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U ovom radu izvršeno je definisanje pojma optimizacije, njen istorijski razvoj i matematička formulacija, sa akcentom na heurističku optimizaciju. Predstavljene su grupe metoda matematičke optimizacije, a heurističke metode su detaljnije opisane. Predstavljene su prednosti metoda GA, PSO, TLBO, koje su odabrane kao reprezentativne heurističke metode. Razvijene su modifikacije, hibridna metoda i nova heuristička optimizaciona metoda. Na osnovu metode GA, njegovim modifikovanjem, dobijena je metoda iGA. Modifikacija rTLBO razvijena je na osnovu originalnog TLBO algoritma. Razvijeni su novi pristupi hibridizacije heurističkih metoda, a „redna“ hibridizacija primenjena je za razvoj hGPT algoritma. Ovaj hibridni algoritam koristi iGA, PSO i TLBO algoritme. Na osnovu heurističke pojave, razvijena je originalna optimizaciona metoda nazvana DINDI. Metoda je izvedena na osnovu eksperimentalnih ispitivanja i praćenja deteta u toku igre (dečak Dindi). Razvijen je originalni optimizacioni softver, a u softver su implementirane razvijene heurističke metode. Softver je samostalan i omogućava opštost u pogledu optimizacije. Moguće je optimizovati bilo koji problem matematički formulisan ovim softverom. On omogućuje korisniku sve potrebne aktivnosti u fazama predprocesiranja, procesiranja i postprocesiranja. Razvijene metode testirane su prema preporukama iz literature i na načine kojima je moguće potvrditi njihove kvalitete. Za testiranja su korišćene test funkcije bez ograničenja, sa ograničenjima i inženjerske test funkcije. Prema preporukama iz literature, izvršeno je poređenje razvijenih metoda, sa atraktivnim metodama iz literature. Razvijena optimizaciona metoda (DINDI) primenjena je za rešavanje praktičnih problema mašinskog konstruisanja. Za problem optimizacije reduktora, razvijen je odgovarajući oblik univerzalnog matematičkog modela i sprovedena je optimizacija za konkretne primere reduktora. Za analizirane primere postižu se značajno bolje karakteristike reduktora prim, This dissertation defines the term optimization, gives its historical development and mathematical formulation, with an accent on heuristic optimization. The mathematical optimization method group is presented, and heuristic methods are described in detail. As representative heuristic methods the advantages of GA, PSO, TLBO methods are shown. Modifications, a hybrid method and a new heuristic optimization method were developed. Based on GA, through its modification, the iGA method was created. The rTLBO modification was developed based on the original TLBO method. New approaches to hybridization of heuristic methods were developed, and “inline” hybridization was used to develop the hGPT algorithm. This hybrid uses iGA, PSO, and TLBO algorithms. Based on heuristic occurrences, an original optimization method was developed named DINDI. The method was developed based on experimental research and monitoring a child playing (a boy named Dindi). An original optimization software was developed which implements the developed heuristic methods. The software is a standalone program and allows for general use in terms of optimization. It is possible to optimize any mathematically formulated problem using this software. The software allows the user to access and use all necessary activities in the phases of preprocessing, processing and post processing. The developed methods of testing are compliant to guidelines from literature and to the methods of confirming their qualities. Unconstrained, constrained, and engineering test functions were used for testing. According to suggestions from literature, a comparison of developed methods with current methods from literature was conducted. The developed optimization method (DINDI) was used for solving practical problems in mechanical constructions. For the problem of gear train optimization a form of universal mathematical model was developed and the optimization for specific examples of gear trains was conducted. For the analyzed ex

A set of plastocyanin (Pc) mutants, probing the small acidic patch (Glu59, Glu60, and Asp61) and a nearby residue, Gln88, has been constructed to provide further insight into the electron transfer process between Pc and photosystem 1. The negatively charged residues were changed into their neutral counterparts or to a positive lysine. All mutant proteins exhibited electron transfer kinetics qualitatively similar to those of the wild type protein over a wide range of Pc concentrations. The kinetics were slightly faster for the Gln88Lys mutant, while they were significantly slower for the Glu59Lys mutant. The data were analyzed with two different models: one involving a conformational change of the Pc-photosystem 1 complex that precedes the electron transfer step (assumed to be irreversible) [Bottin, H., and Mathis, P. (1985) Biochemistry 24, 6453-6460] and another where no conformational change occurs, the electron transfer step is reversible, and dissociation of products is explicitly taken into account [Drepper, F., Hippler, M., Nitschke, W., and Haehnel, W. (1996) Biochemistry 35, 1282-1295]. Both models can account for the observed kinetics in the limits of low and high Pc concentrations. To discriminate between the models, the effects of added magnesium ions on the kinetics were investigated. At a high Pc concentration (0.7 mM), the ionic strength dependence was found to be consistent with the model involving a conformational change but not with the model where the electron transfer is reversible. One residue in the small acidic patch, Glu60, seems to be responsible for the major part of the ionic strength dependence of the kinetics.

