Properties of bounded stochastic processes employed in biophysics

Abstract

Realistic stochastic modeling is increasingly requiring the use of bounded noises. In this work, properties and relationships of commonly employed bounded stochastic processes are investigated within a solid mathematical ground. Four families are object of investigation: the Sine-Wiener (SW), the Doering–Cai–Lin (DCL), the Tsallis–Stariolo–Borland (TSB), and the Kessler–Sørensen (KS) families. We address mathematical questions on existence and uniqueness of the processes defined through Stochastic Differential Equations, which often conceal non-obvious behavior, and we explore the behavior of the solutions near the boundaries of the state space. The expression of the time-dependent probability density of the Sine-Wiener noise is provided in closed form, and a close connection with the Doering–Cai–Lin noise is shown. Further relationships among the different families are explored, pathwise and in distribution. Finally, we illustrate an analogy between the Kessler–Sørensen family and Bessel processes, which allows to relate the respective local times at the boundaries.     

A Hybrid Improvement Heuristic for the One-Dimensional Bin Packing Problem

We propose in this work a hybrid improvement procedure for the bin packing problem. This heuristic has several features: the use of lower bounding strategies; the generation of initial solutions by reference to the dual min-max problem; the use of load redistribution based on dominance, differencing, and unbalancing; and the inclusion of an improvement process utilizing tabu search. Encouraging results have been obtained for a very wide range of benchmark instances, illustrating the robustness of the algorithm. The hybrid improvement procedure compares favourably with all other heuristics in the literature. It improved the best known solutions for many of the benchmark instances and found the largest number of optimal solutions with respect to the other available approximate algorithms.     

Automated and enhanced extraction of a small molecule-drug conjugate using an enzyme-inhibitor interaction based SPME tool followed by direct analysis by ESI-MS

We report a novel, fast, and automatic SPME-based method capable of extracting a small molecule-drug conjugate (SMDC) from biological matrices. Our method relies on the extraction of the drug conjugate followed by direct elution into an electrospray mass spectrometer (ESI-MS) source for qualitative and quantitative analysis. We designed a tool for extracting the targeting head of a recently synthesized SMDC, which includes acetazolamide (AAZ) as high-affinity ligand specific to carbonic anhydrase IX. Specificity of the extraction was achieved through systematic optimization. The design of the extraction tool is based on noncovalent and reversible interaction between AAZ and CAII that is immobilized on the SPME extraction phase. Using this approach, we showed a 330% rise in extracted AAZ signal intensity compared to a control, which was performed in the absence of CAII. A linear dynamic range from 1.2 to 25 μg/ml was found. The limits of detection (LOD) of extracted AAZ from phosphate-buffered saline (PBS) and human plasma were 0.4 and 1.2 μg/ml, respectively. This with a relative standard deviation of less than 14% (n = 40) covers the therapeutic range.

Graphical abstract

     

Acetoxyphenylketene. Reaction with biacetyl

The generation of acetoxyphenylketene (4) in the cold in the presence of biacetyl yields the single β-lactone $\text{12B}$, which undergoes a novel rearrangement to the tricyclic orthoester lactone $\text{11}$ above 130°.     

Molecular and crystal structures of ruthenium and osmium arene clusters

The molecular and crystal structures of a number of ruthenium and osmium clusters of nuclearity between three and six containing arene fragments such as C₆H₆, C₆H₃Me₃, C₆H₄Me₂ and C₆H₅Me have been investigated. Attention has been focused on the relationship between the terminal ( ⁶-coordination) and face-capping ( ₃: ²: ²: ²-coordination) bonding modes. Empirical packing potential energy calculations have been employed to investigate the intermolecular organization in the crystal. It has been shown that the arene fragments in mono-arene clusters form ribbons, while in bis-arene clusters graphitic-like interactions throughout the crystal are established. The factors controlling the ease of arene reorientational motion in the solid state has also been investigated in relation to the shape, size and geometry of the molecules and of their interlocking modes.     

Traceless solid-phase synthesis of 2,4,6-chlorodiamino and triaminopyrimidines

An effective traceless solid-phase synthesis of chloro-diaminopyrimidines via an amino-de-chlorination reaction of polymer-bound 4-alkoxycarbonylamino-2,6-dichloropyrimidines has been developed. After release from the polymer the target molecules were obtained in good to excellent purity, although with modest regiocontrol. Further reaction of solid-supported N-alkoxycarbonyl-chloro-diaminopyrimidines with secondary amines afforded triaminopyrimidines in good purity under mild conditions, whereas less nucleophilic primary amines did not perform well under the conditions explored so far.     

LCAO–MO similarity measures and taxonomy

Similarity measures between pairs of molecular wave functions are described. They are based on the geometrical structure of the LCAO–MO framework and upon multivariate analysis ideas. The theoretical framework is presented, and formulae for some integrals needed are given. Two main measures, distance and correlation coefficients, are used. Distance and correlation matrices induce relationships in the whole MO set, which can be depicted through minimal spanning tree techniques. Furthermore, principal component analysis allows a two-dimensional visualization of the Mo manifold geometrical relationships. Various examples are given in order to obtain information on how basis set, environment, excitation, bending, stretching, and electronegativity affect the induced order. For this purpose “ab initio” SCF–LCAO–MO calculations with double- and single-zeta quality basis sets have been used for various simple molecular structures: H₂O, NH₃, CH₄, N₂, O₂, C₂, NO, CN, and CO. The results obtained can open the way to LCAO–MO taxonomy. Using this information, other areas of interest are connected with similarity measures (SCF and CI , localization procedures, etc.), proving in this manner their potential utility.     

Density functional theory study of the mechanism of the proline-catalyzed intermolecular aldol reaction

Transition structures associated with the C-C bond-formation step of the proline-catalyzed intermolecular aldol reaction between acetone and isobutyraldehyde have been studies using density functional theory methods at the B3LYP/6-31G** computational level. A continuum model has been selected to represent solvent effects. For this step, which is the stereocontrolling and rate-determining step, four reactive channels corresponding to the syn and anti arrangement of the active methylene of the enamine relative to the carboxylic acid group of l-proline and the re and si attack modes to both faces of the aldehyde carbonyl group have been analyzed. The B3LYP/6-31G** energies are in good agreement with experiment, allowing us to explain the origin of the catalysis and stereoselectivity for these proline-catalyzed aldol reactions. Received: 2 April 2002 / Accepted: 18 July 2002 / Published online: 11 October 2002 Acknowledgements. This work was supported by research funds provided by the Ministerio de Educación y Cultura of the Spanish Government by DGICYT (project PB98–1429). All the calculations were performed on a Cray–Silicon Graphics Origin 2000 of the Servicio de Informática de la Universidad de Valencia. We are most indebted to this center for providing us with computer capabilities. Correspondence to: L. R. Domingo e-mail: domingo@utopia.uv.es