Browsing by Author "Bishop, Logan D.C."

Now showing 1 - 4 of 4
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    Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions
    (Springer Nature, 2016) Shuang, Bo; Wang, Wenxiao; Shen, Hao; Tauzin, Lawrence J.; Flatebo, Charlotte; Chen, Jianbo; Moringo, Nicholas A.; Bishop, Logan D.C.; Kelly, Kevin F.; Landes, Christy F.
    Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions.
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    Relating chromatogram lineshape to microscale surface interactions using stochastic theory and chemometrics
    (2021-04-01) Bishop, Logan D.C.; Landes, Christy F
    Pharmaceutical separations are necessary to mass-produce novel treatments for emerging diseases. Rare, heterogeneous surface chemistry hampers separations by generating chromatographic tails that cause peak overlap. The chemical source of tailing is thoroughly detailed in microscopic terms by the stochastic theory but difficult to assess from macroscale measurements that guide optimization. Chemometric-driven chromatogram analysis that achieves a microscale understanding of surface chemistry could help direct tuning of column chemistry to reduce tailing. Here, we improve upon previous graphical metrics with our own metric, the Distribution Function Ratio (DFR), which is compatible with stochastic theory and capable of bridging the gap between macroscale chromatograms and microscale surface chemistry. Further, we prove the DFR can provide predictive analysis of surface chemistry, an application that could be used in online chromatographic instruments. Establishing an analytical metric that is simple to implement provides mechanistic, chemometric guidance for future development of surface chemistry in chromatographic columns.
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    The structure–energy landscape of NMDA receptor gating
    (Springer Nature, 2017) Dolino, Drew M.; Chatterjee, Sudeshna; MacLean, David M.; Flatebo, Charlotte; Bishop, Logan D.C.; Shaikh, Sana A.; Landes, Christy F.; Jayaraman, Vasanthi
    N-Methyl-D-aspartate (NMDA) receptors are the main calcium-permeable excitatory receptors in the mammalian central nervous system. The NMDA receptor gating is complex, exhibiting multiple closed, open, and desensitized states; however, central questions regarding the conformations and energetics of the transmembrane domains as they relate to the gating states are still unanswered. Here, using single-molecule Förster resonance energy transfer (smFRET), we map the energy landscape of the first transmembrane segment of the Rattus norvegicus NMDA receptor under resting and various liganded conditions. These results show kinetically and structurally distinct changes associated with apo, agonist-bound, and inhibited receptors linked by a linear mechanism of gating at this site. Furthermore, the smFRET data suggest that allosteric inhibition by zinc occurs by an uncoupling of the agonist-induced changes at the extracellular domains from the gating motions leading to an apo-like state, while dizocilpine, a pore blocker, stabilizes multiple closely packed transmembrane states.
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    Transforming Separation Science with Single-Molecule Methods
    (American Chemical Society, 2020) Calabrase, William; Bishop, Logan D.C.; Dutta, Chayan; Misiura, Anastasiia; Landes, Christy F.; Kisley, Lydia; Smalley-Curl Institute
    Empirical optimization of the multiscale parameters underlying chromatographic and membrane separations leads to enormous resource waste and production costs. A bottom-up approach to understand the physical phenomena underlying challenges in separations is possible with single-molecule observations of solute–stationary phase interactions. We outline single-molecule fluorescence techniques that can identify key interactions under ambient conditions. Next, we describe how studying increasingly complex samples heightens the relevance of single-molecule results to industrial applications. Finally, we illustrate how separation methods that have not been studied at the single-molecule scale can be advanced, using chiral chromatography as an example case. We hope new research directions based on a molecular approach to separations will emerge based on the ideas, technologies, and open scientific questions presented in this Perspective.