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.     

Measurement of harmonic phase differences by interference of attosecond light pulses

By using a self-referencing technique, we have experimentally measured the influence of the carrier-envelope phase of femtosecond light pulses on the phase of the electric field of the radiation produced by high-order harmonic generation. We show that, in particular experimental conditions, the temporal evolution of the electric field of the attosecond pulses, is directly controlled by the carrier-envelope phase of the driving pulses.     

Oxidative dissolution of chalcopyrite by Acidithiobacillus ferrooxidans analyzed by electrochemical impedance spectroscopy and atomic force microscopy

The microbiological leaching of chalcopyrite (CuFeS(2)) is of great interest because of its potential application to many CuFeS(2)-rich ore materials. However, the efficiency of the microbiological process is very limited because this mineral is one of the most refractory to bacterial attack. Knowledge of bacterial role during chalcopyrite oxidation is very important in order to improve the efficiency of bioleaching operation. The oxidative dissolution of a massive chalcopyrite electrode by Acidithiobacillus ferrooxidans was evaluated by electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM). A massive chalcopyrite electrode was utilized in a Tait-type electrochemical cell in acid medium for different immersion times in the presence or absence of bacterium. The differences observed in the impedance diagrams were correlated with the adhesion process of bacteria on the mineral surface.     

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.     

Close-loop three-laser scheme for chaos-encrypted message transmission

In this paper, we numerically evaluate private data transmission using a three-laser scheme, consisting of a pair of twin semiconductor lasers, driven to chaos by delayed optical feedback in a short cavity, and optically injected by a third chaotic laser which forces them to synchronize. This laser is selected with different internal parameters with respect to the twin pair, so that the emissions of the synchronized, matched lasers, are highly correlated, whereas their correlation with the driver is low. The digital message modulates the emission of the transmitter, as in a standard Chaos Modulation scheme. Message recovery is then obtained by subtracting, from the transmitted chaos-masked message, the chaos, locally generated by the synchronized receiver laser. Simulations have been performed with the Lang-Kobayashi model, and, in view of application to private transmission, we have investigated the effect of the parameter mismatch, between transmitter and receiver, on message recovery. A preliminary experimental evaluation has been also performed using specially designed InP integrated modules.     

Branched spines and contact structures on 3-manifolds

We introduce and analyze the characteristic foliation induced by a contact structure on a branched surface, in particular a branched standard spine of a 3-manifold. We extend to (fairly general) singular foliations of branched surfaces the local existence and uniqueness results which hold for genuine surfaces. Moreover we show that global uniqueness holds when restricting to tight structures. We establish branched versions of the elimination lemma. We prove a smooth version of the Gillman-Rolfsen PL-embedding theorem, deducing that branched spines can be used to construct contact structures in a given homotopy class of plane fields. Entrata in Redazione il 6 novembre 1998.     

Erratum to: Determination of metal ion content of beverages and estimation of target hazard quotients: a comparative study

This is a correction to the following paper: Hague T, Petroczi A, Andrews PR, Barker J, Naughton DP: Determination of metal ion content of beverages and estimation of target hazard quotients: a comparative study. Chem Central J 2008, 2:13.     

On the frequency of oscillations in the pair plasma generated by a strong electric field

We study the frequency of the plasma oscillations of electron–positron pairs created by the vacuum polarization in a uniform electric field with strength E   in the range 0.2Ec<E<10Ec$0.2E_c<E<10E_c$. Following the approach adopted in Ruffini, et al. (2007) [1] we work out one second order ordinary differential equation for a variable related to the velocity from which we can recover the classical plasma oscillation equation when E→0$E\to 0$. Thereby, we focus our attention on its evolution in time studying how this oscillation frequency approaches the plasma frequency. The time-scale needed to approach to the plasma frequency and the power spectrum of these oscillations are computed. The characteristic frequency of the power spectrum is determined uniquely from the initial value of the electric field strength. The effects of plasma degeneracy and pair annihilation are discussed.     

Controllability for systems governed by semilinear evolution inclusions without compactness

In this paper we study the controllability for a class of semilinear differential inclusions in Banach spaces. Since we assume the regularity of the nonlinear part with respect to the weak topology, we do not require the compactness of the evolution operator generated by the linear part. As well we are not posing any conditions on the multivalued nonlinearity expressed in terms of measures of noncompactness. We are considering the usual assumption on the controllability of the associated linear problem. Notice that, in infinite dimensional spaces, the above mentioned compactness of the evolution operator and linear controllability condition are in contradiction with each other. We suppose that the nonlinear term has convex, closed, bounded values and a weakly sequentially closed graph when restricted to its second argument. This regularity setting allows us to solve controllability problem under various growth conditions. As application, a controllability result for hyperbolic integro-differential equations and inclusions is obtained. In particular, we consider controllability of a system arising in a model of nonlocal spatial population dispersal and a system governed by the second order one-dimensional telegraph equation.