Quantum mechanical and quasiclassical investigation of the time domain nonadiabatic dynamics of NO2 close to the bottom of the X2A1-A2B2 conical intersection

We use the effective Hamiltonian that we recently fitted against the first 306 experimentally observed vibronic transitions of NO2 [J. Chem. Phys. 119, 5923 (2003)] to investigate the time domain nonadiabatic dynamics of this molecule on the coupled X2A1 and A2B2 electronic states, using both quantum mechanical and quasiclassical techniques. From the quantum mechanical point of view, we show that the transfer of population to the electronic ground state originating from a wave packet launched on the excited state occurs in a stepwise fashion. The evolution of wave packets launched on the electronic ground state is instead more complex because the crossing seam is located close to the bottom of the electronic excited state. We next use the mapping formalism, which replaces the discrete electronic degrees of freedom by continuous ones, to obtain a classical description of the coupled electronic states. We propagate gaussian swarms of trajectories to show that this approach can be used to calculate the populations in each electronic state. We finally propose a very simple trajectory surface hopping model, which assumes that trajectories have a constant probability to jump onto the other state in a particular region of the phase space and a null hopping probability outside from this region. Quasiclassical calculations show that this model enables a precise estimation of complex quantities, like for example the projection of the instantaneous probability density on given planes.Comment: accepted for publication in J. Chem. Phy

Different mechanics of snap-trapping in the two closely related carnivorous plants Dionaea muscipula and Aldrovanda vesiculosa

The carnivorous aquatic Waterwheel Plant (Aldrovanda vesiculosa L.) and the closely related terrestrial Venus Flytrap (Dionaea muscipula SOL. EX J. ELLIS) both feature elaborate snap-traps, which shut after reception of an external mechanical stimulus by prey animals. Traditionally, Aldrovanda is considered as a miniature, aquatic Dionaea, an assumption which was already established by Charles Darwin. However, videos of snapping traps from both species suggest completely different closure mechanisms. Indeed, the well-described snapping mechanism in Dionaea comprises abrupt curvature inversion of the two trap lobes, while the closing movement in Aldrovanda involves deformation of the trap midrib but not of the lobes, which do not change curvature. In this paper, we present the first detailed mechanical models for these plants, which are based on the theory of thin solid membranes and explain this difference by showing that the fast snapping of Aldrovanda is due to kinematic amplification of the bending deformation of the midrib, while that of Dionaea unambiguously relies on the buckling instability that affects the two lobes.Comment: accepted in Physical Review

Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model

We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the model successfully reproduces some of the observed properties of real systems and predictions of kinetic models. For example, sampling of the DNA sequence by the protein proceeds via a succession of 3d motion in the solvent, 1d sliding along the sequence, short hops between neighboring sites, and intersegmental transfers. Moreover, facilitated diffusion takes place in a certain range of values of the protein effective charge, that is, the combination of 1d sliding and 3d motion leads to faster DNA sampling than pure 3d motion. At last, the number of base pairs visited during a sliding event is comparable to the values deduced from single-molecule experiments. We also point out and discuss some discrepancies between the predictions of this model and some recent experimental results as well as some hypotheses and predictions of kinetic models

Extracting Multidimensional Phase Space Topology from Periodic Orbits

We establish a hierarchical ordering of periodic orbits in a strongly coupled multidimensional Hamiltonian system. Phase space structures can be reconstructed quantitatively from the knowledge of periodic orbits alone. We illustrate our findings for the hydrogen atom in crossed electric and magnetic fields.Comment: 4 pages, 5 figures, accepted for publication in Phys. Rev. Let

Anharmonic stacking in supercoiled DNA

Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation.Comment: In pres

Discovering novel enzymes by functional screening of plurigenomic libraries from alga-associated <i>Flavobacteriia</i> and <i>Gammaproteobacteria</i>

