Bioinformatics

The analysis of gene regulatory networks (GRNs) is a central goal of bioinformatics highly accelerated by the advent of new experimental techniques, such as RNA interference. A battery of reverse engineering methods has been developed in recent years to reconstruct the underlying GRNs from these and other experimental data. However, the performance of the individual methods is poorly understood and validation of algorithmic performances is still missing to a large extent. To enable such systematic validation, we have developed the web application GeNGe (GEne Network GEnerator), a controlled framework for the automatic generation of GRNs. The theoretical model for a GRN is a non-linear differential equation system. Networks can be user-defined or constructed in a modular way with the option to introduce global and local network perturbations. Resulting data can be used, e.g. as benchmark data for evaluating GRN reconstruction methods or for predicting effects of perturbations as theoretical counterparts of biological experiment

Application of classical models of chirality to surface second harmonic generation

International audienceTwo classical models (Kuhn and Kauzmann) are extended to calculate the second-order nonlinear response of an isotropic layer of chiral molecules. Calculation of the various nonlinear susceptibilities (electric dipolar, magnetic dipolar, and electric quadrupolar) is performed and applied to the derivation of the second harmonic field radiated by the molecules. It is shown that the two models give strikingly different results about the origin of the chiral response in such experiments. Previously published results are analyzed in view of this calculation which allows to understand the different interpretations proposed. This calculation emphasizes the interest of surface second harmonic generation to access information about the microscopic origin of optical activity in chiral molecules. © 2001 American Institute of Physics

Cubic optical nonlinearity of free electrons in bulk gold

A fast (τresponse &lt;90 fs) free-electron spin-flipping frequency-degenerate nonlinearity with a significant value of |χ(3)xxyy(ω,ω,ω,-ω) χ(3)xyyx(ω,ω,ω,-ω)| ~ 10-8 esu has been observed in bulk gold at 1260 nm by use of a new pump-probe polarization-sensitive technique. <br/

Wavelength dependence of nonlinear circular dichroism in a chiral ruthenium-tris(bipyridyl) solution

International audienceNonlinear circular dichroism is studied in a solution of ruthenium-tris(bipyridyl) salt in one-beam and pump-probe experiments by tuning the laser wavelength across the circular dichroism structure. The dispersion of the nonlinear circular dichroism is measured. This wavelength dependence is well accounted for by a model calculation where nonlocality is included in the optical response of a two-coupled-oscillator system. This calculation also allows us to address the question of the contribution of electric quadrupolarization to the nonlinear optical activity of an isotropic liquid of chiral molecules. © 2002 The American Physical Societ

Magnetization-induced optical nonlinearity in ferromagnetic GaMnAs

International audienceWe report the observation of a coherent nonlinear signal in pump-probe experiments on a ferromagnetic GaMnAs. The coherent signal, which is originating due to coherent interaction between pump and probe beams, depends on the polarization configuration of each beam and follows the sample magnetization as it changes with the applied magnetic field and/or the sample temperature. Cop. 2007 American Institute of Physics

Size-Dependent Surface Plasmon Dynamics in Metal Nanoparticles

We study the effect of Coulomb correlations on the ultrafast optical dynamics of small metal particles. We demonstrate that a surface-induced dynamical screening of the electron-electron interactions leads to quasiparticle scattering with collective surface excitations. In noble-metal nanoparticles, it results in an interband resonant scattering of d-holes with surface plasmons. We show that this size-dependent many-body effect manifests itself in the differential absorption dynamics for frequencies close to the surface plasmon resonance. In particular, our self-consistent calculations reveal a strong frequency dependence of the relaxation, in agreement with recent femtosecond pump-probe experiments.Comment: 8 pages + 4 figures, final version accepted to PR

Size-dependent Correlation Effects in Ultrafast Optical Dynamics of Metal Nanoparticles

We study the role of collective surface excitations in the electron relaxation in small metal particles. We show that the dynamically screened electron-electron interaction in a nanoparticle contains a size-dependent correction induced by the surface. This leads to new channels of quasiparticle scattering accompanied by the emission of surface collective excitations. We calculate the energy and temperature dependence of the corresponding rates, which depend strongly on the nanoparticle size. We show that the surface-plasmon-mediated scattering rate of a conduction electron increases with energy, in contrast to that mediated by a bulk plasmon. In noble-metal particles, we find that the dipole collective excitations (surface plasmons) mediate a resonant scattering of d-holes to the conduction band. We study the role of the latter effect in the ultrafast optical dynamics of small nanoparticles and show that, with decreasing nanoparticle size, it leads to a drastic change in the differential absorption lineshape and a strong frequency dependence of the relaxation near the surface plasmon resonance. The experimental implications of our results in ultrafast pump-probe spectroscopy are also discussed.Comment: 29 pages including 6 figure