Procedia Computer Science 00 (2010) 1–9 Procedia Computer Science Simulation of Multiphysics Multiscale Systems, 7th International Workshop. In International Conference on Computational Science, ICCS 2010 BS: a spatial shape-based scale-independent simulation environment for biological systems F. Buti, D. Cacciagrano, F. Corradini, E. Merelli and L. Tesei School of Science and Technology, University of Camerino, Via Madonna delle Carceri 9, 62032, Camerino, Italy Abstract The simulation and visualization of biological system models is becoming more and more important both in clin- ical use and in basic research. Since many systems are characterized by interactions involving different scales at the same time, several approaches have been defined to handle such complex systems at different spatial and tem- poral scale. In this context, we propose BS, a 3D particle-based spatial simulator whose novelty consists of providing a uniform and geometry-oriented multiscale modeling environment. These features make BS “scale- independent”, able to express geometric and positional information, and able to support transformations between scales simply defined as mappings between different granularity model instances. To highlight BS peculiari- ties, we sketch a multiscale model of human aortic valve where shapes are used at the cell scale for describing the interaction between a single valvular interstitial cell and its surrounding matrix, at the tissue scale for modeling the valve leaflet tissue mechanical behaviour, and at the organ scale for reproducing, as a 3D structure with fluid-structure interaction, the motion of the valve, blood, and surrounding tissue. Keywords: Particle-based models, Multiscale modeling, Simulation of biological systems, Human aortic valve 1. Introduction Nowadays, it is possible to observe biological systems in great detail: with a light microscope one can distinguish the compartments of a human cell, and with an electron microscope one can even see very small details such as pro- teins. At the same time, models for describing and simulating biological systems have comparable resolution regimes and work on different spatial and temporal scales: in the microscopic approach, molecular dynamics and Monte Carlo methods describe systems at the level of atoms or proteins while, in the macroscopic regime, continuum-based simu- lations model complete biological assemblies (but do not contain any explicit molecular information). Independently from the choice of a suitable resolution degree to observe and to model biological systems, a characteristic of bio- logical complexity is the intimate connection that exists between different length scales - from the nanometer-length scale of molecules to the highly structured meter scale of the whole human body. For instance, as stated in [1], subtle changes in molecular structure as a consequence of a single gene mutation can lead to catastrophic failure at the or- gan level, such as heart failure from reentrant arrhythmias that lead to ventricular fibrillation. But information flows Email address: name.surname@unicam.it (F. Buti, D. Cacciagrano, F. Corradini, E. Merelli and L. Tesei)