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.
Any references on the mechanics of cancer?
Zishun: Very interesting. Would you be willing to point out any specific references on the subject?
In reply to Any references on the mechanics of cancer? by Zhigang Suo
Dear Zhigang, Thanks.
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.
interaction law
Dear Zishun,
What is the interaction law of integrin-collagen and integrin-gelatin, used in your molecular dynamics simulations?
Thanks.
In reply to interaction law by Henry Tan
Re: interaction law
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.
How many atoms and Molecular Dynamics steps are needed?
Zishun,
How many atoms, and how many Molecular Dynamics steps, are needed to simulate a typically cancer related process, such as mechanotransduction, metastasis, and tumorigenesis?
In reply to How many atoms and Molecular Dynamics steps are needed? by Henry Tan
reply your question
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.
Zishun
In reply to reply your question by zishun liu
parallel computing
I parallel computing needed for these large scale simulations?