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JSim Bibliography

This page is for the current JSim version 2.0. Click here for the earlier JSim 1.6 version.

This page lists known published material related to JSim. Last updated 18 May 2006. Contents:


Refereed Papers

Barta E, Sideman S, and Bassingthwaighte JB. Facilitated diffusion and membrane permeation of fatty acid in albumin solutions. Ann Biomed Eng 28: 331-345, 2000.

Bassingthwaighte JB. Strategies for the Physiome Project. Ann Biomed Eng 28: 1043-1058, 2000.

Beard DA and Bassingthwaighte JB. The fractal nature of myocardial blood flow emerges from a whole-organ model of arterial network. J Vasc Res 37: 282-296, 2000.

Beard DA and Bassingthwaighte JB. Advection and diffusion of substances in biological tissues with complex vascular networks. Ann Biomed Eng 28: 253-268, 2000.

Eke A, Herman P, Bassingthwaighte JB, Raymond GM, Cannon M, Balla I, and Ikrenyi C. Fractal analysis of physiological time series. Eur J Physiol 439: 403-415, 2000.

Prinzen FW and Bassingthwaighte JB. Blood flow distributions by microsphere deposition methods. Cardiovasc Res 45: 13-21, 2000.

Qian H and Bassingthwaighte JB. A class of flow bifurcation models with lognormal distribution and fractal dispersion. J Theor Biol 205: 261-268, 2000.

Schwartz LM, Bukowski TR, Ploger JD, and Bassingthwaighte JB. Endothelial adenosine transporter characterization in perfused guinea pig hearts. Am J Physiol Heart Circ Physiol 279: H1502-H1511, 2000.

Wang G, Raymond GM, Li Y, Schweiger GD, Sharafuddin MJ, Stolpen AH, Yang S, Li Z, Bassingthwaighte JB, and Vannier MW. A model for intravenous bolus propagation for optimization of contrast enhancement. Proceedings of the SPIE 3978: 436-447, 2000.

Bassingthwaighte JB. The modelling of a primitive "sustainable" conservative cell. Phil Trans Roy Soc Lond A 359: 1055-1072, 2001.

Bassingthwaighte JB, Beard DA, and Li Z. The mechanical and metabolic basis of myocardial blood flow heterogeneity. Basic Res Cardiol 96: 582-594, 2001.

Beard DA. Taylor dispersion of a solute in a microfluidic channel. J Appl Physics 89: 4667-4669, 2001.

Beard DA. A computational framework for generating transport models from databases of microvascular anatomy. Ann Biomed Eng 29: 837-843, 2001.

Beard DA and Bassingthwaighte JB. Modeling advection and diffusion of oxygen in complex vascular networks. Ann Biomed Eng 29: 298-310, 2001.

Higgins G, Athey B, Bassingthwaighte JB, Burgess J, Champion H, Cleary K, Dev P, Duncan J, Hopmeier M, Jenkins D, Johnson C, Kelly H, Leitch R, Lorensen W, Metaxas D, Spitzer V, Vaidehi N, Vosburgh K, and Winslow R. Modeling and simulation in medicine: Toward an integrated framework. July 20-21, 2000, National Library of Medicine, National Institutes of Health, Bethesda, Maryland. Comput Aided Surg 6: 32-39, 2001.

Wang CY and Bassingthwaighte JB. Capillary supply regions. Math Biosci 173: 103-114, 2001.

Bassingthwaighte JB. The Physiome Project: The Macroethics of Engineering Toward Health. The Bridge 32(3): 24-29, 2002.

Beyer RP, Bassingthwaighte JB, and Deussen AJ. A computational model of oxygen transport from red blood cells to mitochondria. Comput Methods Programs Biomed 67: 39-54, 2002.

Van Oosterhout MFM, Arts T, Bassingthwaighte JB, Reneman RS, and Prinzen FW. Relation between local myocardial growth and blood flow during chronic ventricular pacing. Cardiovasc Res 53: 831-840, 2002.568.

