Beta-agonist- and prostaglandin E1-induced translocation of the beta-adrenergic receptor kinase: evidence that the kinase may act on multiple adenylate cyclase-coupled receptors.

beta-Adrenergic receptor kinase (beta-AR kinase) is a cytosolic enzyme that phosphorylates the beta-adrenergic receptor only when it is occupied by an agonist [Benovic, J. Strasser, R. H., Caron, M. G. & Lefkowitz, R. J. (1986) Proc. Natl. Acad. Sci. USA 83, 2797-2801.] It may be crucially involved in the processes that lead to homologous or agonist-specific desensitization of the receptor. Stimulation of DDT1MF-2 hamster smooth muscle cells or S49 mouse lymphoma cells with a beta-agonist leads to translocation of 80-90% of the beta-AR kinase activity from the cytosol to the plasma membrane. The translocation process is quite rapid, is concurrent with receptor phosphorylation, and precedes receptor desensitization and sequestration. It is also transient, since much of the activity returns to the cytosol as the receptors become sequestered. Stimulation of beta-AR kinase translocation is a receptor-mediated event, since the beta-antagonist propranolol blocks the effect of agonist. In the kin- mutant of the S49 cells (lacks cAMP-dependent protein kinase), prostaglandin E1, which provokes homologous desensitization of its own receptor, is at least as effective as isoproterenol in promoting beta-AR kinase translocation to the plasma membrane. However, in the DDT1MF-2 cells, which contain alpha 1-adrenergic receptors coupled to phosphatidylinositol turnover, the alpha 1-agonist phenylephrine is ineffective. These results suggest that the first step in homologous desensitization of the beta-adrenergic receptor may be an agonist-promoted translocation of beta-AR kinase from cytosol to plasma membrane and that beta-AR kinase may represent a more general adenylate cyclase-coupled receptor kinase that participates in regulating the function of many such receptors.

Waveguide QED: Many-body bound-state effects in coherent and Fock-state scattering from a two-level system

Strong coupling between a two-level system (TLS) and bosonic modes produces dramatic quantum optics effects. We consider a one-dimensional continuum of bosons coupled to a single localized TLS, a system which may be realized in a variety of plasmonic, photonic, or electronic contexts. We present the exact many-body scattering eigenstate obtained by imposing open boundary conditions. Multiphoton bound states appear in the scattering of two or more photons due to the coupling between the photons and the TLS. Such bound states are shown to have a large effect on scattering of both Fock- and coherent-state wave packets, especially in the intermediate coupling-strength regime. We compare the statistics of the transmitted light with a coherent state having the same mean photon number: as the interaction strength increases, the one-photon probability is suppressed rapidly, and the two- and three-photon probabilities are greatly enhanced due to the many-body bound states. This results in non-Poissonian light. © 2010 The American Physical Society.

Control of radiative processes using tunable plasmonic nanopatch antennas.

The radiative processes associated with fluorophores and other radiating systems can be profoundly modified by their interaction with nanoplasmonic structures. Extreme electromagnetic environments can be created in plasmonic nanostructures or nanocavities, such as within the nanoscale gap region between two plasmonic nanoparticles, where the illuminating optical fields and the density of radiating modes are dramatically enhanced relative to vacuum. Unraveling the various mechanisms present in such coupled systems, and their impact on spontaneous emission and other radiative phenomena, however, requires a suitably reliable and precise means of tuning the plasmon resonance of the nanostructure while simultaneously preserving the electromagnetic characteristics of the enhancement region. Here, we achieve this control using a plasmonic platform consisting of colloidally synthesized nanocubes electromagnetically coupled to a metallic film. Each nanocube resembles a nanoscale patch antenna (or nanopatch) whose plasmon resonance can be changed independent of its local field enhancement. By varying the size of the nanopatch, we tune the plasmonic resonance by ∼ 200 nm, encompassing the excitation, absorption, and emission spectra corresponding to Cy5 fluorophores embedded within the gap region between nanopatch and film. By sweeping the plasmon resonance but keeping the field enhancements roughly fixed, we demonstrate fluorescence enhancements exceeding a factor of 30,000 with detector-limited enhancements of the spontaneous emission rate by a factor of 74. The experiments are supported by finite-element simulations that reveal design rules for optimized fluorescence enhancement or large Purcell factors.

