Structure and functional motifs of GCR1, the only plant protein with a GPCR fold?

Whether GPCRs exist in plants is a fundamental biological question. Interest in deorphanizing new G protein coupled receptors (GPCRs), arises because of their importance in signaling. Within plants, this is controversial as genome analysis has identified 56 putative GPCRs, including GCR1 which is reportedly a remote homologue to class A, B and E GPCRs. Of these, GCR2, is not a GPCR; more recently it has been proposed that none are, not even GCR1. We have addressed this disparity between genome analysis and biological evidence through a structural bioinformatics study, involving fold recognition methods, from which only GCR1 emerges as a strong candidate. To further probe GCR1, we have developed a novel helix alignment method, which has been benchmarked against the the class A – class B - class F GPCR alignments. In addition, we have presented a mutually consistent set of alignments of GCR1 homologues to class A, class B and class F GPCRs, and shown that GCR1 is closer to class A and /or class B GPCRs than class A, class B or class F GPCRs are to each other. To further probe GCR1, we have aligned transmembrane helix 3 of GCR1 to each of the 6 GPCR classes. Variability comparisons provide additional evidence that GCR1 homologues have the GPCR fold. From the alignments and a GCR1 comparative model we have identified motifs that are common to GCR1, class A, B and E GPCRs. We discuss the possibilities that emerge from this controversial evidence that GCR1 has a GPCR fol

Physics of Interpulse Emission in Radio Pulsars

The magnetized induced Compton scattering off the particles of the ultrarelativistic electron-positron plasma of pulsar is considered. The main attention is paid to the transverse regime of the scattering, which holds in a moderately strong magnetic field. We specifically examine the problem on induced transverse scattering of the radio beam into the background, which takes place in the open field line tube of a pulsar. In this case, the radiation is predominantly scattered backwards and the scattered component may grow considerably. Based on this effect, we for the first time suggest a physical explanation of the interpulse emission observed in the profiles of some pulsars. Our model can naturally account for the peculiar spectral and polarization properties of the interpulses. Furthermore, it implies a specific connection of the interpulse to the main pulse, which may reveal itself in the consistent intensity fluctuations of the components at different timescales. Diverse observational manifestations of this connection, including the moding behavior of PSR B1822-09, the peculiar temporal and frequency structure of the giant interpulses in the Crab pulsar, and the intrinsic phase correspondence of the subpulse patterns in the main pulse and the interpulse of PSR B1702-19, are discussed in detail. It is also argued that the pulse-to-pulse fluctuations of the scattering efficiency may lead to strong variability of the interpulse, which is yet to be studied observationally. In particular, some pulsars may exhibit transient interpulses, i.e. the scattered component may be detectable only occasionally.Comment: 28 pages, 2 figures. Accepted for publication in Ap

Fermionic Zero Modes of Supergravity Cosmic Strings

Recent developments in string theory suggest that cosmic strings could be formed at the end of brane inflation. Supergravity provides a realistic model to study the properties of strings arising in brane inflation. Whilst the properties of cosmic strings in flat space-time have been extensively studied there are significant complications in the presence of gravity. We study the effects of gravitation on cosmic strings arising in supergravity. Fermion zero modes are a common feature of cosmic strings, and generically occur in supersymmetric models. The corresponding massless currents can give rise to stable string loops (vortons). The vorton density in our universe is strongly constrained, allowing many theories with cosmic strings to be ruled out. We investigate the existence of fermion zero modes on cosmic strings in supergravity theories. A general index theorem for the number of zero modes is derived. We show that by including the gravitino, some (but not all) zero modes disappear. This weakens the constraints on cosmic string models. In particular, winding number one cosmic D-strings in models of brane inflation are not subject to vorton constraints. We also discuss the effects of supersymmetry breaking on cosmic D-strings.Comment: 33 page

Boundary Inflation and the WMAP Data

Inflation in a five-dimensional brane world model with two boundary branes is studied. We make use of the moduli space approximation whereby the low energy theory reduces to a four-dimensional biscalar-tensor gravity plus a minimally coupled scalar field. After a detailed analysis of the inflationary solutions, we derive the evolution equations of the linear perturbations separating the adiabatic mode from two entropy modes. We then examine the primordial scalar and tensor power spectra and show that their tilt depends on the scalar-tensor coupling constant. Finally, the induced CMB anisotropies are computed and we present a Monte Carlo Markov Chains exploration of the parameter space using the first year WMAP data. We find a marginalized probability bound for the associated Eddington parameter at the end of inflation 1 - gamma < 0.002, at 95% confidence level. This suggests that future CMB data could provide crucial information helping to distinguish scalar-tensor and standard inflationary scenarios.Comment: 24 pages, 19 figures, uses RevTex. Qualitative discussions added, matches published versio

Density perturbations in the brane-world

In Randall-Sundrum-type brane-world cosmologies, density perturbations generate Weyl curvature in the bulk, which in turn backreacts on the brane via stress-energy perturbations. On large scales, the perturbation equations contain a closed system on the brane, which may be solved without solving for the bulk perturbations. Bulk effects produce a non-adiabatic mode, even when the matter perturbations are adiabatic, and alter the background dynamics. As a consequence, the standard evolution of large-scale fluctuations in general relativity is modified. The metric perturbation on large-scales is not constant during high-energy inflation. It is constant during the radiation era, except at most during the very beginning, if the energy is high enough.Comment: Additional arguments and minor corrections; version accepted by Phys. Rev.

