Pentopyranosyl Oligonucleotide Systems. 9th Communication

Pyranosyl‐RNA (‘p‐RNA’ ) is an oligonucleotide system isomeric to natural RNA and composed of the very same building blocks as RNA. Its generational, chemical, and informational properties are deemed to be those of an alternative nucleic acid system that could have been a candidate in Nature's evolutionary choice of the molecular basis of genetic function. We consider the study of the chemistry of p‐RNA as etiologically relevant in the sense that knowledge of its structural, chemical, and informational properties on the chemical level offers both a perspective and reference points for the recognition of specific structural assets of the RNA structure that made it the (supposedly) superior system among possible alternatives and, therefore, the system that became part of biology as we know it today. The paper describes the chemical synthesis of β‐d‐ (and L )‐ribopyranosyl‐(4′→2′)‐oligonucleotide sequences, presents a resume of their structural and chemical properties, and cautiously discusses what we may and may not have learned from the pyranosyl isomer of RNA with respect to the conundrum of RNA's origin.     

Multifunctional ToF-SIMS: combinatorial mapping of gradient energy substrates

We present a simple method for chemical modification of chlorosilane self-assembled monolayers (SAMs) on Si surfaces by exposure to a gradient of UV-ozone radiation to create stable substrates with a range of contact angles (θ_H2O≈5–95°) and surface energies on a single substrate. These gradient energy substrates are developed to potentially generate libraries for combinatorial studies of thin film phenomenology, where a systematic variation of interfacial surface energy represents one of the significant parameters along one axis. The graded oxidation process presents a systematic variation of surface chemical composition. We have utilized contact angle measurements and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to investigate this variation for a series of ions, among which are SiCH₃⁺, SiOH⁺ and COOH⁻. We show that the macroscopic measurements of surface free energy/contact angle correlate with the detailed analysis of surface chemistry (as assessed by ToF-SIMS) on these test substrates.     

Tight-binding method modelling of photonic crystal waveguides

We present here a tight-binding-like modelling of two-dimensional (2D) photonic crystals (PCs). Adopted from solid-state physics, the concept of generalized Wannier functions is used to construct a localized state basis that allows a parameter-free ab initio study of defects in PCs. We demonstrate here for a 2D triangular lattice of dielectric rods in air, the existence of this localized basis and the possibility to study large scale complex dielectric structures deviating from periodicity. Specific numerical simulations on a split waveguide embedded in this triangular lattice are performed, and they demonstrate the superiority of this method over plane wave based techniques.     

3D molecular imaging SIMS

Thin monolayer and bilayer films of spin cast poly(methyl methacrylate) (PMMA), poly(2-hydroxyethyl methacrylate) (PHEMA), poly(lactic) acid (PLA) and PLA doped with several pharmaceuticals have been analyzed by dynamic SIMS using SF₅⁺ polyatomic primary ion bombardment. Each of these systems exhibited minimal primary beam-induced degradation under cluster ion bombardment allowing molecular depth profiles to be obtained through the film. By combing secondary ion imaging with depth profiling, three-dimensional molecular image depth profiles have been obtained from these systems. In another approach, bevel cross-sections are cut in the samples with the SF₅⁺ primary ion beam to produce a laterally magnified cross-section of the sample that does not contain the beam-induced damage that would be induced by conventional focussed ion beam (FIB) cross-sectioning. The bevel surface can then be examined using cluster SIMS imaging or other appropriate microanalysis technique.     

Studies of large scale unstable growth formed during GaAs(001) homoepitaxy

Atomic force and scanning tunneling microscopy studies have been performed on GaAs(001) films grown by molecular beam epitaxy. Multilayered mounds are seen to evolve when the growth conditions favor island nucleation. As the epilayer thickness is increased, these features grow in all dimensions but the angle of inclination remains approximately constant at 1°. The mounding does not occur on surfaces grown in step-flow. We propose that the multi-layered features are due to an unstable growth mode which relies on island nucleation and the presence of a step edge barrier.     

Fully adaptive multiresolution finite volume schemes for conservation laws

The use of multiresolution decompositions in the context of finite volume schemes for conservation laws was first proposed by A. Harten for the purpose of accelerating the evaluation of numerical fluxes through an adaptive computation. In this approach the solution is still represented at each time step on the finest grid, resulting in an inherent limitation of the potential gain in memory space and computational time. The present paper is concerned with the development and the numerical analysis of fully adaptive multiresolution schemes, in which the solution is represented and computed in a dynamically evolved adaptive grid. A crucial problem is then the accurate computation of the flux without the full knowledge of fine grid cell averages. Several solutions to this problem are proposed, analyzed, and compared in terms of accuracy and complexity.

     

Branch and win: OR tree search algorithms for solving combinatorial optimisation problems

Currently, most combinatorial optimisation problems have to be solved, if the optimum solution is sought, using general techniques to explore the space of feasible solutions and, more specifically, through exploratory enumerative procedures in trees and search graphs. We propose Branch and Win, a general formulation for understanding and synthesising the different tree search procedures that have been presented in the literature of operations research as well as in that of artificial intelligence. Several general ideas are also presented, whose application allows designing new hybrid search algorithms, in order to implement the procedure.     

Pressure-temperature phase diagrams of smectogenic 4'-alkyl-4-cyanobiphenyls (9CB, 10CB, 11CB and 12CB)

The pressure-temperature ( p - T ) phase diagrams for four smectogenic members of the 4'-alkyl-4-cyanobiphenyl homologous series ( n CB, n =9, 10, 11 and 12) over the temperature range 320-410 K and pressure range 0.1-300 MPa (3 kbar) were constructed using DTA. At 1 atm 9CB exhibits nematic and smectic A d phases, while the other members show only the smectic A d phase. However, at elevated pressures the clearing line splits in the case of 10CB and 11CB which indicates the induction of a nematic phase. It was found that the triple point, where the isotropic, nematic and smectic phases coexist, is strongly shifted to higher pressures with increasing chain length. This was interpreted as being caused by a loss of the rod-like shape of the molecules containing longer alkyl tails which explore a range of conformations. The slope of the clearing line, d T /d p , depends strongly on the length of the alkyl chain for the n CB series, but does not show a step-wise change between the nematogenic and smectogenic members.