of core mission science, or Short Cadence (SC) which is used for applications such as asteroseismology of solar-like stars and transit timing measurements of exoplanets where the 1-minute sampling is critical. We discuss the characteristics of SC data obtained in the 33.5-day long Quarter 1 (Q1) observations with Kepler which completed on 15 June 2009. The truly excellent time series precisions are nearly Poisson limited at 11th magnitude providing per-point measurement errors of 200 parts-per-million per minute. For extremely saturated stars near 7th magnitude precisions of 40 ppm are reached, while for background limited measurements at 17th magnitude precisions of 7 mmag are maintained. We note the presence of two additive artifacts, one that generates regularly spaced peaks in frequency, and one that involves additive offsets in the time domain inversely proportional to stellar brightness. The difference between LC and SC sampling is illustrated for transit observations of TrES-2.Comment: 5 pages, 4 figures, ApJ Letters in pres

Information-theoretic interpretation of quantum error-correcting codes

Quantum error-correcting codes are analyzed from an information-theoretic perspective centered on quantum conditional and mutual entropies. This approach parallels the description of classical error correction in Shannon theory, while clarifying the differences between classical and quantum codes. More specifically, it is shown how quantum information theory accounts for the fact that "redundant" information can be distributed over quantum bits even though this does not violate the quantum "no-cloning" theorem. Such a remarkable feature, which has no counterpart for classical codes, is related to the property that the ternary mutual entropy vanishes for a tripartite system in a pure state. This information-theoretic description of quantum coding is used to derive the quantum analogue of the Singleton bound on the number of logical bits that can be preserved by a code of fixed length which can recover a given number of errors.Comment: 14 pages RevTeX, 8 Postscript figures. Added appendix. To appear in Phys. Rev.

Extending scientific computing system with structural quantum programming capabilities

We present a basic high-level structures used for developing quantum programming languages. The presented structures are commonly used in many existing quantum programming languages and we use quantum pseudo-code based on QCL quantum programming language to describe them. We also present the implementation of introduced structures in GNU Octave language for scientific computing. Procedures used in the implementation are available as a package quantum-octave, providing a library of functions, which facilitates the simulation of quantum computing. This package allows also to incorporate high-level programming concepts into the simulation in GNU Octave and Matlab. As such it connects features unique for high-level quantum programming languages, with the full palette of efficient computational routines commonly available in modern scientific computing systems. To present the major features of the described package we provide the implementation of selected quantum algorithms. We also show how quantum errors can be taken into account during the simulation of quantum algorithms using quantum-octave package. This is possible thanks to the ability to operate on density matrices

Characterizing two solar-type Kepler subgiants with asteroseismology: KIC10920273 and KIC11395018

Determining fundamental properties of stars through stellar modeling has improved substantially due to recent advances in asteroseismology. Thanks to the unprecedented data quality obtained by space missions, particularly CoRoT and Kepler, invaluable information is extracted from the high-precision stellar oscillation frequencies, which provide very strong constraints on possible stellar models for a given set of classical observations. In this work, we have characterized two relatively faint stars, KIC10920273 and KIC11395018, using oscillation data from Kepler photometry and atmospheric constraints from ground-based spectroscopy. Both stars have very similar atmospheric properties; however, using the individual frequencies extracted from the Kepler data, we have determined quite distinct global properties, with increased precision compared to that of earlier results. We found that both stars have left the main sequence and characterized them as follows: KIC10920273 is a one-solar-mass star (M=1.00 +/- 0.04 M_sun), but much older than our Sun (t=7.12 +/- 0.47 Gyr), while KIC11395018 is significantly more massive than the Sun (M=1.27 +/- 0.04 M_sun) with an age close to that of the Sun (t=4.57 +/- 0.23 Gyr). We confirm that the high lithium abundance reported for these stars should not be considered to represent young ages, as we precisely determined them to be evolved subgiants. We discuss the use of surface lithium abundance, rotation and activity relations as potential age diagnostics.Comment: 12 pages, 3 figures, 5 tables. Accepted by Ap

Non-adaptive Measurement-based Quantum Computation and Multi-party Bell Inequalities

Quantum correlations exhibit behaviour that cannot be resolved with a local hidden variable picture of the world. In quantum information, they are also used as resources for information processing tasks, such as Measurement-based Quantum Computation (MQC). In MQC, universal quantum computation can be achieved via adaptive measurements on a suitable entangled resource state. In this paper, we look at a version of MQC in which we remove the adaptivity of measurements and aim to understand what computational abilities still remain in the resource. We show that there are explicit connections between this model of computation and the question of non-classicality in quantum correlations. We demonstrate this by focussing on deterministic computation of Boolean functions, in which natural generalisations of the Greenberger-Horne-Zeilinger (GHZ) paradox emerge; we then explore probabilistic computation, via which multipartite Bell Inequalities can be defined. We use this correspondence to define families of multi-party Bell inequalities, which we show to have a number of interesting contrasting properties.Comment: 13 pages, 4 figures, final version accepted for publicatio