Mid- and Far-Infrared Marker Bands of the Metal Coordination Sites of the Histidine Side Chains in the Protein Cu,Zn-Superoxide Dismutase

International audienceVibrational spectroscopy gives important information on the properties of ligand and metal–ligand bonds in metalloenzymes. Infrared spectroscopy is appealing for the study of metal active sites that are not amenable to Raman spectroscopy. We present a combined experimental and theoretical approach to analyze the mid- and far-IR spectra of Cu,Zn-superoxide dismutase (Cu,Zn-SOD) as a probe of the histidine ligands. This metalloenzyme provides a unique model to identify specific IR signatures of metal–histidine coordination and to study their alterations as a function of the metal (copper/zinc), the copper valence state (+I/+II), the histidine coordination mode (Nτ and Nπ) and the histidine protonation state. DFT calculations combined with normal mode descriptions from potential energy distribution calculations were performed on two slightly different cluster models. Differences in the constraints at the side chain of one histidine Cu ligand sensibly modify the geometric parameters and vibrational properties. Electrochemically induced FTIR difference spectroscopy provided mid- and far-IR fingerprint spectra of the Cu protein in aqueous media that are sensitive to the redox state of the Cu centre at the active site. Comparisons of the DFT predictions with the experimental IR modes of the histidine ligands at the Cu,Zn-SOD active site showed that useful mid-IR markers of histidine Nτ and Nπ coordination were predicted with good accuracy. The DFT analysis further demonstrated a link between the ν(C4–C5) mode frequency of His46 and the specific properties of the His46–Cu bond in Cu,Zn-SOD. A combined theoretical and experimental approach on samples in H2O and 2H2O or 15N-labelled samples identified the contributions from the histidine side chain modes in the 669–629 cm–1 region

Modeling Bitcoin Contracts by Timed Automata

Bitcoin is a peer-to-peer cryptographic currency system. Since its introduction in 2008, Bitcoin has gained noticeable popularity, mostly due to its following properties: (1) the transaction fees are very low, and (2) it is not controlled by any central authority, which in particular means that nobody can "print" the money to generate inflation. Moreover, the transaction syntax allows to create the so-called contracts, where a number of mutually-distrusting parties engage in a protocol to jointly perform some financial task, and the fairness of this process is guaranteed by the properties of Bitcoin. Although the Bitcoin contracts have several potential applications in the digital economy, so far they have not been widely used in real life. This is partly due to the fact that they are cumbersome to create and analyze, and hence risky to use. In this paper we propose to remedy this problem by using the methods originally developed for the computer-aided analysis for hardware and software systems, in particular those based on the timed automata. More concretely, we propose a framework for modeling the Bitcoin contracts using the timed automata in the UPPAAL model checker. Our method is general and can be used to model several contracts. As a proof-of-concept we use this framework to model some of the Bitcoin contracts from our recent previous work. We then automatically verify their security in UPPAAL, finding (and correcting) some subtle errors that were difficult to spot by the manual analysis. We hope that our work can draw the attention of the researchers working on formal modeling to the problem of the Bitcoin contract verification, and spark off more research on this topic

Testing real-time systems using TINA

The paper presents a technique for model-based black-box conformance testing of real-time systems using the Time Petri Net Analyzer TINA. Such test suites are derived from a prioritized time Petri net composed of two concurrent sub-nets specifying respectively the expected behaviour of the system under test and its environment.We describe how the toolbox TINA has been extended to support automatic generation of time-optimal test suites. The result is optimal in the sense that the set of test cases in the test suite have the shortest possible accumulated time to be executed. Input/output conformance serves as the notion of implementation correctness, essentially timed trace inclusion taking environment assumptions into account. Test cases selection is based either on using manually formulated test purposes or automatically from various coverage criteria specifying structural criteria of the model to be fulfilled by the test suite. We discuss how test purposes and coverage criterion are specified in the linear temporal logic SE-LTL, derive test sequences, and assign verdicts

Visibilities and bolometric corrections for stellar oscillation modes observed by Kepler

Kepler produces a large amount of data used for asteroseismological analyses, particularly of solar-like stars and red giants. The mode amplitudes observed in the Kepler spectral band have to be converted into bolometric amplitudes to be compared to models. We give a simple bolometric correction for the amplitudes of radial modes observed with Kepler, as well as the relative visibilities of non-radial modes. We numerically compute the bolometric correction c_{K-bol} and mode visibilities for different effective temperatures Teff within the range 4000-7500 K, using a similar approach to a recent one from the literature (Michel et al. 2009, A&A 495, 979). We derive a law for the correction to bolometric values: c_{K-bol} = 1 + a_1 (Teff-To) + a_2 (Teff-To)^2, with To = 5934 K, a_1 = 1.349e-4 K^{-1}, and a_2 = -3.120e-9 K^{-2} or, alternatively, as the power law c_{K-bol} = (Teff/To)^alpha with alpha = 0.80. We give tabulated values for the mode visibilities based on limb-darkening (LD), computed from ATLAS9 model atmospheres for Teff in [4000,7500] K, log g in [2.5,4.5], and [M/H] in [-1.0,+1.0]. We show that using LD profiles already integrated over the spectral band provides quick and good approximations for visibilities. We point out the limits of these classical visibility estimations.Comment: 5 pages, 4 figures, 1 table, minor language edition. Published in A&

Algorithms for zero-dimensional ideals using linear recurrent sequences

Inspired by Faug\`ere and Mou's sparse FGLM algorithm, we show how using linear recurrent multi-dimensional sequences can allow one to perform operations such as the primary decomposition of an ideal, by computing the annihilator of one or several such sequences.Comment: LNCS, Computer Algebra in Scientific Computing CASC 201

What Fraction of Boron-8 Solar Neutrinos arrive at the Earth as a nu_2 mass eigenstate?

