Combination of RSM and NSGA-II algorithm for optimization and prediction of thermal conductivity and viscosity of bioglycol/water mixture containing SiO2 nanoparticles

The fluids containing nanoparticles have enhanced thermo-physical characteristics in comparison with conventional fluids without nanoparticles. Thermal conductivity and viscosity are thermo-physical properties that strongly determine heat transfer and momentum. In this study, the response surface method was firstly used to derive an equation for the thermal conductivity and another one for the viscosity of bioglycol/water mixture (20:80) containing silicon dioxide nanoparticles as a function of temperature as well as the volume fraction of silicon dioxide. Then, NSGA-II algorithm was used for the optimization and maximizing thermal conductivity and minimizing the nanofluid viscosity. Different fronts were implemented and 20th iteration number was selected as Pareto front. The highest thermal conductivity (0.576 W/m.K) and the lowest viscosity (0.61 mPa.s) were obtained at temperature on volume concentration of (80 °C and 2%) and (80 °C without nanoparticle) respectively. It was concluded that the optimum thermal conductivity and viscosity of nanofluid could be obtained at maximum temperature (80 °C) or a temperature close to this temperature. An increase in the volume fraction of silicon dioxide led to the enhancement of thermal conductivity but the solution viscosity was also increased. Therefore, the optimum point should be selected based on the system requirement.     

Development and optimisation of a novel genetic algorithm for studying model protein folding

Determination of the native state of a protein from its amino acid sequence is the goal of protein folding simulations, with potential applications in gene therapy and drug design. Location of the global minimum structure for a given sequence, however, is a difficult optimisation problem. In this paper, we describe the development and application of a genetic algorithm (GA) to find the lowest-energy conformations for the 2D HP lattice bead protein model. Optimisation of the parameters of our standard GA program reveals that the GA is most successful (at finding the lowest-energy conformations) for high rates of mating and mutation and relatively high elitism. We have also introduced a number of new genetic operators: a duplicate predator—which maintains population diversity by eliminating duplicate structures; brood selection—where two parent structures undergo crossover and give rise to a brood of (not just two) offspring; and a Monte Carlo based local search algorithm—to explore the neighbourhood of all members of the population. It is shown that these operators lead to significant improvements in the success and efficiency of the GA, both compared with our standard GA and with previously published GA studies for benchmark HP sequences with up to 50 beads.     

The lifetime of CFC substitutes studied by a network trained with chaotic mapping modified genetic algorithm and DFT calculations

The hydrohaloalkanes have attracted much attention as potential substitutes of chlorofluorocarbons (CFCs) that deplete the ozone layer and lead to great high global warming. Having a short atmospheric lifetime is very important for the potential substitutes that may also induce ozone depletion and yield high global warming gases to be put in use. Quantitative structure–activity relationship (QSAR) studies were presented for their lifetimes aided by the quantum chemistry parameters including net charges, Mulliken overlaps, E _HOMO and E _LUMO based on the density functional theory (DFT) at B3PW91 level, and the C-H bond dissociation energy based on AM1 calculations. Outstanding features of the logistic mapping, a simple chaotic system, especially the inherent ability to search the space of interest exhaustively have been utilized. The chaotic mapping aided genetic algorithm artificial neural network training scheme (CGANN) showed better performance than the conventional genetic algorithm ANN training when the structure of the data set was not favorable. The lifetimes of HFCs and HCs appeared to be greatly dependent on their energies of the highest occupied molecular orbitals. The perference of the RMSRE comparing to RMSE as objective function of ANN training was better for the samples of interest with relatively short lifetimes. C₂H₆ and C₃H₈ as potential green substitutes of CFCs present relatively short lifetimes.     

Testing an alternative search algorithm for compound identification with the ‘Wiley Registry of Tandem Mass Spectral Data,MSforID’

A tandem mass spectral database system consists of a library of reference spectra and a search program. State‐of‐the‐art search programs show a high tolerance for variability in compound‐specific fragmentation patterns produced by collision‐induced decomposition and enable sensitive and specific ‘identity search’. In this communication, performance characteristics of two search algorithms combined with the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were evaluated. The search algorithms tested were the MSMS search algorithm implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30 000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their setup from tandem‐in‐space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS. Copyright © 2013 John Wiley & Sons, Ltd.     

On the automatic restricted-step rational-function-optimization method

The rational function optimization algorithm is one of the widely used methods to search stationary points on surfaces. However, one of the drawbacks of this method is the step reduction procedure to deal with the overstepping problem. We present and comment on a method such that the step obtained from the solution of the rational function equations possesses the desired correct length. The analysis and discussion of the method is mainly centered on the location and optimization of transition states. Received: 18 June 1998 / Accepted: 17 September 1998 / Published online: 23 November 1998     

Analysis of electrophoretic patterns of arbitrarily primed PCR profiling

We present a mathematical algorithm for the analysis of electrophoretic patterns resulting from arbitrarily primed PCR profiling. The algorithm is based on the established mathematical procedures applied to the analysis of digital images of gel patterns. The algorithm includes (a) transformation of the image into a matrix form, (b) identification of every electrophoretic lane as a set of matrix columns that are further mathematically processed, (c) averaging of matrix columns corresponding to electrophoretic lanes that define lane representatives, (d) elimination of "smiling" bands, (e) solving the problem of a lane offset, and (f) removal of the background. Representation of individual electrophoretic lanes in the form of functions allows interlane comparisons and further mathematical analysis. Direct comparison of selected lanes was obtained by employing correlation analysis. Gel images were those obtained after arbitrarily primed PCR analysis of DNA that underwent damage induced by gamma radiation from a (60)Co source. The applied method proved to be useful for elimination of subjectivity of visual inspection. It offers the possibility to avoid overlooking important differences in case of suboptimal electrophoretic resolution. In addition, higher precision is achieved in the assessment of quantitative differences due to better insight into experimental artifacts. These simple mathematical methods offer an open-type algorithm, i.e., this algorithm enables easy implementation of different parameters that may be useful for other analytical needs.     

On the validity of the counterpoise correction for the basis set superposition error including the fragment relaxation terms

It is demonstrated that relatively large geometrical changes make Emsley et al.'s assumption (J Am Chem Soc (1978) 100:3303) on the counterpoise correction for the basis set superposition error including the fragment relaxation terms unacceptable. Received: 23 September 1997 / Accepted: 31 October 1997