Conformational memories with variable bond angles

Conformational Memories (CM) is a simulated annealing/Monte Carlo method that explores peptide and protein dihedral conformational space completely and efficiently, independent of the original conformation. Here we extend the CM method to include the variation of a randomly chosen bond angle, in addition to the standard variation of two or three randomly chosen dihedral angles, in each Monte Carlo trial of the CM exploratory and biased phases. We test the hypothesis that the inclusion of variable bond angles in CM leads to an improved sampling of conformational space. We compare the results with variable bond angles to CM with no bond angle variation for the following systems: (1) the pentapeptide Met-enkephalin, which is a standard test case for conformational search methods; (2) the proline ring pucker in a 17mer model peptide, (Ala)(8)Pro(Ala)(8); and (3) the conformations of the Ser 7.39 chi(1) in transmembrane helix 7 (TMH7) of the cannabinoid CB1 receptor, a 25-residue system. In each case, analysis of the CM results shows that the inclusion of variable bond angles results in sampling of regions of conformational space that are inaccessible to CM calculations with only variable dihedral angles, and/or a shift in conformational populations from those calculated when variable bond angles are not included. The incorporation of variable bond angles leads to an improved sampling of conformational space without loss of efficiency. Our examples show that this improved sampling leads to better exploration of biologically relevant conformations that have been experimentally validated.     

Multilayer neural network of adaptive bidirectional associative memories

The analysis of the functioning of the brain allows to propose a computational model of multilayer artificial neural network susceptible of associating some response to a particular input, so that when we present that input, we get the required output by the stability of its states and by minimizing the function of energy of the network. The problem of explosion in the number of interconnections has been solved by the introduction of a layer between the input and the output layer of the network. In this paper, we propose the adaptive bidirectional associative memory by conjugate gradient algorithm, so as to study the behavior and performances of the network on pairs of patterns through using the autoassociative or heteroassociative memories.     

Metal ion doped polymers as media for optical memories

Polymer materials are making an impact on optical storage technology to develop high information density and fast access type memories with a high read-out efficiency. The principle and advantages of three-dimensional (3-D) data storage in the form of interference patterns (holograms) have been outlined. Three different information storage materials have been developed by doping metal ions such as Cr(VI) and Fe(III) in water-soluble polymers, namely poly(vinyl alcohol) (PVA) and poly(acrylic acid) (PAA), which need no further thermal or chemical treatment. Volume transmission holograms have been recorded in dichromated poly(vinyl alcohol) (DCPVA), ferric chloride doped poly(vinyl alcohol) (FePVA) and dichromated poly(acrylic acid) (DCPAA), with and without an electron donor (dimethyl formamide), and xanthene dyes (fluorescein, eosin Y and Rose Bengal). Different parameters influencing the holographic performance have been optimized to achieve a high real-time diffraction efficiency (～70%). An electron transfer process from the polymer matrix to Cr(VI)/Fe(III), leading to the photocrosslinking of the polymer in the form of an interference pattern, has been suggested as the mechanism of information storage (hologram recording) in these materials.     

The electronic spectrum and electronic structure of 1,5 dinitronaphthialene

The electronic absorption spectra of the n-heptane and ethanol solutions and the polarized absorption spectrum of the single crystal were measured with 1,5-dinitronaphthalene. 1,5-Dinitronaphthalene shows three absorption bands at 198.7, 230 and 323 m. The 230 m and 323 m. bands are polarized almost parallel with the long and short axes of the naphthalene ring respectively. The assignment of the bands has been made by combining the observed results with the theoretical consideration.

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Zusammenfassung Das UV-Absorptionsspektrum von 1,5-Dinitronaphthalin in Lösung von n-Heptan und Äthanol und das Polarisationsabsorptionsspektrum des Einkristalls wurde aufgenommen. Es zeigt drei Banden bei 198,7, 230 und 323 m, wobei die Polarisationsrichtungen der beiden letzteren nahezu parallel zur langen und kurzen Achse des Naphthalinringes liegen. Die Zuordnung der Banden wurde auf Grund einer Kombination experimenteller und theoretischer Gegebenheiten vorgenommen.

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Résumé Le spectre électronique d'absorption du 1,5-dinitronaphthalène a été mesuré dans l'éthanol, le n-heptane et dans le monocristal. Des bandes à 198,7, 230 et 323 m la deuxième (troisième) est polarisée presque parallèle à l'axe longue (courte) du noyau naphthalénique. La comparison aux résultats théoriques permet l'interprétation des bandes.

     

Interpretation of analytical patterns from the output of chaotic dynamical memories

A fundamental study has been carried out to use a nonlinear dynamic system, Freeman’s KIII model, for pattern recognition in analytical chemistry. Filtering of the output of the neuron activity traces in the gamma range has been studied by applying a fast Fourier transform filter. Different possibilities for interpretation of the system output have been investigated. Preliminary results are demonstrated for classification of drugs based on their spectra in the mid infrared range.     

Interpretation of analytical patterns from the output of chaotic dynamical memories

A fundamental study has been carried out to use a nonlinear dynamic system, Freeman's KIII model, for pattern recognition in analytical chemistry. Filtering of the output of the neuron activity traces in the gamma range has been studied by applying a fast Fourier transform filter. Different possibilities for interpretation of the system output have been investigated. Preliminary results are demonstrated for classification of drugs based on their spectra in the mid infrared range.     

苯并噻二嗪吸电子基取代衍生物电子性质的理论研究

运用量子化学半经验方法对1，2，4-苯并噻二嗪-1，1二氧类化合物的8种取代衍生物进行了量子化学计算，从体系能量、几何构型、电子结构、前线分子轨道等几方面分析了吸电子基-CN，-NO2等取代后体系的电子性质变化规律．结果表明：随着取代基吸电子能力的增强，体系的活性增强，可为药物合成提供一定的理论指导．     

Nucleation and growth phenomena in nanosized electrochemical systems for resistive switching memories

The impact of the electrochemical nucleation on the switching kinetics in many nanoscaled redox-based resistive switching memories is critically discussed. In the case of the atomic switch, the system is site invariant and the nucleation process is strictly localized below the STM tip. Using RbAg₄I₅ solid electrolyte, nucleation was found to be rate limiting. The electrochemical metallization memory cells (gapless type atomic switch) operate at conditions closer to the conventional nucleation. They introduce additional difficulties for interpretation of the experimental results due to formation of hillocks, of surface oxide barrier films, induction of strain, and the influence of the high electric field. In valence change memories, the nucleation seems to be less important because of the higher applied voltages. The results are discussed in the context of the atomistic theory of electrochemical nucleation. We believe that re-analysis of the experimental data for many systems will reveal that the nucleation is limiting the switching time.     

Enzyme nanoparticles-based electronic biosensor

A simple and effective method to prepare an enzyme electronic biosensor by immobilizing enzyme nanoparticles directly onto the gold electrode surface is described; prepared horseradish peroxidase nanoparticles have been successfully used to develop reagentless electronic biosensors for H2O2 detection without promoters and mediators and offer great potential to develop enzyme-based electronic biosensors.     

Molecular electronic virial theorem

The partitioning of the molecular electronic energy into true one-electron quantities defined by a molecular electronic virial theorem (MEVT) is studied for a number of molecules. Since the theorem is derived for exact wavefunctions, its applicability to various ab initio wavefunctions at difierent levels of accuracy is examined. The average percentage deviations of the theorem for near Hartree-Fock, double zeta, STO-6G and STO-3G type wave functions are 0.4, 1.7, 2.3 and 3.3, respectively.