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

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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 ... continued below

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7 p. (0.4 MB)

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Trebotich, D June 24, 2006.

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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.

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7 p. (0.4 MB)

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PDF-file: 7 pages; size: 0.4 Mbytes

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  • Presented at: SciDAC 2006, Denver, CO, United States, Jun 25 - Jun 29, 2006

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  • Report No.: UCRL-CONF-222419
  • Grant Number: W-7405-ENG-48
  • Office of Scientific & Technical Information Report Number: 896571
  • Archival Resource Key: ark:/67531/metadc885011

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  • June 24, 2006

Added to The UNT Digital Library

  • Sept. 22, 2016, 2:13 a.m.

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  • April 17, 2017, 1:05 p.m.

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Trebotich, D. Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework, article, June 24, 2006; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc885011/: accessed September 22, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.