Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Heavy Dirac and Majorana neutrino production ine + e − collisions

The production of heavy Dirac and Majorana neutrinos ine ⁺ e ^? collisions is investigated. The heavy Dirac and/or Majorana neutrinos can be produced in charged and neutral current processes $(e^ + e^ - \to N_1 \bar N_2 )$ . The production of a single heavy neutrino is possible if it mixes with the light neutrino species. The production of heavy neutrinos in Higgs channels is also studied, since in some specific models the Yukawa couplings could be large enough to make the production of heavy neutrinos through Higgs boson exchanges sufficiently large for detection. The most general left-right symmetric model with possibly complexV orA couplings is used in the analytic calculations of the production cross sections, but the numerical examples are given using simplified left-right symmetric model. The interference terms between different production channels have been studied in great detail and in some cases the interference terms are found to be non-negligible in wide range of production spectrum. The pair production cross section is larger in the Dirac case than it is in the Majorana case, but the single heavy Majorana neutrino production cross section is roughly twice as large as that of a Dirac neutrino.     

Determination of Na(2)O from sodium aluminate NaAlO(2)

The aim of the work was to find a suitable method and conditions for determining Na(2)O wt.% from NaAlO(2). Problems were encountered while titrating NaAlO(2) with hydrochloric acid. The problematic area was the pH range 4-10 where aluminum precipitates as hydroxides. The different species of the aluminate solution were determined using potentiometric and complexometric titrations. The equivalent point of the potentiometric titration was detected using Gran's plotting method. Precipitation of aluminum hydroxides did not interfere with titrations, because in potentiometric titrations the pH value was over 10 and in complexometric titrations the pH was 4. The results were accurate and determinations were easy to carry out. Sodium was also determined by DCP-AES.     

Optical sensing of parameters crucial for Japanese woodblock print making

Traditional Japanese woodblock printing is a centuries old art form. This time-honoured form of art is at risk of extinction as a consequence of the increasing lack of availability of wild cherry trees, which are a traditionally used woodblock material. Solutions for this material problem have been investigated for several years, but none of the tested materials has been sufficient when compared with the watercolour print quality imprinted by wild cherry woodblocks. To contribute to overcoming this material problem, we have investigated the physical properties of heat-treated woodblock materials made from different wood species. The International Commission on Illumination (CIE) tristimulus values, the CIELAB coordinates, the total reflectance, and the gloss, as well as, the water contact angle from the woodblock surface is observed to have a strong relation to the surface treatment of a woodblock. The surface treatment of a woodblock, in turn, relates to its water delivery, which is the basis for watercolour printing.     

An overview on the processing of polymers growth rate data and on the methods to verify the accuracy of the input parameters in crystallization regime analysis

This work reviews criteria for the successful application of regime analysis to polymers and also discusses the influence of accuracy of input variables on the results. Despite that it has often been stated that the uncertainty in the input parameters remarkably affects the trustworthiness of the outcomes of the regime analysis, the literature offers on the subject only a fragmentary information and there is no paper looking over all the effects of accuracy of the input parameters. Here the influence of errors in input parameters has been investigated and methods to test the reliability of thermodynamic outcomes have been discussed. Mathematical ways to ascertain the accuracy of the input parameters consist in comparisons between the growth rates expressed by the Hoffman–Lauritzen equation and their derivatives generated by means of the output of the regime analysis. These comparisons, under the hypothesis of validity of the secondary nucleation theory, allow excluding the presence of remarkable errors in input values and variables.     

On the importance of behavioral operational research: The case of understanding and communicating about dynamic systems

We point out the need for Behavioral Operational Research (BOR) in advancing the practice of OR. So far, in OR behavioral phenomena have been acknowledged only in behavioral decision theory but behavioral issues are always present when supporting human problem solving by modeling. Behavioral effects can relate to the group interaction and communication when facilitating with OR models as well as to the possibility of procedural mistakes and cognitive biases. As an illustrative example we use well known system dynamics studies related to the understanding of accumulation. We show that one gets completely opposite results depending on the way the phenomenon is described and how the questions are phrased and graphs used. The results suggest that OR processes are highly sensitive to various behavioral effects. As a result, we need to pay attention to the way we communicate about models as they are being increasingly used in addressing important problems like climate change.     

