Resolving genetic functions within microbial populations: In situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization

Prokaryotes represent one-half of the living biomass on Earth, with the vast majority remaining elusive to culture and study within the laboratory. As a result, we lack a basic understanding of the functions that many species perform in the natural world. To address this issue, we developed complementary population and single-cell stable isotope (C-13)-linked analyses to determine microbial identity and function in situ. We demonstrated that the use of rRNA/mRNA stable isotope probing (SIP) recovered the key phylogenetic and functional RNAs. This was followed by single-cell physiological analyses of these populations to determine and quantify in situ functions within an aerobic naphthalene-degrading groundwater microbial community. Using these culture-independent approaches, we identified three prokaryote species capable of naphthalene biodegradation within the groundwater system: two taxa were isolated in the laboratory (Pseudomonas fluorescens and Pseudomonas putida), whereas the third eluded culture (an Acidovorax sp.). Using parallel population and single-cell stable isotope technologies, we were able to identify an unculturable Acidovorax sp. which played the key role in naphthalene biodegradation in situ, rather than the culturable naphthalene-biodegrading Pseudomonas sp. isolated from the same groundwater. The Pseudomonas isolates actively degraded naphthalene only at naphthalene concentrations higher than 30 mu M. This study demonstrated that unculturable microorganisms could play important roles in biodegradation in the ecosystem. It also showed that the combined RNA SIP-Raman-fluorescence in situ hybridization approach may be a significant tool in resolving ecology, functionality, and niche specialization within the unculturable fraction of organisms residing in the natural environment.

Simulation of whole building coupled hygrothermal-airflow transfer in different climates

The coupled heat, air and moisture transfer between building envelopes and indoor air is complicated, and has a significant influence on the indoor environment and the energy performance of buildings. In the paper, a model for predicting coupled multi-zone hygrothermal-airflow transfer is presented. Both heat and moisture transfer in the building envelope and multi-zone indoor airflow are simultaneously considered; their interactions are modeled. The coupled system model is implemented into Matlab–Simulink, and is validated by using a series of testing tools and experiments. The new program is applied to investigate the moisture transfer effect on indoor air humidity and building energy consumption in different climates (hot-humid, temperate and hot-dry climates). The results show that not accounting for hygrothermal effects in modeling will result in overestimation of energy costs for hot and humid climate situations and possible over sizing of plant leading to inefficient operation.

Optical transmission through single subwavelength apertures using prism coupled input of laser light of annular intensity profile

Light transmission through a single subwavelength aperture in a silver film is examined with a novel input configuration comprising an annular laser beam of variable diameter that is prism-coupled to the back face of the silver. Transmission peaks driven by excitation of the back-face surface plasmon mode or by the aperture resonance itself are separately observed. For both cases, comparison of films with and without a front-face, circular grating implies significantly more efficient coupling from the aperture fields to the front-face surface plasmon than directly to free radiation. (c) 2007 Optical Society of America.

Hot Electrons Transverse Refluxing in Ultraintense Laser-Solid Interactions

We have analyzed the coupling of ultraintense lasers (at similar to 2 X 1019 W/cm(2)) with solid foils of limited transverse extent (similar to 10 s of mu m) by monitoring the electrons and ions emitted from the target. We observe that reducing the target surface area allows electrons at the target surface to be reflected from the target edges during or shortly after the laser pulse. This transverse refluxing can maintain a hotter, denser and more homogeneous electron sheath around the target for a longer time. Consequently, when transverse refluxing takes places within the acceleration time of associated ions, we observe increased maximum proton energies (up to threefold), increased laser-to-ion conversion efficiency (up to a factor 30), and reduced divergence which bodes well for a number of applications.

Nonlinear modulation of transverse dust lattice waves in complex plasma crystals

The occurrence of the modulational instability in transverse dust lattice waves propagating in a one-dimensional dusty plasma crystal is investigated. The amplitude modulation mechanism, which is related to the intrinsic nonlinearity of the sheath electric field, is shown to destabilize the carrier wave under certain conditions, possibly leading to the formation of localized envelope excitations. Explicit expressions for the instability growth rate and threshold are presented and discussed. (C) 2004 American Institute of Physics.

Weakly nonlinear effects associated with transverse oscillations in dusty plasma crystals

We study the amplitude modulation of transverse dust lattice waves (TDLW) propagating in a single- and double-layer dusty plasma (DP) crystal. It is shown that a modulational instability mechanism, which is related to an intrinsic nonlinearity of the sheath electric field, may occur under certain conditions. Possibility of the formation of localized excitations (envelope solitons) in the dusty plasma crystal is discussed.

Modulational instability and localized excitations involving two nonlinearly coupled upper-hybrid waves in plasmas

The nonlinear coupling between two perpendicularly propagating ( with respect to the external magnetic field direction) upper-hybrid ( UH) waves in a uniform magnetoplasma is considered, taking into account quasi-stationary density perturbations which are driven by the UH wave ponderomotive force. This interaction is governed by a pair of coupled nonlinear Schrodinger equations ( CNLSEs) for the UH wave envelopes. The CNLSEs are used to investigate the occurrence of modulational instability. Waves in the vicinity of the UH resonance are considered, so that the group dispersion terms for both waves are approximately equal, but the UH wave group velocities may be different. It is found that a pair of unstable UH waves ( obeying anomalous group dispersion) yields an increased instability growth rate, while a pair of stable UH waves ( individually obeying normal group dispersion) remains stable for equal group velocities, although it is destabilized by a finite group velocity mismatch. Stationary nonlinear solutions of the CNLSEs are presented.

