ISSN 1214-0287 (on-line)
ISSN 1214-021X (printed)

Volume 4 (2006), No 2, p 87-94

GOSA, a Simulated Annealing-Based Program for global optimization of nonlinear problems, also reveals transyears

Jerzy Czaplicki, Germaine Cornelissen, Franz Halberg

Address: Jerzy Czaplicki, Universite Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse France

Received 12th January 2006.
Revised 14th March 2006.
Published online 10th April 2006.

Full text article (pdf)
Full text article (html)

Transyears in biology have been documented thus far by the extended cosinor approach, including linearnonlinear rhythmometry. We here confirm the existence of transyears by simulated annealing, a method originally developed for a much broader use, but described and introduced herein for validating its application to time series. The method is illustrated both on an artificial test case with known components and on biological data. We provide a table comparing results by the two methods and trust that the procedure will serve the budding sciences of chronobiology (the study of mechanisms underlying biological time structure), chronomics (the mapping of time structures in and around us), and chronobioethics, using the foregoing disciplines to add to concern for illnesses of individuals also a budding focus on diseases of societies, like crime, and of nations and civilizations, like war.

simulated annealing; linear-nonlinear rhythmometry; transyears; cosinor

Bohachevsky IO, Johnson MI, Stein ML: Generalized simulated annealing for function optimization. Technometrics 28:209-217, 1986.

Corana A, Marchesi M, Martini C, Ridella S: Minimizing multimodal functions of continuous variables with the ‘simulated annealing algorithm’. ACM Trans Math Softw 13:262-280, 1987.

Cornelissen G, Halberg F: Chronomedicine. In Armitage P, Colton T (eds.): Encyclopedia of Biostatistics, 2nd ed., John Wiley & Sons Ltd., Chichester 2005, pp. 796-812.

Czaplicki J, Cornelissen G, Bakken EE, Halberg F: Simulated annealing software for resolving spectral components close in frequency validates endocrine transyears. Abstract, Meeting on Current Problems of Adaptation under Polar Conditions, Khanty-Manoijsk, Siberia, Russia, 2006.

Goffe WL, Ferrier GD, Rogers J: Global optimization of statistical functions with simulated annealing. J Econom.60:65-99, 1994.

Halberg F: Chronobiology: methodological problems. Acta Med Rom 18:399-440, 1980.

Halberg F, Cornelissen G, Bakken EE et al.: Transyears: new endpoints for gerontology and geriatrics or confusing sources of variability? J Gerontol A Biol Sci Med Sci 59:1344-1347, 2004.

Halberg F, Cornelissen G, Katinas G et al.: Chronobiology’s progress. Part I, season's appreciations 2004-2005: time-, frequency-, phase-, variable-, individual-, age- and sitespecific chronomics. J Appl Biomed 4:1-38, 2006a.

Halberg F, Cornelissen G, Katinas G et al.: Chronobiology’s progress. Part II, chronomics for an immediately applicable biomedicine. J Appl Biomed 4:73-86, 2006b.

Matuska T, Mikulecky M: Chronobiology of spontaneous abortion: Halberg’s paraseasonality is dominating again. Abstract, 27th Seminar on Man in his Terrestrial and Cosmic Environment, Upice, Czech Republic, May 16-18, 2006.

Metropolis N, Rosenbluth AW, Rosenbluth MN et al.: Equations of state calculations by fast computing machines. J Chem Phys 21:1087-1092, 1953.

Nilges M, Clore GM, Gronenborn AM: Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. FEBS Lett 239:129-136, 1988.

Press WH, Flannery B, Teukolsky S, Vetterling WT: Numerical Recipes in Fortran. Cambridge University Press, New York 1992.

Rummel JA, Lee JK, Halberg F: Combined linear-nonlinear chronobiologic windows by least-squares resolve neighboring components in a physiologic rhythm spectrum. In Ferin M, Halberg F, Richart RM, Vande Wiele R (eds.): Biorhythms and Human Reproduction, Int. Inst. for the Study of Human Reproduction Conf. Proc., John Wiley & Sons, New York 1974, pp. 53-82.

Valandro L, Zordan M, Polanska M et al.: Relevance of lunar periodicity in human spontaneous abortions. Gynecol Obstet Invest 58:179-182, 2004.

Vanderbilt D, Louie SG: A Monte Carlo simulated annealing approach to optimization over continuous variables. J Comp Phys 56:259-271, 1984.

Campagne S, Muller I, Milon A, Gervais V. Towards the classification of DYT6 dystonia mutants in the DNA-binding domain of THAP1. Nucleic Acids Res. 40: 9927-9940, 2012.

Iordanov I, Renault M, Reat V, Bosshart PD, Engel A, Saurel O, Milon A. Dynamics of Klebsiella pneumoniae OmpA transmembrane domain: The four extracellular loops display restricted motion behavior in micelles and in lipid bilayers. Biochim Biophys Acta Biomembr. 1818: 2344-2353, 2012.

Zilberman-Peled B, Bransburg-Zabary S, Klein DC, Gothilf Y. Molecular evolution of multiple arylalkylamine N-acetyltransferase (AANAT) in fish. Mar Drugs. 9: 906-921, 2011.

Tourtoglou K, Virvou M. Simulated Annealing in Finding Optimum Groups of Learners of UML. Conference Information: 3rd International Symposium on Intelligent Interactive Multimedia Systems and Services, JUL 28-30, 2010 Baltimore, MD. Intelligent Interactive Multimedia Systems and Services Book Series: Smart Innovation Systems and Technologies. 6: 147-156, 2010.

Holt A, Rougier L, Reat V, Jolibois F, Saurel O, Czaplicki J, Killian JA, Milon A. Order Parameters of a Transmembrane Helix in a Fluid Bilayer: Case Study of a WALP Peptide. Biophys J. 98: 1864-1872, 2010.

Campagne S, Saurel O, Gervais V, Milon A. Structural determinants of specific DNA-recognition by the THAP zinc finger. Nucleic Acids Res. 38: 3466-3476, 2010.

Refinetti R, Cornelissen G, Halberg F. Procedures for numerical analysis of circadian rhythms. Biol Rhytm Res. 38: 275-325, 2007.