Sound production mechanism in carapid fish: first example with a slow sonic muscle

Fish sonic swimbladder muscles are the fastest muscles in vertebrates and have fibers with numerous biochemical and structural adaptations for speed. Carapid fishes produce sounds with a complex swimbladder mechanism, including skeletal components and extrinsic sonic muscle fibers with an exceptional helical myofibrillar structure. To study this system we stimulated the sonic muscles, described their insertion and action and generated sounds by slowly pulling the sonic muscles. We find the sonic muscles contract slowly, pulling the anterior bladder and thereby stretching a thin fenestra. Sound is generated when the tension trips a release system that causes the fenestra to snap back to its resting position. The sound frequency does not correspond to the calculated resonant frequency of the bladder, and we hypothesize that it is determined by the snapping fenestra interacting with an overlying bony swimbladder plate. To our knowledge this tension release mechanism is unique in animal sound generation

Second rapport d'étape du groupe de réflexion sur les aménagements physiques en zone côtière et leur gestion pour l'aquaculture et la pêche

Ce second rapport d'étape fait le point sur le travail engagé depuis la réunion d'ouverture du 18 mai 1998. En premier lieu, il rappelle les principales observations et conclusions des deux premières réunions de travail. Il présente ensuite les principaux enseignements tirés de la récente mission du groupe de travail, centrée sur les Pertuis charentais. A la différence de la côte méditerranéenne, il n'y a pas, sur le littoral atlantique français, de récifs artificiels au sens traditionnel. Les seules structures immergées récentes sont des filières à moules en Charente. Ce rapport inclut une analyse des besoins budgétaires pour mener à bien la réflexion et l'élaboration du rapport final. Les annexes attestent des efforts tantôt théoriques, tantôt pratiques de répondre à des demandes d'origines variées: particuliers, collectivités, administration, élus, médias. Au terme de cette première année d'étude, le premier constat est que les ressources marines vivantes des côtes françaises sont globalement surexploitées, ou mal exploitée. De manière globale, les expertises halieutiques convergent pour souligner l'importance de la bande côtière dans le cycle biologique de nombreuses espèce, et notamment des petits fonds. Le second constat est relatif à la qualité du milieu environnant côtier : les estuaires et baies sont l'aboutissement de bassins versants, collecteurs des effluents issus des diverses activités humaines, agriculture, industrie, habitat. L'approche de la gestion par celle du bassin versant devient prépondérante, d'où la nécessité d'une approche intégrée des problèmes et des enjeux côtiers. Le troisième point prend en compte les tendances lourdes sur les 20 prochaines années : réchauffement général du climat, donc des eaux, modes de vie valorisant l'habitat, le travail et le tourisme en zone littorale, souci de la qualité de la vie, de la variété des activités récréatives. En conséquence, il faut s'attendre à une pression croissante sur les usages du littoral, de la proche bande côtière, notamment pour l'explotation des ressources marines vivantes, ce qui ne manquera pas de contribuer à l'émergence de conflits entre les divers acteurs, face à une ressource limitée et convoitée. La réflexion sur les prochains Contrats de Plan (2000-2006) constitue enfin une remarquable opportunité de réflexions croisées entre chercheurs, promoteurs et décideurs locaux à l'échelle des écosystèmes

S/G-1: An Ab Initio Force-field Blending Frozen Hermite Gaussian Densities and Distributed Multipoles. Proof of Concept and First Applications to Metal Cations

International audienceWe demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar response level. This opens up the possibility of embodying explicit scalar relativistic effects in molecular mechanics thanks to the direct transferability of ab initio pseudopotentials. Therefore, incorporating GEM-like electron density for a metal cation enable the introduction of nonambiguous short-range quantum effects within any point-dipole based polarizable force field without the need of an extensive parametrization

QM/AMOEBA description of properties and dynamics of embedded molecules

We describe the development, implementation, and application of a polarizable QM/MM strategy, based on the AMOEBA polarizable force field, for calculating molecular properties and performing dynamics of molecular systems embedded in complex matrices. We show that polarizable QM/MM is a well-understood, mature technology that can be deployed using a state-of-the-art implementation that combines efficient numerical methods and linear scaling techniques. Thanks to these numerical advances and to the availability of parameters for a wide manifold of systems in the AMOEBA force field, polarizable QM/AMOEBA can be used for advanced production applications, that range from the prediction of spectroscopies to ground- and excited-state multiscale ab initio molecular dynamics simulations. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Combined QM/MM Methods

Addressing the issues of non-isotropy and non-additivity in the development of quantum chemistry-grounded polarizable molecular mechanics

We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM