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Tamara Carla Bidone
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Tamara Carla Bidone

Assistant Professor of Bioengineering
Assistant Professor
Biomedical Engineering, Polytechnic University of Turin, Italy, BS (2005), MS (2008) and PhD (2013)
Massachusetts Institute of Technology, Visiting student (2011-2012)
Lehigh University, Postdoc (2013-2015)
University of Chicago, Postdoc (2016-2018)

Research

Computational Models and Simulations of Biological Systems


Current Research

Computational methods have permeated the field of biology in the last decades. With the increase of computer power and simulation techniques, computational biology now reveals entirely novel concepts of cell dynamics and functions that cannot be extracted by traditional cell biology methods. For example, models of the cell cytoskeleton, which provides cells with shape and resistance to deformation, can now explain the origin of the viscoelastic properties of cells. Similarly, computational simulations of the formation of a contractile ring for cell division provide a framework to understand how disorder-to-order cell dynamics occur during cytokinesis, when cytoskeleton proteins reorganize from a random architecture into an organized bundle.

My current research is in the field of cellular and molecular biomechanics. I develop computational methods in order to understand how emergent properties of cells arise by transient interactions between subcellular components. I have experience in computational biomechanics, biophysics and computational chemistry. I currently develop numerical models of transmembrane receptors for cell mechanosensing, actomyosin contractility and stress transmission.

Our lab at the SCI institute and the Department of Bioengineering will start in January 2019. It will provide a highly interdisciplinary environment, where principles from applied mathematics, statistics, biophysics, computer science and visualization will be used in order to probe the dynamic interactions between cellular structures and components in a quantitative manner, with the ability to make experimentally testable predictions. We will work in collaboration with experimental groups at the University of Utah and other institutions.

Based upon the need for understanding biological mechanisms in both cell physiology and pathology, our lab will have four synergistic focus groups:
- computational models of adhesions in wound healing and cancer cells
- molecular and coarse-grained simulations of actin filaments and bundles
- mesoscale models of virus and drug encapsulation within the cell cytoskeleton
- 3D models of carcinoma cell migration in fibrous matrices


Selected Publications

Oakes PW, Bidone TC, Beckham Y, Skeeters AV, Ramirez-San Juan GR, Winter SP, Voth GA, Gardel ML, Lamellipodium is a myosin-independent mechanosensor. Proc Natl Acad Sci U S A 2018 Mar 13;115(11):2646-2651

Bidone TC, Jung W, Maruri D, Borau C, Kamm RD, Kim T, Morphological Transformation and Force Generation of Active Cytoskeletal Networks. PLoS Comput Biol 2017 Jan;13(1):e1005277

Zhang D, Bidone TC, Vavylonis D, ER-PM Contacts Define Actomyosin Kinetics for Proper Contractile Ring Assembly. Curr Biol 2016 Mar 7;26(5):647-53

Bidone TC, Kim T, Deriu MA, Morbiducci U, Kamm RD, Multiscale impact of nucleotides and cations on the conformational equilibrium, elasticity and rheology of actin filaments and crosslinked networks. Biomech Model Mechanobiol 2015 Oct;14(5):1143-55

Tang H, Bidone TC, Vavylonis D, Computational model of polarized actin cables and cytokinetic actin ring formation in budding yeast. Cytoskeleton (Hoboken) 2015 Oct;72(10):517-33

Bidone TC, Tang H, Vavylonis D, Dynamic network morphology and tension buildup in a 3D model of cytokinetic ring assembly. Biophys J 2014 Dec 2;107(11):2618-28

Deriu MA, Shkurti A, Paciello G, Bidone TC, Morbiducci U, Ficarra E, Audenino A, Acquaviva A, Multiscale modeling of cellular actin filaments: from atomistic molecular to coarse-grained dynamics. Proteins 2012 Jun;80(6):1598-609

Borau C, Kim T, Bidone T, García-Aznar JM, Kamm RD, Dynamic mechanisms of cell rigidity sensing: insights from a computational model of actomyosin networks. PLoS One 2012;7(11):e49174

Deriu MA, Bidone TC, Mastrangelo F, Di Benedetto G, Soncini M, Montevecchi FM, Morbiducci U, Biomechanics of actin filaments: a computational multi-level study. J Biomech 2011 Feb 24;44(4):630-6

Bidone TC, Tang H, Vavylonis D, INSIGHTS INTO THE MECHANICS OF CYTOKINETIC RING ASSEMBLY USING 3D MODELING. Int Mech Eng Congress Expo 2014;9: