Improving chaos-based pseudo-random generators in finite-precision arithmetic

Nonlinear Dynamics - One of the widely-used ways in chaos-based cryptography to generate pseudo-random sequences is to use the least significant bits or digits of finite-precision numbers defined...     

Examining the possibilities of applying high pressure to preserve yoghurt supplemented with probiotic bacteria

Natural yoghurt was subject to pressures of 200 and 250 MPa/4 and 18°C/15 min, after which milk-activated inocula of Lactobacillus acidophilus and Bifidobacterium sp. were added. The yoghurts were stored for 4 weeks at refrigeration temperature. After preparation and each week of storage, the count of bacteria, acidity, antibacterial property and an organoleptic assessment was determined. The highest survival rate was demonstrated by the bacteria of Lactobacillus delbrueckii ssp. bulgaricus, Streptococcus thermophilus and Bifidobacterium sp. in the yoghurt pressurised 200 MPa/15min at 4°C. Acidity increases in the control yoghurts were higher than in the pressurised ones. Pressurised yoghurts demonstrated weaker antibacterial effect in comparison to control yoghurts. Slight changes in the smell and taste were observed after pressurisation. Yoghurts pressurised at 18°C were characterised by more favourable organoleptic properties. Better conciseness of the curd and lower whey seep out were observed in pressurised yoghurt.     

Acid-catalyzed Hydrolysis of the cis-[Cr(1,10-phenanthroline)2(O2CO)]+ Ion Studied by the u.v.–vis Stopped Flow Method

The cis-[Cr(phen)₂(O₂CO)]⁺ ion was prepared through the displacement of two molecules of water from the cis-[Cr(phen)₂(OH₂)₂]³⁺ by the bidentate carbonate anion. It underwent two-phase hydrolysis reactions under acidic conditions (0.1 < [H⁺] < 2.7 m) at 5, 10, 15, 20 and 25 °C. Via slow carbonato chelate ring opening (first step k₁^slow) and a second fast decarboxylation(k₂^fast value). The first step was preceded by protonation of the coordinate bidentate carbonate ligand. The second step exhibited no pH dependence, while k₁^slow values increased with acid concentration that suggested the presence of both protonated and deprotonated reactant species. Based on these observations we have proposed a hydrolysis mechanism featuring H₂O-induced ring-opening of the coordinate CO₃²⁻ group in the first step k₁^slow followed by loss of CO₃²⁻ from two intermediates, [Cr(phen)₂(O₂COH)]²⁺ (k₁^slow) and [Cr(phen)₂(OH₂)(O₂COH)]²⁺ (k₂^fast).     

Modulational instability in one-dimensional saturable waveguide arrays: Comparison with Kerr nonlinearity

Discrete modulational instability within the first band of uniform one-dimensional waveguide arrays possessing a saturable self-defocusing nonlinearity is investigated in detail within the coupled mode approach. Explicit analytical results for both the threshold and the maximal gain of instability are compared with the corresponding data from waveguide arrays exhibiting Kerr nonlinearity. We find that saturation bounds the interval of existence of discrete modulational instability, stabilizes the frequency region of perturbations around ±π/2 and decreases both gain and critical spatial frequency of perturbations.     

Thermal decomposition of basic aluminium potassium sulfate. Part II. Kinetics of the reaction

The kinetics of individual stages of thermal dissociation of basic aluminium potassium sulfate (BAPS) were studied thermogravimetrically under isobaric and isothermal conditions at a reduced pressure of the order of 10^?3 hPa and in the atmosphere of gaseous products of the reaction (H₂O, SO₂).The kinetic parameters of all the reaction stages have been identified and the nature of the stages and the effect of changes of the reaction of conditions on the course of the processes have been determined.     

