535 research outputs found

    Open-Source Workflows for Reproducible Molecular Simulation

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    We apply molecular simulation to predict the equilibrium structure of organic molecular aggregates and how these structures determine material properties, with a focus on software engineering practices for ensuring correctness. Because simulations are implemented in software, there is potential for authentic scientific reproducibility in such work: An entire experimental apparatus (codebase) can be given to another investigator who should be able to use the same processes to find the same answers. Yet in practice, there are many barriers which stand in the way of reproducible molecular simulations that we address through automation, generalization, and software packaging. Collaboration on and application of the Molecular Simulation and Design Framework (MoSDeF) features prominently. We present structural investigations of organic molecule aggregates and the development of infrastructure and workflows that help manage, initialize, and analyze molecular simulation results through the following scientific applications (1) A screening study wherein we validate self-assembled poly-3-hexylthiophene (P3HT) morphologies show the same state dependency as in prior work, and (2) A multi-university collaborative reproducibility study where we examine modeling choices that give rise to differences between simulation engines. In aggregate, we reinforce the need for pipelines and practices emphasizing transferability, reproducibility, useability, and extensibility in molecular simulation

    On the Leaves of Climbing Plants

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    Relations of literature, science & philosophy in university education

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    RELATIONS OF LITERATURE, SCIENCE & PHILOSOHPY: Thought distinguished from feeling;- series of minds founded on this distinction. - The general and the particular distinguished, and a second series of minds suggested;- a corresponding series cf expressions of mentality;- diagram. Summary to this point. Of the scientific method,- ancient philosophy. The development of the inductive method,- Dr» Reid quoted;-the growth of science;- oscillation;- the likeness of the new to the old philosophy recapitulation.*THE FOREGOING ANALYSIS AS BEARING ON UNIVERSITIES: A. Nature & Function of University Education: Meaning of university Education defined,- Professor Butcher quoted. The discussion introduced by a list of materials.B(1) Literature: Why music and fine art are not essential in university education;- literature completely representative of the artistic spirit, but improperly used.- Ancient literature, modern literature.- Common arguments in favour of literary training stated and refuted, The real reason why literature must be studied;- the need for changed method in the study of literature.* Summary and conclusions regarding literature.B.(2) Science & Philosophy Limited nature of most arts courses;- gaps in arts courses;- enough subjects included, but why always the same? The real object of scientific training;- The best plan of education in science & philosophy;- Omission of natural science from most arts courses;- this omission not obviated by Scottish "honours" courses,- comparison of these with those of Cambridge. Advantages of free choice of subjects. Need for philosophy and practical suggestions. The argument confirmed by reference to history. Summary,APPLICATION OF THE FOREGOING TO EDINBURGH UNIVERSITY: The teaching organisation in Edinburgh. The use that is made of this organisation, and the use that might be

    Structures of pyruvate kinases display evolutionarily divergent allosteric strategies

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    The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (k(cat)/S(0.5)). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (k(cat)/S(0.5)) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors
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