The algebra of the general Markov model on phylogenetic trees and networks

It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the K3ST model, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper we rectify this shortcoming by showing how to extend the general Markov model on trees to to include arbitrary splits; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the "splitting" operator that generates the branching process on phylogenetic trees. For simplicity we proceed by discussing the two state case and note that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the previous approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give a tentative argument that our approach to extending to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for the possibility of convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.Comment: 17 pages, 5 figure

Structural analysis of the starfish SALMFamide neuropeptides S1 and S2: The N-terminal region of S2 facilitates self-association

The neuropeptides S1 (GFNSALMFamide) and S2 (SGPYSFNSGLTFamide), which share sequence similarity, were discovered in the starfish Asterias rubens and are prototypical members of the SALMFamide family of neuropeptides in echinoderms. SALMFamide neuropeptides act as muscle relaxants and both S1 and S2 cause relaxation of cardiac stomach and tube foot preparations in vitro but S2 is an order of magnitude more potent than S1. Here we investigated a structural basis for this difference in potency using spectroscopic techniques. Circular dichroism spectroscopy showed that S1 does not have a defined structure in aqueous solution and this was supported by 2D nuclear magnetic resonance experiments. In contrast, we found that S2 has a well-defined conformation in aqueous solution. However, the conformation of S2 was concentration dependent, with increasing concentration inducing a transition from an unstructured to a structured conformation. Interestingly, this property of S2 was not observed in an N-terminally truncated analogue of S2 (short S2 or SS2; SFNSGLTFamide). Collectively, the data obtained indicate that the N-terminal region of S2 facilitates peptide self-association at high concentrations, which may have relevance to the biosynthesis and/or bioactivity of S2 in vivo

A Mission to Explore the Pioneer Anomaly

The Pioneer 10 and 11 spacecraft yielded the most precise navigation in deep space to date. These spacecraft had exceptional acceleration sensitivity. However, analysis of their radio-metric tracking data has consistently indicated that at heliocentric distances of $\sim 20-70$ astronomical units, the orbit determinations indicated the presence of a small, anomalous, Doppler frequency drift. The drift is a blue-shift, uniformly changing with a rate of $\sim(5.99 \pm 0.01)\times 10^{-9}$ Hz/s, which can be interpreted as a constant sunward acceleration of each particular spacecraft of $a_P = (8.74 \pm 1.33)\times 10^{-10} {\rm m/s^2}$. This signal has become known as the Pioneer anomaly. The inability to explain the anomalous behavior of the Pioneers with conventional physics has contributed to growing discussion about its origin. There is now an increasing number of proposals that attempt to explain the anomaly outside conventional physics. This progress emphasizes the need for a new experiment to explore the detected signal. Furthermore, the recent extensive efforts led to the conclusion that only a dedicated experiment could ultimately determine the nature of the found signal. We discuss the Pioneer anomaly and present the next steps towards an understanding of its origin. We specifically focus on the development of a mission to explore the Pioneer Anomaly in a dedicated experiment conducted in deep space.Comment: 8 pages, 9 figures; invited talk given at the 2005 ESLAB Symposium "Trends in Space Science and Cosmic Vision 2020", 19-21 April 2005, ESTEC, Noordwijk, The Netherland

The Advanced Compton Telescope

The Advanced Compton Telescope (ACT), the next major step in gamma-ray astronomy, will probe the fires where chemical elements are formed by enabling high-resolution spectroscopy of nuclear emission from supernova explosions. During the past two years, our collaboration has been undertaking a NASA mission concept study for ACT. This study was designed to (1) transform the key scientific objectives into specific instrument requirements, (2) to identify the most promising technologies to meet those requirements, and (3) to design a viable mission concept for this instrument. We present the results of this study, including scientific goals and expected performance, mission design, and technology recommendations

Fundamental Physics with the Laser Astrometric Test Of Relativity

The Laser Astrometric Test Of Relativity (LATOR) is a joint European-U.S. Michelson-Morley-type experiment designed to test the pure tensor metric nature of gravitation - a fundamental postulate of Einstein's theory of general relativity. By using a combination of independent time-series of highly accurate gravitational deflection of light in the immediate proximity to the Sun, along with measurements of the Shapiro time delay on interplanetary scales (to a precision respectively better than 0.1 picoradians and 1 cm), LATOR will significantly improve our knowledge of relativistic gravity. The primary mission objective is to i) measure the key post-Newtonian Eddington parameter \gamma with accuracy of a part in 10^9. (1-\gamma) is a direct measure for presence of a new interaction in gravitational theory, and, in its search, LATOR goes a factor 30,000 beyond the present best result, Cassini's 2003 test. The mission will also provide: ii) first measurement of gravity's non-linear effects on light to ~0.01% accuracy; including both the Eddington \beta parameter and also the spatial metric's 2nd order potential contribution (never measured before); iii) direct measurement of the solar quadrupole moment J2 (currently unavailable) to accuracy of a part in 200 of its expected size; iv) direct measurement of the "frame-dragging" effect on light by the Sun's gravitomagnetic field, to 1% accuracy. LATOR's primary measurement pushes to unprecedented accuracy the search for cosmologically relevant scalar-tensor theories of gravity by looking for a remnant scalar field in today's solar system. We discuss the mission design of this proposed experiment.Comment: 8 pages, 9 figures; invited talk given at the 2005 ESLAB Symposium "Trends in Space Science and Cosmic Vision 2020," 19-21 April 2005, ESTEC, Noodrwijk, The Netherland

