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Bone remodelling in BioShape. (English) Zbl 1283.92010

Krivine, Jean (ed.) et al., Proceedings of the 1st international workshop on interactions between computer science and biology (CS2Bio’10), Amsterdam, The Netherlands, June 10, 2010. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 268, 17-29 (2010).
Summary: Many biological phenomena are inherently multiscale, i.e., they are characterised by interactions involving different scales at the same time. This is the case of bone remodelling, where macroscopic behaviour (at organ and tissue scale) and microstructure (at cell scale) strongly influence each other. Consequently, several approaches have been defined to model such a process at different spatial and temporal levels and, in particular, in terms of continuum properties, abstracting in this way from a realistic – and more complex – cellular scenario. While a large amount of information is available to validate such models separately, more work is needed to integrate all levels fully in a faithful multiscale model.{ }In this scenario, we propose the use of BioShape, a 3D particle-based, scale-independent, geometry and space oriented simulator. It is used to define and integrate a cell and tissue scale model for bone remodelling in terms of shapes equipped with perception, interaction and movement capabilities. Their in-silico simulation allows for tuning continuum-based tissutal and cellular models, as well as for better understanding – both in qualitative and in quantitative terms – the blurry synergy between mechanical and metabolic factors triggering bone remodelling.
For the entire collection see [Zbl 1281.68031].

MSC:

92C05 Biophysics
Full Text: DOI

References:

