A statistical model for global optimization by means of select and clone

A statistical model tor giobai optimization is constructed generalizing some properties ofthe Wiener process to the multidimensional case. A new approach, which is similar to the Branch and Bound approach, is proposed to the construction of algorithms based on statistical models. A two dimensional version of the algorithm is implemented, and test results are presented     

Efficient implementation of the analytic second derivatives of Hartree–Fock and hybrid DFT energies: a detailed analysis of different approximations

In this paper, various implementations of the analytic Hartree–Fock and hybrid density functional energy second derivatives are studied. An approximation-free four-centre implementation is presented, and its accuracy is rigorously analysed in terms of self-consistent field (SCF), coupled-perturbed SCF (CP-SCF) convergence and prescreening criteria. The CP-SCF residual norm convergence threshold turns out to be the most important of these. Final choices of convergence thresholds are made such that an accuracy of the vibrational frequencies of better than 5 cm^?1 compared to the numerical noise-free results is obtained, even for the highly sensitive low frequencies (<100–200 cm^?1). The effects of the choice of numerical grid for density functional exchange–correlation integrations are studied and various weight derivative schemes are analysed in detail. In the second step of the work, approximations are introduced in order to speed up the computation without compromising its accuracy. To this end, the accuracy and efficiency of the resolution of identity approximation for the Coulomb terms and the semi-numerical chain of spheres approximation to the exchange terms are carefully analysed. It is shown that the largest performance improvements are realised if either Hartree–Fock exchange is absent (pure density functionals) and otherwise, if the exchange terms in the CP-SCF step of the calculation are approximated by the COSX method in conjunction with a small integration grid. Default values for all the involved truncation parameters are suggested. For vancomycine (176 atoms and 3593 basis functions), the RIJCOSX Hessian calculation with the B3LYP functional and the def2-TZVP basis set takes ～3 days using 16 Intel® Xeon® 2.60GHz processors with the COSX algorithm having a net parallelisation scaling of 11.9 which is at least ～20 times faster than the calculation without the RIJCOSX approximation.     

Reactivity profiles of ligands of mammalian retinoic acid receptors: A preliminary COREPA analysis

Retinoic acid and associated derivatives comprise a class of endogenous hormones that bind to and activate different families of retinoic acid receptors (RARs, RXRs), and control many aspects of vertebrate development. Identification of potential RAR and RXR ligands is of interest both from a pharmaceutical and toxicological perspective. The recently developed COREPA (COmmon REactivity PAttern) algorithm was used to establish reactivity profiles for a limited data set of retinoid receptor ligands in terms of activation of three RARs ( f , g , n ) and an RXR ( f ). Conformational analysis of a training set of retinoids and related analogues in terms of thermodynamic stability of conformers and rotational barriers showed that these chemicals tend to be quite flexible. This flexibility, and the observation that relatively small energy differences between conformers can result in significant variations in electronic structure, highlighted the necessity of considering all energetically reasonable conformers in defining common reactivity profiles. The derived reactivity patterns for three different subclasses of the RAR ( f , g , n ) were similar in terms of their global electrophilicity (nucleophilicity) and steric parameters. However, the profile of active chemicals with respect to interaction with the RXR- f differed qualitatively from that of the RARs. Variations in reactivity profiles for the RAR versus RXR families would be consistent with established differences in their affinity for endogenous retinoids, likely reflecting functional differences in the receptors.     

Quantitative prediction of biodegradability,metabolite distribution and toxicity of stable metabolites

An evaluation of the capability of organic chemicals to mineralize is an important factor to consider when assessing their fate in the environment. Microbial degradation can convert a toxic chemical into an innocuous one, and vice versa , or alter the toxicity of a chemical. Moreover, primary biodegradation can convert chemicals into stable products that can be difficult to mineralize. In this paper, we present some new results obtained on the basis of a recently developed probabilistic approach to modeling biodegradation based on microbial transformation pathways. The metabolic transformations and their hierarchy were calibrated by making use of the ready biodegradability data from the MITI-I test and expert knowledge for the most probable transformation pathways. A model was developed and integrated into an expert software system named CATABOL that is able to predict the probability of biodegradation of organic chemicals directly from their structure. CATABOL simulates the effects of microbial enzyme systems, generates the most plausible transformation pathways, and quantitatively predicts the persistence and toxicity of the biodegradation products. A subset of 300 organic chemicals were selected from Canada's Domestic Substances List and subjected to CATABOL to compare predicted properties of the parent chemicals with their respective first stable metabolite. The results show that most of the stable metabolites have a lower acute toxicity to fish and a lower bioaccumulation potential compared to the parent chemicals. In contrast, the metabolites appear to be generally more estrogenic than the parent chemicals.     

A model validation and consensus building environment

Over half of the failures in drug development are due to problems with the absorption, distribution, metabolism, excretion, and toxicity, or ADME/Tox properties of a candidate compound. The utilization of in silico tools to predict ADME/Tox and physicochemical properties holds great potential for reducing the attrition rate in drug research and development, as this technology can prioritize candidate compounds in the pharmaceutical R&D pipeline. However, a major concern surrounding the use of in silico ADME/Tox technology is the reliability of the property predictions. Bio-Rad Laboratories, Inc. has created a computational environment that addresses these concerns. This environment is referred to as KnowItAll®. Within this platform are encoded a number of ADME/Tox predictors, the ability to validate these predictors with/without in-house data and models, as well as build a ‘consensus’ model that may be a much better model than any of the individual predictive model. The KnowItAll® system can handle two types of predictions: real number and categorical classification.     

