Simulation of Stem Cell Differentiation in Nanopattern Based on Focal Adhesion
Achmad Zacky Fairuza(a*), Sparisoma Viridi(a,b), Suprijadi(a,b)

a) Master program of Nanotechnology, Graduate School, Institut Teknologi Bandung, Bandung 40132, Indonesia
*email: fairuza.zacky1[at]gmail.com

b) Physics department, Faculty of Mathematics and Natural Science, Institut Teknologi Bandung, Bandung 40132, Indonesia

Abstract

One of the aims of stem cell research is to control the direction of differentiation. It has been reported that variating nano-topography or nanopattern at the site of cell attachment can control the fate of stem cell differentiation. The mechanism behind this phenomenon is predicted to occur due to focal adhesion which is a condition when integrin proteins on the cell surface bind to ligands on the substrate or to other cell integrin. To help understanding the effect of nanopattern on stem cells through focal adhesion, in this study, the authors created a 2D system to simulate cell differentiation in nanopatterns. One of the characteristics that can be seen in the differentiation process is the shape and area of the cell spreading which affects the cytoskeleton formation which is related to stem cell differentiation fate. Thus, the purpose of this simulation program is to observe the effect of nanopatterns on stem cell shape over time. The program exploits the dynamics of free-moving integrin receptors and static ligands that act as nanopatterns. These integrins will move to nearest ligands or to other unbound cell integrins using the principles of molecular dynamics and agent-based models. If the integrin and the target object are close enough, an integrin-ligand or integrin-integrin complex is formed. As a result of this dynamic, the shape of the cell will be deformed so that the cell spreading is seen in a certain time interval. The program used 160 integrins for each cell. While the distance between the ligands compared to their size \(\left(\frac{d}{r_{lig}}\right) \) varied in the range of 6 to 16 as reported in previous studies. The results of the simulation system are compared with the experimental results to see qualitative similarities. In this research, tests were carried out to determine the effect of parameters in stem cell simulations on nanopatterns. Furthermore, by using parameters that have been obtained from previously reported research, variations of the distance of the nanopattern and the shape of the nanopattern are carried out to observe the spreading area of cell and its effect on interactions between cells. The results obtained show good agreement with the experimental result. The density of integrins in cells is also used as a model to describe the strength of the cytoskeleton formed.

Keywords: cell differentiation, focal adhesion, modeling, molecular dynamic, stem cell, simulation.

Topic: Modelling and Computational Physics