[1] Andrews, S. S.; Bray, D., Stochastic simulation of chemical reactions with spatial resolution and single molecule detail, Phys. Biol., 1, 137-151 (2004)
[2] Ayton, G.; Noid, W.; Voth, G., Multiscale modeling of biomolecular systems: in serial and in parallel, Current Opinion in Structural Biology, 17, 192-198 (2007)
[3] Bartocci, E., F. Corradini, M. R. Di Berardini, E. Merelli and L. Tesei, Shape Calculus. A spatial calculus for 3D colliding shapes, Technical Report 6, Department of Mathematics and Computer Science, University of Camerino (2010), Accepted for publication in the Scientific Annals of Computer Science. To appear in 2010. Available at http://s1report.cs.unicam.it/6/.; Bartocci, E., F. Corradini, M. R. Di Berardini, E. Merelli and L. Tesei, Shape Calculus. A spatial calculus for 3D colliding shapes, Technical Report 6, Department of Mathematics and Computer Science, University of Camerino (2010), Accepted for publication in the Scientific Annals of Computer Science. To appear in 2010. Available at http://s1report.cs.unicam.it/6/. · Zbl 1424.92001
[4] Berendsen, H., GROMACS: A message-passing parallel molecular dynamics implementation, Computer Physics Communications, 91, 43-56 (1995)
[5] Boulianne, L.; Assaad, S.; Dumontier, M.; Gross, W., GridCell: a stochastic particle-based biological system simulator, BMC Systems Biology, 2 (2008)
[6] Boyle, W.; Simonet, W.; Lacey, D., Osteoclast differentiation and activation, Nature, 423, 337-342 (2003)
[7] Brooks, B.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M., CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, Journal of Computational Chemistry, 4, 187-217 (1983)
[8] Burger, E.; Klein-Nulend, J., Mechanosensory transduction in bone role of the lacuno-canalicular network, FASEB J, 13, 101-112 (1999)
[9] Buti, F., D. Cacciagrano, F. Corradini, E. Merelli and L. Tesei, BioShape: a spatial shape-based scale-independent simulation environment for biological systems, in: ICCS 2010: Proceedings of Simulation of Multiphysics Multiscale Systems, 7th International Workshop, 2010, downloadable at http://cosy.cs.unicam.it/bioshape/iccs2010.pdf.; Buti, F., D. Cacciagrano, F. Corradini, E. Merelli and L. Tesei, BioShape: a spatial shape-based scale-independent simulation environment for biological systems, in: ICCS 2010: Proceedings of Simulation of Multiphysics Multiscale Systems, 7th International Workshop, 2010, downloadable at http://cosy.cs.unicam.it/bioshape/iccs2010.pdf. · Zbl 1283.92010
[10] Ciocchetta, F., A. Duguid, S. Gilmore, M. L. Guerriero and J. Hillston, The Bio-PEPA tool suite, International Conference on Quantitative Evaluation of Systems 0 (2009), pp. 309-310.; Ciocchetta, F., A. Duguid, S. Gilmore, M. L. Guerriero and J. Hillston, The Bio-PEPA tool suite, International Conference on Quantitative Evaluation of Systems 0 (2009), pp. 309-310.
[11] Corradini, F.; Merelli, E., Hermes: agent-base middleware for mobile computing, (Mobile Computing. Mobile Computing, LNCS, vol. 3465 (2005)), 234-270
[12] Cowin, C.; Hegedus, D., Bone remodeling i: A theory of adaptive elasticity, Journal of Elasticity, 6, 313-326 (1976) · Zbl 0335.73028
[13] Cowin, C.; Hegedus, D., Bone remodeling ii: small strain adaptive elasticity, Journal of Elasticity, 6, 337-352 (1976) · Zbl 0342.73069
[14] Cowin, S.; Moss-Salentijn, L.; Moss, M., Candidates for the mechanosensory system in bone, J Biomech Eng, 113, 191-197 (1991)
[15] Cristofolini, L.; Taddei, F.; Baleani, M.; Baruffaldi, F.; Stea, S.; Viceconti, M., Multiscale investigation of the functional properties of the human femur, Philos Transact A Math Phys Eng Sci, 366, 3319-3341 (2008)
[16] Evans, D.; Lawford, P.; Gunn, J.; Walker, D.; Hose, D.; Smallwood, R.; Chopard, B.; Krafczyk, M.; Bernsdorf, J.; Hoekstra, A., The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery, Phil. Trans. R. Soc. A, 366, 3343-3360 (2008)
[17] Frost, H., Skeletal structural adaptations to mechanical usage (SATMU): 2. Redefining Wolffs Law: the remodeling problem, Anat. Rec., 226, 414-422 (1990)
[18] Harada, S.; Rodan, G., Control of osteoblast function and regulation of bone mass, Nature, 423, 349-355 (2003)
[19] Hu, Z.; Mellor, J.; Wu, J.; Kanehisa, M.; Stuart, J.; DeLisi, C., Towards zoomable multidimensional maps of the cell, Nature Biotechnology, 25, 547-554 (2007)
[20] Huiskes, R.; Ruimerman, R.; Lenthe, G. V.; Janssen, J., Effects of mechanical forces on maintenance and adaptation of form in trabecular bone, Nature, 405, 704-706 (2000)
[21] Hunter, P.; Li, W.; McCulloch, A.; Noble, D., Multiscale modeling: Physiome project standards, tools, and databases, Computer, 39, 48-54 (2006)
[22] Klein-Nulend, J.; van der Plas, A.; Semeins, C.; Ajubi, N.; Frangos, J.; Nijweide, P.; Burger, E., Sensitivity of osteocytes to biomechanical stress in vitro, FASEB J, 9, 441-445 (1995)
[23] Koumoutsakos, P., Multiscale flow simulations using particles, Annu. Rev. Fluid Mech., 37, 457-487 (2005) · Zbl 1117.76054
[24] Li, H., Y. Cao and L. Petzold, StochKit, a new stochastic simulation toolkit, in: Proceedings of the Sixth International Conference on Systems Biology, 2005.; Li, H., Y. Cao and L. Petzold, StochKit, a new stochastic simulation toolkit, in: Proceedings of the Sixth International Conference on Systems Biology, 2005.
[25] Nauman, E.; Satcher, R.; Keaveny, T.; Halloran, B.; Bikle, D., Osteoblasts respond to pulsatile fluid flow with short-term increases in pge (2) but no change in mineralization, Journal of Applied Physiology, 90, 1849-1854 (2001)
[26] Phillips, J.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.; Kalé, L.; Schulten, K., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, 26, 1781-1802 (2005)
[27] Plimpton, S. J.; Slepoy, A., Microbial cell modeling via reacting diffusive particles, Journal of Physics: Conference Series, 16, 305 (2005)
[28] Priami, C., P. Ballarini and P. Quaglia, BlenX4Bio — BlenX for biologists, in: CMSB ’09: Proceedings of the 7th International Conference on Computational Methods in Systems Biology, 2009, pp. 26-51.; Priami, C., P. Ballarini and P. Quaglia, BlenX4Bio — BlenX for biologists, in: CMSB ’09: Proceedings of the 7th International Conference on Computational Methods in Systems Biology, 2009, pp. 26-51.
[29] Rouhi, G.; Epstein, M.; Sudak, L.; Herzog, W., Modeling bone resorption using mixture theory with chemical reactions, Journal of Mechanics of Materials and Structures, 2, 1141-1156 (2007)
[30] Sloot, P. and A. Hoekstra, Multi-scale modelling in computational biomedicine, Brief. Bioinform. (2009).; Sloot, P. and A. Hoekstra, Multi-scale modelling in computational biomedicine, Brief. Bioinform. (2009).
[31] Stiles, J. R.; Bartol, T. M., Monte Carlo methods for simulating realistic synaptic microphysiology using MCell, (Schutter, E. D., Computational Neuroscience: Realistic Modeling for Experimentalists (2001), CRC Press), 87-127
[32] Turner, C., Toward a mathematical description of bone biology: the principle of cellular accommodation, Calcified Tissue International, 65, 466-471 (1999)
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