Alga-associated microorganisms, in the context of their numerous interactions with the host and the complexity of the marine environment, are known to produce diverse hydrolytic enzymes with original biochemistry. We recently isolated several macroalgal-polysaccharide-degrading bacteria from the surface of the brown alga Ascophyllum nodosum. These active isolates belong to two classes: the Flavobacteriia and the Gammaproteobacteria. In the present study, we constructed two “plurigenomic” (with multiple bacterial genomes) libraries with the 5 most interesting isolates (regarding their phylogeny and their enzymatic activities) of each class (Fv and Gm libraries). Both libraries were screened for diverse hydrolytic activities. Five activities, out of the 48 previously identified in the natural polysaccharolytic isolates, were recovered by functional screening: a xylanase (GmXyl7), a beta-glucosidase (GmBg1), an esterase (GmEst7) and two iota-carrageenases (Fvi2.5 and Gmi1.3). We discuss here the potential role of the used host-cell, the average DNA insert-sizes and the used restriction enzymes on the divergent screening yields obtained for both libraries and get deeper inside the “great screen anomaly”. Interestingly, the discovered esterase probably stands for a novel family of homoserine o-acetyltransferase-like-esterases, while the two iota-carrageenases represent new members of the poorly known GH82 family (containing only 19 proteins since its description in 2000). These original results demonstrate the efficiency of our uncommon “plurigenomic” library approach and the underexplored potential of alga-associated cultivable microbiota for the identification of novel and algal-specific enzymes

Soft-Bottom macrobenthic communities of the Vitória Bay estuarine system, South-eastern Brazil

O presente trabalho analisa e descreve a estrutura das associações faunísticas macrobênticas (epifauna e infauna) do sistema estuarino da Baía de Vitória, sudeste do Brasil, de Janeiro de 1998 a Junho de 1999. Amostras replicadas em níveis de entre-marés e sublitoral foram coletadas em intervalos de três meses em dez estações. Foram caracterizadas as composições dos sedimentos de entre-marés e sublitoral. Os parâmetros físico-químicos da água foram medidos in situ. Foram coletados 10.695 indivíduos, compreendendo a 144 taxa. Os grupos mais abundantes foram moluscos, crustáceos e poliquetos. As espécies mais abundantes foram os bivalves Anomalocardia brasiliana, Mytella guyanensis e M. falcata. Localmente, descargas significativas de esgoto doméstico causaram um aumento da quantidade de matéria orgânica no sedimento (até 30%) e baixa concentração de oxigênio dissolvido na água (< 1mg.l-1). Próximo às duas entradas da baía, o alto hidrodinamismo e a presença de areia grossa reduziram os efeitos deletérios dos aportes de esgotos. A riqueza (S), a diversidade (H') de espécies e a abundância total (A), decresceram das estações externas do estuário (22 < S < 72; 1.99 < H' < 2.85; 320 < A < 1737) em direção às estações internas (2 < S < 45; 0.59 < H' < 2.67; 2 < A < 1317), onde a salinidade e oxigênio dissolvido foram menores e as quantidades de matéria orgânica maiores.The present work describes and analyses the structure of the macrobenthic epi- and infaunal assemblage of the estuarine system of Vitória Bay, South-eastern Brazil, from January 1998 to June 1999. Replicated sampling at intertidal and subtidal levels was conducted quarterly at ten stations. Intertidal and subtidal sediment composition was characterised. Water physico-chemical parameters were measured in situ. A total of 10,695 individuals, belonging to 144 taxa, were collected. Molluscs, crustaceans and polychaetes were the most abundant groups. The bivalves Anomalocardia brasiliana, Mytella guyanensis and M. falcata were the most abundant species. Locally, significant discharges of residential and industrial wastewater resulted in high organic content in the sediment (up to 30%) and low dissolved oxygen concentration in the water (< 1mg.l-1). Near the two entrances of the bay, high hydrodynamic activity and coarse sand reduced the detrimental effects of raw and treated sewage inputs. Species richness (S), diversity (H') and total abundance (A) decreased from outer-bay stations (22 < S < 72; 1.99 < H' < 2.85; 320 < A < 1737) towards inner-bay stations (2 < S < 45; 0.59 < H' < 2.67; 2 < A < 1317), where salinity and dissolved oxygen were lowest and organic matter content highest

Dynamical versus statistical mesoscopic models for DNA denaturation

We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are varied to get predictions in better agreement with experimental results that were not addressed up to now, like mechanical unzipping, the evolution of the critical temperature with sequence length, and temperature resolution. We show that the model with the new parameters provides results that are in quantitative agreement with those obtained from statistical models. Investigation of the critical properties of the dynamical model suggests that DNA denaturation looks like a first-order phase transition in a broad temperature interval, but that there necessarily exists, very close to the critical temperature, a crossover to another regime. The exact nature of the melting dynamics in this second regime still has to be elucidated. We finally point out that the descriptions of the physics of the melting transition inferred from statistical and dynamical models are not completely identical and discuss the relevance of our model from the biological point of view