Identification of Termite Species and Subspecies of the Genus Zootermopsis Using Near-Infrared Reflectance Spectroscopy

Dampwood termites of the genus Zootermopsis (Isoptera: Termopsidae) are an abundant group of basal termites found in temperate forests of western North America. Three species are currently recognized in the genus and one of these species is subdivided into two subspecies. Although morphological and genetic characters are useful in differentiating among the three species and the two subspecies, respectively, only hydrocarbon analysis can enable differentiation both among the three species and the two subspecies. Due to the limitations of hydrocarbon analysis, such as the need for fresh specimens, alternative methods that could rapidly and accurately identify Zootermopsis would be useful. Using a partial least squares analysis of near-infrared spectra, each of the Zootermopsis species and subspecies were identified with greater than 95% and 80% accuracy, respectively. Neural network analysis of the near-infrared spectra successfully enabled the identification of the species and subspecies with greater than 99% accuracy. The inexpensive, reproducible, and rapid nature of near-infrared spectroscopy makes it a viable alternative to morphological, hydrocarbon, or genetic analysis for identifying Zootermopsis

Single electron emission in two-phase xenon with application to the detection of coherent neutrino-nucleus scattering

We present an experimental study of single electron emission in ZEPLIN-III, a two-phase xenon experiment built to search for dark matter WIMPs, and discuss applications enabled by the excellent signal-to-noise ratio achieved in detecting this signature. Firstly, we demonstrate a practical method for precise measurement of the free electron lifetime in liquid xenon during normal operation of these detectors. Then, using a realistic detector response model and backgrounds, we assess the feasibility of deploying such an instrument for measuring coherent neutrino-nucleus elastic scattering using the ionisation channel in the few-electron regime. We conclude that it should be possible to measure this elusive neutrino signature above an ionisation threshold of $\sim$3 electrons both at a stopped pion source and at a nuclear reactor. Detectable signal rates are larger in the reactor case, but the triggered measurement and harder recoil energy spectrum afforded by the accelerator source enable lower overall background and fiducialisation of the active volume

The Schro¨\ddot{o}dinger-Poisson equations as the large-N limit of the Newtonian N-body system: applications to the large scale dark matter dynamics

In this paper it is argued how the dynamics of the classical Newtonian N-body system can be described in terms of the Schr$\ddot{o}$dinger-Poisson equations in the large $N$ limit. This result is based on the stochastic quantization introduced by Nelson, and on the Calogero conjecture. According to the Calogero conjecture, the emerging effective Planck constant is computed in terms of the parameters of the N-body system as $\hbar \sim M^{5/3} G^{1/2} (N/)^{1/6}$, where is $G$ the gravitational constant, $N$ and $M$ are the number and the mass of the bodies, and $$ is their average density. The relevance of this result in the context of large scale structure formation is discussed. In particular, this finding gives a further argument in support of the validity of the Schr$\ddot{o}$dinger method as numerical double of the N-body simulations of dark matter dynamics at large cosmological scales.Comment: Accepted for publication in the Euro. Phys. J.

Applications of Field-Theoretic Renormalization Group Methods to Reaction-Diffusion Problems

We review the application of field-theoretic renormalization group (RG) methods to the study of fluctuations in reaction-diffusion problems. We first investigate the physical origin of universality in these systems, before comparing RG methods to other available analytic techniques, including exact solutions and Smoluchowski-type approximations. Starting from the microscopic reaction-diffusion master equation, we then pedagogically detail the mapping to a field theory for the single-species reaction k A -> l A (l < k). We employ this particularly simple but non-trivial system to introduce the field-theoretic RG tools, including the diagrammatic perturbation expansion, renormalization, and Callan-Symanzik RG flow equation. We demonstrate how these techniques permit the calculation of universal quantities such as density decay exponents and amplitudes via perturbative eps = d_c - d expansions with respect to the upper critical dimension d_c. With these basics established, we then provide an overview of more sophisticated applications to multiple species reactions, disorder effects, L'evy flights, persistence problems, and the influence of spatial boundaries. We also analyze field-theoretic approaches to nonequilibrium phase transitions separating active from absorbing states. We focus particularly on the generic directed percolation universality class, as well as on the most prominent exception to this class: even-offspring branching and annihilating random walks. Finally, we summarize the state of the field and present our perspective on outstanding problems for the future.Comment: 10 figures include