Probing the mechanism of electron capture and electron transfer dissociation using tags with variable electron affinity

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of doubly protonated electron affinity (EA)-tuned peptides were studied to further illuminate the mechanism of these processes. The model peptide FQpSEEQQQTEDELQDK, containing a phosphoserine residue, was converted to EA-tuned peptides via β-elimination and Michael addition of various thiol compounds. These include propanyl, benzyl, 4-cyanobenzyl, perfluorobenzyl, 3,5-dicyanobenzyl, 3-nitrobenzyl, and 3,5-dinitrobenzyl structural moieties, having a range of EA from −1.15 to +1.65 eV, excluding the propanyl group. Typical ECD or ETD backbone fragmentations are completely inhibited in peptides with substituent tags having EA over 1.00 eV, which are referred to as electron predators in this work. Nearly identical rates of electron capture by the dications substituted by the benzyl (EA = −1.15 eV) and 3-nitrobenzyl (EA = 1.00 eV) moieties are observed, which indicates the similarity of electron capture cross sections for the two derivatized peptides. This observation leads to the inference that electron capture kinetics are governed by the long-range electron−dication interaction and are not affected by side chain derivatives with positive EA. Once an electron is captured to high-n Rydberg states, however, through-space or through-bond electron transfer to the EA-tuning tags or low-n Rydberg states via potential curve crossing occurs in competition with transfer to the amide π* orbital. The energetics of these processes are evaluated using time-dependent density functional theory with a series of reduced model systems. The intramolecular electron transfer process is modulated by structure-dependent hydrogen bonds and is heavily affected by the presence and type of electron-withdrawing groups in the EA-tuning tag. The anion radicals formed by electron predators have high proton affinities (approximately 1400 kJ/mol for the 3-nitrobenzyl anion radical) in comparison to other basic sites in the model peptide dication, facilitating exothermic proton transfer from one of the two sites of protonation. This interrupts the normal sequence of events in ECD or ETD, leading to backbone fragmentation by forming a stable radical intermediate. The implications which these results have for previously proposed ECD and ETD mechanisms are discussed

Exoplanet Transit Database. Reduction and processing of the photometric data of exoplanet transits

We demonstrate the newly developed resource for exoplanet researchers - The Exoplanet Transit Database. This database is designed to be a web application and it is open for any exoplanet observer. It came on-line in September 2008. The ETD consists of three individual sections. One serves for predictions of the transits, the second one for processing and uploading new data from the observers. We use a simple analytical model of the transit to calculate the central time of transit, its duration and the depth of the transit. These values are then plotted into the observed - computed diagrams (O-C), that represent the last part of the application.Comment: Accepted to NewAstronom

SLoMo: automated site localization of modifications from ETD/ECD mass spectra

Recently, software has become available to automate localization of phosphorylation sites from CID data and to assign associated confidence scores. We present an algorithm, SLoMo (Site Localization of Modifications), which extends this capability to ETD/ECD mass spectra. Furthermore, SLoMo caters for both high and low resolution data and allows for site-localization of any UniMod post-translational modification. SLoMo accepts input data from a variety of formats (e.g., Sequest, OMSSA). We validate SLoMo with high and low resolution ETD, ECD, and CID data

Restless bandit marginal productivity indices I: singleproject case and optimal control of a make-to-stock M/G/1 queue

This paper develops a framework based on convex optimization and economic ideas to formulate and solve by an index policy the problem of optimal dynamic effort allocation to a generic discrete-state restless bandit (i.e. binary-action: work/rest) project, elucidating a host of issues raised by Whittle (1988)Žs seminal work on the topic. Our contributions include: (i) a unifying definition of a projectŽs marginal productivity index (MPI), characterizing optimal policies; (ii) a complete characterization of indexability (existence of the MPI) as satisfaction by the project of the law of diminishing returns (to effort); (iii) sufficient indexability conditions based on partial conservation laws (PCLs), extending previous results of the author from the finite to the countable state case; (iv) application to a semi-Markov project, including a new MPI for a mixed longrun-average (LRA)/ bias criterion, which exists in relevant queueing control models where the index proposed by Whittle (1988) does not; and (v) optimal MPI policies for service-controlled make-to-order (MTO) and make-to-stock (MTS) M/G/1 queues with convex back order and stock holding cost rates, under discounted and LRA criteria

A Spitzer Five-Band Analysis of the Jupiter-Sized Planet TrES-1

With an equilibrium temperature of 1200 K, TrES-1 is one of the coolest hot Jupiters observed by {\Spitzer}. It was also the first planet discovered by any transit survey and one of the first exoplanets from which thermal emission was directly observed. We analyzed all {\Spitzer} eclipse and transit data for TrES-1 and obtained its eclipse depths and brightness temperatures in the 3.6 {\micron} (0.083 % {\pm} 0.024 %, 1270 {\pm} 110 K), 4.5 {\micron} (0.094 % {\pm} 0.024 %, 1126 {\pm} 90 K), 5.8 {\micron} (0.162 % {\pm} 0.042 %, 1205 {\pm} 130 K), 8.0 {\micron} (0.213 % {\pm} 0.042 %, 1190 {\pm} 130 K), and 16 {\micron} (0.33 % {\pm} 0.12 %, 1270 {\pm} 310 K) bands. The eclipse depths can be explained, within 1$\sigma$ errors, by a standard atmospheric model with solar abundance composition in chemical equilibrium, with or without a thermal inversion. The combined analysis of the transit, eclipse, and radial-velocity ephemerides gives an eccentricity $e = 0.033^{+0.015}_{-0.031}$, consistent with a circular orbit. Since TrES-1's eclipses have low signal-to-noise ratios, we implemented optimal photometry and differential-evolution Markov-chain Monte Carlo (MCMC) algorithms in our Photometry for Orbits, Eclipses, and Transits (POET) pipeline. Benefits include higher photometric precision and \sim10 times faster MCMC convergence, with better exploration of the phase space and no manual parameter tuning.Comment: 17 pages, Accepted for publication in Ap

Long time simulation of a highly oscillatory Vlasov equation with an exponential integrator

We change a previous time-stepping algorithm for solving a multi-scale Vlasov-Poisson system within a Particle-In-Cell method, in order to do accurate long time simulations. As an exponential integrator, the new scheme allows to use large time steps compared to the size of oscillations in the solution

Analysis of Kepler's short-cadence photometry for TrES-2b

We present an analysis of 18 short-cadence (SC) transit lightcurves of TrES-2b using quarter 0 (Q0) and quarter 1 (Q1) from the Kepler Mission. The photometry is of unprecedented precision, 237ppm per minute, allowing for the most accurate determination of the transit parameters yet obtained for this system. Global fits of the transit photometry, radial velocities and known transit times are used to obtain a self-consistent set of refined parameters for this system, including updated stellar and planetary parameters. Special attention is paid to fitting for limb darkening and eccentricity. We place an upper limit on the occultation depth to be <72.9ppm to 3-sigma confidence, indicating TrES-2b has the lowest determined geometric albedo for an exoplanet, of Ag<0.146. We also produce a transit timing analysis using Kepler's short-cadence data and demonstrate exceptional timing precision at the level of a few seconds for each transit event. With 18 fully-sampled transits at such high precision, we are able to produce stringent constraints on the presence of perturbing planets, Trojans and extrasolar moons. We introduce the novel use of control data to identify phasing effects. We also exclude the previously proposed hypotheses of short-period TTV and additional transits but find the hypothesis of long-term inclination change is neither supported nor refuted by our analysis.Comment: Accepted in ApJ. 19 pages, 12 figures, 5 tables, emulateap