Characterization of G‐Quadruplex/Hairpin Transitions of RNAs by 19F NMR Spectroscopy

2′‐O‐[(4‐Trifluoromethyl‐triazol‐1‐yl)methyl] reporter groups have been incorporated into guanosine‐rich RNA models (including a known bistable Qd/Hp RNA and two G‐rich regions of mRNA of human prion protein, PrP) and applied for the ¹⁹F NMR spectroscopic characterization of plausible G‐quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF₃‐labeled RNAs, phosphoramidite building blocks of 2′‐O‐[(4‐CF₃‐triazol‐1‐yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid‐phase RNA synthesis. The obtained ¹⁹F NMR spectra supported the usual characterization data (obtained by UV‐ and CD‐melting profiles and by ¹H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the ¹⁹F NMR signals. For a well‐behaved Qd/Hp transition, thermodynamic parameters could be extracted.     

Numerical study of dynamics of single bubbles and bubble swarms

A systematic computational study of the dynamics of gas bubbles rising in a viscous liquid is presented. Two-dimensional simulations are carried out. Both the dynamics of single bubbles and small groups of bubbles (bubble swarms) are considered. This is a continuation of our previous studies on the two-bubble coalescence and vortex shedding [A. Smolianski, H. Haario, P. Luukka, Vortex shedding behind a rising bubble and two-bubble coalescence: a numerical approach, Appl. Math. Model. 29 (2005) 615–632]. The proposed numerical method allows us to simulate a wide range of flow regimes, accurately capturing the shape of the deforming interface of the bubble and the surface tension effect, while maintaining the mass conservation. The computed time-evolution of bubble’s position and rise velocity shows a good agreement with the available experimental data. At the same time, the results on the dynamics of bubble interface area, which are, up to our knowledge, presented for the first time, show how much the overall mass transfer would be affected by the interface deformation in the case of the bubble dissolution. Another set of experiments that are of interest for chemical engineers modelling bubbly flows concerns the bubble swarms and their behavior in different bubble-shape regimes. The ellipsoidal and spherical shape regimes are considered to represent, respectively, the coalescing and non-coalescing bubble swarms. The average rise velocities of the bubble swarms are computed and analyzed for both regimes.     

Rapid Screening of Indole-3-Acetic Acid and Other Indole Derivatives in Bacterial Culture Broths by Planar Chromatography

JPC – Journal of Planar Chromatography – Modern TLC - The aim of this study was to find suitable separation conditions for the rapid screening of indole derivatives in bacterial culture...     

Optimization studies of single-transverse-mode 980 nm ridge-waveguide lasers

The paper presents a simple and efficient Mode-Solver-based method for determining the ridge profile that ensures stable single-transverse-mode operation in ridge waveguide lasers. A quantitative figure of merit, easily derived from the Mode Solver analysis of the structure, indicates the likelihood of single transverse modal behavior over the whole bias range. The transverse mode analysis performed with the in-house developed software has been compared with the results of the commercial simulation package LASTIP and with experiments. The simulation and experimental results have been used to derive processing guidelines for achieving a stable single-transverse-mode operation in ridge waveguide lasers.     

Time-resolved coherent anti-Stokes Raman-scattering measurements of I2 in solid Kr: vibrational dephasing on the ground electronic state at 2.6-32 K

Time-resolved coherent anti-Stokes Raman-scattering (CARS) measurements are carried out for iodine (I2) in solid krypton matrices. The dependence of vibrational dephasing time on temperature and vibrational quantum number v is studied. The v dependence is approximately quadratic, while the temperature dependence of both vibrational dephasing and spectral shift, although weak, fits the exponential form characteristic of dephasing by pseudolocal phonons. The analysis of the data indicates that the frequency of the pseudolocal phonons is approximately 30 cm(-1). The longest dephasing times are observed for v = 2 being approximately 300 ps and limited by inhomogeneous broadening. An increase in the dephasing rate of v = 2 as the temperature is lowered to T = 2.6 K is taken as a clear indication of lattice-strain-induced inhomogeneity of the ensemble coherence.