Kinetics of the reactions of C2H5, n‐C3H7, and n‐C4H9 radicals with Cl2 at the temperature range 190–360 K

The kinetics of the C₂H₅ + Cl₂, n‐C₃H₇ + Cl₂, and n‐C₄H₉ + Cl₂ reactions has been studied at temperatures between 190 and 360 K using laser photolysis/photoionization mass spectrometry. Decays of radical concentrations have been monitored in time‐resolved measurements to obtain reaction rate coefficients under pseudo‐first‐order conditions. The bimolecular rate coefficients of all three reactions are independent of the helium bath gas pressure within the experimental range (0.5–5 Torr) and are found to depend on the temperature as follows (ranges are given in parenthesis): k(C₂H₅ + Cl₂) = (1.45 ± 0.04) × 10^?11 (T/300 K)^{?1.73 ± 0.09} cm³ molecule^?1 s^?1 (190–359 K), k(n‐C₃H₇ + Cl₂) = (1.88 ± 0.06) × 10^?11 (T/300 K)^{?1.57 ± 0.14} cm³ molecule^?1 s^?1 (204–363 K), and k(n‐C₄H₉ + Cl₂) = (2.21 ± 0.07) × 10^?11 (T/300 K)^{?2.38 ± 0.14} cm³ molecule^?1 s^?1 (202–359 K), with the uncertainties given as one‐standard deviations. Estimated overall uncertainties in the measured bimolecular reaction rate coefficients are ±20%. Current results are generally in good agreement with previous experiments. However, one former measurement for the bimolecular rate coefficient of C₂H₅ + Cl₂ reaction, derived at 298 K using the very low pressure reactor method, is significantly lower than obtained in this work and in previous determinations. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 614–619, 2007     

First direct kinetic measurement of i-C4H5 (CH2CHCCH2) + O2 reaction: Toward quantitative understanding of aromatic ring formation chemistry

The kinetics of the i-C₄H₅ (buta-1,3-dien-2-yl) radical reaction with molecular oxygen has been measured over a wide temperature range (275–852 K) at low pressures (0.8–3 Torr) in direct, time-resolved experiments. The measurements were performed using a laminar flow reactor coupled to photoionization mass spectrometer (PIMS), and laser photolysis of either chloroprene (2-chlorobuta-1,3-diene) or isoprene was used to produce the resonantly stabilized i-C₄H₅ radical. Under the experimental conditions, the measured bimolecular rate coefficient of i-C₄H₅ + O₂ reaction is independent of bath gas density and exhibits weak, negative temperature dependency, and can be described by the expression k₃ = (1.45 ± 0.05) × 10^?12 × (T/298 K)^{?(0.13±0.05)} cm³ s^?1. The measured bimolecular rate coefficient is surprisingly fast for a resonantly stabilized radical. Under combustion conditions, the reactions of i-C₄H₅ radical with ethylene and acetylene are believed to play an important role in forming the first aromatic ring. However, the current measurements show that i-C₄H₅ + O₂ reaction is significantly faster under combustion conditions than previous estimations suggest and, consequently, inhibits the soot forming propensity of i-C₄H₅ radicals. The bimolecular rate coefficient estimates used for the i-C₄H₅ + O₂ reaction in recent combustion simulations show significant variation and are up to two orders of magnitude slower than the current, measured value. All estimates, in contrast to our measurements, predict a positive temperature dependency. The observed products for the i-C₄H₅ + O₂ reaction were formaldehyde and ketene. This is in agreement with the one theoretical study available for i-C₄H₅ + O₂ reaction, which predicts the main bimolecular product channels to be H₂CO + C₂H₃ + CO and H₂CCO + CH₂CHO.