This is a comparative study of the photoinduced (so-called forward) electron-transfer reaction 3Zncyt/pc(II) --> Zncyt+/pc(I), between the triplet state of zinc cytochrome c (3Zncyt) and cupriplastocyanin [pc(II)], and the thermal (so-called back) electron-transfer reaction Zncyt+/pc(I) --> Zncyt/pc(II), between the cation (radical) of zinc cytochrome c (Zncyt+) and cuproplastocyanin [pc(I)], which follows it. Both reactions occur between associated (docked) reactants, and the respective unimolecular rate constants are kF and kB. Our previous studies showed that the forward reaction is gated by a rearrangement of the diprotein complex. Now we examine the back reaction and complare the two. We study the effects of temperature (in the range 273.3-302.9 K) and viscosity (in the range 1.00-17.4 cP) on the rate constants and determine enthalpies (DeltaH), entropies (DeltaS), and free energies (DeltaG) of activation. We compare wild-type spinach plastocyanin, the single mutants Tyr83Leu and Glu59Lys, and the double mutant Glu59Lys/Glu60Gln. The rate constant kB for wild-type spinach plastocyanin and its mutants markedly depends on viscosity, an indication that the back reaction is also gated. The activation parameters DeltaH and DeltaS show that the forward and back reactions have similar mechanisms, involving a rearrangement of the diprotein complex from the initial binding configuration to the reactive configuration. The rearrangements of the complexes 3Zncyt/pc(II) and Zncyt+/pc(I) that gate their respective reactions are similar but not identical. Since the back reaction of all plastocyanin variants is faster than the forward reaction, the difference in free energy between the docking and the reactive configuration is smaller for the back reaction than for the forward reaction. This difference is explained by the change in the electrostatic potential on the plastocyanin surface as Cu(II) is reduced to Cu(I). It is the smaller DeltaH that makes DeltaG smaller for

The unimolecular rate constant for the photoinduced electron-transfer reaction 3Zncyt/pc(II) --> Zncyt+/pc(I) within the electrostatic complex of zinc cytochrome c and spinach cupriplastocyanin is kF. We report the effects on kF of the following factors, all at pH 7.0: 12 single mutations on the plastocyanin surface (Leu12Asn, Leu12Glu, Leu12Lys, Asp42Asn, Asp42Lys, Glu43Asn, Glu59Gln, Glu59Lys, Glu60Gln, Glu60Lys, Gln88Glu, and Gln88Lys), the double mutation Glu59Lys/Glu60Gln, temperature (in the range 273.3-302.9 K), and solution viscosity (in the range 1. 00-116.0 cP) at 283.2 and 293.2 K. We also report the effects of the plastocyanin mutations on the association constant (Ka) and the corresponding free energy of association (DeltaGa) with zinc cytochrome c at 298.2 K. Dependence of kF on temperature yielded the activation parameters DeltaH, DeltaS, and DeltaG. Dependence of kF on solution viscosity yielded the protein friction and confirmed the DeltaG values determined from the temperature dependence. The aforementioned intracomplex reaction is not a simple electron-transfer reaction because donor-acceptor electronic coupling (HAB) and reorganizational energy (lambda), obtained by fitting of the temperature dependence of kF to the Marcus equation, deviate from the expectations based on precedents and because kF greatly depends on viscosity. This last dependence and the fact that certain mutations affect Ka but not kF are two lines of evidence against the mechanism in which the electron-transfer step is coupled with the faster, but thermodynamically unfavorable, rearrangement step. The electron-transfer reaction is gated by the slower, and thus rate determining, structural rearrangement of the diprotein complex; the rate constant kF corresponds to this rearrangement. Isokinetic correlation of DeltaH and DeltaS parameters and Coulombic energies of the various configurations of the Zncyt/pc(II) complex consistently show that the rearrangement is a facile config