Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

Mechanistic studies of single bubble growth using interface-tracking methods

The growth of a vapour bubble at a heated surface involves various fluid mechanics, heat transfer and phase change phenomena. In this paper we present recent work under the auspices of the NURESAFE project aimed at developing mechanistic modelling of this. Evaporation at the curved surface of the bubble requires evaluation of the unsteady heat conduction within the surrounding liquid, coupled to an appropriate phase change model at the vapour–liquid interface. Issues around the development and implementation of such a phase change model are addressed. For low-pressure bubbles, however, a large fraction of the total evaporation takes place from the “microlayer”; a thin layer of water coating the heated substrate, which is left behind as the bubble expands. This microlayer evaporation requires careful, sub-grid modelling, as heat fluxes through the thin layer are very high. In particular, we demonstrate here the need both for modelling of the conjugate heat transfer within the substrate, and the importance of the incorporation of evaporative thermal resistance at the vapour–liquid interface. Despite the important role it plays in bubble growth, the mechanisms governing the formation, and resulting dimensions, of this microlayer are very little understood. We finish with a presentation of some early results attempting to investigate mechanistically the hydrodynamics of microlayer formation

Broadband laser cooling of trapped atoms with ultrafast pulses

We demonstrate broadband laser cooling of atomic ions in an rf trap using ultrafast pulses from a modelocked laser. The temperature of a single ion is measured by observing the size of a time-averaged image of the ion in the known harmonic trap potential. While the lowest observed temperature was only about 1 K, this method efficiently cools very hot atoms and can sufficiently localize trapped atoms to produce near diffraction-limited atomic images

Tunneling Ionization Rates from Arbitrary Potential Wells

We present a practical numerical technique for calculating tunneling ionization rates from arbitrary 1-D potential wells in the presence of a linear external potential by determining the widths of the resonances in the spectral density, rho(E), adiabatically connected to the field-free bound states. While this technique applies to more general external potentials, we focus on the ionization of electrons from atoms and molecules by DC electric fields, as this has an important and immediate impact on the understanding of the multiphoton ionization of molecules in strong laser fields.Comment: 13 pages, 7 figures, LaTe

Slow Light in Doppler Broadened Two level Systems

We show that the propagation of light in a Doppler broadened medium can be slowed down considerably eventhough such medium exhibits very flat dispersion. The slowing down is achieved by the application of a saturating counter propagating beam that produces a hole in the inhomogeneous line shape. In atomic vapors, we calculate group indices of the order of 10^3. The calculations include all coherence effects.Comment: 6 pages, 5 figure

A kinetic and theoretical study of the borate catalysed reactions of hydrogen peroxide: the role of dioxaborirane as the catalytic intermediate for a wide range of substrates

Our recent work has provided new insights into the equilibria and species that exist in aqueous solution at different pHs for the boric acid – hydrogen peroxide system, and the role of these species in oxidation reactions. Most recently, (M. C. Durrant, D. M. Davies and M. E. Deary, Org. Biomol. Chem., 2011, 9,7249–7254), we have produced strong theoretical and experimental evidence for the existence of a previously unreported monocyclic three membered peroxide species, dioxaborirane, that is the likely catalytic species in borate mediated electrophilic reactions of hydrogen peroxide in alkaline solution. In the present paper, we extend our study of the borate–peroxide system to look at a wide range of substrates that include substituted dimethyl anilines, methyl-p-tolyl sulfoxide, halides, hydrogen sulfide anion, thiosulfate ,thiocyanate, and hydrazine. The unusual selectivity–reactivity pattern of borate catalysed reactions compared with hydrogen peroxide and inorganic or organic peracids previously observed for theorganic sulfides (D. M. Davies, M. E. Deary, K. Quill and R. A. Smith, Chem.–Eur. J., 2005, 11, 3552–3558) is also seen with substituted dimethyl aniline nucleophiles. This provides evidence that the pattern is not due to any latent electrophilic tendency of the organic sulfides and further supports dioxaborirane being the likely reactive intermediate, thus broadening the applicability of this catalytic system. Moreover, density functional theory calculations on our proposed mechanism involving dioxaborirane are consistent with the experimental results for these substrates. Results obtained at high concentrations of both borate and hydrogen peroxide require the inclusion the diperoxodiborate dianion in the kinetic analysis .A scheme detailing our current understanding of the borate–peroxide system is presented

Extreme ultraviolet interferometry measurements with high-order harmonics

We demonstrate that high-order harmonics generated by short, intense laser pulses in gases provide an interesting radiation source for extreme ultraviolet interferometry, since they are tunable, coherent, of short pulse duration, and simple to manipulate. Harmonics from the 9th to the 15th are used to measure the thickness of an aluminum layer. The 11th harmonic is used to determine the spatial distribution of the electron density of a plasma produced by a 300-ps laser. Electronic densities higher than 2-10(20) electrons/cm(3) are measured. (C) 2000 Optical Society of America. OCIS codes: 190.0190, 190.4160, 190.7110, 120.3180, 140.7240, 350.4500