Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations

An algorithm for encoding long strings of building blocks, like 4 DNA bases (adenine-A, cytosine-C, thymine-T, and guanidine-G), 20 natural amino acids (from Alanine Ala to Valine-Val, plus the stop triplet), or all 64 possible base triplets (from AAA to TTT), into "zigzag" or "spectrum-like" representations is suggested. The new encoding scheme can be derived in the 3-, 2-, or 1-dimensional form depending on the user's wishes. The only information, besides the string for which the "spectrum-like" representation is sought, is the initial positioning of the complete set of units from which the string is composed, i.e., four positions for A, C, G, and T, or 20 positions for natural amino acids plus stop, etc. This initial positioning can be initialized in either the 3-, 2-, or 1-D form. As an illustration of the suggested encoding scheme of the visual and chemometric comparison of the first 10 exon strings of the beta globin gene of 10 different species, each string consisting of about 100 basic amino acids long is shown.     

Shedding light on the structure of a photoinduced transient excimer by time-resolved diffraction

Time-resolved single-crystal diffraction performed with synchrotron radiation shows that the 53(1) micros phosphorescent state, generated in the crystalline phase of trimeric {[3,5-(CF3)(2)Pyrazolate]Cu}(3) molecules by exposure to 355 nm of light at 17 K, is due to the formation of an excimer rather than the shortening of the intramolecular Cu...Cu distances within the trimeric units, or the formation of a continuous chain of interacting molecules. One of the intermolecular Cu...Cu distances contracts by 0.56 Angstroms from 4.018(1) to 3.46(1) Angstroms;, whereas the interplanar spacing of the trimers is reduced by 0.65 Angstroms; from 3.952(1) to 3.33(1) Angstroms. Density-functional theory calculations support the formation of a Cu...Cu bond through the intermetallic transfer of a Cu 3d electron to a molecular orbital with a large 4p contribution on the reacting Cu atoms.     

Potential formation in a bounded two-electron temperature plasma system with floating collector that emits electrons

Formation of the plasma potential in a plasma that contains energetic electrons and is bounded by a floating collector that emits electrons is studied theoretically. The problem is treated by a static. kinetic plasma-sheath model of Schwager and Birdsall [Phys. Fluids B2 (1990) 1057], which we have extended in order to include additional energetic electron population. The distribution of these electrons is assumed to be a high-temperature Maxwellian. They are called hot electrons. In the paper we study effects of the density and temperature of the hot electrons on the formation of the plasma potential. The model shows that for certain densities and temperatures of the hot electron population plasmas with two different plasma potentials can coexist in the system. These two plasmas are separated spatially by a double layer. For the case when there is no emission of electrons from the collector, results of the model are compared with computer simulation and very good agreement between the model and the simulation is found. The simulation also confirms existence of two plasmas with two different potentials separated by a double layer.     

Evaluation of in situ electrodeposition technique in electrothermal atomic absorption spectrometry

Conventional electrothermal atomic absorption spectrometric (ETAAS) equipment was extensively modified to enable automated in situ electrodeposition. The original autosampler injection Teflon capillary was replaced by a composite Pt/Teflon capillary which served as an anode in the electrodeposition circuit. Incorporation of a peristaltic pump and of a three-way solenoid under computer control into the sample dispenser circuit provided all necessary steps for automated electrodeposition-ETAAS determination. The automated sequence controlled addition of Pd modifier and of the analyte, electrolysis, withdrawal of spent electrolyte, rinsing, drying and atomization. Performance of the system was evaluated by analyzing Pb in 3% m/v NaCl. Optimization using factorial design yielded 3sigma detection limit of 20 pg Pb and reproducibility of 1.0-1.4% (for constant current electrodeposition), these values being superior to the results of conventional ETAAS of Pb in 0.5% m/v NaCl. Sensitivity of Pb determination is not affected by NaCl, NaOH, NaNO3 and NH4H2PO4, up to 4.6% m/v, demonstrating efficient matrix removal in the electrodeposition step.     

