A new look at NICMOS transmission spectroscopy of HD189733, GJ-436 and XO-1: no conclusive evidence for molecular features

We present a re-analysis of archival HST/NICMOS transmission spectroscopy of three exoplanet systems; HD 189733, GJ-436 and XO-1. Detections of several molecules, including H20, CH4 and CO2, have been claimed for HD 189733 and XO-1, but similarly sized features are attributed to systematic noise for GJ-436. The data consist of time-series grism spectra covering a planetary transit. After extracting light curves in independent wavelength channels, we use a linear decorrelation technique account for instrumental systematics (which is becoming standard in the field), and measure the planet-to-star radius ratio as a function of wavelength. For HD 189733, the uncertainties in the transmission spectrum are significantly larger than those previously reported. We also find the transmission spectrum is considerably altered when using different out-of-transit orbits to remove the systematics, when some parameters are left out of the decorrelation procedure, or when we perform the decorrelation with quadratic functions rather than linear functions. Given that there is no physical reason to believe the baseline flux should be modelled as a linear function of any particular set of parameters, we interpret this as evidence that the linear decorrelation technique is not a robust method to remove systematic effects from the light curves for each wavelength channel. For XO-1, the parameters measured to decorrelate the light curves would require extrapolation to the in-transit orbit to remove the systematics, and we cannot reproduce the previously reported results. We conclude that the resulting NICMOS transmission spectra are too dependent on the method used to remove systematics to be considered robust detections of molecular species in planetary atmospheres, although the presence of these molecules is not ruled out.Comment: 17 pages, 28 figures, accepted in MNRA

BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling

Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx

Facile: a command-line network compiler for systems biology

<p>Abstract</p> <p>Background</p> <p>A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unknown. It is therefore important to be able to easily investigate the effects of adding or removing reactions and to easily perform a bifurcation analysis, which shows the qualitative dynamics of a model for a range of parameter values.</p> <p>Results</p> <p>We present Facile, a Perl command-line tool for analysing the dynamics of a systems biology model. Facile implements the law of mass action to automatically compile a biochemical network (written as, for example, <monospace>E + S <-> C</monospace>) into scripts for analytical analysis (Mathematica and Maple), for simulation (XPP and Matlab), and for bifurcation analysis (AUTO). Facile automatically identifies mass conservations and generates the reduced form of a model with the minimum number of independent variables. This form is essential for bifurcation analysis, and Facile produces a C version of the reduced model for AUTO.</p> <p>Conclusion</p> <p>Facile is a simple, yet powerful, tool that greatly accelerates analysis of the dynamics of a biochemical network. By acting at the command-line and because of its intuitive, text-based input, Facile is quick to learn and can be incorporated into larger programs or into automated tasks.</p

Optimal squeezing, pure states, and amplification of squeezing in resonance fluorescence

It is shown that 100% squeezed output can be produced in the resonance fluorescence from a coherently driven two-level atom interacting with a squeezed vacuum. This is only possible for $N=1/8$ squeezed input, and is associated with a pure atomic state, i.e., a completely polarized state. The quadrature for which optimal squeezing occurs depends on the squeezing phase $\Phi ,$ the Rabi frequency $\Omega ,$ and the atomic detuning $\Delta$. Pure states are described for arbitrary $\Phi ,$ not just $\Phi =0$ or $\pi$ as in previous work. For small values of $N,$ there may be a greater degree of squeezing in the output field than the input - i.e., we have squeezing amplification.Comment: 6 pages & 7 figures, Submitted to Phys. Rev.

Excitations in time-dependent density-functional theory

An approximate solution to the time-dependent density functional theory (TDDFT) response equations for finite systems is developed, yielding corrections to the single-pole approximation. These explain why allowed Kohn-Sham transition frequencies and oscillator strengths are usually good approximations to the true values, and why sometimes they are not. The approximation yields simple expressions for G\"orling-Levy perturbation theory results, and a method for estimating expectation values of the unknown exchange-correlation kernel.Comment: 4 pages, 1 tabl

Quantum interference in optical fields and atomic radiation

We discuss the connection between quantum interference effects in optical beams and radiation fields emitted from atomic systems. We illustrate this connection by a study of the first- and second-order correlation functions of optical fields and atomic dipole moments. We explore the role of correlations between the emitting systems and present examples of practical methods to implement two systems with non-orthogonal dipole moments. We also derive general conditions for quantum interference in a two-atom system and for a control of spontaneous emission. The relation between population trapping and dark states is also discussed. Moreover, we present quantum dressed-atom models of cancellation of spontaneous emission, amplification on dark transitions, fluorescence quenching and coherent population trapping.Comment: To be published in Journal of Modern Optics Special Issue on Quantum Interferenc

