@article{Pardi2023.12.15.571789,

title = {pyQCM-BraTaDio: A tool for visualization, data mining, and modelling of Quartz crystal microbalance with dissipation data},

author = {Brandon M. Pardi and Syeda Tajin Ahmed and Silvia Jonguitud Flores and Warren Flores and Laura L. E. Mears and Bernardo Yá nez Soto and Roberto C. Andresen Eguiluz},

url = {https://www.biorxiv.org/content/early/2023/12/15/2023.12.15.571789},

doi = {10.1101/2023.12.15.571789},

year  = {2023},

date = {2023-12-15},

urldate = {2023-12-15},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Here, we present a Python based software that allows for the rapid visualization, data mining, and basic model applications of quartz crystal microbalance with dissipation data. Our implementation begins with a Tkinter GUI to prompt the user for all required information, such as file name/location, selection of baseline time, and overtones for visualization (with customization capabilities). These inputs are then fed to a workflow that will use the baseline time to scrub and temporally shift data using the Pandas and Numpy libraries and carry out the plot options for visualization. The last stage consists of an interactive plot, that presents the data and allows the user to select ranges in MatPlotLib-generated panels, followed by application of data models, including Sauerbrey, thin films in liquid, among others, that are carried out with NumPy and SciPy. The implementation of this software allows for simple and expedited data analysis, in lieu of time consuming and labor-intensive spreadsheet analysis.View this table:Competing Interest StatementThe authors have declared no competing interest.},

keywords = {GUI, MatPlotLib, openQCM, pyQCM-BraTaDio, Python, QCM-D, Software},

pubstate = {published},

tppubtype = {article}

}

@article{millan2023degradation,

title = {Degradation kinetics of medium chain length Polyhydroxyalkanoate degrading enzyme: a quartz crystal microbalance study},

author = {Fabien Millan and Nils Hanik},

url = {https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2023.1303267/full},

doi = {https://doi.org/10.3389/fbioe.2023.1303267},

year  = {2023},

date = {2023-12-14},

urldate = {2023-12-14},

journal = {Frontiers in Bioengineering and Biotechnology},

volume = {11},

pages = {1303267},

publisher = {Frontiers Media SA},

abstract = {This study investigates the enzymatic degradation processes of different classes of polyhydroxyalkanoates (PHAs), a group of biopolymers naturally synthesized by various microorganisms. Medium chain length PHAs (mcl-PHAs) are distinguished biopolymers due to their biodegradability and diverse material properties. Using quartz crystal microbalance measurements as a valuable tool for accurate real-time monitoring of the enzymatic degradation process, the research provides detailed kinetic data, describing the interaction between enzymes and substrates during the enzymatic degradation process. Thin films of poly-3-hydroxybutyrate (PHB) and polyhydroxyoctanoate copolymer (PHO), containing molar fractions of about 84% 3-hydroxyoctanoate and 16% 3-hydroxyhexanoate, were exposed to scl-depolymerases from Pseudomonas lemoignei LMG 2207 and recombinant mcl-depolymerase produced in Escherichia coli DH5α harboring the plasmid pMAD8, respectively. Analyses based on a heterogeneous kinetic model for the polymer degradation indicated a six-fold stronger adsorption equilibrium constant of mcl-depolymerase to PHO. Conversely, the degradation rate constant was approximately twice as high for scl-depolymerases acting on PHB. Finally, the study highlights the differences in enzyme-substrate interactions and degradation mechanisms between the investigated scl- and mcl-PHAs.},

keywords = {biodegradable polymers, degradation kinetics, depolymerase enzymes, enzymatic degradation, openQCM, openQCM Q-1, polyhydroxyalkanoates, Python, Quartz Crystal Microbalance},

pubstate = {published},

tppubtype = {article}

}