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.     

π-Electron currents in fixed π-sextet aromatic benzenoids

In view of different patterns of π-electron density currents in benzenoid aromatic compounds it is of interest to investigate the pattern of ring currents in various classes of compounds. Recently such a study using a graph theoretical approach to calculating CC bond currents was reported for fully benzenoid hydrocarbons, that is, benzenoid hydrocarbons which have either π-sextets rings or “empty” rings in the terminology of Clar. In this contribution we consider π-electron currents in benzenoid hydrocarbons which have π-electron sextets and C=C bonds fully fixed. Our approach assumes that currents arise from contributions of individual conjugated circuits within the set of Kekulé valence structures of these molecules.     

CZE study on adsorption processes of aliphatic and aromatic amines on PMMA chip

Adsorption processes on a PMMA chip linked with CZE separations of a group of 13 aliphatic and aromatic mono‐ and di‐amines were studied. Due to the lack of chromophores within aliphatic amines, contact conductivity detection implemented directly onto the chip was used for monitoring of cationic CZE separations. To prevent an adsorption of studied amines to the chip channels, the surface of PMMA chip was modified by dynamic coating. Different surface modifiers, such as aliphatic oligoamines (diethylenetriamine and triethylenetetramine), were added to the BGE solutions filling the chip channels. The effect of various concentrations of surface modifiers on peak profiles and separation parameters of amines was monitored. Of these, mainly, aliphatic di‐amines and aromatic mono‐amines adversely affected the CZE resolution of a whole group of analytes by their strong adsorption to the chip channels. A propionate BGE with pH 3.2 containing 100 μM triethylenetetramine and 25 mM 18‐crown‐6‐ether was found suitable for CZE resolution of 12 from a total of 13 amines studied. Simple dynamic modification of the surface of PMMA chip enabled fast (analysis time lasted 9 min), sensitive (sub‐μM LODs reached) and reproducible (1–3% RSD of the peak areas) CZE analysis of the aliphatic and aromatic amines.     

Using controlled radical polymerization to confirm the lower critical solution temperature of an N‐(alkoxyalkyl) acrylamide polymer in aqueous solution

N‐(3‐Methoxypropyl) acrylamide (MPAM) was polymerized by controlled radical polymerization (CRP) methods such as nitroxide‐mediated polymerization (NMP) and reversible addition–fragmentation chain‐transfer polymerization (RAFT). CRP was expected to yield well‐defined polymers with sharp lower critical solution temperature (LCST) transitions. NMP with the BlocBuilder (2‐([tert‐butyl[1‐(diethoxyphosphoryl)‐2,2‐dimethylpropyl]amino]oxy)‐2‐methylpropanoic acid) and SG1 ([tert‐butyl[1‐(diethoxyphosphoryl)‐2,2‐dimethylpropyl]amino] oxidanyl) initiating system revealed low yields and lack of control (high dispersity, ? ～ 1.5–1.6, and inhibition of chain growth). However, RAFT was far more effective, with linear number average molecular weight, , versus conversion, X, plots, low ? ～ 1.2–1.4 and the ability to form block copolymers using N,N‐diethylacrylamide (DEAAM) as the second monomer. Poly(MPAM) (with = 13.7–25.3 kg mol^?1) thermoresponsive behavior in aqueous media revealed cloud point temperatures (CPT)s between 73 and 92 °C depending on solution concentration (ranging from 1 to 3 wt %). The and the molecular weight distribution were the key factors determining the CPT and the sharpness of the response, respectively. Poly(MPAM)‐b‐poly(DEAAM) block copolymer ( = 22.3 kg mol^?1, ? = 1.41, molar composition F_DEAAM = 0.38) revealed dual LCSTs with both segments revealing distinctive CPTs (at 75 and 37 °C for poly(MPAM) and poly(DEAAM) blocks, respectively) by both UV–Vis and dynamic light scattering. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 59–67     

From a point-like to an arbitrarily shaped sample: A survey of equations for electron paramagnetic resonance signal intensity calculations

A set of original, analytical equations useful for theoretical calculation of the electron paramagnetic resonance (EPR) signal intensity are presented for the multitude of sample shapes, which range from point-like, line-like, planar, rectangular, cubical, circular, cylindrical, spherical to an irregularly shaped sample. The samples can be situated at any available position within the prescribed part of the microwave cavity (a central cylinder of diameter 11 mm and length 23.5 mm, in either a Bruker single TE₁₀₂ or double TE₁₀₄ rectangular cavity, with the modulation coils situated in the left and right side cavity walls, which is connected to a X-band, field-modulated CW Bruker EPR spectrometer). The theoretical computations of EPR signal intensity can be used in the computer simulations in which: (i) the EPR signal intensity profiles are constructed; (ii) the optimal sample positions in the cavity to give a maximum value of signal intensity are found; (iii) the errors associated with sample positioning within the cavity when compared to a second sample of a different size, shape or position are studied.