Discrete aqueous solvent effects and possible attractive forces

We study discrete solvent effects on the interaction of two parallel charged surfaces in ionic aqueous solution. These effects are taken into account by adding a bilinear non-local term to the free energy of Poisson-Boltzmann theory. We study numerically the density profile of ions between the two plates, and the resulting inter-plate pressure. At large plate separations the two plates are decoupled and the ion distribution can be characterized by an effective Poisson-Boltzmann charge that is smaller than the nominal charge. The pressure is thus reduced relative to Poisson-Boltzmann predictions. At plate separations below ~2 nm the pressure is modified considerably, due to the solvent mediated short-range attraction between ions in the the system. For high surface charges this contribution can overcome the mean-field repulsion giving rise to a net attraction between the plates.Comment: 12 figures in 16 files. 19 pages. Submitted to J. Chem. Phys., July 200

Ion condensation on charged patterned surfaces

We study ion condensation onto a patterned surface of alternating charges. The competition between self-energy and ion-surface interactions leads to the formation of ionic crystalline structures at low temperatures. We consider different arrangements of underlying ionic crystals, including single ion adsorption, as well as the formation of dipoles at the interface between charged domains. Molecular dynamic simulation illustrates existence of single and mixed phases. Our results contribute to understanding pattern recognition, and molecular separation and synthesis near patterned surfaces.Comment: 3 figure

The Role of the Gouy Phase in the Coherent Phase Control of the Photoionization and Photodissociation of Vinyl Chloride

We demonstrate theoretically and experimentally that the Gouy phase of a focused laser beam may be used to control the photo-induced reactions of a polyatomic molecule. Quantum mechanical interference between one- and three-photon excitation of vinyl chloride produces a small phase lag between the dissociation and ionization channels on the axis of the molecular beam. Away from the axis, the Gouy phase introduces a much larger phase lag that agrees quantitatively with theory without any adjustable parameters.Comment: 4 pages, 4 figure

Theory and simulations of rigid polyelectrolytes

We present theoretical and numerical studies on stiff, linear polyelectrolytes within the framework of the cell model. We first review analytical results obtained on a mean-field Poisson-Boltzmann level, and then use molecular dynamics simulations to show, under which circumstances these fail quantitatively and qualitatively. For the hexagonally packed nematic phase of the polyelectrolytes we compute the osmotic coefficient as a function of density. In the presence of multivalent counterions it can become negative, leading to effective attractions. We show that this results from a reduced contribution of the virial part to the pressure. We compute the osmotic coefficient and ionic distribution functions from Poisson-Boltzmann theory with and without a recently proposed correlation correction, and also simulation results for the case of poly(para-phenylene) and compare it to recently obtained experimental data on this stiff polyelectrolyte. We also investigate ion-ion correlations in the strong coupling regime, and compare them to predictions of the recently advocated Wigner crystal theories.Comment: 32 pages, 15 figures, proceedings of the ASTATPHYS-MEX-2001, to be published in Mol. Phy

Radius of a Photon Beam with Orbital Angular Momentum

We analyze the transverse structure of the Gouy phase shift in light beams carrying orbital angular momentum and show that the Gouy radius $r_G$ characterizing the transverse structure grows as $\sqrt{2p+|\ell|+1}$ with the nodal number $p$ and photon angular momentum number $\ell$. The Gouy radius is shown to be closely related to the root-mean-square radius of the beam, and the divergence of the radius away from the focal plane is determined. Finally, we analyze the rotation of the Poynting vector in the context of the Gouy radius.Comment: 11 page

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

<p>Abstract</p> <p>Background</p> <p>To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.</p> <p>Results</p> <p>We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.</p> <p>Conclusions</p> <p>The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.</p> <p>Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: <url>http://pbil.univ-lyon1.fr/software/prunier</url></p

Description beyond the mean field approximation of an electrolyte confined between two planar metallic electrodes

We study an electrolyte confined in a slab of width $W$ composed of two grounded metallic parallel electrodes. We develop a description of this system in a low coupling regime beyond the mean field (Poisson--Boltzmann) approximation. There are two ways to model the metallic boundaries: as ideal conductors in which the electric potential is zero and it does not fluctuate, or as good conductors in which the average electric potential is zero but the thermal fluctuations of the potential are not zero. This latter model is more realistic. For the ideal conductor model we find that the disjoining pressure is positive behaves as $1/W^3$ for large separations with a prefactor that is universal, i.e. independent of the microscopic constitution of the system. For the good conductor boundaries the disjoining pressure is negative and it has an exponential decay for large $W$. We also compute the density and electric potential profiles inside the electrolyte. These are the same in both models. If the electrolyte is charge asymmetric we find that the system is not locally neutral and that a non-zero potential difference builds up between any electrode and the interior of the system although both electrodes are grounded.Comment: 16 pages, 5 figures, added a new appendix B and a discussion on ideal conductors vs. good conductor