Bassingthwaighte JB. The macro-ethics of genomics to health: The Physiome Project. Comptes Rendus Biologies de l’Academie des sciences francaise 326: 1105-1110, 2003.

Kellen MR and Bassingthwaighte JB. Transient transcapillary exchange of water driven by osmotic forces in the heart. Am J Physiol Heart Circ Physiol 285: H1317-H1331, 2003.

Kellen MR and Bassingthwaighte JB. An integrative model of coupled water and solute exchange in the heart. Am J Physiol Heart Circ Physiol 285: H1303-H1316, 2003.

Raymond GM, Percival DB, and Bassingthwaighte JB. The spectra and periodograms of anticorrelated discrete fractional Gaussian noise.. Physica A 322: 169-179, 2003.

Wang CY and Bassingthwaighte JB. Blood flow in small curved tubes. J Biomech Eng 125: 910-914, 2003.

White RJ, Bassingthwaighte JB, Charles JB, Kushmerick MJ, and Newman DJ. Issues of exploration: Human health and wellbeing during a mission to Mars. Adv Space Res 31: 7-16, 2003.

Bassingthwaighte JB and Vinnakota KC. The computational integrated myocyte. A view into the virtual heart. Modeling in Cardiovascular Systems. Ann. New York Acad. Sci. 1015, edited by S. Sideman and R. Beyar. 2004, p. 391-404.

Dash RK and Bassingthwaighte JB. Blood HbO2 and HbCO2 dissociation curves at varied O2, CO2, pH, 2,3-DPG and temperature levels. Ann Biomed Eng 32: 1676-1693, 2004.

Vinnakota K and Bassingthwaighte JB. Myocardial density and composition: A basis for calculating intracellular metabolite concentrations. Am J Physiol Heart Circ Physiol 286: H1742-H1749, 2004.

Bassingthwaighte JB, Chizeck HJ, Atlas LE, and Qian H. Multiscale modeling of cardiac cellular interactions. The Communicative Cardiac Cell. Ann. New York Acad. Sci. 1047: , edited by Sideman S, Beyar R, and Landesberg A. 2005, p. 395-424.

Beard DA, Bassingthwaighte JB, and Greene A. Computational modeling of physiological systems. Physiol Genomics 23: 1-3, 2005.

Bassingthwaighte JB. A practical extension of hydrodynamic theory of porous transport for hydrophilic solutes. Microcirculation 13: 111-118, 2006.

Bassingthwaighte JB, Chizeck HJ, and Atlas LE. Strategies and tactics in multiscale modeling of cell-to-organ systems. Proc IEEE 94: 819-831, 2006.

Bassingthwaighte JB, Raymond GR, Ploger JD, Schwartz LM, and Bukowski TR. GENTEX, a general multiscale model for in vivo tissue exchanges and intraorgan metabolism. Phil Trans Roy Soc A: Mathematical, Physical and Engineering Sciences 364(1843): 1423-1442, 2006.

Musters MWJM, Bassingthwaighte JB, van Riel NAW, and van der Vusse GJ. Computational evidence for protein-mediated fatty acid transport across the sarcolemma.. Biochem J 393: 669-678, 2006.

Dash RK, Li Z, and Bassingthwaighte JB. Simultaneous blood-tissue exchange of oxygen, carbon dioxide, bicarbonate, and hydrogen ion. Ann Biomed Eng 2006 (in press).

Bassingthwaighte JB, Kushmerick M, Qian H, and Beard DA. Multiscale modeling of cardiac intermediary metabolism and exciation. Interactive and Integrated Cardiology. Ann. New York Acad. Sci., edited by Sideman S, Beyar R, and Landesberg A. 2006 (in press).

Bassingthwaighte JB, Carlson BE, Raymond GR, and Butterworth E. Transport phenomena and ATP generation: An hypothesis on how myocardial regional flow heterogeneity is driven by regional cellular demands. Ann New York Acad Sci 2006 (in preparation).

Qian H and Beard DA. Metabolic futile cycles and their functions: A systems analysis of energy and control. Bioch J 2006 (in preparation).

