Dave Parker is Senior Principal Software Engineer in the Bio/Nano/Programmable Matter group at Autodesk. His focus is on developing scientific software for the modeling and visualization of nanoscale biological structures.
Prior to joining Autodesk, Dave developed software for simulating transient nonlinear heat conduction and thermo-plastic deformations for 3D metal printing processes. Before that he worked on various projects involving the analysis of next generation DNA sequencing data, finite element simulations of shock wave propagation in complex materials, scientific visualization, computational blood flow simulations of the human vasculature, image-based geometric modeling for surgical planning, and image processing of 3D/4D medical imaging data.
For his thesis Dave developed computational models of molecular motors to study their mechanism of movement. This work included implementing an open source software system called Protein Mechanica (https://simtk.org/projects/protmech) used for constructing coarse-grained models from protein crystal structures and simulating them based on multibody dynamics methods. As a Postdoctoral Research Fellow in the Bryant Molecular Motors Lab at Stanford University Dave developed software to aid in the design of genetically engineered molecular motors.
Dave received his Ph.D. in Biomechanical Engineering from Stanford University. While at the Georgia Institute of Technology he completed his B.S. in Computer Science and did graduate work in Applied Mathematics, concentrating on research in fractals and nonlinear dynamics.
Background / CV
Chen, L., Nakamura, M., Schindler, T.D., Parker, D., Bryant, Z. (2012) Engineering controllable bidirectional molecular motors based on myosin. Nature Nanotechnology, 7(4):252-6
Parker, D., Bryant, Z., Delp, S.L. (2009) Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics, Cellular and Molecular Bioengineering, 2(3):366-374.
Liao, J.-C., Spudich, J.A., Parker, D., Delp, S.L. (2007) Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways. Proceedings of the National Academy of Sciences, USA, 104:3171-3716.
Spilker, R.L., Feinstein, J.A., Parker, D., Reddy, V.M., Taylor, C.A. (2007) Morphometry-Based Impedance Boundary Conditions for Patient-Specific Modeling of Blood Flow in Pulmonary Arteries, Annals of Biomedical Engineering, 35(4):546-59.
Loboa, E.G., Fang, T.D., Parker, D., Warren, S.M., Fong, K.D., Longaker, M.T., Carter, D.R. (2005) Mechanobiology of mandibular distraction osteogenesis: Finite element analyses with a rat model, Journal of Orthopaedic Research, 23(3):663-670.
Markl, M., Chan, F.P., Alley, M.T., Wedding, K.L., Draney, M.T., Elkins, C., Parker, D., Wicker, R., Taylor, C.A., Herfkens, R.J., Pelc, N.J. (2003) Time Resolved Three Dimensional Phase Contrast MRI (4D-Flow), Journal of Magnetic Resonance Imaging 17:499-506.
Cheng, C.P., Parker, D., Taylor, C.A. (2002) Quantification of Wall Shear Stress in Large Blood Vessels Using Langrangian interpolation Functions with cine PC-MRI, Annals of Biomedical Engineering, 30(8):1020-1032.
Taylor, C.A., Cheng, C.P., Espinosa, L.A., Tang, B.T., Parker, D., Herfkens, R.J. (2002) In Vivo Quantification of Blood Flow and Wall Shear Stress in the Human Abdominal Aorta during Lower Limb Exercise, Annals of Biomedical Engineering, 30(3):402-408.
Taylor, C.A., Draney, M.T., Ku, J.P., Parker, D., Steele, B.N., Wang, K.C., Zarins, C.K. (1999) Predictive Medicine: Computational Techniques in Therapeutic Decision-Making, Computer Aided Surgery, 4:231-247.
Parker, D., Liao, J.-C., Delp, S.L. (2007) Toward a Coarse-Grained Model of the Myosin V Neck. 9th U.S National Congress on Computational Mechanics, July 22-26, 2007, San Francisco, CA
Parker, D., Liao, J.-C., Delp, S.L. (2006) Toward a Coarse-Grained Model of the Myosin V Neck using the Normal Mode Analysis. 50th Annual Biophysical Society Meeting, Salt Lake City, UT. December 11-14, 2005
Parker, D., Pande, V.J., Delp, S.L. (2004) A 3D Model of Myosin V Structure, Biomedical Computation at Stanford 2004 Symposium Proceedings, Stanford, CA.
Spilker, R.A., Parker, D., Taylor C.A. (2003) Image-Based Modeling of Blood Flow in Pulmonary Arteries Using a One-Dimensional Finite Element Method Coupled to a Morphometry-Based Model of the Distal Vessels, Summer Bioengineering Conference June 25-29, Sonesta Beach Resort in Key Biscayne, Florida.
Loboa, E.G., Fang, T.D., Parker, D., Warren, S.M., Fong, K.D., Longaker, M.T., Carter, D.R. (2003) Mechanobiology of Mandibular Distraction Osteogenesis - Finite Element Analyses with a Rat Model, 49th Annual Meeting, Orthopaedic Research Society. New Orleans, LA.
Cheng, C.P., Parker, D., Taylor, C.A. (2001) Wall Shear Stress Quantification from Magnetic Resonance Imaging Data Using Lagrangian Interpolation Functions, Proceedings of the 2001 ASME Summer Bioengineering Meeting, Snowbird, UT.
Parker, D., Wang, K.C., Taylor, C.A. (1999) Image Based Geometric Modeling of the Human Vasculature in Computational Hemodynamics, Proceedings of the 1999 ASME Summer Bioengineering Meeting, Big Sky, MT.
San Francisco, CA 94111