Consistency of Markov chain quasi-Monte Carlo on continuous state spaces

The random numbers driving Markov chain Monte Carlo (MCMC) simulation are usually modeled as independent U(0,1) random variables. Tribble [Markov chain Monte Carlo algorithms using completely uniformly distributed driving sequences (2007) Stanford Univ.] reports substantial improvements when those random numbers are replaced by carefully balanced inputs from completely uniformly distributed sequences. The previous theoretical justification for using anything other than i.i.d. U(0,1) points shows consistency for estimated means, but only applies for discrete stationary distributions. We extend those results to some MCMC algorithms for continuous stationary distributions. The main motivation is the search for quasi-Monte Carlo versions of MCMC. As a side benefit, the results also establish consistency for the usual method of using pseudo-random numbers in place of random ones.Comment: Published in at http://dx.doi.org/10.1214/10-AOS831 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Nonlinear spectroscopic studies using sum- and difference-frequency generation

A detailed study is presented of resonant sum- and difference-frequency generation for the mixed-crystal system azulene in naphthalene. The S0 -> S1, S0 -> S2 and S1 -> S2 transitions of azulene provide the 3 needed dipoles for the existence of c(2), and a relatively small static elec. field was used to break the interference between the waves generated in the 2 crystal sublattices. Second-order nonlinear processes can occur sep. in each sublattice. All the theor. predicted resonances, except the DICE effect, were obsd. The generated field intensity satd. at higher fields, and in certain circumstances exhibited hysteresis as a function of the d.c. field strength. The line-narrowing capabilities of these new forms of spectroscopy were explored

Specificity and Kinetics of Haloalkane Dehalogenase

Haloalkane dehalogenase converts halogenated alkanes to their corresponding alcohols. The active site is buried inside the protein and lined with hydrophobic residues. The reaction proceeds via a covalent substrate-enzyme complex. This paper describes a steady-state and pre-steady-state kinetic analysis of the conversion of a number of substrates of the dehalogenase. The kinetic mechanism for the “natural” substrate 1,2-dichloroethane and for the brominated analog and nematocide 1,2-dibromoethane are given. In general, brominated substrates had a lower Km, but a similar kcat than the chlorinated analogs. The rate of C-Br bond cleavage was higher than the rate of C-Cl bond cleavage, which is in agreement with the leaving group abilities of these halogens. The lower Km for brominated compounds therefore originates both from the higher rate of C-Br bond cleavage and from a lower Ks for bromo-compounds. However, the rate-determining step in the conversion (kcat) of 1,2-dibromoethane and 1,2-dichloroethane was found to be release of the charged halide ion out of the active site cavity, explaining the different Km but similar kcat values for these compounds. The study provides a basis for the analysis of rate-determining steps in the hydrolysis of various environmentally important substrates.

Absorption and emission spectroscopies of homogeneous and inhomogeneously broadened multilevel systems in strong light fields

A method is introduced to calc., for a model set of mol. levels, the spectral line shapes expected for a variety of conventional laser expts. including absorption, hole burning, fluorescence line narrowing, and Raman scattering. The method allows the incident laser field to have arbitrary intensity. Furthermore, the effects of model gaussian or lorenzian inhomogeneous distributions are readily incorporated. Earlier results for a 2-level system are easily obtained and new results are presented for inhomogeneously broadened 2- and 3-level systems, and for the effects of pure dephasing on the strong field spectra. The differences between fluorescence and Raman in strong fields, and the effect of strong fields on the spontaneous emission of inhomogeneously broadened transitions were described. Some predictions are made regarding line narrowing expts. in the strong-field limit

Influence of mutations of Val226 on the catalytic rate of haloalkane dehalogenase

Haloalkane dehalogenase converts haloalkanes to their corresponding alcohols. The 3D structure, reaction mechanism and kinetic mechanism have been studied. The steady state kcat with 1,2-dichloroethane and 1,2-dibromoethane is limited mainly by the rate of release of the halide ion from the buried active-site cavity. During catalysis, the halogen that is cleaved off (Clα) from 1,2-dichloroethane interacts with Trp125 and the Clβ interacts with Phe172. Both these residues have van der Waals contacts with Val226. To establish the effect of these interactions on catalysis, and in an attempt to change enzyme activity without directly mutating residues involved in catalysis, we mutated Val226 to Gly, Ala and Leu. The Val226Ala and Val226Leu mutants had a 2.5-fold higher catalytic rate for 1,2-dibromoethane than the wild-type enzyme. A pre-steady state kinetic analysis of the Val226Ala mutant enzyme showed that the increase in kcat could be attributed to an increase in the rate of a conformational change that precedes halide release, causing a faster overall rate of halide dissociation. The kcat for 1,2-dichloroethane conversion was not elevated, although the rate of chloride release was also faster than in the wild-type enzyme. This was caused by a 3-fold decrease in the rate of formation of the alkyl-enzyme intermediate for 1,2-dichloroethane. Val226 seems to contribute to leaving group (Clα or Brα) stabilization via Trp125, and can influence halide release and substrate binding via an interaction with Phe172. These studies indicate that wild-type haloalkane dehalogenase is optimized for 1,2-dichloroethane, although 1,2-dibromoethane is a better substrate.

