Archaeal ubiquity

In the seventeenth century, Antoine von Leeuwenhook used a simple microscope to discover that we live within a previously undetected microbial world containing an enormously diverse population of creatures. The late nineteenth and early twentieth century brought advances in microbial culture techniques and in biochemistry, uncovering the roles that microbes play in all aspects of our world, from causing disease to modulating geochemical cycles. In the last 25 years, molecular biology has revealed the complexity and pervasiveness of the microbial world and its importance for understanding the interactions that maintain living systems on the planet. The paper by Preston et al. (1) in this issue of the Proceedings provides a clear illustration of the power of these molecular techniques to describe new biological relationships and to pose important questions about the mechanisms that drive evolution. The analysis of ribosomal RNA gene sequences is one molecular approach that has radically altered our view of microbial diversity. Its application can be extended and expedited by the use of PCR. The confluence of these techniques has stimulated the rapid assembly of sequence information from homologues rRNA gene regions derived from virtually all classes of organisms. The data collected thus far support the scheme first presented by Woese et al. (2), which holds that the relationships among organisms can be summarized in the form of a universal phylogenetic tree comprised of one eukaryotic and two prokaryotic domains: the Eucarya, the Bacteria, and the Archaea (Fig. 1)

The Order of Phase Transitions in Barrier Crossing

A spatially extended classical system with metastable states subject to weak spatiotemporal noise can exhibit a transition in its activation behavior when one or more external parameters are varied. Depending on the potential, the transition can be first or second-order, but there exists no systematic theory of the relation between the order of the transition and the shape of the potential barrier. In this paper, we address that question in detail for a general class of systems whose order parameter is describable by a classical field that can vary both in space and time, and whose zero-noise dynamics are governed by a smooth polynomial potential. We show that a quartic potential barrier can only have second-order transitions, confirming an earlier conjecture [1]. We then derive, through a combination of analytical and numerical arguments, both necessary conditions and sufficient conditions to have a first-order vs. a second-order transition in noise-induced activation behavior, for a large class of systems with smooth polynomial potentials of arbitrary order. We find in particular that the order of the transition is especially sensitive to the potential behavior near the top of the barrier.Comment: 8 pages, 6 figures with extended introduction and discussion; version accepted for publication by Phys. Rev.

Photonic band mixing in linear chains of optically coupled micro-spheres

The paper deals with optical excitations arising in a one-dimensional chain of identical spheres due optical coupling of whispering gallery modes (WGM). The band structure of these excitations depends significantly on the inter-mixing between WGMs characterized by different values of angular quantum number, $l$. We develop a general theory of the photonic band structure of these excitations taking these effects into account and applied it to several cases of recent experimental interest. In the case of bands originating from WQMs with the angular quantum number of the same parity, the calculated dispersion laws are in good qualitative agreement with recent experiment results. Bands resulting from hybridization of excitations resulting from whispering gallery modes with different parity of $l$ exhibits anomalous dispersion properties characterized by a gap in the allowed values of \emph{wave numbers} and divergence of group velocity.Comment: RevTex, 28 pages, 7 Figure

Giant Spin Relaxation Anisotropy in Zinc-Blende Heterostructures

Spin relaxation in-plane anisotropy is predicted for heterostructures based on zinc-blende semiconductors. It is shown that it manifests itself especially brightly if the two spin relaxation mechanisms (D'yakonov-Perel' and Rashba) are comparable in efficiency. It is demonstrated that for the quantum well grown along the [0 0 1] direction, the main axes of spin relaxation rate tensor are [1 1 0] and [1 -1 0].Comment: 3 pages, NO figure

Numerical MHD Simulations of Solar Magnetoconvection and Oscillations in Inclined Magnetic Field Regions

