Department of Physical Sciences

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Now showing 1 - 5 of 263
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    A nanometric probe of the local proton concentration in microtubule-based biophysical systems
    (2022) Kalra, Aarat P.; Eakins, Boden B.; Vagin, Sergei I.; Wang, Hui; Patel, Sahil D.; Winter, Philip; Aminpour, Maral; Lewis, John D.; Rezania, Vahid; Shankar, Karthik; Scholes, Gregory D.; Tuszynski, Jack A.; Rieger, Bernhard; Meldrum, Alkiviathes
    We show a double-functional fluorescence sensing paradigm that can retrieve nanometric pH information on biological structures. We use this method to measure the extent of protonic condensation around microtubules, which are protein polymers that play many roles crucial to cell function. While microtubules are believed to have a profound impact on the local cytoplasmic pH, this has been hard to show experimentally due to the limitations of conventional sensing techniques. We show that subtle changes in the local electrochemical surroundings cause a double-functional sensor to transform its spectrum, thus allowing a direct measurement of the protonic concentration at the microtubule surface. Microtubules concentrate protons by as much as one unit on the pH scale, indicating a charge storage role within the cell via the localized ionic condensation. These results confirm the bioelectrical significance of microtubules and reveal a sensing concept that can deliver localized biochemical information on intracellular structures.
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    Scanning the auroral skies: the Athabasca University robotic telescope
    (2019) Cartledge, Stefan; Schofield, Ian; Connors, Martin; Langill, Phil
    The Athabasca University Robotic Telescope (AURT) is a moderate aperture (0.36 m) networked robotic telescope that supports teaching and research at Athabasca University, a pioneering and prominent distance learning university in Canada. This paper reviews the establishment and implementation of a robotic, Internet-based astronomical observatory whose development parallels and complements Athabasca University’s auroral observatory. We discuss the unique features and challenges of the northern observing environment, give examples of teaching and research activities underway at AURT, and discuss an investigation into dark sky conditions over the AURT site.
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    Multifractality nature of microtubule dynamic instability process
    (2021) Rezania, Vahid; Sudirga, Ferry C.; Tuszyński, Jack A.
    The irregularity of growing and shortening patterns observed experimentally in microtubules and their ensembles reflects a dynamical system that fluctuates stochastically between assembly and disassembly phases. The observed time series of microtubule lengths have been extensively analyzed to shed light on structural and dynamical properties of microtubules. Here, for the first time, Multifractal Detrended Fluctuation analysis (MFDFA) has been employed to investigate the multifractal and topological properties of both experimental and simulated microtubule time series. We find that the time dependence of microtubule length possesses true multifractal characteristics and cannot be described by mono-fractal distributions. Based on the multifractal spectrum profile, a set of multifractal indices have been calculated that can be related to the level of dynamical processes in microtubules. We also show that the resulting multifractal spectra for the simulated data might not be comparable with experimental data.
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    A new method for protein characterization and classification using geometrical features for 3D face analysis: an example of tubulin structures
    (2021) Di Grazia, Luca; Aminpour, Maral; Vezzetti, Enrico; Rezania, Vahid; Marcolin, Federica; Tuszyński, Jack A.
    This article reports on the results of research aimed to translate biometric 3D face recognition concepts and algorithms into the field of protein biophysics in order to precisely and rapidly classify morphological features of protein surfaces. Both human faces and protein surfaces are free-forms and some descriptors used in differential geometry can be used to describe them applying the principles of feature extraction developed for computer vision and pattern recognition. The first part of this study focused on building the protein dataset using a simulation tool and performing feature extraction using novel geometrical descriptors. The second part tested the method on two examples, first involved a classification of tubulin isotypes and the second compared tubulin with the FtsZ protein, which is its bacterial analog. An additional test involved several unrelated proteins. Different classification methodologies have been used: a classic approach with a support vector machine (SVM) classifier and an unsupervised learning with a k-means approach. The best result was obtained with SVM and the radial basis function kernel. The results are significant and competitive with the state-of-the-art protein classification methods. This leads to a new methodological direction in protein structure analysis.
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    Revealing and attenuating the electrostatic properties of tubulin and its polymers
    (2021) Kalra, Aarat P.; Patel, Sahil; Eakins, Boden; Riddell, Saralyn; Kumar, Pawan; Winter, Philip; Preto, Jordane; Carlson, Kris W.; Lewis, John D.; Rezania, Vahid; Tuszyński, Jack A.; Shankar, Karthik
    Tubulin is an electrostatically negative protein that forms cylindrical polymers termed microtubules, which are crucial for a variety of intracellular roles. Exploiting the electrostatic behavior of tubulin and microtubules within functional microfluidic and optoelectronic devices is limited due to the lack of understanding of tubulin behavior as a function of solvent composition. This work displays the tunability of tubulin surface charge using dimethyl sulfoxide (DMSO) for the first time. Increasing the DMSO volume fractions leads to the lowering of tubulin's negative surface charge, eventually causing it to become positive in solutions >80% DMSO. As determined by electrophoretic mobility measurements, this change in surface charge is directionally reversible, i.e., permitting control between −1.5 and + 0.2 cm2 (V s)−1. When usually negative microtubules are exposed to these conditions, the positively charged tubulin forms tubulin sheets and aggregates, as revealed by an electrophoretic transport assay. Fluorescence-based experiments also indicate that tubulin sheets and aggregates colocalize with negatively charged g-C3N4 sheets while microtubules do not, further verifying the presence of a positive surface charge. This study illustrates that tubulin and its polymers, in addition to being mechanically robust, are also electrically tunable.