Book Chapters

Bassingthwaighte JB. Compound delivery and local blood flows. Molecular Nuclear Medicine , edited by Feinendegen LE, Shreeve WW, Eckelman WC, Bahk YW, and Wagner HN Jr. Berlin Heidelberg New York: 2003, p. 171-198.

Beard DA, Qian H, and Bassingthwaighte JB. Stoichiometric Foundation of Large-Scale Biochemical System Analysis. Modeling in Molecular Biology , edited by G. Ciobanu and G.Rozenberg. Berlin Heidelberg New York: Natural Computing Series, Springer-Verlag, 2004, p. 1-19.

Musters MWJM, Bassingthwaighte JB, Panday V, Riel NAW, and van der Vusse GJ. Computational modeling of muscle fatty acid uptake and utilization.. Lipobiology , edited by van der Vusse GJ. Elsevier, Amsterdam: 2004, p. 173-224.

Bassingthwaighte JB. Capillary Permeability New York: Encyclopedia of Biomedical Engineering, John Wiley and Sons, Inc, 2006 (in press).

Abstracts

Bassingthwaighte JB. Strategies for large scale systems modeling. Ann Biomed Eng 28: S28, 2000.

Bassingthwaighte JB. The Physiome Project: Systems approaches to understanding everything about biology. 4th Annual Hilton Head Workshop, February 23-27, 2000. Computational Modeling of Biological Systems: From Gene to Organ , Hilton Head, S.C.: 2000, p. 27.

Bassingthwaighte JB. The Physiome Project: Integrating from genomics to function or vice versa. Proc Transcriptome 2000, Paris, 6-9 November 2000 1-2, 2000.

Bassingthwaighte JB and Li Z. Strategies for large scale modeling in the Physiome Project. Nat Inst Environmental Health Sciences Virtual Body Workshop 3-4, 2000.

Bassingthwaighte JB and Li Z. Simulation Resource Facility in Circulatory Mass Transport and Exchange. NCRR Principal Investigators Meeting 2000 37-38, 2000.

Kellen MR and Bassingthwaighte JB. Application of transcapillary exchange model to prediction of lymph to plasma concentration ratios. FASEB J 14: A141, 2000.

Kellen MR and Bassingthwaighte JB. Analysis of osmotic transients in rabbit heart. Ann Biomed Eng 28: S32, 2000.

Kim Y, Spelman F, and Bassingthwaighte JB. Bioengineering degree programs and curricula at the University of Washington. Ann Biomed Eng 28: S107, 2000.

Lacoin M, Byrd GF, and Bassingthwaighte JB. 3-D arterial cast reconstruction and fluorescent microsphere deposition to obtain regional flows in the heart. FASEB J 14: A160, 2000.

Li Z, Butterworth E, and Bassingthwaighte JB. Building an infrastructure for the Physiome Project. Ann Biomed Eng 28: S28, 2000.

Prinzen FW, van Oosterhout MFM, Arts T, Bassingthwaighte JB, and Reneman RS. Mismatch of local myocardial hypertrophy and blood flow during chronic ventricular pacing. Circulation 102(Suppl.II): 196, 2000.

Thomas W and Bassingthwaighte JB. A barrier can cause a hyperbolic enzyme to have switch-like kinetics. Ann Biomed Eng 28: S105, 2000.

Van Oosterhout MFM, Arts T, Bassingthwaighte JB, Reneman RS, and Prinzen FW. Relation between local hypertrophy and blood flow during chronic ventricular pacing. Eur J Cardiol 21: 516, 2000.

Bassingthwaighte JB. Constructing a set of conservative cell models. Ann Biomed Eng 29: S-9, 2001.

Bassingthwaighte JB. Linking metabolic pathway models. Am Soc Cell Biol 2001.

Bassingthwaighte JB. Bioinformatics and the Physiome Project. IEEE Trans on Biomed Eng 2001.

Kellen MR and Bassingthwaighte JB. Reflection Coefficient Estimates depend on flux partitioning among transcapillary exchange pathways. Ann Biomed Eng 29: S-73, 2001.

