Kinetics of comet formation in single‐cell gel electrophoresis: Loops and fragments

We investigated the mechanisms of DNA exit during single‐cell gel electrophoresis (the comet assay) by measuring the kinetics of the comet tail formation. In the neutral comet assay, the rate of DNA exit was found to be dependent on the topological state of DNA, which was influenced by either ethidium bromide or a low radiation dose. The results clearly show that the comet tail is formed by extended DNA loops: the loop extension, being reversible when the DNA torsional constraint remains in the loops, is favored when the constraint is relaxed. The kinetics of the comet formation in the case of a high radiation dose points out that accumulation of the single‐strand breaks causes DNA fragmentation. In contrast to the neutral comet assay, the alkaline comet assay is not related to the chromatin loops. Our results imply that the alkaline treatment induces detachment of the loops from the nuclear matrix, and the comet tail is formed by ssDNA fragments, the ends of which are pulled out from the comet head by electric force. We suggest that the kinetic approach can be considered as an important improvement of the comet assay.     

Kinetics and Mechanism of Cr(VI) Reduction in a Water Cathode Induced by Atmospheric Pressure DC Discharge in Air

The process of reduction of Cr⁶⁺ ions (solution of potassium dichromate, K₂Cr₂O₇) in a water cathode was studied during a DC discharge in air. The concentration range of Cr⁶⁺ was (5.7–19) ×10^?5 mol/l and discharge current range was 20–80 mA. Cr⁶⁺ ions were shown to be reversibly reduced under a discharge action. The equilibrium degree of reduction increased with increasing initial concentration of the solution at fixed discharge current. At fixed initial concentration the reduction degree increased with increasing discharge current. The reduction degrees so obtained were 0.34–0.84. A kinetic scheme of the processes taking place in a solution was proposed. The calculated data obtained as a result of application of this scheme described well the experimental results on Cr⁶⁺ kinetics. The main processes of Cr⁶⁺ reduction and Cr³⁺ oxidation were revealed. HO ₂ ^· radicals and hydrogen peroxide were shown to be responsible for Cr⁶⁺ reduction whereas ^·OH radicals and O₂ molecules provide the reverse process of Cr³⁺ oxidation to Cr⁶⁺. The mechanism of action of phenol additives improving the process efficiency is discussed. The efficiency of phenol action as a radical scavenger was shown to be determined with its mass-transfer to the reaction area rather than chemical reaction rate.     

Two-dimensional optical three-pulse photon echo spectroscopy. II. Signatures of coherent electronic motion and exciton population transfer in dimer two-dimensional spectra

Using the nonperturbative approach to the calculation of nonlinear optical spectra developed in a foregoing paper [Mancal et al., J. Chem. Phys. 124, 234504 (2006), preceding paper], calculations of two-dimensional electronic spectra of an excitonically coupled dimer model system are presented. The dissipative exciton transfer dynamics is treated within the Redfield theory and energetic disorder within the molecular ensemble is taken into account. The manner in which the two-dimensional spectra reveal electronic couplings in the aggregate system and the evolution of the spectra in time is studied in detail. Changes in the intensity and shape of the peaks in the two-dimensional relaxation spectra are related to the coherent and dissipative dynamics of the system. It is shown that coherent electronic motion, an electronic analog of a vibrational wave packet, can manifest itself in two-dimensional optical spectra of molecular aggregate systems as a periodic modulation of both the diagonal and off-diagonal peaks.     

Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes

In this and the following paper, we describe the ultrafast structural fluctuations and rearrangements of the hydrogen bonding network of water using two-dimensional (2D) infrared spectroscopy. 2D IR spectra covering all the relevant time scales of molecular dynamics of the hydrogen bonding network of water were studied for the OH stretching absorption of HOD in D2O. Time-dependent evolution of the 2D IR line shape serves as a spectroscopic observable that tracks how different hydrogen bonding environments interconvert while changes in spectral intensity result from vibrational relaxation and molecular reorientation of the OH dipole. For waiting times up to the vibrational lifetime of 700 fs, changes in the 2D line shape reflect the spectral evolution of OH oscillators induced by hydrogen bond dynamics. These dynamics, characterized through a set of 2D line shape analysis metrics, show a rapid 60 fs decay, an underdamped oscillation on a 130 fs time scale induced by hydrogen bond stretching, and a long time decay constant of 1.4 ps. 2D surfaces for waiting times larger than 700 fs are dominated by the effects of vibrational relaxation and the thermalization of this excess energy by the solvent bath. Our modeling based on fluctuations with Gaussian statistics is able to reproduce the changes in dispersed pump-probe and 2D IR spectra induced by these relaxation processes, but misses the asymmetry resulting from frequency-dependent spectral diffusion. The dynamical origin of this asymmetry is discussed in the companion paper.     

Thermal analysis and kinetic study of Petro?ani bituminous coal from Romania in comparison with a sample of Ural bituminous coal

Solid fuels represent one of the most used sources of energy in many countries. In terms of ranking for the coal deposits, Romania occupies the 26th place in the world, and the 11th place in Europe, with reserves of 22 million tones of bituminous coal (BC) and 472 million tones of lignite. The National Bituminous Coal Company extracts the most significant amount of BC from the Jiu Valley area, a Subcharpatian basin in the Parang Mountains. In the present article, the BC extracted from the Livezeni depth mine next to Petro?ani city is investigated from the microstructural, thermal, and kinetic point of view, in comparison with a sample from Ural Mountains in Russia. Scanning electron microscopy, FTIR spectroscopy, and thermal analysis (TG/DSC/DTA in air and inert atmosphere) measurements were performed. The KAS isoconversional kinetic method was applied for the in-depth understanding of thermal decompositions and burning processes that occur. Even if the thermal behavior of the two samples is generally similar, the non-isothermal kinetic study revealed important differences in the pathways of the oxidative decomposition of volatiles and formation of coke. Also, the kinetics of coke burning depends only on the amount of fix carbon, regardless of the provenience of BC.