The sunspot penumbra is a transition zone between the strong vertical magnetic field area (sunspot umbra) and the quiet Sun. The penumbra has a fine filamentary structure that is characterized by magnetic field lines inclined toward the surface. Numerical simulations of solar convection in inclined magnetic field regions have provided an explanation of the filamentary structure and the Evershed outflow in the penumbra. In this paper, we use radiative MHD simulations to investigate the influence of the magnetic field inclination on the power spectrum of vertical velocity oscillations. The results reveal a strong shift of the resonance mode peaks to higher frequencies in the case of a highly inclined magnetic field. The frequency shift for the inclined field is significantly greater than that in vertical field regions of similar strength. This is consistent with the behavior of fast MHD waves.Comment: 9 pages, 6 figures, Solar Physics (in press

The Poisson-Boltzmann model for implicit solvation of electrolyte solutions: Quantum chemical implementation and assessment via Sechenov coefficients.

We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the solute. A hierarchy of approximations for this model includes a linear approximation for weak electrostatic potentials, finite size of the mobile electrolyte ions, and a Stern-layer correction. Recasting the Poisson-Boltzmann equations into Euler-Lagrange equations then significantly simplifies the derivation of the free energy of solvation for these approximate models. The parameters of the model are either fit directly to experimental observables-e.g., the finite ion size-or optimized for agreement with experimental results. Experimental data for this optimization are available in the form of Sechenov coefficients that describe the linear dependence of the salting-out effect of solutes with respect to the electrolyte concentration. In the final part, we rationalize the qualitative disagreement of the finite ion size modification to the Poisson-Boltzmann model with experimental observations by taking into account the electrolyte concentration dependence of the Stern layer. A route toward a revised model that captures the experimental observations while including the finite ion size effects is then outlined. This implementation paves the way for the study of electrochemical and electrocatalytic processes of molecules and cluster models with accurate electronic structure methods

Simulations of Oscillation Modes of the Solar Convection Zone

We use the three-dimensional hydrodynamic code of Stein and Nordlund to realistically simulate the upper layers of the solar convection zone in order to study physical characteristics of solar oscillations. Our first result is that the properties of oscillation modes in the simulation closely match the observed properties. Recent observations from SOHO/MDI and GONG have confirmed the asymmetry of solar oscillation line profiles, initially discovered by Duvall et al. In this paper we compare the line profiles in the power spectra of the Doppler velocity and continuum intensity oscillations from the SOHO/MDI observations with the simulation. We also compare the phase differences between the velocity and intensity data. We have found that the simulated line profiles are asymmetric and have the same asymmetry reversal between velocity and intensity as observed. The phase difference between the velocity and intensity signals is negative at low frequencies and jumps in the vicinity of modes as is also observed. Thus, our numerical model reproduces the basic observed properties of solar oscillations, and allows us to study the physical properties which are not observed.Comment: Accepted for publication in ApJ Letter

Pointwise consistency of the kriging predictor with known mean and covariance functions

This paper deals with several issues related to the pointwise consistency of the kriging predictor when the mean and the covariance functions are known. These questions are of general importance in the context of computer experiments. The analysis is based on the properties of approximations in reproducing kernel Hilbert spaces. We fix an erroneous claim of Yakowitz and Szidarovszky (J. Multivariate Analysis, 1985) that the kriging predictor is pointwise consistent for all continuous sample paths under some assumptions.Comment: Submitted to mODa9 (the Model-Oriented Data Analysis and Optimum Design Conference), 14th-19th June 2010, Bertinoro, Ital

Is Quantum Mechanics Compatible with an Entirely Deterministic Universe?

A b s t r a c t It will be argued that 1) the Bell inequalities are not equivalent with those inequalities derived by Pitowsky and others that indicate the Kolmogorovity of a probability model, 2) the original Bell inequalities are irrelevant to both the question of whether or not quantum mechanics is a Kolmogorovian theory as well as the problem of determinism, whereas 3) the Pitowsky type inequalities are not violated by quantum mechanics, hence 4) quantum mechanics is a Kolmogorovian probability theory, therefore, 5) it is compatible with an entirely deterministic universe.Comment: 15 pages, (compressed and uuencoded) Postscript (188 kb), preprint 94/0