A molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide

In this paper, we report on the conformational profile of the pentacyclo-undecane (PCU) cage tripeptide carried out by molecular dynamics (MD) simulation using water as an explicit solvent. The MD solution phase studies carried on the model peptide analogues (A)=Ac–Ala–Ala–Ala–NHMe; (B)=Ac–Cage–Cage–Cage–NHMe; (C)=Ac–Ala–Cage–Ala–NHMe and (D)=Ac–Ala–Pro–Ala–NHMe, are used as a complimentary technique to the corresponding gas phase simulated annealing (SA) study previously carried out in our laboratory. No significant structural changes were observed over the MD trajectories. However, the results reported here provide further evidence that the (PCU) cage amino acid exhibits C_7eq, C_7aq, _R and _L conformations, and the theoretical results suggest that the PCU cage amino acid is a strong β-turn inducer. These results support the prediction that when the PCU cage residues are in the (i) and (i+2) positions, the β-turn can be extended in either direction to form anti-parallel β-pleated sheets, thereby forming the basis of the mechanism for the folding back of the chain in a cross-β-turn structure.     

Penultimate Approximations in Statistics of Extremes and Reliability of Large Coherent Systems

In reliability theory any coherent system can be represented as either a series-parallel or a parallel-series system. Its lifetime can thus be written as the minimum of maxima or the maximum of minima. For large-scale coherent systems it is sensible to assume that the number of system components goes to infinity. Then, the possible non-degenerate extreme value laws either for maxima or for minima are eligible candidates for the system reliability or at least for the finding of adequate lower and upper bounds for the reliability. The identification of the possible limit laws for the system reliability of homogeneous series-parallel (or parallel-series) systems has already been done under different frameworks. However, it is well-known that in most situations such non-degenerate limit laws are better approximated by an adequate penultimate distribution. Dealing with regular and homogeneous parallel-series systems, we assess both theoretically and through Monte-Carlo simulations the gain in accuracy when a penultimate approximation is used instead of the ultimate one.     

Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics

The present study describes an extensive conformational search of substance P using two different computational methods. On the one hand, the peptide was studied using the iterative simulated annealing, and on the other, molecular dynamics simulations at 300 and 400 K. With the former method, the peptide was studied in vacuo with a dielectric constant of 80, whereas using the latter study the peptide was studied in a box of TIP3P water molecules. Analysis of the results obtained using both methodologies was carried out using an in-house methodology using a cluster analysis method based on information theory. Comparison of the two sampling methodologies and the different environment used in the calculations is also analyzed. Finally, the conformational motifs that are characteristic of substance P in a hydrophilic environment are presented and compared with the experimental results available in the literature.     

Dynamics of Si-H vibrations in an amorphous environment

We present results of the first vibrational photon-echo, transient-grating, and temperature dependent transient-bleaching experiments on a-Si:H. Using these techniques, and the infrared light of a free electron laser, the vibrational population decay and phase relaxation of the Si-H stretching mode were investigated. Careful analysis of the data indicates that the vibrational energy relaxes directly into Si-H bending modes and Si phonons, with a distribution of rates determined by the amorphous host. Conversely, the pure dephasing appears to be single exponential, and can be modeled by dephasing via two-phonon interactions.     

Diabolic pair transfer and oscillating behavior of backbending in rotating nuclei

Quantum effects generate “channels” which guide a nucleus from ground state to scission. We present here the channels of²⁵⁸Fm and relate them to the measured kinetic energies of the fission products, to the mass asymmetry and to the relative abundance of the various fission components. The microscopic reason is discussed.     

New Asymptotic Formulae for the Point Coulomb Phase Shift

We investigate the Coulomb phase shift, and derive and analyze new and more precise analytical formulae. We consider next to leading order terms to the Stirling’s approximation, and show that they are important at small values of the angular momentum l and other regimes. We employ the uniform approximation. The use of our expressions in low-energy scattering of charged particles is discussed and some comparisons are made with other approximation methods. Potential use of our results in the search for deviations from pure Mott scattering of sub-barrier scattering of very heavy ions is pointed out.     

Photo-controlled release of zinc metal ions by spiropyran receptors anchored to single-walled carbon nanotubes

Light controllable release of antinflammatory zinc ions by a smart multifunctional material composed of spiropyrans and single walled carbon nanotubes (SWNTs) is demonstrated. The exploitation of a number of complementary characterization techniques allows the investigation of both composition and performance of the multifunctional SP/SWNT nanomaterial developed. Moreover, its suitability for potential applications in bio-systems is suggested by the effective removal of the metal catalyst and the introduction of biocompatible linkers into the SP/SWNT material. The realization of potential photo controllable SP/SWNTs based drug delivery systems (DDSs) is envisaged, where nanotubes act as intracellular carriers of light modulated receptors for bioactive agents.