Chemputation and the standardization of chemical informatics

The explosion in the use of machine learning for automated chemical reaction optimization is gathering pace. However, the lack of a standard architecture that connects the concept of chemical transformations universally to software and hardware provides a barrier to using the results of these optimizations and could cause the loss of relevant data and prevent reactions from being reproducible or unexpected findings verifiable or explainable. In this Perspective, we describe how the development of the field of digital chemistry or chemputation, that is the universal code-enabled control of chemical reactions using a standard language and ontology, will remove these barriers allowing users to focus on the chemistry and plug in algorithms according to the problem space to be explored or unit function to be optimized. We describe a standard hardware (the chemical processing programming architecture—the ChemPU) to encompass all chemical synthesis, an approach which unifies all chemistry automation strategies, from solid-phase peptide synthesis, to HTE flow chemistry platforms, while at the same time establishing a publication standard so that researchers can exchange chemical code (χDL) to ensure reproducibility and interoperability. Not only can a vast range of different chemistries be plugged into the hardware, but the ever-expanding developments in software and algorithms can also be accommodated. These technologies, when combined will allow chemistry, or chemputation, to follow computation—that is the running of code across many different types of capable hardware to get the same result every time with a low error rate

An autonomous electrochemical discovery robot that utilises probabilistic algorithms: probing the redox behaviour of inorganic materials

The discovery of new electroactive materials is slow due to the large combinatorial chemical space of possible experiments. Efficient exploration of redox‐active chemical space requires a machine learning assisted robotic platform with real‐time feedback. Here, we developed a closed‐loop robotic platform which is capable of synthesis and electrochemical characterisation controlled using a probabilistic algorithm. This was used to probe the redox behaviour of different polyoxometalates (POMs) precursors and explore the formation of redox‐active coordination complexes. The system can run accurate analytical electrochemical measurements whilst maintaining the performance and accuracy of both the working and reference electrodes. The platform successfully ran and analysed 336 coordination chemistry reactions by performing ca. 2500 cyclic voltammetry (CV) scans for analysis and electrode cleaning. Overall, the platform carried out over 9900 operations in 350 hours at a rate of 28 operations per hour, and we identified 24 complex solutions which showed significantly different redox activity. Experiments were performed using a universal chemical synthesis language (χDL) with variable inputs. The platform was used autonomously to investigate a range of POM precursor materials demonstrating 45 % increase in capacitance. The experiments ran for 36 hours with more than 6400 operations during which we analysed 200 POM precursor solutions

Data acquisition process for an intelligent decision support in gynecology and obstetrics emergency triage

Manchester Triage System is a reliable system of triage in the emergency department of a hospital. This system when applied to a specific patients’ condition such the pregnancy has several limitations. To overcome those limitations an alternative triage IDSS was developed in the MJD. In this approach the knowledge was obtained directly from the doctors’ empirical and scientific experience to make the first version of decision models. Due to the particular gynecological and/or obstetrics requests other characteristics had been developed, namely a system that can increase patient safety for women in need of immediate care and help low-risk women avoid high-risk care, maximizing the use of resources. This paper presents the arrival flowchart, the associated decisions and the knowledge acquisition cycle. Results showed that this new approach enhances the efficiency and the safety through the appropriate use of resources and by assisting the right patient in the right place.The work of Filipe Portela was supported by the grant SFRH/BD/70156/2010 from FC

Electromagnetic corrections in eta --> 3 pi decays

We re-evaluate the electromagnetic corrections to eta --> 3 pi decays at next-to-leading order in the chiral expansion, arguing that effects of order e^2(m_u-m_d) disregarded so far are not negligible compared to other contributions of order e^2 times a light quark mass. Despite the appearance of the Coulomb pole in eta --> pi+ pi- pi0 and cusps in eta --> 3 pi0, the overall corrections remain small.Comment: 21 pages, 11 figures; references updated, version published in EPJ

An integrated self-optimizing programmable chemical synthesis and reaction engine

Robotic platforms for chemistry are developing rapidly but most systems are not currently able to adapt to changing circumstances in real-time. We present a dynamically programmable system capable of making, optimizing, and discovering new molecules which utilizes seven sensors that continuously monitor the reaction. By developing a dynamic programming language, we demonstrate the 10-fold scale-up of a highly exothermic oxidation reaction, end point detection, as well as detecting critical hardware failures. We also show how the use of in-line spectroscopy such as HPLC, Raman, and NMR can be used for closed-loop optimization of reactions, exemplified using Van Leusen oxazole synthesis, a four-component Ugi condensation and manganese-catalysed epoxidation reactions, as well as two previously unreported reactions, discovered from a selected chemical space, providing up to 50% yield improvement over 25–50 iterations. Finally, we demonstrate an experimental pipeline to explore a trifluoromethylations reaction space, that discovers new molecules

Measurement of the ratio B(D0->pi+pi-pi0)/B(D0->K-pi+pi0) and the time-integrated CP asymmetry in D0->pi+pi-pi0

