17th SEACOMP 2019 and 3rd PIT-FMB 2019, 8-10 August 2019, Badung, Indonesia

1. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 1
Simulation of Blood Cell Separation
System Based on Inertia and Elasticity
using Molecular Dynamics Method
(a simulation design)
S. Viridi1
, F. Haryanto1
, Isa Anshori2
1
Department of Physics, Institut Teknologi Bandung, Bandung 40132 Indonesia
2
Department of Biomedical Engineering, Institut Teknologi Bandung, Bandung 40132
Indonesia
v201890809_3

2. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 2
Outline
• Introduction
• Previous works
• Molecular dynamics
• Proposed simulation design
• Summaries

3. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 3
Introduction

4. Blood seperation: MOFF & DEP
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 4
H.-S. Moon, K. Kwon, S.-I. Kim, H. Han, J. Sohn, S. Lee, H.-I. Jung Lab. Chip 11 1118-1125 (2011), url
https://doi.org/10.1039/C0LC00345J
CTCs (circulating tumor cells), multi-orifice flow fractination, dielectroporesis
Human breast cancer cells

5. Blood seperation: PFF
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 5
M. Pødenphant, N. Ashley, K. Koprowska, K. U. Mir, M. Zalkovskij, B. Bilenberg, W. Bodmer, A. Kristensen, R. Marie,
Lab. Chip 15 4598-4606 (2015), url https://doi.org/10.1039/C5LC01014D
Pinched flow fractination
Critical
diameter

6. Blood seperation: μChannel (PDMS)
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 6
J. K. S. Tan, S.-Y. Park, H. L. Leo, S. Kim, IEEE Trans. Biomed. Circuits Syst. 11 1431-1437 (2017), url
https://doi.org/10.1109/TBCAS.2017.2748232
Polydimethylsiloxane
WBC, RBC

7. WBC capture and release: 2LHPM
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 7
Javier Alejandro Hernández-Castro, Kebin Li, Jamal Daoud, David Juncker, Teodor Veres, "Two-level submicron high
porosity membranes (2LHPM) for the capture and release of white blood cells (WBCs)", Lab. Chip. 19 589-597 (2019),
url https://doi.org/10.1039/C8LC01256C
Two-level submicron high porosity membranes

8. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 8
Previous works

9. Clogging: Initial model
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 9
L. Haris, S. Viridi, S. N. Khotimah, "Formulasi Interaksi antara Eritrosit dan Trombosit dalam Peristiwa Penyumbatan
Pembuluh Kapiler pada Kasus Malaria Serebral Menggunakan Metoda Dinamika Molekular", Prosiding Simposium
Nasional Inovasi Pembelajaran dan Sains 2012 (SNIPS 2012), Eds. F. D. E. Latief et al., Bandung, Indonesia, 7-8 Juni
2012, pp. 88-91.

10. Clogging: All spheres
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 10
L. Haris, S. Viridi, S. N. Khotimah, F. Haryanto, "Two-Dimensional Coulomb Model of Capillary Vessel in the Case of
Cerebral Malaria using Molecular Dynamics", Proceedings of the 12th Asia-Oceania Congress of Medical Physics
(AOCMP) and the 10th South-East Asian Congress of Medical Physics (SEACOMP), Eds. A. Krisanachinda et al.,
Chiang Mai, Thailand, 11-14 December 2012, pp. 170-172.

11. Clogging: Orientation
17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 11
L. Haris, S. N. Khotimah, F. Haryanto, S. Viridi, "Physics Modeling for Medical Purposes: Molecular Dynamics
Simulation on Malaria-Infected Blood Flow in 2-D Channel", Prosiding Simposium Nasional Inovasi dan Pembelajaran
Sains 2013 (SNIPS 2013), Eds. A. Purqon et al., Bandung, Indonesia, 3-4 Juli 2013, pp. 142-145.

12. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 12
L. Haris, S. N. Khotimah, F. Haryanto, S. Viridi, "Molecular Dynamics Simulation of Soft Grains: Malaria-Infected Red
Blood Cells Motion within Obstructed 2-D Capillary Vessel", in Symposium on Biomathematics-2013, edited by H.
Arimura et al., AIP Conference Proceedings 1587, American Institute of Physics, Melville, NY, 2014, pp. 43-46., urll
https://dx.doi.org/10.1063/1.4866530
Clogging: Position, orientation, charge

13. Single RBC
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 13
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.
Variation of
spring initial
length ≠
stable
structure

14. Collision of two RBCs
17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 14
Sparisoma Viridi and Ismi Yasifa, "Simulation of two red blood cells (RBC) collision based on granular model: case of
one-dimensional collision", Journal of Physics: Conference Series 1248 (1), 012083 (2019),url
https://doi.org/10.1088/1742-6596/1248/1/012083

15. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 15
Molecular dynamics

16. • Normal force: Collision between (sperical) cell
where ξij is overlab between two spheres
Considered forces
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 16
.
ijijNijijNij rrkN 
ξγξ −=
( )ijjiij rRR −+= ,0minξ

17. • Drag force: Motion of cells due to fluid flow
Considered forces (cont.)
17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 17
.
( )ififi vvRD

−−= πη6
iv

fv


18. • Sum of forces at time t
• Acceleration at time t
Newton’s second law of motion
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 18
.
( )∑∑ =
−+=
N
j
ijijNDF i
1
1 δ

∑= F
m
a
i
 1

19. Euler algorithm
• Velocity at time t + Δt
• Position at time t + Δt
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 19
( ) ( ) tatvttv ∆+=∆+

( ) ( ) tvtrttr ∆+=∆+


20. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 20
Proposed simulation
design

21. • It alows the use of previous formulation of
normal force
Channel wall builts from spheres
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 21
` `
` `
`
.

22. A (minor) problem
• Proposed approach requires flow velocity
profile, which is only known mathematically
for fully developed flow between two parallel
plates or in a cylindrical channel
which known as Poiseuille flow
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8-10 August 2019, Badung, Indonesia 22
url http://brennen.caltech.edu/fluidbook/basicfluiddynamics/Navierstokesexactsolutions/poiseuilleflow.pdf [20190809]
( ) ( )22
4
1
rR
dz
dp
ruz −





−=
η

23. Fluid flow velocity profile
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 23
url https://www.engineersedge.com/fluid_flow/flow_velocity_profiles.htm [20190809]

24. Developing velocity profile
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3rd PIT-FMB 2019
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url https://www.theseus.fi/bitstream/handle/10024/106991/Acharya_Saroj.pdf?sequence=1&isAllowed=y [20190809]

25. Fluid flow velocity profile of a junction
• There is no analytical solution, it seems com-
plicated: phase φ, junction angle α, radius ρ
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 25
X. Li, S. Wang, "Flow field and pressure loss analysis of junction and its structure optimization of aircraft hydraulic pipe
system", Chinese Journal of Aeronautics[], vol. 26, no. 4, pp. 1080–1092, Aug 2013 url
https://doi.org/10.1016/j.cja.2013.04.004

26. Suggestion
• Is there any suggested solution?
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3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 26

27. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 27
Summaries

28. Summaries
• Simulation design for blood cell separation
based on inertial and elasticity using mole-
cular dynamics method implementing Euler
algorithm in JavaScript has been proposed
• Experiment confirmation is required for
tuning the system and also for the fluid flow v
profile
• Source is avalable at
https://github.com/dudung/butiran.js17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 28

29. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 29
https://osf.io/tg79j/

30. 17th SEACOMP 2019
3rd PIT-FMB 2019
8-10 August 2019, Badung, Indonesia 30
Thank you