On the global optimization properties of finite-difference local descent algorithms

The paper is devoted to the convergence properties of finite-difference local descent algorithms in global optimization problems with a special -convex structure. It is assumed that the objective function can be closely approximated by some smooth convex function. Stability properties of the perturbed gradient descent and coordinate descent methods are investigated. Basing on this results some global optimization properties of finite-difference local descent algorithms, in particular, coordinate descent method, are discovered. These properties are not inherent in methods using exact gradients.The paper was presented at the II. IIASA-Workshop on Global Optimization, Sopron (Hungary), December 9–14, 1990.     

Optimization of Glycosylation Reactions in a Microreactor

Glycosylations are notoriously difficult reactions that require extensive optimization regarding the type of anomeric leaving group, solvent, reaction temperature, and reaction time. Described is the use of a silicon‐based microreactor to screen reaction conditions and to scale‐up synthetic procedures. For the first time, glycosyl phosphates were employed in a microreactor. The optimized reaction conditions were successfully transferred to a batch process.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Thermodynamical approach to the traveling salesman problem: An efficient simulation algorithm

We present a Monte Carlo algorithm to find approximate solutions of the traveling salesman problem. The algorithm generates randomly the permutations of the stations of the traveling salesman trip, with probability depending on the length of the corresponding route. Reasoning by analogy with statistical thermodynamics, we use the probability given by the Boltzmann-Gibbs distribution. Surprisingly enough, using this simple algorithm, one can get very close to the optimal solution of the problem or even find the true optimum. We demonstrate this on several examples.We conjecture that the analogy with thermodynamics can offer a new insight into optimization problems and can suggest efficient algorithms for solving them.The author acknowledges stimulating discussions with J. Piút concerning the main ideas of the present paper. The author is also indebted to P. Brunovský, J. erný, M. Hamala, . Peko, . Znám, and R. Zajac for useful comments.     

Global optimization and stochastic differential equations

Let ⁿ be then-dimensional real Euclidean space,x=(x ₁,x ₂, ...,x _n)^{T n} , and letf: ⁿ R be a real-valued function. We consider the problem of finding the global minimizers off. A new method to compute numerically the global minimizers by following the paths of a system of stochastic differential equations is proposed. This method is motivated by quantum mechanics. Some numerical experience on a set of test problems is presented. The method compares favorably with other existing methods for global optimization.This research has been supported by the European Research Office of the US Army under Contract No. DAJA-37-81-C-0740.The third author gratefully acknowledges Prof. A. Rinnooy Kan for bringing to his attention Ref. 4.     

Optimization and validation of an enzyme immunoassay for the insect growth regulator fenoxycarb

A competitive enzyme-linked immunosorbent assay (ELISA) was developed for the quantitative detection of the insect growth regulator fenoxycarb. Polyclonal rabbit antisera, raised against protein conjugates of four haptenic derivatives of fenoxycarb, were utilized in immobilized antigen-based, competitive immunoassays. With ELISA systems that were both hapten- and carrier-heterologous, most antiserum titers fell in the range of 1:1000-1:30,000. Assay conditions, including concentrations of antisera and coating antigens, were optimized. The effect of pH, organic solvents, and various blocking agents was also investigated. A hapten-homologous and two hapten-heterologous indirect ELISAs allowed fenoxycarb determination in the range of 0.1-85 ng ml⁻¹ with apparent IC₅₀ values of 1.2-2.8 ng ml⁻¹. Cross-reactivities with a number of compounds (e.g. pesticides of related structure, hapten synthesis intermediates, fenoxycarb metabolite, photodegradation products) were determined, and the assay proved highly selective for fenoxycarb. In particular, no significant interference was found with selected pyrethroid and juvenile hormone analog insecticides, phenoxyacetic acid herbicides, and photodegradation products of fenoxycarb. Using spiked water samples, assay performance was validated by SPME/GC-MS.     

Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation

New equations are derived and implemented for efficient and accurate computation of solvation energy derivatives for the conductor-like polarizable continuum model (C-PCM) and the isotropic integral equation formalism polarizable continuum model (IEF-PCM). Two new molecular surface tessellation procedures GEPOL-RT and GEPOL-AS that generate near continuous potential energy surfaces are proposed for PCM geometry optimization. The combined use of these new techniques leads to efficient and convergent geometry optimizations with the PCMs.     

Comparison of polydimethyl siloxane stationary phases with 5% and 50% phenyl substitution for the separation of organophosphorus and organonitrogen pesticides under optimized gas chromatographic conditions

The CGC analysis of 25 organophosphorus and organonitrogen pesticides was optimized on two different stationary phases, namely a 5% diphenyl dimethyl silicone (SE-54 type) and a 50% diphenyl dimethyl silicone (OV-17 type) by selecting the best temperature program conditions, using computer simulation.     

Electronic structure of BeH2

Nonorthogonal single‐configuration and multiconfiguration ab initio calculations are carried out on the BeH₂ molecule in its equilibrium (D_∞h) geometry, using a highly optimized even‐tempered Slater‐type orbital (STO) basis set. The results are used as a basis for a discussion of the electronic structure of the molecule in modern‐VB terms. A value of R_e = 1.329 Å is obtained. Values are also obtained for the symmetric‐stretch harmonic frequency (2053 cm^?1), electric quadrupole moment (?5.60 Buckingham), and nuclear quadrupole coupling constants (?3.59 MHz for ⁹Be and 0.0915 MHz for ²H). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Polarized basis sets of Slater-type orbitals: H to Ne atoms

We present three Slater-type atomic orbital (STO) valence basis (VB) sets for the first and second row atoms, referred to as the VB1, VB2, and VB3 bases. The smallest VB1 basis has the following structure: [3, 1] for the H and He atoms, [5, 1] for Li and Be, and [5, 3, 1] for the B to Ne series. For the VB2 and VB3 bases, both the number of shells and the number of functions per shell are successively increased by one with respect to VB1. With the exception of the H and Li atoms, the exponents for the VB1 bases were obtained by minimizing the sum of the Hartree-Fock (HF) and frozen-core singles and doubles configuration interaction (CISD FC) energies of the respective atoms in their ground state. For H and Li, we minimized the sum of the HF and CISD FC energies of the corresponding diatoms (i.e., of H(2) or Li(2)) plus the ground-state energy of the atom. In the case of the VB2 basis sets, the sum that was minimized also included the energies of the positive and negative ions, and for the VB3 bases, the energies of a few lowest lying excited states of the atom. To account for the core correlations, the VBx (x = 1, 2, and 3) basis sets for the Li to Ne series were enlarged by one function per shell. The exponents of these extended (core-valence, CV) basis sets, referred to, respectively, as the CVBx (x = 1, 2, and 3) bases, were optimized by relying on the same criteria as in the case of the VBx (x = 1, 2, and 3) bases, except that the full CISD rather than CISD FC energies were employed. We show that these polarized STO basis sets provide good HF and CI energies for the ground and excited states of the atoms considered, as well as for the corresponding ions.