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Vivi Andasari, PhD

Position
(Former) Postdoctoral Associate in Zaman lab (BU) and Kamm lab (MIT)

Email
andasariatbu.edu


Research Interests
My research interests lie in the area of mathematical modeling and computational simulation studies of cellular processes focusing on cell migration, which is a complex yet highly organized cellular activity that drives many physiological and pathological conditions in the human body. Depending on the viewpoint of cellular phenomena being investigated, I have used continuum approaches for modeling at the tissue/macroscopic level and individual cell (agent)-based approaches for multiscale modeling combining cellular models and intracellular dynamics. I am also interested in integrating molecular and intracellular scale models using meshless or particle-based methods into cellular scale methods of free and moving boundaries.

Skills
Python for high performance computing and visualization applied in numerical methods for ODEs, computational Galerkin methods, particle-based methods, and individual cell (agent)-based models (particularly the Cellular Potts Model). Visit my teaching page, for more information on these methods and how to implement them in Python.

Research Experience
  • Postdoctoral Fellow with Dr Xiaobo Zhou, from July 2013 to February 2014 in the Department of Radiology, Wake Forest School of Medicine in Winston-Salem, North Carolina, USA
  • Postdoctoral Research Assistant with Prof Mark Chaplain, FRSE, from July 2011 to December 2012 in the Division of Mathematics, University of Dundee, Dundee, Scotland, UK
  • Research Assistant Trainee in Mathematics for Industry, at Eindhoven University of Technology, Eindhoven, the Netherlands


Publications
  1. V. Andasari, D. Lü, M. Swat, S. Feng, F. Spill, L. Chen, X. Luo, M.H. Zaman, M. Long (2018) Computational model of wound healing: EGF secreted by fibroblasts promotes delayed re-epithelialization of epithelial keratinocytes, Integrative Biology, PMID: 30206629, doi: 10.1039/c8ib00048d
  2. F. Spill, V. Andasari, M. Mak, R. Kamm, M.H. Zaman (2016) Effects of 3D Geometries on Cellular Gradient Sensing and Polarization, Physical Biology, 13(3):036008, PMID: 27345945, doi: 10.1088/1478-3975/13/3/036008
  3. V. Andasari, F. Spill, R. Ouifki, M.H. Zaman. Modeling temporal dynamic of nascent adhesions. in revision
  4. V. Andasari, A. Gerisch, A.P. South, M.A.J. Chaplain, Mathematical modelling of cancer cell invasion of tissue: the development of an in silico organotypic assay, in revision.
  5. L. Tang, A. L. van de Ven, D. Guo, V. Andasari, V. Cristini, K. C. Li, X. Zhou (2014) Computational Modeling of 3D Tumor Growth and Angiogenesis for Chemotherapy Evaluation, PLoS ONE, 9(1):e83962, PMID: 24404145, doi: 10.1371/journal.pone.0083962, [pdf]
  6. V. Andasari, R.T. Roper, M.H. Swat, M.A.J. Chaplain (2012) Integrating intracellular dynamics using CompuCell3D and Bionetsolver: applications to multiscale modelling of cancer cell growth and invasion, PLoS ONE, 7(3):e33726, PMID: 22461894, doi: 10.1371/journal.pone.0033726, [pdf]
  7. V. Andasari and M.A.J. Chaplain (2012) Intracellular modelling of cell-matrix adhesion during cancer cell invasion, Mathematical Modelling of Natural Phenomena, 7(1):29-48, doi: 10.1051/mmnp/20127103
  8. V. Andasari, A. Gerisch, G. Lolas, A.P. South, M.A.J. Chaplain (2011) Mathematical modelling of cancer cell invasion of tissue: biological insight from mathematical analysis and computational simulation, Journal of Mathematical Biology, 63(1):141-171, PMID: 20872264, doi: 10.1007/s00285-010-0369-1
  9. A.C.T. Aarts, V. Andasari, S.J.L.v. Eijndhoven (2009) Vallende polymeerdraden vormen Lissajouspatronen (Liquid Rope Lissajous Patterns), Nieuw Archief voor Wiskunde, 5/10, nr. 3, [pdf], English version [pdf].


