Project details

Organization	Institute of High Performance Computing (IHPC), A*STAR
Mentors	Mr. Zeng Yukai & Dr. Chiam Keng Hwee
Student	Lee Yuexian Elis
Name of Project	Computational Exploration of Transport Mechanisms in Cells

A. Brief description of the project

The main objective of this computational project is to explore a few intracellular transport mechanisms and intracellular structures in order to better understand how the cell works. For example, living cells interact and adapt to the external environment through responding to mechanical stimuli and converting them into biochemical signals. Intracellular transport plays a central role in fundamental processes such as cell growth, cell motility and cell death.

More about the project

In this project, model cytoskeletons have been constructed, using the computer programme Matlab, to investigate the proposal that the interconnected filamentous structure of the cytoskeleton can act as both a mechano- and signal transducer. The model cytoskeleton is composed of rigid rods (that represent actin filaments), which are connected with springs (that represent filamin – which link the actin filaments together). The model eukaryotic cell is submitted to mechanical perturbations at its membrane. By using the computer programme C++, the efficiency of this network to transmit energy to the nuclerar wall can be calculated.

The cytoskeleton

The cytoplasm of eukaryotic cells is spatially organized by a network of protein filaments known as the cytoskeleton. This network contains three principal types of filaments – microtubules, actin filaments and intermediate filaments. Differences in the structures of the subunits and the manner of their self-assembly give the filaments different mechanical properties. Actin filaments are the thinnest of the three, and are hard but brittle.

Experimental Objectives

1. To investigate the relationship between the number of rods and the number of springs.
2. To investigate how the number of springs affects the Energy Transfer Ratio.
3. To investigate how the Energy Transfer Ratio changes with time.

B. Results

1. Relationship between the number of rods and the number of springs:



In the graph above, the x-axis represents the number of rods at each point, while the y-axis represents the number of springs at each point.
By changing the number of rods while keeping all other factors in the cytoskeleton system constant, this affected the number of springs in the system – an increase in the number of rods leads to an increase in the number of springs. Moreover, this increase occurs quadratically.

2. Relationship between time and Energy Transfer Ratio:



In the graph above, the x-axis represents the time (in seconds), while the y-axis represents the Energy Transfer Ratio (ETR) at each point of time.
The graph generated reflected that Energy ETR increases rapidly with time until it reaches its optimum point. After which, there is a sharp decrease in the ETR – indicating that energy transfer through the cytoskeleton is increasing inefficient after 0.01 seconds. At 0.02 seconds, the rate of decrease slows down.

3. Relationship between number of springs and Energy Transfer Ratio (with respect to time):



In the graph above, the x-axis represents the time (in seconds), while the y-axis represents the logarithm of the Energy Transfer Ratio (ETR) at each point of time. The rate of change of ETR of three systems (represented by each graph) with 700 rods each but a different number of springs was calculated.

From the graph, it is evident that an increase in the number of springs would generally lead to an increase in ETR. However, should there be too little springs in the system (less than 500), ETR would be zero as the percolation threshold has been reached – no energy is transferred as the cytoskeleton cannot function due to a lack of springs.

C. Reflection

Content and/or skill I learnt the most of:

1. Writing and using computer programmes C++ and Matlab - writing such programmes can be tedious, but they are useful especially since I needed them to plot models and calculate mathematical values.
2. Knowing about the existence of the cytoskeleton in all animal cells, as well as its complex structure and multiple functions.
3. Realising how various components of the cytoskeleton are inter-related and any alteration can affect the rate of energy transfer in the cell (which is the main function of the cytoskeleton).

Most interesting observation of people at work in attachment organization/ Interesting aspects of learning:

1. The scientists at my attachment are heavily reliant on computer programmes to aid them in their research tasks – from this, I realized the importance of computer programmes, its wonderful fuctions and how it is impossible (at this point of time at least) to work without them at IHPC.
2. The scientists tend to have lunch together as this provides opportunities for the research team to bond, hence strengthening team dynamics and ensuring better communication at work.

Important traits necessary to do well and enjoy work/ A life skill I took away from this attachment

Scientific research is really about taking small steps in the dark (i.e. venturing into fields of science that has yet to be discovered). Clearly, perseverance and passion are key characteristics that scientists need to possess in order to succeed. The scientists working at my attachment clearly had passion for what they were doing, hence providing them with the thirst for scientific knowledge and enabling them to persevere even if comprehensive results could not be obtained despite putting in much effort.

D. Gallary