Accelerated Poisson-Boltzmann calculations for static and dynamic systems

We report here an efficient implementation of the finite difference Poisson-Boltzmann solvent model based on the Modified Incomplete Cholsky Conjugate Gradient algorithm, which gives rather impressive performance for both static and dynamic systems. This is achieved by implementing the algorithm with Eisenstat's two optimizations, utilizing the electrostatic update in simulations, and applying prudent approximations, including: relaxing the convergence criterion, not updating Poisson-Boltzmann-related forces every step, and using electrostatic focusing. It is also possible to markedly accelerate the supporting routines that are used to set up the calculations and to obtain energies and forces. The resulting finite difference Poisson-Boltzmann method delivers efficiency comparable to the distance-dependent dielectric model for a system tested, HIV Protease, making it a strong candidate for solution-phase molecular dynamics simulations. Further, the finite difference method includes all intrasolute electrostatic interactions, whereas the distance dependent dielectric calculations use a 15-A cutoff. The speed of our numerical finite difference method is comparable to that of the pair-wise Generalized Born approximation to the Poisson-Boltzmann method.     

Photogenotoxicity of mammalian cells: a review of the different assays for in vitro testing

During the past several years, phototoxicity has been studied at the molecular level, and these studies have provided new insights in the field of DNA lesion characterization, DNA repair and cell response to ultraviolet (UV)-induced stress. The development of new antibiotics and antiinflammatory drugs has highlighted the necessity to develop the assessment of phototoxicity in the safety evaluation of new chemical compounds. This paper aims at reviewing the known molecular mechanisms of the cellular response to UV-induced stress, the in vitro methods that can be proposed and used to screen for toxicity of sunlight and the photosensitization process resulting from the activation of drugs by light. UV sources, biological systems and endpoints of interest in that particular objective are listed. Phototoxic effects span from the cytotoxic-apoptotic effect to the induction of primary DNA damage, DNA repair and a variety of stress genes acting on the cell cycle and the fate of the cell. Ultimately, it can lead to the induction of hereditary DNA modification. A variety of assays are proposed to specifically address all these particular consequences of UV-induced toxicity.     

One-step stereoselective synthesis and NMR chiral shift properties of a novel hexacoordinated phosphorus cation

[reaction: see text] Tropolone, binol, and PCl(5) react in CH(2)Cl(2) at reflux to generate in one step a novel C(2)-symmetric hexacoordinated phosphorus cation of configuration controlled by the binol ligand. It behaves as an efficient NMR chiral shift agent for chiral anionic phosphate and borate anions.     

Multiscale clustering in granular surface flows

We investigate steady granular surface flows in a rotating drum and demonstrate the existence of rigid clusters of grains embedded in the flowing layer. These clusters appear to be fractal and their size is power law distributed from the grain size scale up to the thickness of the flowing layer. The implications of the absence of a characteristic length scale on available theoretical models of dense granular flows are discussed. Finally, we suggest a possible explanation of the difference between velocity profiles observed in surface flows and in flows down a rough inclined plane.     

Spatial trapping of short pulses in Ti-indiffused LiNbO(3) waveguides

We show numerically and experimentally that spatial trapping can be induced in quadratic media even if the pump pulse's duration is shorter than the group-delay mismatch between fundamental wave and second-harmonic components. The influence of phase mismatch and pulse power on the trapping effect is discussed. Spatial, temporal, and spectral behaviors that accompany self-trapped propagation are highlighted.     

Etude comparative des méthyl-borazines par RMN

A comparative study of borazine ( 0 ) and six methyl borazines ( 1 to 6 ) has been conducted by NMR. It becomes evident that the chemical shift of N? CH₃ protons hardly varies between mono-, di- and tri-N-methyl borazines, whereas this parameter undergoes a strong change (in all 0·21 ppm, to high field) when one passes from N-trimethyl borazine (HB? NCH₃)₃ to hexamethyl borazine (CH₃B? NCH₃)₃ through a gradual substitution on the three boron atoms ( 3, 4, 5 and 6 ). Moreover, a systematic variation of the parameter δ has been found between compounds 3, 4 and 5 for the protons which keep precisely the same immediate environment. A qualitative interpretation of this experimental result is proposed in terms of electronic effects general to the hexagonal planar boron/nitrogen ring which characterises these molecules.