On a Construction of Fast Direct Solvers

Fast direct solvers for the Poisson equation with homogeneous Dirichlet and Neumann boundary conditions on special triangles and tetrahedra are constructed. The domain given is extended by symmetrization or skew symmetrization onto a rectangle or a rectangular parallelepiped and a fast direct solver is used there. All extendable domains are found. Eigenproblems are also considered.     

Stochastic processes with sample paths in reproducing kernel Hilbert spaces

A theorem of M. F. Driscoll says that, under certain restrictions, the probability that a given Gaussian process has its sample paths almost surely in a given reproducing kernel Hilbert space (RKHS) is either or . Driscoll also found a necessary and sufficient condition for that probability to be .

Doing away with Driscoll's restrictions, R. Fortet generalized his condition and named it nuclear dominance. He stated a theorem claiming nuclear dominance to be necessary and sufficient for the existence of a process (not necessarily Gaussian) having its sample paths in a given RKHS. This theorem - specifically the necessity of the condition - turns out to be incorrect, as we will show via counterexamples. On the other hand, a weaker sufficient condition is available.

Using Fortet's tools along with some new ones, we correct Fortet's theorem and then find the generalization of Driscoll's result. The key idea is that of a random element in a RKHS whose values are sample paths of a stochastic process. As in Fortet's work, we make almost no assumptions about the reproducing kernels we use, and we demonstrate the extent to which one may dispense with the Gaussian assumption.

     

Optical properties of semiconducting iron disilicide thin films

The iron silicides samples were prepared by annealing of iron films evaporated onto silicon wafers and capped with amorphous silicon thin overlayers. Semiconducting FeSi₂ phase is formed by annealing at the temperatures from 550°C to 850°C. The optical properties of the FeSi₂ layers have been deduced from reflectance and transmittance measurements carried out in the temperature range of (77–380) K. The spectral dependence of the absorption coefficient favours direct allowed transitions with forbidden energy gap of 0.87eV at the room temperature. The application of a simple three-parameter semiempirical formula to the temperature dependence of the direct energy gaps leads to the following best fit parameters: the band gap at zero temperature E _g (0) = (0.895 ± 0.004)eV, the dimensionless coupling parameter S = 2.0 ± 0.3, and the average phonon energy <hw> = (46 ± 8)meV. By examining all the reported triplets of parameters for -FeSi₂ fabricated by different techniques and thermal processes, an obvious discrepancy can be found for the lattice coupling parameter and average phonon energy, although the bandgaps at 0 K are very similar. Unlike the theoretical prediction and the earlier reported result, our results do not show any evidence of a particularly strong electron-phonon interaction, which would give the lower carrier mobilities. -FeSi₂ seems to be an intriguing material where states with energies near the band edges permit ambiguous interpretation of the character of transitions. From optical model for the thin film-substrate system we found the index of refraction to be (5–5.9) in the photon energy interval from 0.65 to 1.15eV. There is also indication of an additional higher-energy absorption edge at l.05eV.     

Thin layers of bovine serum albumin by matrix assisted pulsed laser evaporation

Thin films of bovine serum albumin were prepared by cryogenic matrix assisted pulsed laser evaporation technique under various deposition conditions. Energy density of laser beam changed in the range 0.1-0.5 J cm⁻². Films were deposited in vacuum or in nitrogen ambient. Targets were prepared from bovine serum albumin solution in phosphate buffered physiological saline and with an addition of UV absorbers as dimethylsulphoxide, phthalic acid, or adenine. Polyethylene and silicon (1 1 1) were used as substrates. Film properties were studied with atomic force microscopy and Fourier transform infrared spectroscopy attenuated total reflection. The deposition changed native conformation of albumin, resulting in the formation of water-insoluble aggregates. Addition of laser light absorbers in target solutions did not prevent the damage of albumin structure.