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs) that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength, hundreds of them confirmed by directly observable allele-specific binding bias. The majority of QTLs were either within 1 kb of the CTCF binding motif, or in linkage disequilibrium with a variant within 1 kb of the motif. On the X chromosome we observed three classes of binding sites: a minority class bound only to the active copy of the X chromosome, the majority class bound to both the active and inactive X, and a small set of female-specific CTCF sites associated with two non-coding RNA genes. In sum, our data reveal extensive genetic effects on CTCF binding, both direct and indirect, and identify a diversity of patterns of CTCF binding on the X chromosome.

Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates.

Cells have evolved oscillators with different frequencies to coordinate periodic processes. Here we studied the interaction of two oscillators, the cell division cycle (CDC) and the yeast metabolic cycle (YMC), in budding yeast. Previous work suggested that the CDC and YMC interact to separate high oxygen consumption (HOC) from DNA replication to prevent genetic damage. To test this hypothesis, we grew diverse strains in chemostat and measured DNA replication and oxygen consumption with high temporal resolution at different growth rates. Our data showed that HOC is not strictly separated from DNA replication; rather, cell cycle Start is coupled with the initiation of HOC and catabolism of storage carbohydrates. The logic of this YMC-CDC coupling may be to ensure that DNA replication and cell division occur only when sufficient cellular energy reserves have accumulated. Our results also uncovered a quantitative relationship between CDC period and YMC period across different strains. More generally, our approach shows how studies in genetically diverse strains efficiently identify robust phenotypes and steer the experimentalist away from strain-specific idiosyncrasies.

Cell cycle start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates

© 2016 Burnetti et al. Cells have evolved oscillators with different frequencies to coordinate periodic processes. Here we studied the interaction of two oscillators, the cell division cycle (CDC) and the yeast metabolic cycle (YMC), in budding yeast. Previous work suggested that the CDC and YMC interact to separate high oxygen consumption (HOC) from DNA replication to prevent genetic damage. To test this hypothesis, we grew diverse strains in chemostat and measured DNA replication and oxygen consumption with high temporal resolution at different growth rates. Our data showed that HOC is not strictly separated from DNA replication; rather, cell cycle Start is coupled with the initiation of HOC and catabolism of storage carbohydrates. The logic of this YMC-CDC coupling may be to ensure that DNA replication and cell division occur only when sufficient cellular energy reserves have accumulated. Our results also uncovered a quantitative relationship between CDC period and YMC period across different strains. More generally, our approach shows how studies in genetically diverse strains efficiently identify robust phenotypes and steer the experimentalist away from strain-specific idiosyncrasies.

The numerical simulation of enclosure fires using a Cfd fire field model coupled with a pyrolysis based solid fuel combustion submodel—a first approximation

In this paper, we present some early work concerned with the development of a simple solid fuel combustion model incorporated within a Computational Fluid Dynamics (CFD) framework. The model is intended for use in engineering applications of fire field modeling and represents an extension of this technique to situations involving the combustion of solid cellulosic fuels. A simple solid fuel combustion model consisting of a thermal pyrolysis model, a six flux radiation model and an eddy-dissipation model for gaseous combustion have been developed and implemented within the CFD code CFDS-FLOW3D. The model is briefly described and demonstrated through two applications involving fire spread in a compartment with a plywood lined ceiling. The two scenarios considered involve a fire in an open and closed compartment. The model is shown to be able to qualitatively predict behaviors similar to "flashover"—in the case of the open room—and "backdraft"— in the case of the initially closed room.

Coupled 3-D finite difference time domain and finite volume methods for solving microwave heating in porous media

Computational results for the microwave heating of a porous material are presented in this paper. Combined finite difference time domain and finite volume methods were used to solve equations that describe the electromagnetic field and heat and mass transfer in porous media. The coupling between the two schemes is through a change in dielectric properties which were assumed to be dependent both on temperature and moisture content. The model was able to reflect the evolution of temperature and moisture fields as the moisture in the porous medium evaporates. Moisture movement results from internal pressure gradients produced by the internal heating and phase change.

Modelling the fluid dynamics and coupled phenomena in arc weld pools

A 3D model of melt pool created by a moving arc type heat sources has been developed. The model solves the equations of turbulent fluid flow, heat transfer and electromagnetic field to demonstrate the flow behaviour phase-change in the pool. The coupled effects of buoyancy, capillary (Marangoni) and electromagnetic (Lorentz) forces are included within an unstructured finite volume mesh environment. The movement of the welding arc along the workpiece is accomplished via a moving co-ordinator system. Additionally a method enabling movement of the weld pool surface by fluid convection is presented whereby the mesh in the liquid region is allowed to move through a free surface. The surface grid lines move to restore equilibrium at the end of each computational time step and interior grid points then adjust following the solution of a Laplace equation.

