Figure 1 : Actin in the endocytosis process simulated with cytosim. The actin filaments are depicted in red (yellow for the growing ends), Arp2/3 (an actin nucleator) in green, the membrane in blue, and the crosslinkers in transparent red.
The cytoskeleton is an ensemble of semi-rigid filaments and their associated effectors. The most famous examples are the actin and microtubule cytoskeleton, that play a dominant role in cell mechanics and intra-cellular transport. In the cellular architecture group in EMBL, we are developing a state-of-the-art simulations of the cytoskeleton : Cytosim.
The core of the simulation is the mechanics of the cytoskeletal fibers, i.e. microtubules and actin fibers. They are modeled as elastic incompressible fibers. These fibers can interact with one another, either by direct contact (i.e. steric interactions), or by the means of motors and crosslinkers. The fibers can interact mechanically with other elements : surfaces (e.g. the cell membrane), objects in the cells (e.g. chromatin beads), etc.
We also take into account fiber dynamics : growth, shrinkage, treadmilling, dynamic instabilities… Moreover, many biochemical factors can be inserted : nucleation factors, polymerization/depolymerization agents. All these can also be submitted to chemical reactions, e.g. activation/deactivation, adsorbtion…
While the possibilities offered by Cytosim are extremely large, the learning curve is gentle, as no programming knowledge is required : a system can be described by a configuration file that will be read by the simulation, and many configuration examples are provided. Moreover, Cytosim comes with a rich built-in graphical interface. I even used Cytosim to make music video, as part of the EMBL lab day contest.
For a more scientific application, it allowed me to understand the size scaling of (non mamalian) red blood cells, and the shape changes in platelets : see this article.
The program is available on http://www.cytosim.org.