We calculate the fraction of B^8 solar neutrinos that arrive at the Earth as a nu_2 mass eigenstate as a function of the neutrino energy. Weighting this fraction with the B^8 neutrino energy spectrum and the energy dependence of the cross section for the charged current interaction on deuteron with a threshold on the kinetic energy of the recoil electrons of 5.5 MeV, we find that the integrated weighted fraction of nu_2's to be 91 \pm 2 % at the 95% CL. This energy weighting procedure corresponds to the charged current response of the Sudbury Neutrino Observatory (SNO). We have used SNO's current best fit values for the solar mass squared difference and the mixing angle, obtained by combining the data from all solar neutrino experiments and the reactor data from KamLAND. The uncertainty on the nu_2 fraction comes primarily from the uncertainty on the solar delta m^2 rather than from the uncertainty on the solar mixing angle or the Standard Solar Model. Similar results for the Super-Kamiokande experiment are also given. We extend this analysis to three neutrinos and discuss how to extract the modulus of the Maki-Nakagawa-Sakata mixing matrix element U_{e2} as well as place a lower bound on the electron number density in the solar B^8 neutrino production region.Comment: 23 pages, 8 postscript figures, latex. Dedicated to the memory of John Bahcall who championed solar neutrinos for many lonely year

The derivation of performance expressions for communication protocols from timed Petri net models

Petri Net models have been extended in a variety of ways and have been used to prove the correctness and evaluate the performance of communication protocols. Several extensions have been proposed to model time. This work uses a form of Timed Petri Nets and presents a technique for symbolically deriving expressions which describe system performance. Unlike past work on performance evaluation of Petri Nets which assumes a priori knowledge of specific time delays, the technique presented here applies to a wide range of time delays so long as the delays satisfy a set of timing constraints. The technique is demonstrated using a simple communication protocol

Angular momentum transport by internal gravity waves III - Wave excitation by core convection and the Coriolis effect

This is the third in a series of papers that deal with angular momentum transport by internal gravity waves. We concentrate on the waves excited by core convection in a 3Msun, Pop I main sequence star. Here, we want to examine the role of the Coriolis acceleration in the equations of motion that describe the behavior of waves and to evaluate its impact on angular momentum transport. We use the so-called traditional approximation of geophysics, which allows variable separation in radial and horizontal components. In the presence of rotation, the horizontal structure is described by Hough functions instead of spherical harmonics. The Coriolis acceleration has two main effects on waves. It transforms pure gravity waves into gravito-inertial waves that have a larger amplitude closer to the equator, and it introduces new waves whose restoring force is mainly the conservation of vorticity. Taking the Coriolis acceleration into account changes the subtle balance between prograde and retrograde waves in non-rotating stars. It also introduces new types of waves that are either purely prograde or retrograde. We show in this paper where the local deposition of angular momentum by such waves is important.Comment: 9 pages, 10 figures, accepted for publication by A&

Hydrogen bonding to the cysteine ligand of superoxide reductase: acid–base control of the reaction intermediates

International audienceSuperoxide reductase SOR is a non-heme iron metalloenzyme that detoxifies superoxide radical in microorganisms. Its active site consists of an unusual non-heme Fe2+ center in a [His4 Cys1] square pyramidal pentacoordination, with the axial cysteine ligand proposed to be an essential feature in catalysis. Two NH peptide groups from isoleucine 118 and histidine 119 establish H-bondings with the sulfur ligand (Desulfoarculus baarsii SOR numbering). In order to investigate the catalytic role of these H-bonds, the isoleucine 118 residue of the SOR from Desulfoarculus baarsii was mutated into alanine, aspartate or serine residues. Resonance Raman spectroscopy showed that the mutations specifically induced an increase of the strength of the Fe3+-S(Cys) and S-Cβ(Cys) bonds as well as a change in conformation of the cysteinyl side chain, which was associated with the alteration of the NH hydrogen bonding to the sulfur ligand. The effects of the isoleucine mutations on the reactivity of SOR with O2●- were investigated by pulse radiolysis. These studies showed that the mutations induced a specific increase of the pKa of the first reaction intermediate, recently proposed to be an Fe2+-O2●- species. These data were supported by DFT calculations carried out on three models of the Fe2+-O2●- intermediate, with one, two or no H-bonds on the sulfur ligand. Our results demonstrated that the hydrogen bonds between the NH (peptide) and the cysteine ligand tightly control the rate of protonation of the Fe2+-O2●- reaction intermediate to form an Fe3+-OOH species

Efficient Emptiness Check for Timed B\"uchi Automata (Extended version)

The B\"uchi non-emptiness problem for timed automata refers to deciding if a given automaton has an infinite non-Zeno run satisfying the B\"uchi accepting condition. The standard solution to this problem involves adding an auxiliary clock to take care of the non-Zenoness. In this paper, it is shown that this simple transformation may sometimes result in an exponential blowup. A construction avoiding this blowup is proposed. It is also shown that in many cases, non-Zenoness can be ascertained without extra construction. An on-the-fly algorithm for the non-emptiness problem, using non-Zenoness construction only when required, is proposed. Experiments carried out with a prototype implementation of the algorithm are reported.Comment: Published in the Special Issue on Computer Aided Verification - CAV 2010; Formal Methods in System Design, 201