Theses


Teachings
BE 503/703 - Computational Methods in Biomedical Engineering (Fall 2014)
BE 503/703 - Numerical Methods and Modeling in Biomedical Engineering (Fall 2015)
Numerical Methods using Python
Stochastic Modeling using Python


Other Publications


Contributed Talks
  1. Modelling Cancer Cell Invasion of Tissue: The Roles of Cell Adhesion (October 2012). Presented at the Modeling of Multicellular Development and Cancer: European CompuCell3D/SBW Hands-on Workshop, organized by Lorentz Center at Leiden University, Leiden, the Netherlands, 8 - 13 October 2012.
  2. Integrating Intracellular Dynamics using CompuCell3D and Bionetsolver with an Application to Multiscale Modelling of Cancer Invasion (21 June 2011). Presented at the Casablanca International Workshop on Mathematical Biology: Control and Analysis, the Hassan II University Mohammedia, Casablanca, Morocco, 20 - 24 June 2011 (check out my report about the conference on the SMB Newsletter vol. 25, issue 1, Jan 2012.
  3. Modelling Cancer Cell Invasion of Tissue: The Roles of Cell Adhesion (3 March 2011). Presented at the Numerical Analysis Group seminar, Fachbereich Mathematik, Technische Universität Darmstadt, Darmstadt, Germany.
  4. Mathematical Modelling of Cancer Cell Invasion of Tissue: Cell Adhesion in the uPA System, (6 April 2010). Presented at the 2010 BMC/BAMC Joint Meeting at the University of Edinburgh, Edinburgh, UK, 6 - 9 April 2010.
  5. Mathematical Modelling of Cancer Cell Invasion: The Roles of Cell Adhesion (18 August 2009). Presented at the CompuCell3D 3rd AnnualWorkshop: Developing Multi-Cell Developmental and Biomedical Simulations with CompuCell3D at the Biocomplexity Institute, Indiana University, Bloomington Indiana, USA, 17 - 21 August 2009.
  6. Mathematical Modelling of the Cell-Matrix Adhesion Pathway for Cancer Cell Invasion of Tissue (27 July 2009). Presented at the International Conference on Mathematical Biology and Annual Meeting of The Society for Mathematical Biology (SMB) at the University of British Columbia, Vancouver, Canada, 27 - 30 July 2009.
  7. Modelling Cancer Cell Invasion of Tissue: Non-local Effects in the uPA System (28 October 2008). Presented at the Centenary Symposium on Mathematical and Statistical Modelling in Medicine and Health Science at Queen's University Belfast, Belfast, Northern Ireland, UK, 28 October 2008.
  8. Mathematical Modelling of Cancer Cell Invasion of Tissue (23 September 2008). Presented at the Numerical Mathematics Research Group seminar, Institut Für Mathematik, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Halle an der Saale, Germany.
  9. Mathematical Modelling of Cancer Cell Invasion of Tissue (22 May 2008). Presented at a student research seminar at the IGTC Summer School in Mathematical Biology organized by PIMS (the Pacific Institute for Mathematical Sciences) Department of Mathematics, University of British Columbia, Vancouver, Canada, 11 May - 11 June 2008.


Poster Presentations
  1. EGF Secreted by Fibroblasts Promote the Biphasic Feature of Asymmetric Keratinocyte Migration in Wound Healing, presented at the Postdoc Annual Retreat at Boston University, 5 - 6 April 2016.
  2. A Compartmental Model for Temporal Dynamics of Cell-Matrix Adhesion, presented at the Cellular Dynamics and Models Meeting 2015 at Cold Spring Harbor Laboratory, 3 - 6 March 2015.
  3. Multiscale Aspects of Cell-cell and Cell-matrix Adhesion for Cancer Cell Invasion, presented at the CMMB Conference 2012 on Multiscale Modelling in Medicine and Biology at the University of Nottingham, UK, 3 - 5 September 2012. The poster has won the 1st prize of the conference's poster competition.
  4. Mathematical Modelling of Cancer Invasion of Tissue: The Roles of Cell Adhesion, presented at the London Mathematical Society Durham Symposium: Numerical Analysis of Multiscale Problems at the University of Durham, Durham, UK, 5 - 15 July 2010.
  5. Modelling Cancer Cell Invasion: The Roles of Cell-cell & Cell-matrix Adhesion, presented at the Workshop on Cancer Development, Angiogenesis, Progression, and Invasion at the Mathematical Biosciences Institute (MBI), Ohio State University, Columbus Ohio, USA, 26 - 30 January 2009.
  6. Modelling cancer cell invasion of tissue: Non-local effects in the uPA system, presented at the ECMTB08 at the University of Edinburgh, Edinburgh, Scotland, UK, 29 June - 4 July 2008.


Grants, Awards & Prizes


Last modified:  5th April 2016