Bayesian phylogenetic estimation of fossil ages

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized data sets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two data sets of 5.7% and 13.2% respectively. The median relative standard error (RSD) was 9.2% and 7.2% respectively, suggesting good precision, although with some outliers. In fact in the two data sets we analyze the phylogenetic estimates of fossil age is on average < 2 My from the midpoint age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the "morphological clock", and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.Comment: 28 pages, 8 figure

Screening effects in a density functional theory based description of molecular junctions in the Coulomb blockade regime

We recently introduced a method based on density functional theory (DFT) and non-equilibrium Green's function techniques (NEGF) for calculating the addition energies of single molecule nano-junctions in the Coulomb blockade (CB) regime. Here we apply this approach to benzene molecules lying parallel and at various distances from two aluminum fcc (111) surfaces, and discuss the distance dependence in our calculations in terms of electrostatic screening effects. The addition energies near the surface are reduced by about a factor of two, which is comparable to previously reported calculations employing a computationally far more demanding quasi-particle description

Dynamical diversity and metastability in a hindered granular column near jamming

Granular media jam into a panoply of metastable states. The way in which these states are achieved depends on the nature of local and global constraints on grains; here we investigate this issue by means of a non-equilibrium stochastic model of a hindered granular column near its jamming limit. Grains feel the constraints of grains above and below them differently, depending on their position. A rich phase diagram with four dynamical phases (ballistic, activated, logarithmic and glassy) is revealed. The statistics of the jamming time and of the metastable states reached as attractors of the zero-temperature dynamics is investigated in each of these phases. Of particular interest is the glassy phase, where intermittency and a strong deviation from Edwards' flatness are manifest.Comment: 23 pages, 12 figure

Metastable States in High Order Short-Range Spin Glasses

The mean number of metastable states in higher order short-range spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination numbers. For lattices with small connectivities, numerical simulations do not show any significant dependence on the relative positions of the interacting spins on the lattice, indicating thus that these systems can be described by a few macroscopic parameters. As an extremely anisotropic model we consider the low autocorrelated binary spin model and we show through numerical simulations that its landscape has an exceptionally large number of local optima

Glassy states in a shaken sandbox

Our model of shaken sand, presented in earlier work, has been extended to include a more realistic `glassy' state, i.e., when the sandbox is shaken at very low intensities of vibration. We revisit some of our earlier results, and compare them with our new results on the revised model. Our analysis of the glassy dynamics in our model shows that a variety of ground states is obtained; these fall in two categories, which we argue are representative of regular and irregular packings.Comment: 10 pages. 3 figures. To appear in Proceedings of Research Workshop on "Challenges in Granular Physics" (ICTP, Trieste, August 7-11, 2001). Special issue of Advances in Complex System

Dynamic Response of a Cylindrical Shell Segment Subjected to an Arbitrary Loading

Dynamic response analysis for underground cylindrical shell segments subjected to blast loadin

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently Bayesian MCMC has become the dominant method of divergence time estimation and fossil evidence has been re-interpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting has not been carefully investigated. Here we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis

Qualification model spacecraft tests for DEMP, SGEMP, and ESD effects

The development of a satellite design demonstration test program is described. The test approach is comprehensive in that it includes the effects from electrostatic discharge (ESD), system generated electromagnetic pulse (SGEMP), as well as dispersed electromagnetic pulses (DEMP). The comprehensive test concept is based on the similarity of the satellite's response to several environments