Comparison of Monte Carlo simulations of cytochrome b6f with experiment using Latin hypercube sampling.
نویسندگان
چکیده
We have programmed a Monte Carlo simulation of the Q-cycle model of electron transport in cytochrome b(6)f complex, an enzyme in the photosynthetic pathway that converts sunlight into biologically useful forms of chemical energy. Results were compared with published experiments of Kramer and Crofts (Biochim. Biophys. Acta 1183:72-84, 1993). Rates for the simulation were optimized by constructing large numbers of parameter sets using Latin hypercube sampling and selecting those that gave the minimum mean square deviation from experiment. Multiple copies of the simulation program were run in parallel on a Beowulf cluster. We found that Latin hypercube sampling works well as a method for approximately optimizing very noisy objective functions of 15 or 22 variables. Further, the simplified Q-cycle model can reproduce experimental results in the presence or absence of a quinone reductase (Q(i)) site inhibitor without invoking ad hoc side-reactions.
منابع مشابه
An Empirical Evaluation of Sampling Methods in Risk Analysis Simulation: Quasi-monte Carlo, Descriptive Sampling, and Latin Hypercube Sampling
This paper compares the performance, in terms of convergence rates and precision of the estimates, for six Monte Carlo Simulation sampling methods: Quasi-Monte Carlo using Halton, Sobol, and Faure numeric sequences; Descriptive Sampling, based on the use of deterministic sets and Latin Hypercube Sampling, based on stratified numerical sets. Those methods are compared to the classical Monte Carl...
متن کاملExploring multi-dimensional spaces: a Comparison of Latin Hypercube and Quasi Monte Carlo Sampling Techniques
Three sampling methods are compared for efficiency on a number of test problems of various complexity for which analytic quadratures are available. The methods compared are Monte Carlo with pseudo-random numbers, Latin Hypercube Sampling, and Quasi Monte Carlo with sampling based on Sobol’ sequences. Generally results show superior performance of the Quasi Monte Carlo approach based on Sobol’ s...
متن کاملLatin hypercube sampling and the propagation of uncertainty in analyses of complex systems
The following techniques for uncertainty and sensitivity analysis are briefly summarized: Monte Carlo analysis, differential analysis, response surface methodology, Fourier amplitude sensitivity test, Sobol’ variance decomposition, and fast probability integration. Desirable features of Monte Carlo analysis in conjunction with Latin hypercube sampling are described in discussions of the followi...
متن کاملOn Reduction of Finite Sample Variance by Extended Latin Hypercube Sampling
McKay, Conover and Beckman (1979) introduced Latin hypercube sampling (LHS) for reducing variance of Monte Carlo simulations. More recently Owen (1992a) and Tang (1993) generalized LHS using orthogonal arrays. In the Owen's class of generalized LHS, we de ne extended Latin hypercube sampling of strengthm (henceforth denoted as ELHS(m)), such that ELHS(1) reduces to LHS. We rst derive explicit f...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bulletin of mathematical biology
دوره 73 9 شماره
صفحات -
تاریخ انتشار 2011