Bagging statistical network inference from large-scale gene expression data.

Modern biology and medicine aim at hunting molecular and cellular causes of biological functions and diseases. Gene regulatory networks (GRN) inferred from gene expression data are considered an important aid for this research by providing a map of molecular interactions. Hence, GRNs have the potential enabling and enhancing basic as well as applied research in the life sciences. In this paper, we introduce a new method called BC3NET for inferring causal gene regulatory networks from large-scale gene expression data. BC3NET is an ensemble method that is based on bagging the C3NET algorithm, which means it corresponds to a Bayesian approach with noninformative priors. In this study we demonstrate for a variety of simulated and biological gene expression data from S. cerevisiae that BC3NET is an important enhancement over other inference methods that is capable of capturing biochemical interactions from transcription regulation and protein-protein interaction sensibly. An implementation of BC3NET is freely available as an R package from the CRAN repository. © 2012 de Matos Simoes, Emmert-Streib.

Ubiquitous Nature of Multimode Vibrational Resonances in Positron-Molecule Annihilation

Positron annihilation on many molecules occurs via positron capture into vibrational Feshbach resonances, with annihilation rates often further enhanced by energy transfer to vibrational excitations weakly coupled to the positron continuum. Data presented here uncover another scenario in which the positron couples directly to a quasicontinuum of multimode vibrational states. A model that assumes excitation and escape from a statistically complete ensemble of multimode vibrations is presented that reproduces key features of the data.

The Biomuse Trio in Conversation

The Biomuse Trio (R. Benjamin Knapp, Eric Lyon, Gascia Ouzounian) was formed in 2008 to perform computer chamber music integrating performance, laptop processing of sound and the transduction of bio-signals for the control of musical gesture. The work of the ensemble encompasses hardware design, audio signal processing, bio-signal processing, composition, improvisation and gesture choreography. The Biomuse Trio has performed and lectured across North America and Europe, including at BEAM Festival, CHI, Diapason Gallery, Green Man Festival, Issue Project Room, NIME, Science Gallery Dublin, STEIM and TheatreLab NYC.

Fauna

Stapleton’s self designed instrument, the BoSS (Bonsai Sound Sculpture, 2010) combines with Rose’s circular breathed baritone, multi-phonic and harmonic textures, to explore other sound worlds through real time interaction/composition. The method of exploration commits to a free improvisation aesthetic whereby the music is created at the point of performance. Encountering one another’s music while performing at the ‘Call them Improvisers’ performance at SARC, an ensemble directed by Evan Parker (November 2010) an affinity to the possibilities of one another’s particular approach became immediately apparent. This strongly identified connection led them to further explore the musical possibilities within the parameters created by the duo setting. Duo activities include concerts at Ausland (Berlin), SARC (Belfast), Sowieso (Berlin), Wendel (Berlin), and a recording with Elmar Susse in Hoffnungskirche, Pankow released by the California-based pfMENTUM record label in 2013.

This output is published in the form of an audio CD on the pfMENTUM record label.

Audley's Remix 2012

Commissioned by Esther Lamneck and Premiered by the NYU New Music Ensemble

Strong Coupling and Long-Range Collective Interactions in Optomechanical Arrays

We investigate the collective optomechanics of an ensemble of scatterers inside a Fabry-Pérot resonator and identify an optimized configuration where the ensemble is transmissive, in contrast to the usual reflective optomechanics approach. In this configuration, the optomechanical coupling of a specific collective mechanical mode can be several orders of magnitude larger than the single-element case, and long-range interactions can be generated between the different elements since light permeates throughout the array. This new regime should realistically allow for achieving strong single-photon optomechanical coupling with massive resonators, realizing hybrid quantum interfaces, and exploiting collective long-range interactions in arrays of atoms or mechanical oscillators.