Dynamics of nonlinearly coupled magnetic-field-aligned electromagnetic electron-cyclotron waves near the zero-group-dispersion point in magnetized plasmas

The nonlinear coupling between two magnetic-field-aligned electromagnetic electron-cyclotron (EMEC) waves in plasmas is considered. Evaluating the ponderomotive coupling between the EMEC waves and quasistationary plasma density perturbations, a pair of coupled nonlinear Schrodinger equations (CNLSEs) is obtained. The CNLSEs are then used to investigate the occurrence of modulational instability in magnetized plasmas. Waves in the vicinity of the zero-group-dispersion point are considered, so that the group dispersion terms may either bear the same or different signs. It is found that a stable EMEC wave can be destabilized due to its nonlinear interactions with an unstable one, while a pair of unstable EMEC waves yields an increased instability growth rate. Individually stable waves remain stable while interacting with one another. Stationary nonlinear solutions of the coupled equations are presented. The relevance of our investigation to nonlinear phenomena in space plasmas is discussed. (c) 2005 American Institute of Physics.

Localized excitations of charged dust grains in dusty plasma lattices

The nonlinear aspects of charged dust grain motion in a one-dimensional dusty plasma (DP) monolayer are discussed. Both horizontal (longitudinal, acoustic mode) and vertical (transverse, optic mode) displacements are considered, and various types of localized excitations are reviewed, in a continuum approximation. Dust crystals are shown to support nonlinear kink-shaped supersonic longitudinal solitary excitations, as well as modulated envelope (either longitudinal or transverse) localized modes. The possibility for Discrete Breather (DB-) type excitations (Intrinsic Localized Modes, ILMs) to occur is investigated, from first principles. These highly localized excitations owe their existence to lattice discreteness, in combination with the interaction and/or
substrate (sheath) potential nonlinearity. This possibility may open new directions in DP- related research. The relation to previous results on atomic chains as well as to experimental results on strongly-coupled dust layers in gas discharge plasmas is discussed.

Nonlinearly coupled whistlers and dust-acoustic perturbations in dusty plasmas

The nonlinear interaction between magnetic-field-aligned coherent whistlers and dust-acoustic perturbations (DAPs) in a magnetized dusty plasma is considered. The interaction is governed by a pair of equations consisting of a nonlinear Schrodinger equation for the modulated whistler wave packet and an equation for the nonresonant DAPs in the presence of the ponderomotive force generated by the whistlers. The coupled equations are employed to investigate the occurrence of modulational instability, in addition to the formation of whistler envelope solitons. This investigation is relevant to amplitude modulated electron whistlers in magnetized space dusty plasmas. (c) 2005 American Institute of Physics.

Stability of dust lattice modes in the presence of charged dust grain polarization in plasmas

We discuss the effect of the attractive force associated with overlapping Debye spheres on the dispersion properties of the longitudinal and transverse dust lattice waves in strongly coupled dust crystals. The dust grain attraction is shown to contribute to a destabilization of the longitudinal dust lattice oscillations. The (optic-like) transverse mode dispersion law is shown to change. due to the Debye sphere dressing effect, from the known inverse-dispersive ("backward wave") form into a normal dispersive law (i.e. the group velocity changes sign). The stability of one-dimensionless bi-layers, consisting of (alternating) negatively and positively charged dust particles, is also discussed. The range of parameter values (mainly in terms of the lattice parameter kappa) where the above predictions are valid, are presented. (c) 2005 Elsevier B.V. All rights reserved.

Parametric instabilities and localization of nonlinearly coupled electromagnetic modes in astrophysical dusty plasmas

The nonlinear coupling between the Alfven-Rao (AR) and dust-Alfven (DA) modes in a uniform magnetized dusty plasma is considered. For this purpose, multi- fluid equations (composed of the continuity and momentum equations), the laws of Faraday and Ampere and the quasi-neutrality condition are adopted to derive a set of equations, which show how the fields of the modes are nonlinearly coupled. The equations are then used to investigate decay and modulational instabilities in magnetized dusty plasmas. Stationary nonlinear solutions of the coupled AR and DA equations are presented. The relevance of the investigation to nonlinear phenomena (instabilities and localized structures) in interstellar molecular clouds is also discussed.

Modulated transverse off-plane dust-lattice wave packets in hexagonal two-dimensional dusty plasma crystals

The propagation of nonlinear dust-lattice waves in a two-dimensional hexagonal crystal is investigated. Transverse (off-plane) dust grain oscillatory motion is considered in the form of a backward propagating wave packet whose linear and nonlinear characteristics are investigated. An evolution equation is obtained for the slowly varying amplitude of the first (fundamental) harmonic by making use of a two-dimensional lattice multiple scales technique. An analysis based on the continuum approximation (spatially extended excitations compared to the lattice spacing) shows that wave packets will be modulationally stable and that dark-type envelope solitons (density holes) may occur in the long wavelength region. Evidence is provided of modulational instability and of the occurrence of bright-type envelopes (pulses) at shorter wavelengths. The role of second neighbor interactions is also investigated and is shown to be rather weak in determining the modulational stability region. The effect of dissipation, assumed negligible in the algebra throughout the article, is briefly discussed.