Quantum Bayesian computation

Quantum Bayesian computation is an emerging field that levers the computational gains available from quantum computers. They promise to provide an exponential speed-up in Bayesian computation. Our article adds to the literature in three ways. First, we describe how quantum von Neumann measurement provides quantum versions of popular machine learning algorithms such as Markov chain Monte Carlo and deep learning that are fundamental to Bayesian learning. Second, we describe quantum data encoding methods needed to implement quantum machine learning including the counterparts to traditional feature extraction and kernel embeddings methods. Third, we show how quantum algorithms naturally calculate Bayesian quantities of interest such as posterior distributions and marginal likelihoods. Our goal then is to show how quantum algorithms solve statistical machine learning problems. On the theoretical side, we provide quantum versions of high dimensional regression, Gaussian processes and stochastic gradient descent. On the empirical side, we apply a quantum FFT algorithm to Chicago house price data. Finally, we conclude with directions for future research.     

Structure Elucidation and Activity of Kolossin A,the D‐/L‐Pentadecapeptide Product of a Giant Nonribosomal Peptide Synthetase

The largest continuous bacterial nonribosomal peptide synthetase discovered so far is described. It consists of 15 consecutive modules arising from an uninterrupted, fully functional gene in the entomopathogenic bacterium Photorhabdus luminescens. The identification of its cryptic biosynthesis product was achieved by using a combination of genome analysis, promoter exchange, isotopic labeling experiments, and total synthesis of a focused collection of peptide candidates. Although it belongs to the growing class of D ‐/ L ‐peptide natural products, the encoded metabolite kolossin A was found to be largely devoid of antibiotic activity and is likely involved in interspecies communication. A stereoisomer of this peculiar natural product displayed high activity against Trypanosoma brucei rhodesiense, a recalcitrant parasite that causes the deadly disease African sleeping sickness.     

Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

Investigation of confined ionic liquid in nanostructured materials by a combination of SANS, contrast-matching SANS, and nitrogen adsorption

Small-angle neutron scattering (SANS), contrast-matching SANS, and nitrogen adsorption have been utilized to investigate the confined ionic liquid (IL) [bmim][PF(6)] phase in ordered mesoporous silica MCM-41 and SBA-15. The results suggest that the pores of SBA-15 are completely filled with IL whereas a small fraction of the pore volume, the pore "core", of MCM-41 is empty. The contrast-matching SANS measurements confirm the enhanced solubility of water in IL. In addition, they provide strong evidence that water does not enter the empty pore core of MCM-41, possibly because of the preferred orientation of the IL molecules in the adsorbed layer.     

Spectroscopic and electronic structure studies of a dimethyl sulfoxide reductase catalytic intermediate: implications for electron- and atom-transfer reactivity

The electronic structure of a genuine paramagnetic des-oxo Mo(V) catalytic intermediate in the reaction of dimethyl sulfoxide reductase (DMSOR) with (CH(3))(3)NO has been probed by electron paramagnetic resonance (EPR), electronic absorption, and magnetic circular dichroism (MCD) spectroscopies. EPR spectroscopy reveals rhombic g- and A-tensors that indicate a low-symmetry geometry for this intermediate and a singly occupied molecular orbital that is dominantly metal centered. The excited-state spectroscopic data were interpreted in the context of electronic structure calculations, and this has resulted in a full assignment of the observed MCD and electronic absorption bands, a detailed understanding of the metal-ligand bonding scheme, and an evaluation of the Mo(V) coordination geometry and Mo(V)-S(dithiolene) covalency as it pertains to the stability of the intermediate and electron-transfer regeneration. Finally, the relationship between des-oxo Mo(V) and des-oxo Mo(IV) geometric and electronic structures is discussed relative to the reaction coordinate in members of the DMSOR enzyme family.     

Disjoint Hamilton cycles in the random geometric graph

We consider the standard random geometric graph process in which n vertices are placed at random on the unit square and edges are sequentially added in increasing order of edge‐length. For fixed k?1, weprove that the first edge in the process that creates a k‐connected graph coincides a.a.s. with the first edge that causes the graph to contain k/2 pairwise edge‐disjoint Hamilton cycles (for even k), or (k?1)/2 Hamilton cycles plus one perfect matching, all of them pairwise edge‐disjoint (for odd k). This proves and extends a conjecture of Krivelevich and M ler. In the special case when k = 2, our result says that the first edge that makes the random geometric graph Hamiltonian is a.a.s. exactly the same one that gives 2‐connectivity, which answers a question of Penrose. (This result appeared in three independent preprints, one of which was a precursor to this article.) We prove our results with lengths measured using the ?_p norm for any p>1, and we also extend our result to higher dimensions. © 2011 Wiley Periodicals, Inc. J Graph Theory 68:299‐322, 2011     