Monte Carlo radiation hydrodynamics:Methods, tests and application to Type Ia supernova ejecta

In astrophysical systems, radiation-matter interactions are important in transferring energy and momentum between the radiation field and the surrounding material. This coupling often makes it necessary to consider the role of radiation when modelling the dynamics of astrophysical fluids. During the last few years, there have been rapid developments in the use of Monte Carlo methods for numerical radiative transfer simulations. Here, we present an approach to radiation hydrodynamics that is based on coupling Monte Carlo radiative transfer techniques with finite-volume hydrodynamical methods in an operator-split manner. In particular, we adopt an indivisible packet formalism to discretize the radiation field into an ensemble of Monte Carlo packets and employ volume-based estimators to reconstruct the radiation field characteristics. In this paper the numerical tools of this method are presented and their accuracy is verified in a series of test calculations. Finally, as a practical example, we use our approach to study the influence of the radiation-matter coupling on the homologous expansion phase and the bolometric light curve of Type Ia supernova explosions. © 2012 The Authors Monthly Notices of the Royal Astronomical Society © 2012 RAS.

Simulations of Biased Agonists in the β2 Adrenergic Receptor with Accelerated Molecular Dynamics

The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signalling pathway a GPCR promotes intracellular signals though ß-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signalling through the G protein and ß-arrestin. Here we report on the dynamics of the ß2 adrenergic receptor bound to the ß-arrestin and G protein biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring the transition within the nanosecond timescale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the ß-arrestin biased agonist, N-cyclopentylbutanepherine we observe a different pattern of motions in helix 7 when compared to simulations with the G protein biased agonist, Salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs. © 2013 American Chemical Society

Dialogic Instruments: Virtuosity (Re)Located in Improvised Performance

This paper introduces a series of new musical instruments that have been designed to
address questions relating to performative virtuosity in the area of ensemble-based
improvisation. The intentionally exploited inconsistent nature of these instruments
raises questions around traditional notions of instrument mastery and opens up
possible methods of recon?guring the performer-instrument relationship.

When Casimir meets Kibble-Zurek

Verification of the dynamical Casimir effect (DCE) in optical systems is still elusive due to the very demanding requirements for its experimental implementation. This typically requires very fast changes in the boundary conditions of the problem. We show that an ensemble of two-level atoms collectively coupled to the electromagnetic field of a cavity, driven at low frequencies and close to a quantum phase transition, stimulates the production of photons from the vacuum. This paves the way for an effective simulation of the DCE through a mechanism that has recently found experimental demonstration. The spectral properties of the emitted radiation reflect the critical nature of the system and allow us to link the detection of DCE to the Kibble-Zurek mechanism for the production of defects when crossing a continuous phase transition.

Starbog: The Garden Virtuoso and the Turing Machine

This article will discuss a recent ensemble composition entitled Starbog which was toured and broadcast in Britain in 2006 . The composition of Starbog focused on developing working methods which combined computer-based techniques (using OpenMusic) with more subconscious means of generating musical ideas. The challenge in achieving this was as much aesthetic/philosophical as it was technical and the present article is intending as a ‘sounding’ which focuses on the influence OpenMusic has had on the composer’s music, rather than documenting the nature of the often simple application of algorithms.

The persistent activity of Jupiter-family comets at 3-7 AU

We present an analysis of comet activity based on the Spitzer Space Telescope component of the Survey of the Ensemble Physical Properties of Cometary Nuclei. We show that the survey is well suited to measuring the activity of Jupiter-family comets at 3-7 AU from the Sun. Dust was detected in 33 of 89 targets (37 ± 6%), and we conclude that 21 comets (24 ± 5%) have morphologies that suggest ongoing or recent cometary activity. Our dust detections are sensitivity limited, therefore our measured activity rate is necessarily a lower limit. All comets with small perihelion distances (q <1.8 AU) are inactive in our survey, and the active comets in our sample are strongly biased to post-perihelion epochs. We introduce the quantity ɛfρ, intended to be a thermal emission counterpart to the often reported Afρ, and find that the comets with large perihelion distances likely have greater dust production rates than other comets in our survey at 3-7 AU from the Sun, indicating a bias in the discovered Jupiter-family comet population. By examining the orbital history of our survey sample, we suggest that comets perturbed to smaller perihelion distances in the past 150 yr are more likely to be active, but more study on this effect is needed.

