1,911 research outputs found

    A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase

    Get PDF
    AbstractThe formation of water chains in cytochrome c oxidase (CcO) is studied by molecular dynamics (MD). Focus is on water chains in the K channel that can supply a proton to the binuclear center (the heme a3 Fe/CuB region), the site of O2 reduction. By assessing the presence of chains of any length on a short time scale (0.1 ps), a view of the kinds of chains and their persistence is obtained. Chains from the entry of the channel on the inner membrane to Thr359 (Rhodobacter sphaeroides numbering) are often present but are blocked at that point until a rotation of the Thr359 side chain occurs, permitting formation of chains from Thr359 towards the binuclear center. No continuous hydrogen-bonded water chains are found connecting Thr359 and the binuclear center. Instead, waters hydrogen bond from Thr359 to the hydroxyl of the heme a3 farnesyl and then continue to the binuclear center via Tyr288, which has been identified as a source of a proton for O2 reduction. Three hydrogen-bonded waters are found to be present in the binuclear center after a sufficiently long simulation time. One is ligated to the CuB and could be associated with a water (or hydroxyl) identified in the crystal structure as the fourth ligand of CuB. The water hydrogen-bonded to the hydroxyl of Tyr288 is extremely persistent and well positioned to participate in O2 reduction. The third water is located where O2 is often suggested to reside in mechanistic studies of O2 reduction

    Three Variations on Variational Autoencoders

    Full text link
    Variational autoencoders (VAEs) are one class of generative probabilistic latent-variable models designed for inference based on known data. We develop three variations on VAEs by introducing a second parameterized encoder/decoder pair and, for one variation, an additional fixed encoder. The parameters of the encoders/decoders are to be learned with a neural network. The fixed encoder is obtained by probabilistic-PCA. The variations are compared to the Evidence Lower Bound (ELBO) approximation to the original VAE. One variation leads to an Evidence Upper Bound (EUBO) that can be used in conjunction with the original ELBO to interrogate the convergence of the VAE.Comment: 21 pages. This version, v2, has added an explicit evaluation of our VAE A variational encoder. The new result is summarized in new Section 4 VAE A explicitly and detailed in Appendices B and

    The effect of a strong external field on the electronic dephasing of a solute that is strongly coupled to a solvent

    Get PDF
    A recent theory of strong field spectroscopy (SFS) [R. I. Cukier and M. Morillo, Phys. Rev. B 57, 6972 (1998), M. Morillo and R. I. Cukier, J. Chem. Phys. (110, 7966 (1999)] is generalized to apply to strong solute–solvent coupling. In SFS, a strong external field is used to connect, with the transition dipole, two electronic states of a solute immersed in a medium. In contrast to weak fields, z̄(t), the average population difference of the solute electronic states is changing significantly. For resonant, strong fields, z̄(t) and the average absorbed power, ��̄(t), exhibit oscillatory decays in time that reflect the changing z̄(t) and the dissipation arising from the coupling to the medium. When the solute–solvent coupling is relatively weak, the time evolution of the solvent only depends on the initial solute state (autonomous behavior). In this work, appropriate to strong coupling, we derive an equation of motion for the solvent dynamics that depends on the solute’s instantaneous state (nonautonomous behavior). The consequences to z̄(t) and ��̄(t) are explored. We find that instead of equalizing the solute populations at long times, now the population is inverted relative to its initial state. We also find that the degree of long-time population inversion can be controlled by turning off the external field before the system has fully relaxed.Center for Fundamental Materials Research at Michigan State UniversityDirección General de Enseñanza Superior de España B95-0536Junta de Andalucí

    HbA1c: chasing numbers or considering context?

    Full text link
    Glycated haemoglobin (HbA<sub>1c</sub>) reflects the average blood glucose level in the three months preceding the test. Changes in consecutive HbA<sub>1c</sub> tests indicate deteriorating, or improved, glycaemic control. HbA<sub>1c</sub> is considered to be the "gold standard" measure of blood glucose control and is often used as the basis for prescribing choices and other care decisions. A number of factors can affect the accuracy of the HbA<sub>1c</sub> result, for example, the life span of red blood cells, assay methods and clinicians\u27 awareness of possible interfering factors. The aim of this article is to outline how HbA<sub>1c</sub> is used as a diagnostic test, how it is used to monitor glycaemic control and how it can guide management decisions. It is also important to emphasise the importance of considering HbA<sub>1c</sub> in the context of the individual rather than as an isolated number

    Artisanal Fashion Design: Entrepreneurs on Thinking, Process, and Decision Making

    Get PDF
    This paper examines the ways in which fashion designers think about themselves, the design process, and the fashion industry. Recent interest in design thinking (Brown, 2009; Martin 2009) has focused attention on the interaction between creativity and rationality in the design process. Within the fashion design literature there are studies of processes in large fashion manufacturing enterprises but very little research has focused on small-scale fashion design entrepreneurs. This study is important given the emergent significance of fashion design and the creative industries in the global economy and the growing importance of entrepreneurs. Understanding how these fashion entrepreneurs operate and the factors influencing their success or failure is, therefore, of interest
    corecore