Soft Constraint Logic Programming and Generalized Shortest Path Problems

In this paper we study the relationship between Constraint Programming (CP) and Shortest Path (SP) problems. In particular, we show that classical, multicriteria, partially ordered, and modality-based SP problems can be naturally modeled and solved within the Soft Constraint Logic Programming (SCLP) framework, where logic programming is coupled with soft constraints. In this way we provide this large class of SP problems with a high-level and declarative linguistic support whose semantics takes care of both finding the cost of the shortest path(s) and also of actually finding the path(s). On the other hand, some efficient algorithms for certain classes of SP problems can be exploited to provide some classes of SCLP programs with an efficient way to compute their semantics.     

Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k

Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1-43) and EF2 (residues 44-75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitro experiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutated calbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 A with respect to the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independent in silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, that is, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2 homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linear correlations between thermodynamic data and ZDOCK scores were built, providing a tested tool for very fast in silico predictions of the free energy of association of protein-protein complexes solved at the atomic level and known to not undergo significant conformational changes upon binding.     

From X- to O-shaped spatiotemporal spectra of light filaments in water

We show that the angle-wavelength spectra of light filaments excited by ultrashort pulses experience a transition from X- to O-like structures when their carrier wavelengths are switched from normal to anomalous dispersion. Calculations confirm that the O-shaped conical emission follows the elliptic geometry of the nonlinear Schr?dinger equation with anomalous dispersion.     

Ozone monitoring in a Mediterranean forest using diffusive and continuous sampling

Ambient ozone was measured in a forest in Castelporziano (Italy) characterised by the prevailing presence of Holm-oak trees (Quercus ilex L.) from June to November 2003. Two methods for measuring ozone were used: long-term monitoring using diffusive samplers at three heights within the canopy, and continuous monitoring at two heights using the UV method. Results for one week mean ozone levels above and below the canopy from the diffusive samplers were compared to those obtained using the automatic analyser at the same levels. A good correlation between the two sampling techniques was found. Continuous monitoring showed a daily cycle with a midday maximum and a nocturnal minimum. While the forest floor consistently had the lowest ozone concentration, there were no differences during most daytime hours. The midday maximum is clearly due to downward mixing with O₃-rich air from above. The night-time ozone decay within the canopy is the result of dry deposition of O₃ and most likely due to reaction with biogenically produced NO. AOT40 within and above the canopy mostly exceeded the critical levels.     

Empirical estimates of the average orders of orbits period lengths in Euler groups

The averaged growth rate of period's length of the geometrical progressions $\text{{q}{}^{\mathrm{t}}\text{mod}\text{n,}\text{t=0,1,…}}$ for increasing n is empirically estimated for different values of q. The experimental results, obtained for n up to 10⁶, allow us to conjecture that the average order of period's length is $\text{C}\text{n}\text{ln}\text{(n)}$, where constant C depends on q. To cite this article: F. Aicardi, C. R. Acad. Sci. Paris, Ser. I 339 (2004).     

Catalytic activity of myoglobin immobilized on zirconium phosphonates

The adsorption and catalytic activity of myoglobin (Mb) on zirconium phosphonates (a-zirconium benzenephosphonate (alpha-ZrBP), a-zirconium carboxyethanephosphonate (alpha-ZrCEP), and a novel layered zirconium fluoride aminooctyl-N,N-bis(methylphosphonate) (ZrC8)) were investigated. The maximum adsorption was reached after 16 h of contact and was greater on hydrophobic supports such as alpha-ZrBP and ZrC8 compared to hydrophilic supports such as alpha-ZrCEP. The equilibrium adsorption isotherms fitted the Langmuir equation, suggesting the presence of a monolayer of protein molecules on the support surfaces. The catalytic activities of free Mb and of the obtained biocomposites were studied in terms of the oxidation of two aromatic substrates, o-phenylenediamine and 2-methoxyphenol (guaiacol), by hydrogen peroxide. The oxidation catalyzed by immobilized myoglobin followed the Michaelis-Menten kinetics, similar to oxidation by free Mb. The kinetic parameters, kcat and KM, were significantly affected by the adsorption process. Mb/alpha-ZrCEP was the most efficient biocatalyst obtained, probably because of the hydrophilic nature of the support. The effect of immobilization on the stability of Mb toward inactivation by hydrogen peroxide was also investigated, and an increased resistance was found. The biocomposites obtained can be stored at 4 degrees C for months without a significant loss of catalytic activity.     

Probing the different stages in contacting a single molecular wire

A crucial problem in molecular electronics is the control of the electronic contact between a molecule and its electrodes. As a model system, we investigated the contact between the molecular wire group of a C90H98 (Lander) molecule and the edge of a Cu(111) monatomic step. The reproducible contact and decontact of the wire was obtained by manipulating the Lander with a low temperature scanning tunneling microscope. The electronic standing wave patterns on the Cu(111) surface serve to monitor the local electronic perturbation caused by the interaction of the wire end with the step edge, giving information on the quality of the contact.     

Molecular dynamics simulations of the ligand-induced chemical information transfer in the 5-HT(1A) receptor

Comparative molecular dynamics simulations of the 5-HT(1A) receptor in its empty as well as agonist- (i.e. active) and antagonist-bound (i.e. nonactive) forms have been carried out. The agonists 5-HT and (R)-8-OH-DPAT as well as the antagonist WAY100635 have been employed. The results of this study strengthen the hypothesis that the receptor portions close to the E/DRY/W motif, with prominence to the cytosolic extensions of helices 3 and 6, are particularly susceptible to undergo structural modification in response to agonist binding. Despite the differences in the structural/dynamics behavior of the two agonists when docked into the 5-HT(1A) receptor, they both exert a destabilization of the intrahelical and interhelical interactions found in the empty and antagonist-bound receptor forms between the arginine of the E/DRY sequence and both D133(3.49) and E340(6.30). For both agonists, the chemical information transfer from the extracellular to the cytosolic domains is mediated by a cluster of aromatic amino acids in helix 6, following the ligand interaction with selected amino acids in the extracellular half of the receptor, such as D116(3.32), S199(5.42), Y195(5.38), and F361(6.51). A significant reduction in the bend at P360(6.50), as compared to the empty and the antagonist-bound receptor forms, is one of the features of the agonist-bound forms that is related to the breakage of the interhelical salt bridge between the E/DRY arginine and E340(6.30). Another structural feature, shared by the agonist-bound receptor forms and not by the empty and antagonist-bound forms, is the detachment of helices 2 and 4, as marked by the movement of W161(4.50) away from helix 2, toward the membrane space.