Affine Constellations Without Mutually Unbiased Counterparts

It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations, mostly in dimension six. The observed discrepancies make a deeper relation between the two existence problems unlikely.Comment: 8 page

A Model Approach to the Electrochemical Cell: An Inquiry Activity

In an attempt to address some student misconceptions in electrochemistry, this guided-inquiry laboratory was devised to give students an opportunity to use a manipulative that simulates the particulatelevel activity within an electrochemical cell, in addition to using an actual electrochemical cell. Students are led through a review of expected prior knowledge relating to oxidation and reduction half-reactions. Then, the students examine the macroscopic level by constructing and using an electrochemical cell. Finally, students use the manipulative and make connections between the two levels through class discussion. The misconceptions involve the movement of electrons and ions through solution and the salt bridge, the resulting charges of the half-cells, and the charge sign given to the anode and cathode on electrochemical and electrolytic cells. Additionally, the activity covers oxidation and reduction reactions in electrochemical cells and provides practice drawing and labeling parts of an electrochemical cell. Results, pre- and post-testing and student comments, indicate that this laboratory facilitates students’ understanding of electrochemical cells

Age Constraints on Brane Models of Dark Energy

Inspired by recent developments in particle physics, the so-called brane world cosmology seems to provide an alternative explanation for the present dark energy problem. In this paper, we use the estimated age of high-$z$ objects to constrain the value of the cosmological parameters in some particular scenarios based on this large scale modification of gravity. We show that such models are compatible with these observations for values of the crossover distance between the 4 and 5 dimensions of the order of $r_c \leq 1.67H_o^{-1}$.Comment: 4 pages, 2 figures, 1 table, to appear in Phys. Rev.

Scalar perturbations from brane-world inflation

We investigate the scalar metric perturbations about a de Sitter brane universe in a 5-dimensional anti de Sitter bulk. We compare the master-variable formalism, describing metric perturbations in a 5-dimensional longitudinal gauge, with results in a Gaussian normal gauge. For a vacuum brane (with constant brane tension) there is a continuum of normalizable Kaluza-Klein modes, with m>3H/2, which remain in the vacuum state. A light radion mode, with m=\sqrt{2}H, satisfies the boundary conditions for two branes but is not normalizable in the single-brane case. When matter is introduced (as a test field) on the brane, this mode, together with the zero-mode and an infinite ladder of discrete tachyonic modes, become normalizable. However, the boundary condition requires the self-consistent 4-dimensional evolution of scalar field perturbations on the brane and the dangerous growing modes are not excited. These normalizable discrete modes introduce corrections at first-order to the scalar field perturbations computed in a slow-roll expansion. On super-Hubble scales, the correction is smaller than slow-roll corrections to the de Sitter background. However on small scales the corrections can become significant.Comment: 15 page

Accelerated Sizing of a Power Split Electrified Powertrain

Component sizing generally represents a demanding and time-consuming task in the development process of electrified powertrains. A couple of processes are available in literature for sizing the hybrid electric vehicle (HEV) components. These processes employ either time-consuming global optimization techniques like dynamic programming (DP) or near-optimal techniques that require iterative and uncertain tuning of evaluation parameters like the Pontryagin's minimum principle (PMP). Recently, a novel near-optimal technique has been devised for rapidly predicting the optimal fuel economy benchmark of design options for electrified powertrains. This method, named slope-weighted energy-based rapid control analysis (SERCA), has been demonstrated producing results comparable to DP, while limiting the associated computational time by near two orders of magnitude. In this paper, sizing parameters for a power split electrified powertrain are considered that include the internal combustion engine size, the two electric motor/generator sizes, the transmission ratios, and the final drive ratio. The SERCA approach is adopted to rapidly evaluate the fuel economy capabilities of each sizing option in various driving missions considering both type-approval drive cycles and real-world driving profiles. While screening out for optimal sizing options, the implemented methodology includes drivability criteria along with fuel economy potential. Obtained results will demonstrate the agility of the developed sizing tool in identifying optimal sizing options compared to state-of-the-art sizing tools for electrified powertrains