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.     

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°.     

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     

Synthesis and Characterization of a [Mn12O12(O2CR)16(H2O)4] Complex Bearing Paramagnetic Carboxylate Ligands. Use of a Modified Acid Replacement Synthetic Approach

Summary.  A new modified approach for the synthesis of Mn₁₂ clusters, based on the use of complex [Mn₁₂O₁₂(O₂C ^t Bu)₁₆(H₂O)₄] (2) as starting material to promote the acidic ligand replacement, is presented here. This new synthetic approach allowed us to obtain complex [Mn₁₂O₁₂(O₂CC₆H₄N(O^•) ^t Bu)₁₆(H₂O)₄] (3), whose preparation remained elusive by direct replacement of the acetate groups of Mn₁₂Ac (1). Complex 3 bearing open-shell radical units, was prepared to increase the total spin number of its ground state, and consequently, to increase T _B , with the expectation that the radical ligands may couple ferromagnetically with the Mn₁₂ core. Unfortunately, magnetic measurements of complex 3 revealed that the sixteen radical carboxylate ligands interact antiferromagnetically with the Mn₁₂ core to yield a S = 2 magnetic ground state. Corresponding author. E-mail: vecianaj@icmab.es Received March 27, 2002; accepted May 2, 2002     

Rigidity of harmonic maps of maximum rank

Thehomotopical rank of a mapf:M →N is, by definition, min{dimg(M) ¦g homotopic tof}. We give upper bounds for this invariant whenM is compact Kähler andN is a compact discrete quotient of a classical symmetric space, e.g., the space of positive definite matrices. In many cases the upper bound is sharp and is attained by geodesic immersions of locally hermitian symmetric spaces. An example is constructed (Section 9) to show that there do, in addition, exist harmonic maps of quite a different character. A byproduct is construction of an algebraic surface with large and interesting fundamental group. Finally, a criterion for lifting harmonic maps to holomorphic ones is given, as is a factorization theorem for representations of the fundamental group of a compact Kähler manifold. The technique for the main result is a combination of harmonic map theory, algebra, and combinatorics; it follows the path pioneered by Siu in his ridigity theorem and later extended by Sampson.     

The influence of the brewing process on the formation of biogenic amines in beers

Biogenic amines, as dabsyl derivatives, were determined in beer samples, intermediate products, and raw materials (malt and maize) by HPLC. A procedure for the extraction of the amines from malt and maize with diluted hydrochloric acid was optimised by combining a Response Surface Methodology with a Simultaneous Decision Making Approach. The results of the analysis indicate that, in brewing, technology and hygiene are the decisive factors that determine the amine concentrations in the final product.     

On Transition Structures for Hydride Transfer Step in Enzyme Catalysis. A Comparative Study on Models of Glutathione Reductase Derived from Semiempirical, HF, and DFT Methods

As a model of the chemical reactions that take place in the active site of gluthatione reductase, the nature of the molecular mechanism for the hydride transfer step has been characterized by means of accurate quantum chemical characterizations of transition structures. The calculations have been carried out with analytical gradients at AM1 and PM3 semiempirical procedures, ab initio at HF level with 3-21G, 4-31G, 6-31G, and 6-31G basis sets and BP86 and BLYP as density functional methods. The results of this study suggest that the endo relative orientation on the substrate imposed by the active site is optimal in polarizing the C4-Ht bond and situating the system in the neighborhood of the quadratic region of the transition structure associated to the hydride transfer step on potential energy surface. The endo arrangement of the transition structure results in optimal frontier HOMO orbital interaction between NADH and FAD partners. The geometries of the transition structures and the corresponding transition vectors, that contain the fundamental information relating reactive fluctuation patterns, are model independent and weakly dependent on the level of theory used to determine them. A comparison between simple and complex molecular models shows that there is a minimal set of coordinates describing the essentials of hydride transfer step. The analysis of transition vector components suggests that the primary and secondary kinetic isotope effects can be strongly coupled, and this prompted the calculation of deuterium and tritium primary, secondary, and primary and secondary kinetic isotope effects. The results obtained agree well with experimental data and demonstrate this coupling.     

Duality and intersection theory in complex manifolds. I

We introduce the concept of a twisting cochain and a twisted complex associated to a coherent sheaf. For sheaves of submanifolds these twisted complexes are used to construct on cochain level the Grothendieck theory of dual class and Gysin map. These explicit constructions give, for instance, a local formula for dual class of higher codimensional submanifolds. We prove a refined version of the Hirzebruch Riemann Roch using such local formulas. We also prove a theorem on when global analytic intersection classes can be computed from first order geometric data. This theory will be used to prove the Holomorphic Lefschetz formula (in Part II) and the Hirzebruch Riemann Roch for analytic coherent sheaves.The first author is supported in part by NSF grants GP-36418X1 and MCS 76-08478. The second by MCS 75-07986 and Sonderforschungsbereich Theoretische Mathematik at Bonn University     

Eigenvectors and cyclic vectors of bilateral weighted shifts. II: Simply invariant subspaces

Let T be an injective bilateral weighted shift onl ² thought as "multiplication by λ" on a space of formal Laurent series L²(β). (a) If L²(β) is contained in a space of quasi-analytic class of functions, then the point spectrum σ_p(T^?) of T^? contains a circle and the cyclic invariant subspaceM _f of T generated by f is simply invariant (i.e., ∩{(T^k M _f)^?: k ≥ 0}= {0}) for each f in L²(β); (b) If L²(β) contains a non-quasi-analytic class of functions (defined on a circle г) of a certain type related with the weight sequence of T, then there exists f in L²(ß) such thatM _f is a non-trivial doubly invariant subspace (i.e., (TM _f)^? =M _f); furthermore, if г ? σ_p(T^*), then σ_p (T^*) = г and f can be chosen so that σ_p([T∣M _f]^*) = г?{α}, for some α ε г. Several examples show that the gap between operators satisfying (a) and operators satisfying (b) is rather small.