Influence of solvent and counter ion on copper complexes with N-alkyl-pyridine-2-carboxamides as studied by electrospray ionization mass spectrometry

The interactions of copper(II) with N-alkyl-pyridine-2-carboxamides (M) were studied by electrospray ionization mass spectrometry. The influence of solvent and counter ion (Cl-, ClO4-) on the type of ions (complexes) observed was discussed. By cone voltage increase, the fragmentation "in source" of the ions discussed was achieved. In methanol solution containing N-alkyl-pyridine-2-carboxamide (M) and CuCl2 the singly- and doubly charged-ions [M+CuCl]+ and [M2+Cu]+2 were detected. In acetonitrile solution containing N-alkyl-pyridine-2-carboxamide and CuCl2, the copper(I)-containing ions [M+CH3CN+Cu]+ were formed. The use of Cu(ClO4)2 instead of CuCl2 resulted in more abundant doubly-charged ions in both methanol and acetonitrlile solutions and, for the former solution, the ions containing methoxyl anion, namely [M+CuOCH3]+, were observed. When water was used as a solvent, the abundant ions corresponding to the protonated ligands were formed, while the ions corresponding to copper complexes were characterised by low abundances.     

Dealing with repetitions in sequencing by hybridization

DNA sequencing by hybridization (SBH) induces errors in the biochemical experiment. Some of them are random and disappear when the experiment is repeated. Others are systematic, involving repetitions in the probes of the target sequence. A good method for solving SBH problems must deal with both types of errors. In this work we propose a new hybrid genetic algorithm for isothermic and standard sequencing that incorporates the concept of structured combinations. The algorithm is then compared with other methods designed for handling errors that arise in standard and isothermic SBH approaches. DNA sequences used for testing are taken from GenBank. The set of instances for testing was divided into two groups. The first group consisted of sequences containing positive and negative errors in the spectrum, at a rate of up to 20%, excluding errors coming from repetitions. The second group consisted of sequences containing repeated oligonucleotides, and containing additional errors up to 5% added into the spectra. Our new method outperforms the best alternative procedures for both data sets. Moreover, the method produces solutions exhibiting extremely high degree of similarity to the target sequences in the cases without repetitions, which is an important outcome for biologists. The spectra prepared from the sequences taken from GenBank are available on our website http://bio.cs.put.poznan.pl/.     

Functionalization of carbon nanotubes with silver clusters

In this paper, an advanced method of one-step functionalization of single and multi walled carbon nanotubes (SWCNTs and MWCNTs) using γ-irradiation was described. Two synthesis procedures, related with different reduction species, were employed. For the first time, poly(vinyl alcohol) PVA is successfully utilized as a source to reduce silver (Ag) metal ions without having any additional reducing agents to obtain Ag nanoparticles on CNTs. The decoration of carbon nanotubes with Ag nanoparticles takes place through anchoring of (PVA) on nanotube's surface. Optical properties of as-prepared samples and mechanism responsible for the functionalization of carbon nanotubes were investigated using UV-vis and FTIR spectroscopy, respectively. Decorated carbon nanotubes were visualized using microscopic techniques: transmission electron microscopy and scanning tunneling microscopy. Also, the presence of Ag on the nanotubes was confirmed using energy dispersive X-ray spectroscopy. This simple and effective method of making a carbon nanotube type of composites is of interest not only for an application in various areas of technology and biology, but for investigation of the potential of radiation technology for nanoengineering of materials.     

Graph algorithms for DNA sequencing – origins,current models and the future

With the ubiquitous presence of next-generation sequencing in modern biological, genetic, pharmaceutical and medical research, not everyone pays attention to the underlying computational methods. Even fewer researchers know what were the origins of the current models for DNA assembly. We present original graph models used in DNA sequencing by hybridization, discuss their properties and connections between them. We also explain how these graph models evolved to adapt to the characteristics of next-generation sequencing. Moreover, we present a practical comparison of state-of-the-art DNA de novo assembly tools representing these transformed models, i.e. overlap and decomposition-based graphs. Even though the competition is tough, some assemblers perform better and certainly large differences may be observed in hardware resources utilization. Finally, we outline the most important trends in the sequencing field, and try to predict their impact on the computational models in the future.