Inversion of particle-stabilized emulsions of partially miscible liquids by mild drying of modified silica particles

Using a system of modified silica particles and mixtures of water and 2,6-lutidine to form particle-stabilized emulsions, we show that subtle alterations to the hydration of the particle surface can cause major shifts in emulsion structure. We use fluorescence confocal microscopy, solid state nuclear magnetic resonance (NMR) and thermo-gravimetric analysis (TGA) to explore this sensitivity, along with other shifts caused by modifications to the silica surface chemistry. The silica particles are prepared by a variant of the St?ber procedure and are modified by the inclusion of 3-(aminopropyl)triethoxysilane and the dye fluorescein isothiocyanate. Treatment prior to emulsification consists of gently drying the particles under carefully controlled conditions. In mixtures of water and 2,6-lutidine of critical composition, the particles stabilize droplet emulsions and bijels. Decreasing particle hydration yields an inversion of the emulsions from lutidine-in-water (L/W) to water-in-lutidine (W/L), with bijels forming around inversion. So dependent is the emulsion behavior on particle hydration that microscopic differences in drying within a particle sample can cause differences in the wetting behavior of that sample, which helps to stabilize multiple emulsions. The formation of bijels at emulsion inversion is also crucially dependent on the surface modification of the silica.     

Simultaneous determination of estrogenic and androgenic hormones in water by isotope dilution gas chromatography-tandem mass spectrometry

A rapid gas chromatography-tandem mass spectrometry (GC-MS/MS) analytical method was developed for the simultaneous analysis of 7 estrogenic hormones (17α-estradiol, 17β-estradiol, estrone, mestranol, 17α-ethynylestradiol, levonorgestrel, estriol) and 5 androgenic hormones (testosterone, androsterone, etiocholanolone, dihydrotestosterone, androstenedione) in aqueous matrices. This method is unique in its inclusion of all 12 of these estrogens and androgens and is of particular value due to its very short chromatographic run time of 15 min. The use of isotope dilution for all analytes ensures the accurate quantification, accounting for analytical variabilities that may be introduced during sample processing and instrumental analysis. Direct isotopically labelled analogues were used for 8 of the 12 hormones and satisfactory isotope standards were identified for the remaining 4 hormones. Method detection levels (MDLs) were determined to describe analyte concentrations sufficient to provide a signal with 99% certainty of detection. The established MDLs for most analytes were 1-5 ngL(-1) in a variety of aqueous matrices. However, slightly higher MDLs were observed for etiocholanolone, androstenedione, testosterone, levonorgestrel and dihydrotestosterone in some aqueous matrices. Sample matrices were observed to have only a minor impact on MDLs and the method validation confirmed satisfactory method stability over intra-day and inter-day analyses of surface water and tertiary treated effluent samples.     

A microfluidic device for self-synchronised production of droplets

The primary requirement for a mixing operation in droplet-based microfluidic devices is an accurate pairing of droplets of reaction fluids over an extended period of time. In this paper, a novel device for self-synchronous production of droplets has been demonstrated. The device uses a change in impedance across a pair of electrodes introduced due to the passage of a pre-formed droplet to generate a second droplet at a second pair of electrodes. The device was characterised using image analysis. Droplets with a volume of ~23.5 ± 3.1 nl (i.e.~93% of the volume of pre-formed droplets) were produced on applying a voltage of 500 V. The synchronisation efficiency of the device was 83%. As the device enables self-synchronised production of droplets, it has a potential to increase the reliability and robustness of mixing operations in droplet-based microfluidic devices.     

Bis(methyltri‐o‐tolylphosphonium) octaiodide

In the crystal structure of the title compound, 2C₂₂H₂₄P⁺·I₈²⁻, the I₈²⁻ anion is located on a crystallographic inversion centre and consists of two tri‐iodide anions linked by di‐iodine at angles of 89.92 (4)° to form a planar `Z'‐shaped dianion. The octaiodides are linked via long‐range interactions [3.877 (11) Å] into infinite polyiodide ribbons. This is the first example of a structure containing an [(o‐tolyl)₃PMe]⁺ cation, and the C_Me—P—C—C_Me torsion angles of −54.0 (11), −51.3 (11) and −48.2 (11)° indicate that the configuration is exo₃.