Department of Physical Sciences

Permanent link for this collection

Browse

Recent Submissions

Now showing 1 - 5 of 261
  • Item
    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.
  • Item
    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.
  • Item
    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.
  • Item
    All wired up: an exploration of the electrical properties of microtubules and tubulin
    (2020) Kalra, Aarat P.; Eakins, Boden; Patel, Sahil; Ciniero, Gloria; Rezania, Vahid; Shankar, Karthik; Tuszynski, Jack A.
    Microtubules are hollow, cylindrical polymers of the protein α, β tubulin, that interact mechanochemically with a variety of macromolecules. Due to their mechanically robust nature, microtubules have gained attention as tracks for precisely directed transport of nanomaterials within lab-on-a-chip devices. Primarily due to the unusually negative tail-like C-termini of tubulin, recent work demonstrates that these biopolymers are also involved in a broad spectrum of intracellular electrical signaling. Microtubules and their electrostatic properties are discussed in this Review, followed by an evaluation of how these biopolymers respond mechanically to electrical stimuli, through microtubule migration, electrorotation and C-termini conformation changes. Literature focusing on how microtubules act as nanowires capable of intracellular ionic transport, charge storage, and ionic signal amplification is reviewed, illustrating how these biopolymers attenuate ionic movement in response to electrical stimuli. The Review ends with a discussion on the important questions, challenges, and future opportunities for intracellular microtubule-based electrical signaling.
  • Item
    A revised shock history for the youngest unbrecciated lunar basalt – Northwest Africa 032
    (2020) Mijajlovic, Tatiana; Xue, Xie; Walton, Erin
    Northwest Africa (NWA) 032 is considered to be the youngest radiometrically-dated mare basalt, with concordant Rb-Sr and Sm-Nd ages of 2.947 ± 0.016 Ga and 2.931 ± 0.092, respectively [1]. These ages are ~175 Ma older than those from 40Ar39Ar (2.779 ± 0.014 Ga) [2]. NWA 032 contains a high modal abundance of pyroxene (50.7 vol%), plagioclase (29.4 vol%), and olivine (11.3 vol%) [3]. The texture is that of an unbrecciated olivine-pyroxene phyric basalt. Olivine phenocrysts are zoned with Mg rich cores (Fo34-50) and thin, discontinuous Fe-rich rims (Fo30). Fine grained (≤ 1μm) elongated, tapered plagioclase crystals (An80-90) are present within the groundmass, interspersed with pyroxene (En1-25Wo15-25) of similar shape and size. These two minerals occur in a plumose texture, radiating from a common nucleation point. Pyroxene may be categorized based on grain size as either groundmass (<1 μm), intermediate crystals (~50 μm) or larger phenocrysts (~100 μm) [3]. The mineralogy of NWA 032 makes it ideal for the study and classification of shock features based on the updated shock classification scheme [4], which relies on petrographic observations of deformation and transformation in olivine, pyroxene and plagioclase – the three most abundant minerals in NWA 032. A previous description of shock effects in NWA 032 allowed for a shock pressure estimate of ~40-60 GPa [3]; however, the shock state of plagioclase feldspar (shock-amorphized vs crystalline) was inconclusive, owing to the fine grain size of this mineral (≤1μm). The purpose of our study is to characterize the shock deformation and transformation effects in NWA 032 using a combination of field emission scanning electron microscopy (FESEM) and Raman spectroscopy, focusing on the shock state of feldspar, as well as characterizing the crystallization products of shock melting. The latter have been demonstrated as useful criteria to evaluate shock conditions [5]. Our results more tightly constrain the shock history experienced by NWA 032.