Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework

Conference · Sat Jun 24 00:00:00 EDT 2006

DOI:https://doi.org/10.1088/1742-6596/46/1/044· OSTI ID:896571

Trebotich, D

We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

• Research Organization: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: W-7405-ENG-48
• OSTI ID: 896571
• Report Number(s): UCRL-CONF-222419; TRN: US200703%%825
• Resource Relation: Journal Volume: 46; Conference: Presented at: SciDAC 2006, Denver, CO, United States, Jun 25 - Jun 29, 2006
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ALGORITHMS
FINITE DIFFERENCE METHOD
GEOMETRY
POLYMERS
SIMULATION
VISCOUS FLOW