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Computational Cancer Mechanics

zishun liu's picture

Since Dec. 2006, Institute of High Performance Computing (IHPC) has set up a biophysics research team that comprises research scientists in the fields of biophysics, solid mechanics and fluid mechanics, and has kicked off the "Computational Cancer Mechanics" project. The key of the project is to use computational modeling to answer fundamental research questions pertaining to the mechanics of cancer. The research team will focus on three sub-projects: mechanotransduction, metastasis, and tumorigenesis.


Zhigang Suo's picture

Zishun: Very interesting. Would you be willing to point out any specific references on the subject?

zishun liu's picture

Dear Zhigang, Thanks.

In this project we will investigate the topics of mechanotransduction, metastasis, tumorigenesis by computational mechanics techniques. From mechanics point of view, we will focus on: Dynamics of integrins receptors under stress, the objective is to study the dynamics and conformational changes of integrin receptors under force and their interaction with lipid bilayer membrane using molecular dynamics (MD) simulations; Clustering of focal adhesion on lipid membrane, the objective is to investigate the interaction of lipid membrane and integrins and to develop the simulation model through MD Coarse-Grained (CG) modeling for determining mechanical processes and behavior of biomolecular systems (cell); Deformation of cells during extravastation.

Unfortunately, we have not published papers in this project.

Henry Tan's picture

Dear Zishun,

What is the interaction law of integrin-collagen and integrin-gelatin, used in your molecular dynamics simulations?


zishun liu's picture

Dear Henry,
In our MD simulation, the molecules are represented by detailed atom structures linked by different covalent bonds, such as hydrogen bond. The interaction between atoms are represented by van der Waals potential function, such as L-J potential.

Henry Tan's picture


How many atoms, and how many Molecular Dynamics steps, are needed to simulate a typically cancer related process, such as mechanotransduction, metastasis, and tumorigenesis?

zishun liu's picture

Dear Henry,
In our model, one computational cell (or element) of lipid bilayer, e.g. DPPC, includes a few hundreds DPPC molecules and a few thousand TIP4 water molecules. Total number of atoms in one computational cell is about few hundred thousand. The time step is about 1~2 fs.

Henry Tan's picture

I parallel computing needed for these large scale simulations?

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