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UConn Health Richard D. Berlin
Center for Cell Analysis & Modeling

People

Masoud Nickaeen

I am a Postdoctoral fellow at Center for Cell Analysis and Modeling (CCAM) at the University of Connecticut Health Center. I joined Prof. Leslie Loew and Dr. Boris Slepchenko labs in October 2014. Currently, I’m developing algorithms for modeling cells with dynamic membranes, in particular migrating cells. This involves implementing tools for modeling interdependence of cell biochemistry and kinematics, the implementation of robust front tracking algorithms (kinematics) combined with the development of conservative algorithms for solving reaction-diffusion-advection systems on domains with moving boundaries. This research was motivated by the need to develop a capability of modeling cell migration within the Virtual Cell (VCell), a computational framework for simulating cellular phenomena in realistic geometries.
Additionally, I study, through continuum mechanics modeling, the dendritic actin filament networks that are formed during endocytosis in fission yeast to understand the role of mechanical forces generated by actin polymerization, turgor pressure and membrane tension in the membrane tube formation.

Education
  • PhD, Mathematics, Applied mathematics, 2010 – 2014
  • Dortmund University of Technology, Dortmund, Germany
  • Thesis: “Efficient FEM and Multigrid Solvers for the Least-squares Method with Application to Non-Newtonian Fluid Flows”, under the supervision of
    Prof. Dr. Stefan Turek
  • MEng, Mechanical Engineering, Fluid Mechanics, 2013 – 2014
  • Rutgers, The State University of New Jersey, Piscataway, NJ, USA
  • Project: “Relaxation of Deformed Vesicles: A Small Deformation Analysis”, under the supervision of Dr. Hao Lin
  • M.Sc., Mechanical Engineering, Energy Conversion, 2007 - 2010
  • K.N. Toosi University of Technology, Tehran, Iran
  • Thesis: “Design of a characteristic–based split finite volume algorithm”, under the supervision of Dr. Ali Ashrafizadeh
  • B.Sc., Mechanical Engineering, Thermo-fluids, 2003 - 2007
  • Persian Gulf University, Bushehr, Iran
  • Thesis: “Numerical analysis of convective-radiative annular fins using FDM”, under the supervision of Dr. Parviz Malekzadeh
Research Interest
  • Computational cell biology
  • Biochemistry and biomechanics of cell motility
  • Computational fluid dynamics and heat transfer
  • Finite element, finite volume and differential quadrature methods
  • Domain decomposition, multilevel and multigrid methods
Publications
Journal Papers
  1. M. Nickaeen, Boris M. Slepchenko, Coupling Cell Biochemistry and Kinematics: Applications to Cell Migration, under preparation, 2015
  2. M. Nickaeen, A. Ouazzi, S. Turek, Monolithic Least-Squares Finite Element Simulation Techniques for the Solution of non-Newtonian Fluid Flows, under preparation, 2015
  3. A. Schwarz, M. Nickaeen, S. Serdas, A. Ouazzi, J. Schroder and S. Turek, A comparative study of mixed least-squares FEMs for the incompressible Navier-Stokes equations, submitted to IJCSE, 2015
  4. Y. Demiryureka, M. Nickaeen, M. Zheng, M. Yu, J. D. Zahn, D. I. Shreiber, H. Lin, J. W. Shan, Transport, Resealing, and Re-poration Dynamics of Two-Pulse Electroporation-Mediated Molecular Delivery, BBA – Biomembranes, 1848,1706-1714, 2015
  5. M. Nickaeen, A. Ashrafizadeh, S. Turek, An Alternative Strategy for the Solution of Heat and Incompressible Fluid Flow Problems via the Finite Volume Method, Numerical Heat Transfer: Part A, 62:393-411, 2012
  6. M. Nickaeen, A. Ouazzi, S. Turek, Newton Multigrid Least-squares FEM for the V-V-P formulation of the Navier-Stokes equations, J. Comp. Phys., 256:416-427, 2014
  7. P. Malekzadeh, M.A. Moghimi, M. Nickaeen, The radiation and variable viscosity effects on electrically conducting fluid over a vertically moving plate subjected to suction and heat flux, Energy Conversion and Management, 52:2040–2047, 2011
Book Chapters
  1. A. Ouazzi, M. Nickaeen, S. Turek, M. Waseem, Newton-Multigrid Least-Squares FEM for S-V-P Formulation of the Navier-Stokes Equations, In A. Abdulle, S. Deparis, D. Kressner, F. Nobile and M. Picasso (Eds.), Numerical Mathematics and Advanced Applications - ENUMATH 2013, volume 103 of Lecture Notes in Computational Science and Engineering, 651-659, Springer, 2015
Conference Proceedings and Presentations
  1. Igor L. Novak, M. Nickaeen, Boris M. Slepchenko, Developing numerical tools for modeling motile cells in VCell, Cellular Dynamics & Models meeting, Cold Spring Harbor Laboratory, NY, March 3-6 2015
  2. A. Schwarz, J. Schröder, S. Serdas, S. Turek, A. Ouazzi, M. Nickaeen, Performance Aspects of a Mixed s-v LSFEM for the Incompressible Navier-Stokes Equations with Improved Mass Conservation, PAMM• Proc. Appl. Math. Mech. 13, 513 – 514, 2013
  3. M. Nickaeen, A. Ashrafizadeh, A Characteristic-Based Split Finite Volume Algorithm for the Solution of Incompressible Flow Problems, Proceedings of the European Conference on Computational Fluid Dynamics ECCOMAS CFD 2010 J. C. F. Pereira, A. Sequeira and J. M. C. Pereira (Eds) Lisbon, Portugal,14-17 June 2010, ISBN: 978-989-96778-1-4