We report a high-statistics measurement of the relative branching fraction B(D0->pi+pi-pi0)/B(D0->K-pi+pi0) using a 532 fb^{-1} data sample collected with the Belle detector at the KEKB asymmetric-energy e+e- collider. The measured value of the relative branching fraction is B(D0->pi+pi-pi0)/B(D0->K-pi+pi0) = (10.12 +/- 0.04(stat) +/- 0.18(syst))x10^{-2} which has an accuracy comparable to the world average. We also present a measurement of the time-integrated CP asymmetry in D0->pi+pi-pi0 decay. The result, A_{CP} = (0.43 +/- 1.30)%, shows no significant CP violation.Comment: 15 pages, 11 figures, submitted to Physics Letters

Gamma-Ray Bursts: The Underlying Model

A pedagogical derivation is presented of the ``fireball'' model of gamma-ray bursts, according to which the observable effects are due to the dissipation of the kinetic energy of a relativistically expanding wind, a ``fireball.'' The main open questions are emphasized, and key afterglow observations, that provide support for this model, are briefly discussed. The relativistic outflow is, most likely, driven by the accretion of a fraction of a solar mass onto a newly born (few) solar mass black hole. The observed radiation is produced once the plasma has expanded to a scale much larger than that of the underlying ``engine,'' and is therefore largely independent of the details of the progenitor, whose gravitational collapse leads to fireball formation. Several progenitor scenarios, and the prospects for discrimination among them using future observations, are discussed. The production in gamma- ray burst fireballs of high energy protons and neutrinos, and the implications of burst neutrino detection by kilometer-scale telescopes under construction, are briefly discussed.Comment: In "Supernovae and Gamma Ray Bursters", ed. K. W. Weiler, Lecture Notes in Physics, Springer-Verlag (in press); 26 pages, 2 figure

Measurement of the Branching Fraction for B->eta' K and Search for B->eta'pi+

We report measurements for two-body charmless B decays with an eta' meson in the final state. Using 11.1X10^6 BBbar pairs collected with the Belle detector, we find BF(B^+ ->eta'K^+)=(79^+12_-11 +-9)x10^-6 and BF(B^0 -> eta'K^0)=(55^+19_-16 +-8)x10^-6, where the first and second errors are statistical and systematic, respectively. No signal is observed in the mode B^+ -> eta' pi^+, and we set a 90% confidence level upper limit of BF(B^+-> eta'pi^+) eta'K^+- decays is investigated and a limit at 90% confidence level of -0.20<Acp<0.32 is obtained.Comment: Submitted to Physics Letters

Measurement of CP asymmetry in Cabibbo suppressed D0 decays

We measure the CP-violating asymmetries in decays to the D0 -> K+K- and D0 -> pi+pi- CP eigenstates using 540 fb^{-1} of data collected with the Belle detector at or near the Upsilon(4S) resonance. Cabibbo-favored D0 -> K-pi+ decays are used to correct for systematic detector effects. The results, A_{CP}^{KK} = (-0.43 +- 0.30 +- 0.11)% and A_{CP}^{pipi} = (+0.43 +- 0.52 +- 0.12)%, are consistent with no CP violation.Comment: Submitted to Phys. Lett.

Heavy quarkonium: progress, puzzles, and opportunities

A golden age for heavy quarkonium physics dawned a decade ago, initiated by the confluence of exciting advances in quantum chromodynamics (QCD) and an explosion of related experimental activity. The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress. However, the broad spectrum of subsequent breakthroughs, surprises, and continuing puzzles could only be partially anticipated. Since the release of the YR, the BESII program concluded only to give birth to BESIII; the $B$-factories and CLEO-c flourished; quarkonium production and polarization measurements at HERA and the Tevatron matured; and heavy-ion collisions at RHIC have opened a window on the deconfinement regime. All these experiments leave legacies of quality, precision, and unsolved mysteries for quarkonium physics, and therefore beg for continuing investigations. The plethora of newly-found quarkonium-like states unleashed a flood of theoretical investigations into new forms of matter such as quark-gluon hybrids, mesonic molecules, and tetraquarks. Measurements of the spectroscopy, decays, production, and in-medium behavior of c\bar{c}, b\bar{b}, and b\bar{c} bound states have been shown to validate some theoretical approaches to QCD and highlight lack of quantitative success for others. The intriguing details of quarkonium suppression in heavy-ion collisions that have emerged from RHIC have elevated the importance of separating hot- and cold-nuclear-matter effects in quark-gluon plasma studies. This review systematically addresses all these matters and concludes by prioritizing directions for ongoing and future efforts.Comment: 182 pages, 112 figures. Editors: N. Brambilla, S. Eidelman, B. K. Heltsley, R. Vogt. Section Coordinators: G. T. Bodwin, E. Eichten, A. D. Frawley, A. B. Meyer, R. E. Mitchell, V. Papadimitriou, P. Petreczky, A. A. Petrov, P. Robbe, A. Vair