Recent progress in protein 3D structure comparison

Quantitation of protein 3-D structure similarity is crucial in such fields as evolutionary studies, structural modeling and prediction of biological function. There are various approaches, many of which are tailored to specific problems. This review summarizes the recent developments in this field with particular interest in two main areas: i) improvements to and statistical interpretation of the root-man-square distance between equivalent atoms, rmsd; and ii) methods of protein structural classification based on geometrical features. Special attention is given to fast methods capable of analyzing large structural databases.     

Rheology of a lyotropic mesophase through a stress-relaxation experiment

We report on the first rheological study of the structural relaxations in a nematic liquid crystalline phase. Linear dynamic and transient shear experiments were applied to a polydomain nematic phase of the CTAB/water system: a liquid crystalline mixture composed of 28 wt% CTAB at 35 degrees C. The decay of the shear modulus, G(t), was analyzed using the CONTIN inverse Laplace transform to obtain a distribution of relaxation times which were compared with ones from the usual fitting procedure based on a generalized Maxwell model. The behavior of the nematic lyotropic structure of the CTAB/water system is characterized by the presence of both slow and fast relaxation times. These were interpreted as being due to a progressive loss of the lyotropic domain orientation and to the breaking/reforming process of the cylindrical aggregates, respectively.     

A simulation model for aircraft sequencing in the near terminal area

The objective of this study is the development of a simulation model to assist in aircraft sequencing operations in the terminal area. After the definition of the main characteristics of the model, a general structure of a terminal area is considered with a variable number of feeder fixes and alternative paths from the fixes to the runways. The model is designed so as to evaluate different operating policies. A discrete events simulation philosophy, using Fortran as simulation language, is employed. Finally a model application to the Rome terminal area is illustrated. The results obtained show that the model, here presented, is general enough to simulate the terminal area behaviour of any airport.     

A biofunctional polymeric coating for microcantilever molecular recognition

An innovative route to activate silicon microcantilevers (MCs) for label free molecular recognition is presented. The method consists in coating the underivatized MCs with a functional ter-polymer based on N,N-dimethylacrylamide (DMA) bearing N-acryloyloxysuccinimide (NAS) and 3-(trimethoxysilyl)propyl-methacrylate (MAPS), two functional monomers that confer to the polymer the ability to react with nucleophilic species on biomolecules and with glass silanols, respectively. The polymer was deposited onto MCs by dip coating. Polymer coated MCs were tested in both static and dynamic modes of actuation, featuring detection of DNA hybridization as well as protein/protein interaction. In the dynamic experiments, focused on protein detection, the MCs showed an average mass responsivity of 0.4 Hz/pg for the first resonant mode and of 2.5 Hz/pg for the second resonant mode. The results of the static experiments, dedicated to DNA hybridization detection, allowed for direct estimation of the DNA duplex formation energetics, which resulted fully consistent with the nominal expected values. These results, together with easiness and cheapness, high versatility, and excellent stability of the recognition signal, make the presented route a reliable alternative to standard SAM functionalization (for microcantilevers (MCs) and for micro-electro-mechanical systems (MEMS) in general).     

A solid-phase approach to the synthesis of N-1-alkyl analogues of cyclic inosine-diphosphate-ribose (cIDPR)

We report here an efficient solid-phase synthesis of N-1-alkyl-substituted analogues of cyclic inosine-diphosphate-ribose (cIDPR), a mimic of cyclic ADP-ribose (cADPR). Our synthetic strategy makes use of a polystyrene support to which inosine was bonded through a 2′,3′-acetal linkage. Insertion of a ω-hydroxy-polymethylene chain of variable length on N-1, followed by conversion into N-1-alkylinosine-bis-phosphate derivatives and cyclization, allowed to obtain analogues of cIDPR of various ring size. The cyclization step was carried out both in solid-phase and in solution by pyrophosphate bond formation. The effect of the N-1-polymethylene chain length on the cyclization yields as well as the reaction conditions, which led to the solid-phase pyrophosphate bond formation, were thoroughly investigated.     

Experimental evidence of non-standard bifurcations in non-smooth oscillator dynamics

Analytical and experimental investigations are performed in order to characterize the dynamic behaviour of a non-smooth rotational oscillator, which exhibits multiple discontinuity boundaries in the phase space. The physical system consists of a rotating body subjected to an elastic restoring force and in contact with one or two rough discs rotating with constant driving velocities. The presence of multiple discontinuity boundaries caused by frictional contacts leads to non-standard bifurcations that are studied by means of a simple mechanical model.A test set-up has then been built to investigate the correctness of modelling of the friction force and the validity of the proposed model for technical applications: the experimental measurements qualitatively and quantitatively capture the basic scenarios anticipated by the model while a strong robustness of the phenomena pointed out by the theoretical analyses has been revealed in the experiments.     

Experimental evidence of bifurcating nonlinear normal modes in piecewise linear systems

A system with piecewise linear restoring forces, typical of damaged beams with a breathing crack, exhibits bifurcations characterized by the onset of superabundant modes in internal resonance with a significantly different shape than that of modes on a fundamental branch. A 2-DOF frame with piecewise linear stiffness is analyzed by means of an experimental investigation; the frame is forced by an harmonic base excitation and the operative modal shapes as well as the response amplitude are directly measured; the results are compared with numerical outcomes for different damping values. This study shows that the shapes and the frequencies of certain nonlinear normal modes (NNMs) of the related autonomous system strongly affect the forced response, in both the numerical and the experimental environments. Therefore, it is possible to match the NNM with the forced response of the system, leading to the prospect of identifying the severity and position of the damage from experimental tests.     

An investigation of void fraction in liquid slugs for horizontal and inclined gas—liquid pipe flow

The void fraction in liquid slugs has been determined for air—water fiow in horizontal and near-horizontal pipes by a newly-developed conductance probe technique. A semi-empirical correlation has been developed and compared with the present measurements and available data. This correlation predicts reasonably well the observed effects of diameter, inclination and physical properties.     

Absolute cross section of p(<Superscript>7</Superscript>Be,γ)<Superscript>8</Superscript>B using a novel approach

The absolute cross section σ (E) of the radiative capture reaction p(⁷Be,γ)⁸B at the center-of-mass energy E = 992 keV has been measured using a radioactive ⁷Be ion beam and a windowless gas target system filled with H₂ gas. The ⁸B residual nuclides were detected with a recoil separator consisting of momentum and velocity filters and a ΔE-E detector telescope. The ⁸B yield was observed concurrently with the ⁷Be + p elastic scattering yield, relating σ(E) to the Rutherford scattering cross section. The resulting value, σ(E) = 0.41 ± 0.11 μb, leads to an S(E) factor at zero energy of S(0) = 16 ± 4 eV b, in fair agreement with recommended values. Received: 8 February 2000