Degradation of Toluene and Trichloroethylene by Burkholderia cepacia G4 in Growth-Limited Fed-Batch Culture

Burkholderia (Pseudomonas) cepacia G4 was cultivated in a fed-batch bioreactor on either toluene or toluene plus trichloroethylene (TCE). The culture was allowed to reach a constant cell density under conditions in which the amount of toluene supplied equals the maintenance energy demand of the culture. Compared with toluene only, the presence of TCE at a toluene/TCE ratio of 2.3 caused a fourfold increase in the specific maintenance requirement for toluene from 22 to 94 nmol mg of cells (dry weight)-1 h-1. During a period of 3 weeks, approximately 65% of the incoming TCE was stably converted to unidentified products from which all three chlorine atoms were liberated. When toluene was subsequently omitted from the culture feed while TCE addition continued, mutants which were no longer able to grow on toluene or to degrade TCE appeared. These mutants were also unable to grow on phenol or m- or o-cresol but were still able to grow on catechol and benzoate. Plasmid analysis showed that the mutants had lost the plasmid involved in toluene monooxygenase formation (pTOM). Thus, although strain G4 is much less sensitive to TCE toxicity than methanotrophs, deleterious effects may still occur, namely, an increased maintenance energy demand in the presence of toluene and plasmid loss when no toluene is added.

Clustering outdoor soundscapes using fuzzy ants

A classification algorithm for environmental sound recordings or "soundscapes" is outlined. An ant clustering approach is proposed, in which the behavior of the ants is governed by fuzzy rules. These rules are optimized by a genetic algorithm specially designed in order to achieve the optimal set of homogeneous clusters. Soundscape similarity is expressed as fuzzy resemblance of the shape of the sound pressure level histogram, the frequency spectrum and the spectrum of temporal fluctuations. These represent the loudness, the spectral and the temporal content of the soundscapes. Compared to traditional clustering methods, the advantages of this approach are that no a priori information is needed, such as the desired number of clusters, and that a flexible set of soundscape measures can be used. The clustering algorithm was applied to a set of 1116 acoustic measurements in 16 urban parks of Stockholm. The resulting clusters were validated against visitor's perceptual measurements of soundscape quality

Evaluation of a new trauma-related drinking to cope measure: Latent structure and heritability

Posttraumatic stress disorder (PTSD) and alcohol use disorder (AUD) commonly co-occur, share latent genetic risk, and are associated with many negative public health outcomes. Via a self-medication framework, trauma-related drinking to cope (TRD), an unexplored phenotype to date, may help explain why these two disorders co-occur, thus serving as an essential target for treatment and prevention efforts. This study sought to create a novel measure of TRD and to investigate its indirect influences on the association between PTSD and AUD, as well as its potential shared molecular genetic risk with PTSD in a genetically-informative study of college students. A sample of 1,896 undergraduate students with a history of trauma and alcohol use provided genotypic data and completed an online assessment battery. The psychometric properties of TRD and how it relates to relevant constructs were examined using descriptive statistics and structural equation modeling. Results of a correlated multiple mediator model indicated that, while accounting for the effects of generalized drinking motives, TRD partially mediated the relation between PTSD and alcohol use problems (β = 0.213, p \u3c .001), consistent with the self-medication hypothesis, and that this relationship was stronger for males (β = 0.804, p \u3c .001) than for females (β = 0.463, p \u3c .001). Results were substantiated using longitudinal data. Genotypic analyses to be presented will include univariate genome wide complex trait analyses (GCTA) to establish SNP-based heritability associated with TRD and PTSD, separately, as well as bivariate GCTA to examine potential overlap in heritability between TRD and PTSD.https://scholarscompass.vcu.edu/gradposters/1047/thumbnail.jp