The document describes a proposed simulation system to model stem cell deposition on nanopatterned surfaces using molecular dynamics and agent-based modeling methods. It first reviews previous works on simulating stem cell differentiation and proliferation influenced by extracellular matrix properties. The proposed simulation system would represent stem cells as layers of cells that can deposit on configurable nanopatterned substrates, including nanopillars and nanopits. The document acknowledges that further development is still needed, as an initial configuration of the simulation system has been established.

1. 2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 1
Molecular Dynamics (MD) Method and
Agent-Based Model (AMB) in Simulation
of Stem Cell Deposition on the Surface
with Nanopattern: Simulator Design
S. Viridi*, Suprijadi, A. Barlian, D. R. Adhika
Institut Teknologi Bandung, Jalan Ganesha 10, Bandung 40132, Indonesia
Pusat Penelitian Nanosans dan Nanoteknologi, Bandung 40132, Indonesia
*dudung@fi.itb.ac.id

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Jakarta, Indonesia
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Outline
• Stem cell
• Previous works
• Simulation system (a design)
• Summaries

3. Hematopoietic stem cell differentiation
2020-06-20
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Stemcell
"Stem Cell Basics for Life Science Researchers", Bio-Rad Labs Inc., Brochure, Rev A, Aug 2010

4. Differentiation of ES and iPS cells
2020-06-20
Jakarta, Indonesia
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Stemcell
"Stem Cell Basics for Life Science Researchers", Bio-Rad Labs Inc., Brochure, Rev A, Aug 2010

5. To mimic extracellular tissues matrix
2020-06-20
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Sander Dobbenga, Lidy E. Fratila-Apachitei, Amir A. Zadpoor, "Nanopattern-induced osteogenic
differentiation of stem cells – A systematic review", Acta Biomaterialia 46 () 3-14 (2016).
Stemcell

6. .. extracellular tissues matrix (cont.)
2020-06-20
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Sander Dobbenga, Lidy E. Fratila-Apachitei, Amir A. Zadpoor, "Nanopattern-induced osteogenic
differentiation of stem cells – A systematic review", Acta Biomaterialia 46 () 3-14 (2016).
Stemcell disordered, nm

7. Experiment with nanopillars
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Stemcell
Hayriye Özçelik, Celestino Padeste, Vasif Hasirci, "Systematically organized nanopillar arrays reveal
differences in adhesion and alignment properties of BMSC and Saos-2 cells", Colloids and Surfaces B:
Biointerfaces 119, 71-81, Jul 2014.

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Stemcell

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Stemcell
Hilary J. Anderson, Jugal Kishore Sahoo, Rein V. Ulijn, Matthew J. Dalby, "Mesenchymal Stem Cell
Fate: Applying Biomaterials for Control of Stem Cell Behavior", Frontiers in Bioengineering and
Biotechnology 4 () 38, May 2016.

10. Effect of matrix stiffness
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Jakarta, Indonesia
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Stemcell
Kai Ye, Xuan Wang, Luping Cao, Shiyu Li, Zhenhua Li, Lin Yu, Jiandong Ding, "Matrix Stiffness and
Nanoscale Spatial Organization of Cell-Adhesive Ligands Direct Stem Cell Fate", Nano Letters 15 (7)
4720-4729, Jun 2015.

11. Due to cell communication?
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Jakarta, Indonesia
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Stemcell
Kai Ye, Xuan Wang, Luping Cao, Shiyu Li, Zhenhua Li, Lin Yu, Jiandong Ding, "Matrix Stiffness and
Nanoscale Spatial Organization of Cell-Adhesive Ligands Direct Stem Cell Fate", Nano Letters 15 (7)
4720-4729, Jun 2015.

12. Deposition simulation
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S. Viridi, Suprijadi, V. Suendo, "Simulasi Deposisi Berdasarkan Penumbuhan ButiranMenggunakan
Dinamika Molekular", Research and Development on Nanotechnology in Indonesia 2 (2), 68-79
(2015).
Previousworks
• Very sticky
contact grains

13. Yeast cell proliferation
2020-06-20
Jakarta, Indonesia
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D Aprianti, S. N. Khotimah, S. Viridi, "Budding Yeast Colony Growth Study Based on
Circular Granular Cell", Journal of Physics: Conference Series 739 (1), 012026 (2016).
reported observation simulation
Previousworks

14. Grid-based channel system
2020-06-20
Jakarta, Indonesia
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S. Viridi, F. D. E. Latief, S. N. Khotimah, "Construction of Maximum Tortuosity of Single Fluid Path in
Grid-based 2-d System (5×20) and 3-d system (5×20×3) for Certain Value of Porosity", Journal of
Physics: Conference Series 877 (1), 012044 (2017).
Previousworks

15. Red blood cell model #1
• Grains and springs
(linear + bending)
2020-06-20
Jakarta, Indonesia
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Ismi Yasifa, Sparisoma Viridi, "Pemodelan Dua Dimensi Deformabilitas Sel Darah Merah berbasis
Granular", Prosiding Simposium Nasional Inovasi dan Pembelajaran Sains 2018 (SNIPS 2018), Eds.
G. Hikmawan et al., Bandung, Indonesia, 9-10 Juli 2018, pp. 86-91.
Previousworks

16. Red blood cell model #2
2020-06-20
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Ismi Yasifa, Sparisoma Viridi, "The spring variation in two-dimensional modeling of red blood cell
deformability based granular", Spektra: Jurnal Fisika dan Aplikasinya 4 (2), 51-60 (2019).
Previousworks

17. Microfluidic device
2020-06-20
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Sparisoma Viridi, Freddy Haryanto, Isa Anshori and Mohammad Haekal, "Simulation of single particle
flowing in a microfluidic device using molecular dynamics method", Journal of Physics: Conference
Series 1505 (1) 012062, Jun 2020.
Previousworks
former design simulation results

18. Simulation system
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Simulation

19. Cell layers
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Simulation

20. Cell separation distance
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Simulation

21. Substrat configuration
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Simulation

22. Substrat configuration (cont.)
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Simulation

23. Nanopillars
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Simulation

24. Nanopits
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Simulation

25. Summaries
• Simulation system for initial configuration has
been built
• Further development must be conducted
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Thank you