Toward a Computational Model of Actin Filament Networks

Andrew Schumann


Actin is one of the most important proteins responsible for a reaction of cells to external stimuli (stresses). There are monomeric actin or G-actin and polimeric actin or F-actin. Monomers of G-actin are connected into double helical filaments of F-actin by the processes of nucleation, polymerization, and depolymerization. Filaments are of 7-8 nm in diameter. They are of several microns in length. Furthermore, filaments can be organized as complex networks of different forms: unstable bunches (parallel unbranched filaments), trees (branched filaments), stable bunches (cross-linked filaments). Actin filament networks can be considered a natural computational model of cells to perform different responses to different external stimuli. So, in this model we have inputs as different stresses and outputs as formations and destructions of filaments, on the one hand, and as assemblies and disassemblies of actin filament networks, on the other hand. Hence, under different external conditions we observe dynamic changes in the length of actin filaments and in the outlook of filament networks. As we see, the main difference of actin filament networks from others including neural networks is that the topology of actin filament networks changes in responses to dynamics of external stimuli. For instance, a neural network is a sorted triple (N,V,w), where N is the set of neurons/processors, V is a set of connections among neurons/processors, and w is a weight for each connection. In the case of actin filament networks we deal with a variability of filaments/processors. Some new filaments/processors can appear in one conditions and they can disappear in other conditions. The same situation when the computational substratum changes during the time of computations is faced in the so-called swarm computing, e.g. in slime mould computing. In this paper we propose a swarm computing on the medium of actin filament networks.