A generic time and space accurate numerical approach to closely coupled fluid-structure interaction problems

Fluid structure interaction, as applied to flexible structures, has wide application in diverse areas such as flutter in aircraft, flow in elastic pipes and blood vessels and extrusion of metals through dies. However a comprehensive computational model of these multi-physics phenomena is a considerable challenge. Until recently work in this area focused on one phenomenon and represented the behaviour of the other more simply even to the extent in metal forming, for example, that the deformation of the die is totally ignored. More recently, strategies for solving the full coupling between the fluid and soild mechanics behaviour have developed. Conventionally, the computational modelling of fluid structure interaction is problematical since computational fluid dynamics (CFD) is solved using finite volume (FV) methods and computational structural mechanics (CSM) is based entirely on finite element (FE) methods. In the past the concurrent, but rather disparate, development paths for the finite element and finite volume methods have resulted in numerical software tools for CFD and CSM that are different in almost every respect. Hence, progress is frustrated in modelling the emerging multi-physics problem of fluid structure interaction in a consistent manner. Unless the fluid-structure coupling is either one way, very weak or both, transferring and filtering data from one mesh and solution procedure to another may lead to significant problems in computational convergence. Using a novel three phase technique the full interaction between the fluid and the dynamic structural response are represented. The procedure is demonstrated on some challenging applications in complex three dimensional geometries involving aircraft flutter, metal forming and blood flow in arteries.

A computational model of coupled heat and moisture transfer with phase change in granular sugar during varying environmental conditions

As part of a comprehensive effort to predict the development of caking in granular materials, a mathematical model is introduced to model simultaneous heat and moisture transfer with phase change in porous media when undergoing temperature oscillations/cycling. The resulting model partial differential equations were solved using finite-volume procedures in the context of the PHYSICA framework and then applied to the analysis of sugar in storage. The influence of temperature on absorption/desorption and diffusion coefficients is coupled into the transport equations. The temperature profile, the depth of penetration of the temperature oscillation into the bulk solid, and the solids moisture content distribution were first calculated, and these proved to be in good agreement with experimental data. Then, the influence of temperature oscillation on absolute humidity, moisture concentration, and moisture migration for different parameters and boundary conditions was examined. As expected, the results show that moisture near boundary regions responds faster than farther away from them with surface temperature changes. The moisture absorption and desorption in materials occurs mainly near boundary regions (where interactions with the environment are more pronounced). Small amounts of solids moisture content, driven by both temperature and vapour concentration gradients, migrate between boundary and center with oscillating temperature.

Use of a coupled mechanical-acoustic computational model to identify failure mechanisms in paper production

In this paper, a couple mechanical-acoustic system of equations is solved to determine the relationship between emitted sound and damage mechanisims in paper under controlled stress conditions. The simple classical expression describing the frequency of a plucked string to its material properties is used to generate a numberical representation of the microscopic structue of the paper, and the resulting numerical model is then used to simulate the vibration of a range of simple fibre structures when undergoing two distinct types of damange mechanisms: (a)fibre/fibre bond failure, (b) fibre failure. The numercial results are analysed to determine whether there is any detectable systematic difference between the resulting acoustic emissions of the two damage processes. Fourier techniques are then used to compare th computeed results against experimental measurements. Distinct frequency components identifying each type of damage are shown to exist, and in this respect theory and experiments show good correspondece. Hence, it is shown, that althrough the mathematical model represents a grossly-simplified view of the complex structure of the paper, it nevertheless provides a good understanding of the underlying micro-mechanisms characterising its proeperties as a stress-resisting structure. Use of the model and acoompanying software will enable operators to identify approaching failure conditions in the continuous production of paper from emitted sound signals and take preventative action.

Predicting HCl concentrations in fire enclosures using an HCl decay model coupled to a CFD-based fire field model

The amount of atmospheric hydrogen chloride (HCl) within fire enclosures produced from the combustion of chloride-based materials tends to decay as the fire effluent is transported through the enclosure due to mixing with fresh air and absorption by solids. This paper describes an HCl decay model, typically used in zone models, which has been modified and applied to a computational fluid dynamics (CFD)-based fire field model. While the modified model still makes use of some empirical formulations to represent the deposition mechanisms, these have been reduced from the original three to two through the use of the CFD framework. Furthermore, the effect of HCl flow to the wall surfaces on the time to reach equilibrium between HCl in the boundary layer and on wall surfaces is addressed by the modified model. Simulation results using the modified HCl decay model are compared with data from three experiments. The model is found to be able to reproduce the experimental trends and the predicted HCl levels are in good agreement with measured values