Time evolution of the Rabi Hamiltonian from the unexcited vacuum

The Rabi Hamiltonian describes a single mode of electromagnetic radiation interacting with a two-level atom. Using the coupled cluster method, we investigate the time evolution of this system from an initially empty field mode and an unexcited atom. We give results for the atomic inversion and field occupation, and find that the virtual processes cause the field to be squeezed. No anti-bunching occurs.Comment: 25 pages, 8 figures, RevTe

Exploring the inner region of Type 1 AGNs with the Keck interferometer

The exploration of extragalactic objects with long-baseline interferometers in the near-infrared has been very limited. Here we report successful observations with the Keck interferometer at K-band (2.2 um) for four Type 1 AGNs, namely NGC4151, Mrk231, NGC4051, and the QSO IRAS13349+2438 at z=0.108. For the latter three objects, these are the first long-baseline interferometric measurements in the infrared. We detect high visibilities (V^2 ~ 0.8-0.9) for all the four objects, including NGC4151 for which we confirm the high V^2 level measured by Swain et al.(2003). We marginally detect a decrease of V^2 with increasing baseline lengths for NGC4151, although over a very limited range, where the decrease and absolute V^2 are well fitted with a ring model of radius 0.45+/-0.04 mas (0.039+/-0.003 pc). Strikingly, this matches independent radius measurements from optical--infrared reverberations that are thought to be probing the dust sublimation radius. We also show that the effective radius of the other objects, obtained from the same ring model, is either roughly equal to or slightly larger than the reverberation radius as a function of AGN luminosity. This suggests that we are indeed partially resolving the dust sublimation region. The ratio of the effective ring radius to the reverberation radius might also give us an approximate probe for the radial structure of the inner accreting material in each object. This should be scrutinized with further observations.Comment: accepted for publication in A&A Letter

Surface induced disorder in body-centered cubic alloys

We present Monte Carlo simulations of surface induced disordering in a model of a binary alloy on a bcc lattice which undergoes a first order bulk transition from the ordered DO3 phase to the disordered A2 phase. The data are analyzed in terms of an effective interface Hamiltonian for a system with several order parameters in the framework of the linear renormalization approach due to Brezin, Halperin and Leibler. We show that the model provides a good description of the system in the vicinity of the interface. In particular, we recover the logarithmic divergence of the thickness of the disordered layer as the bulk transition is approached, we calculate the critical behavior of the maxima of the layer susceptibilities, and demonstrate that it is in reasonable agreement with the simulation data. Directly at the (110) surface, the theory predicts that all order parameters vanish continuously at the surface with a nonuniversal, but common critical exponent. However, we find different exponents for the order parameter of the DO3 phase and the order parameter of the B2 phase. Using the effective interface model, we derive the finite size scaling function for the surface order parameter and show that the theory accounts well for the finite size behavior of the DO3 ordering but not for that of B2 ordering. The situation is even more complicated in the neighborhood of the (100) surface, due to the presence of an ordering field which couples to the B2 order.Comment: To appear in Physical Review

Quantum Mechanical Aspects of Cell Microtubules: Science Fiction or Realistic Possibility?

Recent experimental research with marine algae points towards quantum entanglement at ambient temperature, with correlations between essential biological units separated by distances as long as 20 Angstr\"oms. The associated decoherence times, due to environmental influences, are found to be of order 400 fs. This prompted some authors to connect such findings with the possibility of some kind of quantum computation taking place in these biological entities: within the decoherence time scales, the cell "quantum calculates" the optimal "path" along which energy and signal would be transported more efficiently. Prompted by these experimental results, in this talk I remind the audience of a related topic proposed several years ago in connection with the possible r\^ole of quantum mechanics and/or field theory on dissipation-free energy transfer in microtubules (MT), which constitute fundamental cell substructures. Quantum entanglement between tubulin dimers was argued to be possible, provided there exists sufficient isolation from other environmental cell effects. The model was based on certain ferroelectric aspects of MT. In the talk I review the model and the associated experimental tests so far and discuss future directions, especially in view of the algae photo-experiments.Comment: 31 pages latex, 11 pdf figures, uses special macros, Invited Plenary Talk at DICE2010, Castello Pasquini, Castiglioncello (Italy), September 13-18 201