  1. Adamatzky, A., Erokhin, V., Grube, M., Schubert, Th., Schumann, A. 2012. Physarum Chip Project: Growing Computers From Slime Mould. International Journal of Unconventional Computing. 8(4):319-323.
  2. Balaban, N. Q., Schwarz, U. S., Riveline, D., Goichberg, P., Tzur, G., Sabanay, I., Mahalu, D., Safran, S., Bershadsky, A., Addadi, L. et al. 2001. Force and focal adhesion assembly: a close relationship studied using elastic micropatterned substrates. Nat. Cell Biol. 3:466-472.
  3. ben Avraham, D., Tirion, M. M. 1995. Dynamic and elastic properties of F-actin: a normalmodes analysis. Biophys. J. 68:1231-45.
  4. Carlier, M. F., Valentin, R. C., Combeau, C., Fievez, S., Pantoloni, D. 1994. Actin polymerization: regulation by divalent metal ion and nucleotide binding, ATP hydrolysis and binding of myosin. Adv. Exp. Med. Biol. 358:71-81.
  5. Chhabra, E. S., Higgs, H. N. 2007. The many faces of actin: matching assembly factors with cellular structures. Nature Cell Biology 9:11101121.
  6. Choi, C. K., Vicente-Manzanares, M., Zareno, J., Whitmore, L. A., Mogilner, A. and Horwitz, A. R. 2008. Actin and alpha-actinin orchestrate the assembly and maturation of nascent adhesions in a myosin II motorindependent manner. Nat. Cell Biol. 10:1039-1050.
  7. Coluccio, L. M., Tilney, L. G. 1983. Under physiological conditions actin disassembles slowly from the nonpreferred end of an actin filament. J. Cell. Biol. 97:1629- 1634.
  8. Fackler, O. T., Grosse, R. 2008. Cell motility through plasma membrane blebbing. J. Cell Biol. 181:879- 884.
  9. Furuhashi, K., Ishigami, M., Suzuki, M., Titani, K. 1998. Dry stress-induced phosphorylation of physarum actin. Biochem. Biophys. Res. Commun. 242:653-658.
  10. Furukawa, R., Kundra, R., Fechheimer, M. 1993. Formation of liquid crystals from actin filaments. Biochem. 32:12346-52.
  11. Gimona, M., Mital, R. 1998. The single CH domain of calponin is neither sufficient nor necessary for F-actin binding. J. Cell. Sci.
  12. Goldmann, W. H., Guttenberg, Z., Tang, J. X., Kroy, K., Isenberg, G., Ezzell, R. M. 1998. Analysis of the Factin binding fragments of vinculin using stoppedflow and dynamic lightscattering measurements. Eur. J. Biochem. 254:413-419.
  13. Guo, W. H., Wang, Y. L. 2007. Retrograde fluxes of focal adhesion proteins in response to cell migration and mechanical signals. Mol. Biol. Cell. 18:4519-4527.
  14. Higuchi, H., Yanagida, T., Goldman, Y. E. 1995. Compliance of thin filaments in skinned fibers of rabbit skeletal muscle. Biophys. J. 69:1000-1010.
  15. Holmes, K., Popp, D., Gebhard, W., Kabsch, W. 1990. Atomic model of the actin filament. Nature. 347:44- 49.
  16. Hotulainen, P., Lappalainen, P. 2006. Stress fibers are generated by two distinct actin assembly mechanisms in motile cells. J. Cell. Biol. 173:383-394.
  17. Hu, J., Matzavinos, A., Othmer, H. G. 2007. A theoretical approach to actin lament dynamics. Journal of Statistical Physics. 128(1/2):111138.
  18. Hu, K., Ji, L., Applegate, K. T., Danuser, G., WatermanStorer, C. M. 2007. Differential transmission of actin motion within focal adhesions. Science. 315:111-115.
  19. Iwasa, J.H., and R. D. Mullins. 2007. Spatial and temporal relationships between actin-lament nucleation, capping, and disassembly. Current Biology. 17:395406.
  20. Kas, J., H. Strey, J. X. Tang, D. Finger, R. Ezzell, E. Sackmann, and P. A. Janmey. 1995. F-actin, a model polymer for semiflexible chains in dilute, semidilute and liquid crystalline solutions. Biophys. J. 70:609-625.
  21. Pollard, T. D. and Borisy, G. G. 2003. Cellular motility driven by assembly and disassembly of actin filaments. Cell 112:453-465.
  22. Ridley, A. J., Schwartz, M. A., Burridge, K., Firtel, R. A., Ginsberg, M. H., Borisy, G., Parsons, J. T. and Horwitz, A. R. 2003. Cell migration: integrating signals from front to back. Science. 302, 1704-1709.
  23. Schumann, A. 2015. Conventional and unconventional reversible logic gates on Physarum polycephalum. International Journal of Parallel, Emergent and Distributed Systems. DOI: 10.1080/17445760.2015.1068775 .
  24. Steinmetz, M., K. Goldie, and U. Aebi. 1997. A correlative analysis of actin filament assembly, structure, and dynamics. J. Cell Biol. 138:559-574.
  25. Svitkina, T. M. and Borisy, G. G. 1999. Arp2/3 complex and actin depolymerizing factor/cofilin in dendritic organization and treadmilling of actin filament array in lamellipodia. J. Cell Biol. 145:1009-1026.
  26. Van Haastert, P. J. and Devreotes, P. N. 2004. Chemotaxis: signalling the way forward. Nat. Rev. Mol. Cell Biol. 5:626-634.
  27. Xu, J. Y., Schwarz, W. H., Kas, J. A., Stossel, T. P., Janmey, P. A., Pollard, T. D. 1998. Mechanical properties of actin filament networks depend on preparation, polymerization conditions, and storage of actin monomers. Biophys. J. 74:2731-2740.

Paper Citation

in Harvard Style

Schumann A. (2016). Toward a Computational Model of Actin Filament Networks . In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 4: BIOSIGNALS, (BIOSTEC 2016) ISBN 978-989-758-170-0, pages 290-297. DOI: 10.5220/0005828902900297

in Bibtex Style

author={Andrew Schumann},
title={Toward a Computational Model of Actin Filament Networks},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 4: BIOSIGNALS, (BIOSTEC 2016)},

in EndNote Style

JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 4: BIOSIGNALS, (BIOSTEC 2016)
TI - Toward a Computational Model of Actin Filament Networks
SN - 978-989-758-170-0
AU - Schumann A.
PY - 2016
SP - 290
EP - 297
DO - 10.5220/0005828902900297