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

Fractional bidromy in the vibrational spectrum of HOCl

We introduce the notion of fractional bidromy which is the combination of fractional monodromy and bidromy, two recent generalizations of Hamiltonian monodromy. We consider the vibrational spectrum of the HOCl molecule which is used as an illustrative example to show the presence of nontrivial fractional bidromy. To our knowledge, this is the first example of a molecular system where such a generalized monodromy is exhibited.Comment: 9 pages, 2 figue

An effective model for the X 2A1-A 2B2 conical intersection in NO2

International audienceWe propose an efficient method for calculating the eigenstates and adjusting the parameters of an effective Hamiltonian, which reproduces the experimentally observed energy levels of NO2 up to 11 800 cm-1 above the quantum mechanical ground state, that is a few thousands of cm-1 above the X 2A1-A 2B2 conical intersection, with a rms error less than 4 cm-1. This method principally relies on the determination, through first-order perturbation theory, of an optimal basis for each surface, which takes into account the nonresonant energy shifts experienced by the states of this surface. As a result, the size of the matrix, which one has to build and diagonalize to converge the spectrum up to 11 800 cm-1, is of the order of 500-1000 instead of several tens of thousands. Thank to this Hamiltonian, the analysis of the experimental spectrum up to 11 800 cm-1 could be completed. A detailed description of all states located above 9500 cm-1 is proposed, those lying below 9500 cm-1 being already known and tabulated

Monodromy of the LiNC/NCLi molecule

Using the potential surface of Essers, Tennyson, and Wormer in [Chem. Phys. Lett. 89 (1982) 223], we show that the system of bending vibrational states of the isomerizing molecule LiNC/NCLi has monodromy. On the basis of a deformed spherical pendulum model, we explain dynamical and geometric reasons of this phenomenon and of its absence in the similar system HCN/CNH

The CO A-X System for Constraining Cosmological Drift of the Proton-Electron Mass Ratio

The $\textrm{A}^1\Pi-\textrm{X}^1\Sigma^+$ band system of carbon monoxide, which has been detected in six highly redshifted galaxies ($z=1.6-2.7$), is identified as a novel probe method to search for possible variations of the proton-electron mass ratio ($\mu$) on cosmological time scales. Laboratory wavelengths of the spectral lines of the A-X ($v$,0) bands for $v=0-9$ have been determined at an accuracy of $\Delta\lambda/\lambda=1.5 \times 10^{-7}$ through VUV Fourier-transform absorption spectroscopy, providing a comprehensive and accurate zero-redshift data set. For the (0,0) and (1,0) bands, two-photon Doppler-free laser spectroscopy has been applied at the $3 \times 10^{-8}$ accuracy level, verifying the absorption data. Sensitivity coefficients $K_{\mu}$ for a varying $\mu$ have been calculated for the CO A-X bands, so that an operational method results to search for $\mu$-variation.Comment: 7 pages (main article), 3 figures, includes supplementary materia

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

Cellular protection by erythropoietin: new therapeutic implications

ABSTRACT Erythropoietin (EPO), the principal hematopoietic hormone produced by the kidney and the liver in fetuses, regulates mammalian erythropoiesis and exhibits diverse cellular effects in nonhematopoietic tissues. The introduction of recombinant human EPO (rhEPO) has marked a significant advance in the management of anemia associated with chronic renal failure. At the same time, experimental studies have unveiled its potential neuroprotective and cardioprotective properties, occurring independently of its hematopoietic action. As with other cytoprotective agents, administration of exogenous rhEPO can confer cerebral and myocardial protection against ischemia-reperfusion injury in terms of reduction in cellular apoptosis and necrosis, as well as improvement in functional recovery. Very recent studies even suggest that this drug could have beneficial applications in oncology, protecting against chemotherapy cardiotoxicity. The purpose of this letter is to review current information regarding the various conditions in which rhEPO and its derivates could confer cellular protection. We also address clinical perspectives and novel therapeutic strategies that could be developed based on these studies. Thus, EPO seems to be a very promising agent for protecting cellular survival during both acute and chronic diseases, and its future should be considered with enthusiasm. The hormone erythropoietin (EPO), produced by the kidney and the liver in fetuses, is well known in regulating mammalian erythropoiesis. Exogenous EPO, the recombinant human EPO (rhEPO), introduced approximately two decades ago, is presently used for the treatment of anemia resulting from a variety of conditions, such as chronic renal failure and chemotherapy. However, since the last decade, the existence of EPO and its receptor (EPOR) localized outside of the liver and the kidney, such as the brain and heart, has been shown. At the same time, several experimental studies using rhEPO have unveiled the potential neuroprotective and cardioprotective role of EPO against ischemia, occurring independently of its hematopoietic action The cell possesses a remarkable ability to adapt to stress by changing its phenotype in a manner that renders it more resistant to subsequent injury. This powerful adaptative phenomenon called preconditioning is illustrated by the fact that a sublethal stress (such as ischemia or pharmacological agent administration) applied to an organ enhances its tolerance to a subsequent lethal stress. When preventively administered, rhEPO is able to mimic ischemic preconditioning, protecting neuronal and cardiac cell against various stresses, such as lethal ischemia or cytotoxic drugs In this article, we review current information regarding the various conditions in which rhEPO and its derivates could confer cellular protection. We also report recent data concerning the mechanisms underlying the cytoprotective effects of rhEPO, such as the role of EPOR and the activation of the following cellular signaling pathways. Finally, we adArticle, publication date, and citation information can be found a

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

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

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