Open Access Publications

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Open access publications by faculty, postdocs, and graduate students in the Department of Chemical and Biomolecular Engineering


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Now showing 1 - 5 of 68
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    Tuning High-Density Polyethylene Hydrocracking through Mordenite Zeolite Crystal Engineering
    (ACS Sustainable Chemistry and Engineering, 2023-06-19) Kots, Pavel A.; Doika, Panagiota A.; Vance, Brandon C.; Najmi, Sean; Vlachos, Dionisios G.
    We investigate the hydrocracking of high-density polyethylene using a bifunctional Pt/Al2O3 and modified mordenite acid catalyst. Mass transport limitations impact polymer diffusion into the mordenite pore complex. Initial reaction intermediates are formed on the zeolite’s outer surface. Intercrystallite open-end mesopores improve the diffusion of reaction intermediates deeper into the crystal. Recrystallization and desilication of mordenite lead to a higher polymer conversion and shift the product distribution maximum from pentanes to hexanes and heptanes. The nature of mesopores (occluded or open) and total Brønsted acidity significantly impact zeolite activity and selectivity.
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    Unpacking the multimodal, multi-scale data of the fast and slow lanes of the cardiac vagus through computational modelling
    (Experimental Physiology, 2023-04-30) Gee, Michelle M.; Hornung, Eden; Gupta, Suranjana; Newton, Adam J. H.; Cheng, Zixi (Jack); Lytton, William W.; Lenhoff, Abraham M.; Schwaber, James S.; Vadigepalli, Rajanikanth
    New Findings What is the topic of this review? The vagus nerve is a crucial regulator of cardiovascular homeostasis, and its activity is linked to heart health. Vagal activity originates from two brainstem nuclei: the nucleus ambiguus (fast lane) and the dorsal motor nucleus of the vagus (slow lane), nicknamed for the time scales that they require to transmit signals. What advances does it highlight? Computational models are powerful tools for organizing multi-scale, multimodal data on the fast and slow lanes in a physiologically meaningful way. A strategy is laid out for how these models can guide experiments aimed at harnessing the cardiovascular health benefits of differential activation of the fast and slow lanes. The vagus nerve is a key mediator of brain–heart signaling, and its activity is necessary for cardiovascular health. Vagal outflow stems from the nucleus ambiguus, responsible primarily for fast, beat-to-beat regulation of heart rate and rhythm, and the dorsal motor nucleus of the vagus, responsible primarily for slow regulation of ventricular contractility. Due to the high-dimensional and multimodal nature of the anatomical, molecular and physiological data on neural regulation of cardiac function, data-derived mechanistic insights have proven elusive. Elucidating insights has been complicated further by the broad distribution of the data across heart, brain and peripheral nervous system circuits. Here we lay out an integrative framework based on computational modelling for combining these disparate and multi-scale data on the two vagal control lanes of the cardiovascular system. Newly available molecular-scale data, particularly single-cell transcriptomic analyses, have augmented our understanding of the heterogeneous neuronal states underlying vagally mediated fast and slow regulation of cardiac physiology. Cellular-scale computational models built from these data sets represent building blocks that can be combined using anatomical and neural circuit connectivity, neuronal electrophysiology, and organ/organismal-scale physiology data to create multi-system, multi-scale models that enable in silico exploration of the fast versus slow lane vagal stimulation. The insights from the computational modelling and analyses will guide new experimental questions on the mechanisms regulating the fast and slow lanes of the cardiac vagus toward exploiting targeted vagal neuromodulatory activity to promote cardiovascular health.
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    Insights into solvent and surface charge effects on Volmer step kinetics on Pt (111)
    (Nature Communications, 2023-04-25) Wilson, Jon C.; Caratzoulas, Stavros; Vlachos, Dionisios G.; Yan, Yushan
    The mechanism of pH-dependent hydrogen oxidation and evolution kinetics is still a matter of significant debate. To make progress, we study the Volmer step kinetics on platinum (111) using classical molecular dynamics simulations with an embedded Anderson-Newns Hamiltonian for the redox process and constant potential electrodes. We investigate how negative electrode electrostatic potential affects Volmer step kinetics. We find that the redox solvent reorganization energy is insensitive to changes in interfacial field strength. The negatively charged surface attracts adsorbed H as well as H+, increasing hydrogen binding energy, but also trapping H+ in the double layer. While more negative electrostatic potential in the double layer accelerates the oxidation charge transfer, it becomes difficult for the proton to move to the bulk. Conversely, reduction becomes more difficult because the transition state occurs farther from equilibrium solvation polarization. Our results help to clarify how the charged surface plays a role in hydrogen electrocatalysis kinetics.
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    Anisotropy factors in small-angle scattering for dilute rigid-rod suspensions
    (Journal of Applied Crystallography, 2023-06) Rooks, J.; Gilbert, P. H.; Porcar, L.; Liu, Y.; Butler, P.
    Alignment of anisotropic particles along specific orientations influences the mechanical and rheological properties of a material. Small-angle scattering techniques are widely used to probe this alignment through analysis of anisotropic two-dimensional scattering intensity patterns. The anisotropy factor is the simplest and most common quantitative parameter for describing scattering anisotropy, especially in systems containing rod-like particles, and there are several methods for calculating this factor. However, there has been no systematic study comparing these methods while also evaluating the limitations imposed by non-idealities from instrumentation or polydisperse morphology. Three of the most common methods for calculating an anisotropy factor are examined here and their effectiveness for describing the orientation of a theoretical cylinder is evaluated. It is found that the maximum theoretical value of 1 for the anisotropy factor is only accessible at certain values of scattering vector q. The analysis details recommendations for q-range selection and data binning, as these influence the calculations. The theoretical results are supported by experimental small-angle neutron scattering data for a wormlike micelle solution undergoing shear, where different calculation methods yield distinct quantifications of anisotropy.
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    High-efficiency and multilocus targeted integration in CHO cells using CRISPR-mediated donor nicking and DNA repair inhibitors
    (Biotechnology and Bioengineering, 2023-04-11) Hamaker, Nathaniel K.; Lee, Kelvin H.
    Efforts to leverage clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) for targeted genomic modifications in mammalian cells are limited by low efficiencies and heterogeneous outcomes. To aid method optimization, we developed an all-in-one reporter system, including a novel superfolder orange fluorescent protein (sfOrange), to simultaneously quantify gene disruption, site-specific integration (SSI), and random integration (RI). SSI strategies that utilize different donor plasmid formats and Cas9 nuclease variants were evaluated for targeting accuracy and efficiency in Chinese hamster ovary cells. Double-cut and double-nick donor formats significantly improved targeting accuracy by 2.3–8.3-fold and 19–22-fold, respectively, compared to standard circular donors. Notably, Cas9-mediated donor linearization was associated with increased RI events, whereas donor nicking minimized RI without sacrificing SSI efficiency and avoided low-fidelity outcomes. A screen of 10 molecules that modulate the major mammalian DNA repair pathways identified two inhibitors that further enhance targeting accuracy and efficiency to achieve SSI in 25% of transfected cells without selection. The optimized methods integrated transgene expression cassettes with 96% efficiency at a single locus and with 53%–55% efficiency at two loci simultaneously in selected clones. The CRISPR-based tools and methods developed here could inform the use of CRISPR/Cas9 in mammalian cell lines, accelerate mammalian cell line engineering, and support advanced recombinant protein production applications.
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