Encoding Threshold Boolean Networks into Reaction Systems for the Analysis of Gene Regulatory Networks

Gene regulatory networks represent the interactions among genes regulating the activation of specific cell functionalities and they have been successfully modeled using threshold Boolean networks. In this paper we propose a systematic translation of threshold Boolean networks into reaction systems. Our translation produces a non redundant set of rules with a minimal number of objects. This translation allows us to simulate the behavior of a Boolean network simply by executing the (closed) reaction system we obtain. This can be very useful for investigating the role of different genes simply by “playing” with the rules. We developed a tool able to systematically translate a threshold Boolean network into a reaction system. We use our tool to translate two well known Boolean networks modelling biological systems: the yeast-cell cycle and the SOS response in Escherichia coli. The resulting reaction systems can be used for investigating dynamic causalities among genes.

Adsorption–desorption oscillations of nanoparticles on a honeycomb-patterned pH-responsive hydrogel surface in a closed reaction system

Adsorption–desorption oscillations of nanoparticles on a honeycomb-patterned pH-responsive hydrogel surface were derived from a pH-oscillator in a closed reaction system.

Experimental Study of Closed System in the Chlorine Dioxide-Iodide-Sulfuric Acid Reaction by UV-Vis Spectrophotometric Method

The mole ratior(r=[I−]0/[ClO2]0)has great influence on ClO2-I−-H2SO4closed reaction system. By changing the initiate concentration of potassium iodide, the curve of absorbance along with the reaction time was obtained at 350 nm and 297 nm for triiodide ion, and 460 nm for iodine. The changing point of the absorbance curve's shape locates atr=6.00. For the reaction of ClO2-I−in the absence of H2SO4, the curve of absorbance along with the reaction time can be obtained at 350 nm for triiodide ion, 460 nm for iodine. The mole ratioris equal to 1.00 is the changing point of the curve's shape no matter at which wavelength to determine the reaction. For the reaction of ClO2-I−-H+in different pH buffer solution, the curve of absorbance along with the reaction time was recorded at 460 nm for iodine. Whenris greater than 1.00, the transition point of the curve's shape locates at pH 2.0, which is also the point of producing chlorite or chloride for chlorine dioxide at different pH. Whenris less than 1.00, the transition point locates at pH 7.0.

A NEW TECHNIQUE FOR THE STUDY OF HIGH-POLYMER DEGRADATION REACTIONS

A quartz spoon gauge, recording pressures automatically, is described. The gauge, representing a closed reaction system, can be used for investigations of the degradation of polymers. It has been tested by degrading polymethylmethacrylate over a temperature range of 300 to 400 °C. The important features of the gauge are as follows: (1) The pressure exerted by gases during degradation is continuously recorded at appropriate chart speeds via an electrical transducer (maximum displacement ± 0.038 cm; spoon gauges used in this work had sensitivities in the region of 0.035 cm/atm). (2) Only small quantities of polymers are needed; 20 to 40 mg of polymer in the form of films was deposited on the walls of the reaction vessels; however, much smaller samples could be used, the limit being given by mechanical vibrations set up in the system. (3) Temperature equilibrium between the reaction vessels and a thermostated bath is reached within about 30 seconds.Useful results for polymethylmethacrylate were obtained up to 400 °C, which is a temperature about 100° higher than that reached by previous workers, not neglecting the initial parts of the reactions. The reproducibility of the results has been indicated by average curves obtained from several runs at any one particular temperature and their standard deviations.