Interactions between apolar,basic and acidic model oils and a calcite surface

Abstract

In this study, the atomic force microscopy colloidal probe technique was employed to investigate the interaction between apolar, basic and acidic model oil probes and a calcite surface in solutions containing different concentrations of NaCl, CaCl₂ and Na₂SO₄. In the presence of SO₄^2?, hydration and structural forces were observed between apolar model oil probes and a calcite surface on approach. Relatively low adhesion forces were observed between the basic model oil probes and the calcite surface, while higher adhesion forces were observed between the acidic model oil probes and the calcite surface. Furthermore, the adhesion forces between the basic model oil probes and the calcite surface significantly increased in the presence of SO₄^2?, while the adhesion force between the acidic model oil probes and the calcite surface decreased in the presence of Ca²⁺ or SO₄^2?. The differences in the adhesion forces are related to electrostatic attraction and ion bridging forces between the model oil probes and the calcite surface.     

木质素及其模型化合物的加氢脱氧反应研究进展

随着化石能源的不断枯竭,以及所产生的环境问题-温室效应及其高硫含量引起的酸雨,迫使人类寻找新型替代能源.在众多可再生能源中,生物质因其碳中性,易获取,作为唯一可转化为液体燃料的可再生资源,正日益受到重视.全球每年生物质产出高达1.7×1011t,其中,含75%的碳水化合物如纤维素、甲壳素和淀粉,20%木质素,其他占     

带连续变利率风险模型最终破产概率上界

考虑了带二元连续变利息力的Sparre Andersen风险模型.研究了积累值盈余过程的表达式与性质;在利率递增环境下,利用推广后的调节系数方程组与递归技术推导了最终破产概率的上界,结论表明得到的破产概率上界是更为一般的Lundberg指数上界.     

Interaction between ions and substituted buckybowls: A comprehensive computational study

Complexes formed by substituted buckybowls derived from corannulene and sumanene with sodium cation or chloride anion have been computationally studied by using a variety of methods. Best results have been obtained with the SCS‐MP2 method extrapolated to basis set limit, which reproduces the highest‐level values obtained with the MP2.X method. All bowls form stable complexes with chloride anion, with stabilities ranging from ?6 kcal/mol in the methylated corannulene derivative to ?45 kcal/mol in the CN‐substituted sumanene. The opposite trend is observed in sodium complexes, going from deeply attractive complexes with the methylated derivatives (?36 kcal/mol with sumanene derivative) to slightly repulsive ones in the CN‐substituted bowls (2 kcal/mol in the corannulene derivative). Anion complexes are stabilized by large electrostatic interactions combined with smaller though significant dispersion and induction contributions. Conversely, cation complexes are stabilized by large induction contributions capable of holding together the bowl and the cation even in cases where the electrostatic interaction is repulsive. The effect of substitution is mainly reflected on changes in the molecular electrostatic potential of the bowl and, thus, in the electrostatic contribution to the interaction. Therefore, the variations in the stability of the complexes on substitution could be roughly predicted just considering the changes in the electrostatic interaction. However, other contributions also register changes mainly as a consequence of displacements on the position of the ion at the minimum, so the accurate prediction of the stability of this kind of complexes requires going further than the electrostatic approach. © 2014 Wiley Periodicals, Inc.     

A Theoretical Model for Release Dynamics of an Antifungal Agent Covalently Bonded to the Chitosan

The aim of the study was to create a mathematical model useful for monitoring the release of bioactive aldehydes covalently bonded to the chitosan by reversible imine linkage, considered as a polymer–drug system. For this purpose, two hydrogels were prepared by the acid condensation reaction of chitosan with the antifungal 2-formyl-phenyl-boronic acid and their particularities; influencing the release of the antifungal aldehyde by shifting the imination equilibrium to the reagents was considered, i.e., the supramolecular nature of the hydrogels was highlighted by polarized light microscopy, while scanning electron microscopy showed their microporous morphology. Furthermore, the in vitro fungicidal activity was investigated on two fungal strains and the in vitro release curves of the antifungal aldehyde triggered by the pH stimulus were drawn. The theoretical model was developed starting from the hypothesis that the imine-chitosan system, both structurally and functionally, can be assimilated, from a mathematical point of view, with a multifractal object, and its dynamics were analyzed in the framework of the Scale Relativity Theory. Thus, through Riccati-type gauges, two synchronous dynamics, one in the scale space, associated with the fungicidal activity, and the other in the usual space, associated with the antifungal aldehyde release, become operational. Their synchronicity, reducible to the isomorphism of two SL(2R)-type groups, implies, by means of its joint invariant functions, bioactive aldehyde compound release dynamics in the form of “kink–antikink pairs” dynamics of a multifractal type. Finally, the theoretical model was validated through the experimental data.