Paper Citing NAMD - Abstract
Burti, F.; Cacciagrano, D.; Corradini, F.; Merelli, E.; Tesei, L.
BIOSHAPE: a spatial shape-based scale-independent simulation environment for biological systems
ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS, 1:827-835, 2010
The simulation and visualization of biological system models is becoming more and more important both in clinical 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 temporal scale. In this context, we propose BIOSAFE, a 3D particle-based spatial simulator whose novelty consits of providing a uniform and geometry-oritented multiscale modeling environment. These features make BIOSHAPE "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 BIOSHAPE peculiarities, 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. (C) 2010 Published by Elsevier Ltd.
