SNF2020 | ABS-260 | IS-2, 20 June 2020, Jakarta, Indonesia.

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

2. 2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 2
Outline
• Stem cell
• Previous works
• Simulation system (a design)
• Summaries

3. Hematopoietic stem cell differentiation
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 3
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
SNF2020 | ABS-260 | IS-2 4
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
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 5
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
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 6
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
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 7
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.

8. 2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 8
Stemcell

9. 2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 9
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
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 10
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?
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 11
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
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 12
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
SNF2020 | ABS-260 | IS-2 13
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
SNF2020 | ABS-260 | IS-2 14
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
SNF2020 | ABS-260 | IS-2 15
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
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 16
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
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 17
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
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 18
Simulation

19. Cell layers
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 19
Simulation

20. Cell separation distance
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 20
Simulation

21. Substrat configuration
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 21
Simulation

22. Substrat configuration (cont.)
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 22
Simulation

23. Nanopillars
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 23
Simulation

24. Nanopits
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 24
Simulation

25. Summaries
• Simulation system for initial configuration has
been built
• Further development must be conducted
2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 25

26. 2020-06-20
Jakarta, Indonesia
SNF2020 | ABS-260 | IS-2 26
Thank you