Teaching computers to fold proteins

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. In a test with 24 peptides of known structure, none folded correctly with the initial potential functions, but two-thirds came within 3{\AA} to their native fold after optimizing the potential functions.Comment: 4 pages, 3 figure

Robust statistics for deterministic and stochastic gravitational waves in non-Gaussian noise I: Frequentist analyses

Gravitational wave detectors will need optimal signal-processing algorithms to extract weak signals from the detector noise. Most algorithms designed to date are based on the unrealistic assumption that the detector noise may be modeled as a stationary Gaussian process. However most experiments exhibit a non-Gaussian ``tail'' in the probability distribution. This ``excess'' of large signals can be a troublesome source of false alarms. This article derives an optimal (in the Neyman-Pearson sense, for weak signals) signal processing strategy when the detector noise is non-Gaussian and exhibits tail terms. This strategy is robust, meaning that it is close to optimal for Gaussian noise but far less sensitive than conventional methods to the excess large events that form the tail of the distribution. The method is analyzed for two different signal analysis problems: (i) a known waveform (e.g., a binary inspiral chirp) and (ii) a stochastic background, which requires a multi-detector signal processing algorithm. The methods should be easy to implement: they amount to truncation or clipping of sample values which lie in the outlier part of the probability distribution.Comment: RevTeX 4, 17 pages, 8 figures, typos corrected from first version

Computing the merger of black-hole binaries: the IBBH problem

Gravitational radiation arising from the inspiral and merger of binary black holes (BBH's) is a promising candidate for detection by kilometer-scale interferometric gravitational wave observatories. This paper discusses a serious obstacle to searches for such radiation and to the interpretation of any observed waves: the inability of current computational techniques to evolve a BBH through its last ~10 orbits of inspiral (~100 radians of gravitational-wave phase). A new set of numerical-relativity techniques is proposed for solving this ``Intermediate Binary Black Hole'' (IBBH) problem: (i) numerical evolutions performed in coordinates co-rotating with the BBH, in which the metric coefficients evolve on the long timescale of inspiral, and (ii) techniques for mathematically freezing out gravitational degrees of freedom that are not excited by the waves.Comment: 6 pages RevTe

Academic Freedom

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Influence of Dopamine D2-type Receptors on Motor Behaviors and Conditioning in the Green Tree Frog, Hyla cinerea

Dopamine modulates a range of behaviors that include motor processes, learning, and incentive motivation. Neuroanatomical research supports conservation of dopaminergic populations in the midbrain across vertebrate species, however, less evidence is available for dopamine receptor distributions and function. In order to test the behavioral role of dopamine in a conserved dopaminergic system, the effects of D2-type receptor manipulation on motor behaviors were examined in the anuran amphibian green tree frog, Hyla cinerea. In two different experiments, frogs were treated with a D2 receptor-specific drug, quinpirole or haloperidol, and exposed to a testing session to measure changes in motor behaviors. Quinpirole generally inhibited some motor behaviors, while haloperidol generally stimulated some motor behaviors, as predicted based on receptor mechanisms. A pattern of performance improvement also appeared in frogs in each experiment. Overall, the results support general conservation of DA in motor processes in vertebrate species

Advanced LIGO's ability to detect apparent violations of the cosmic censorship conjecture and the no-hair theorem through compact binary coalescence detections

We study the ability of the advanced Laser Interferometer Gravitational-wave Observatory (aLIGO) to detect apparent violations of the cosmic censorship conjecture and the no-hair theorem. The cosmic censorship conjecture, which is believed to be true in the theory of general relativity, limits the spin-to-mass-squared ratio of a Kerr black hole. The no-hair theorem, which is also believed to be true in the theory of general relativity, suggests a particular value for the tidal Love number of a non-rotating black hole. Using the Fisher matrix formalism, we examine the measurability of the spin and tidal deformability of compact binary systems involving at least one putative black hole. Using parameter measurement errors and correlations obtained from the Fisher matrix, we determine the smallest detectable violation of bounds implied by the cosmic censorship conjecture and the no-hair theorem. We examine the effect of excluding unphysical areas of parameter space when determining the smallest detectable apparent violations, and we examine the effect of different post-Newtonian corrections to the amplitude of the compact binary coalescence gravitational waveform. In addition, we perform a brief study of how the recently calculated 3.0 pN and 3.5 pN spin-orbit corrections to the phase affect spin and mass parameter measurability. We find that physical priors on the symmetric mass ratio and higher harmonics in the gravitational waveform could significantly affect the ability of aLIGO to investigate cosmic censorship and the no-hair theorem for certain systems.Comment: 21 pages, 7 figures, 6 table

Upper limits on gravitational-wave signals based on loudest events

Searches for gravitational-wave bursts have often focused on the loudest event(s) in searching for detections and in determining upper limits on astrophysical populations. Typical upper limits have been reported on event rates and event amplitudes which can then be translated into constraints on astrophysical populations. We describe the mathematical construction of such upper limits.Comment: 8 pages, 1 figur