Thermal properties, sizes, and size distribution of Jupiter-family cometary nuclei

We present results from SEPPCoN, an on-going Survey of the Ensemble Physical Properties of Cometary Nuclei. In this report we discuss mid-infrared measurements of the thermal emission from 89 nuclei of Jupiter-family comets (JFCs). All data were obtained in 2006 and 2007 using imaging capabilities of the Spitzer Space Telescope. The comets were typically 4-5 AU from the Sun when observed and most showed only a point-source with little or no extended emission from dust. For those comets showing dust, we used image processing to photometrically extract the nuclei. For all 89 comets, we present new effective radii, and for 57 comets we present beaming parameters. Thus our survey provides the largest compilation of radiometrically-derived physical properties of nuclei to date. We have six main conclusions: (a) The average beaming parameter of the JFC population is 1.03 ± 0.11, consistent with unity; coupled with the large distance of the nuclei from the Sun, this indicates that most nuclei have Tempel 1-like thermal inertia. Only two of the 57 nuclei had outlying values (in a statistical sense) of infrared beaming. (b) The known JFC population is not complete even at 3 km radius, and even for comets that approach to ˜2 AU from the Sun and so ought to be more discoverable. Several recently-discovered comets in our survey have small perihelia and large (above ˜2 km) radii. (c) With our radii, we derive an independent estimate of the JFC nuclear cumulative size distribution (CSD), and we find that it has a power-law slope of around -1.9, with the exact value depending on the bounds in radius. (d) This power-law is close to that derived by others from visible-wavelength observations that assume a fixed geometric albedo, suggesting that there is no strong dependence of geometric albedo with radius. (e) The observed CSD shows a hint of structure with an excess of comets with radii 3-6 km. (f) Our CSD is consistent with the idea that the intrinsic size distribution of the JFC population is not a simple power-law and lacks many sub-kilometer objects.

Dynamics of interacting Dicke model in a coupled-cavity array

We consider the dynamics of an array of mutually interacting cavities, each containing an ensemble of N two-level atoms. By exploring the possibilities offered by ensembles of various dimensions and a range of atom-light and photon-hopping values, we investigate the generation of multisite entanglement, as well as the performance of excitation transfer across the array, resulting from the competition between on-site nonlinearities of the matter-light interaction and intersite photon hopping. In particular, for a three-cavity interacting system it is observed that the initial excitation in the first cavity completely transfers to the ensemble in the third cavity through the hopping of photons between the adjacent cavities. Probabilities of the transfer of excitation of the cavity modes and ensembles exhibit characteristics of fast and slow oscillations governed by coupling and hopping parameters, respectively. In the large-hopping case, by seeding an initial excitation in the cavity at the center of the array, a tripartite W state, as well as a bipartite maximally entangled state, is obtained, depending on the interaction time. Population of the ensemble in a cavity has a positive impact on the rate of excitation transfer between the ensembles and their local cavity modes. In particular, for ensembles of five to seven atoms, tripartite W states can be produced even when the hopping rate is comparable to the cavity-atom coupling rate. A similar behavior of the transfer of excitation is observed for a four-coupled-cavity system with two initial excitations.

Collectively enhanced optomechanical coupling in periodic arrays of scatterers

We investigate the optomechanical properties of a periodic array of identical scatterers placed inside an optical cavity and extend our previous results. We show that operating at the points where the array is transmissive results in linear optomechanical coupling strengths between the cavity field and collective motional modes of the array that may be several orders of magnitude larger than is possible with an equivalent reflective ensemble. We describe and interpret these effects in detail and investigate the nature of the scaling laws of the coupling strengths for the different transmissive points in various regimes. © 2013 American Physical Society.