La chimiohyperthermie intrapéritonéale (CHIP) dans les cancers ovariens

RésuméLe cancer de l’ovaire reste, en France, la quatrième cause de décès par cancer chez la femme. Il s’agit d’une maladie souvent diagnostiquée à un stade évolué avec carcinose péritonéale (CP) et dont l’histoire naturelle est marquée par des récidives essentiellement péritonéales et l’acquisition d’un profil de chimiorésistance. Malgré les nombreuses lignes de chimiothérapie systémique et les chirurgies de cytoréduction (CCR), le pronostic de ces récidives reste sombre. Depuis plus de 20ans, plusieurs équipes spécialisées ont développé un traitement combiné des CP, associant une chirurgie de cytoréduction complète à une chimiohyperthermie intrapéritonéale (CHIP). Cette thérapeutique a une large place dans le traitement des CP d’origine non gynécologiques. Le rationnel pour une utilisation de la CHIP dans le traitement des CP d’origine ovarienne est important. D’une part, 3 études prospectives randomisées ont démontré la supériorité de l’utilisation de la chimiothérapie intrapéritonéale (sans hyperthermie) par rapport à la chimiothérapie systémique sur des patientes sélectionnées. D’autre part, des études rétrospectives et cas-témoins évaluant la CHIP font état de données de survie encourageantes, en particulier en cas de récidive chimiorésistante. Néanmoins, la morbidité et la mortalité associées doivent appeler à une sélection rigoureuse des patientes éligibles, et à une prise en charge multidisciplinaire dans des centres spécialisés. L’évaluation de la CHIP doit se faire par le moyen d’études randomisées à différents stades évolutifs : 1re ligne, consolidation, récidives qu’elles soient chimiorésistantes ou chimiosensibles. Plusieurs études européennes sont en cours.SummaryOvarian cancer remains the fourth leading cause of cancer death in women in France. It is all too often diagnosed at an advanced stage with peritoneal carcinomatosis (PC), but remains confined to the peritoneal cavity throughout much of its natural history. Because of cellular selection pressure over time, most tumor recurrences eventually develop resistance to systemic platinum. Options for salvage therapy include alternative systemic chemotherapies and further cytoreductive surgery (CRS), but the prognosis remains poor. Over the past two decades, a new therapeutic approach to PC has been developed that combines CRS with hyperthermic intraperitoneal chemotherapy (HIPEC). This treatment strategy has already been shown to be effective in non-gynecologic carcinomatosis in numerous reports. There is a strong rationale for the use of HIPEC for PC of ovarian origin. On the one hand, three prospective randomized trials have demonstrated the superiority of intraperitoneal chemotherapy (without hyperthermia) in selected patients compared to systemic chemotherapy. Moreover, retrospective studies and case-control studies of HIPEC have reported encouraging survival data, especially when used to treat chemoresistant recurrence. However, HIPEC has specific morbidity and mortality; this calls for very careful selection of eligible patients by a multidisciplinary team in specialized centers. HIPEC needs to be evaluated by means of randomized trials for ovarian cancer at different developmental stages: as first line therapy, as consolidation, and for chemoresistant recurrence. Several European Phase III studies are currently ongoing

Heterodyne non-demolition measurements on cold atomic samples: towards the preparation of non-classical states for atom interferometry

We report on a novel experiment to generate non-classical atomic states via quantum non-demolition (QND) measurements on cold atomic samples prepared in a high finesse ring cavity. The heterodyne technique developed for the QND detection exhibits an optical shot-noise limited behavior for local oscillator optical power of a few hundred \muW, and a detection bandwidth of several GHz. This detection tool is used in single pass to follow non destructively the internal state evolution of an atomic sample when subjected to Rabi oscillations or a spin-echo interferometric sequence.Comment: 23 page

X-ray Near Field Speckle: Implementation and Critical Analysis

We have implemented the newly-introduced, coherence-based technique of x-ray near-field speckle (XNFS) at 8-ID-I at the Advanced Photon Source. In the near field regime of high-brilliance synchrotron x-rays scattered from a sample of interest, it turns out, that, when the scattered radiation and the main beam both impinge upon an x-ray area detector, the measured intensity shows low-contrast speckles, resulting from interference between the incident and scattered beams. We built a micrometer-resolution XNFS detector with a high numerical aperture microscope objective and demonstrate its capability for studying static structures and dynamics at longer length scales than traditional far field x-ray scattering techniques. Specifically, we characterized the structure and dynamics of dilute silica and polystyrene colloidal samples. Our study reveals certain limitations of the XNFS technique, which we discuss.Comment: 53 pages, 16 figure