Kellen MR and Bassingthwaighte JB. An integrative model describes whole organ measurements of coupled fluid and solute exchange. FASEB J 15: A46, 2001.

Subramaniam S, Loew L, and Bassingthwaighte J. Bioinformatics in Biology and Engineering. Experimental Biology Meeting Program Online: Available from http://www.the-aps.org/meetings/eb/abstracts/bioinformatics.htm . 2001 (Accessed 5apr02.), p. 1 screen.

Kellen MR and Bassingthwaighte JB. Using whole organ experiments to understand microcirculatory exchange. FASEB J 16: Abstr 410.12, 2002.

Wang CY and Bassingthwaighte JB. Blood flow in small curved vessels. Proceedings of the Fourteenth US National Congress of Applied Mechanics, June 23-28, 2002, Blacksburg, VA. Blacksburg, VA: Virgina Tech, 2002, p. 574.

Bassingthwaighte JB. Cardiac endothelial purine handling. Exper Biol 2003 97.8, p35, 2003.

Bassingthwaighte JB, Barta E, Caldwell JH, and Sideman S. Facilitation of fatty acid transmembrane transport by an albumin receptor. Am J Physiol 28: 2003.

Bassingthwaighte JB, Vinnakota K, and Raymond GM. Morphometric substrate for modeling cardiac function. Exper Biol 2003 465.4, p181, 2003.

Dash RK and Bassingthwaighte JB. New model equations for oxyhemoglobin and carbaminohemoglobin dissociation curves. Biophys J 84: 460A, 2003.

Dash RK and Bassingthwaighte JB. A computational model for oxygen and carbon dioxide transport and exchange in the microcirculation. Exper Biol 2003 327.20, p120, 2003.

Raymond GM, Butterworth E, and Bassingthwaighte JB. JSIM: Free software package for teaching phyiological modeling and research. Exper Biol 2003 280.5, p102, 2003.

Vinnakota KC and Bassingthwaighte JB. Anatomical basis for modeling cardiac metabolic functions. Exper Biol 2003 350.5, p135, 2003.

Bassingthwaighte JB. Capillary permeation through the endothelial barriers. The Microcirculatory Society Newsletter 32: 15, 2004.

Bassingthwaighte JB. Modelling transport, exchange, and reaction in cardiac endothelium and myocytes. J Physiol Abstract Issue: J. Physiol.: SA18, 2004.

Neal ML and Bassingthwaighte JB. Blood gas dynamics in a human cardiopulmonary model. Proc 2004 BMES Annual Fall Meeting 107, 2004.

Bassingthwaighte JB. Multiscale modeling of cardiac cellular energetics. Proc 3rd Fairberg Workshop: The Communicative Cardiac Cell 24, 2005.

Bassingthwaighte JB. Strategies in the design and modulation of multilevel cardiorespiratory models. International symposium for Leading Project for Biosimulation, Keio Univ., Tokyo: 19, 2005.

Musters MWJM, Bassingthwaighte JB, van der Vusse GJ, and van Riel NAW. Transmembrane diffusion of unbound fatty acids is insufficient for cardiac energy requirements: model analysis. Biophys J Abstracts: 718, 2005.

Bassingthwaighte JB, Matuszkiewicz A, Krueger MB, Park JS, Raymond GM, Butterworth E, Neal M, and Hlastala M. The Physiome in Pharmacokinetics, Pharmacodynamics and Toxicology. Proceedings of the SOT: 45th Annual Meeting of the Society of Toxicology, 34, 2006.

Kerckhoffs R, Cole M, Sachse F, Healy S, Neal M, Jones G, Bassingthwaighte JB, and McCulloch A. From myocyte to torso: Spatially and temporally multi-scale simulation of cardiac injury. 2006, p. 49.

Neal M, Bassingthwaighte JB, Kerckhoffs R, McCulloch A, Sachse F, Cole M, and Jones G. Hemodynamics of hemorrhage simulated with an open-loop cardiopulmonary model. 2006, p. 58.

Non-refereed Chapters and References

Bassingthwaighte JB. Editorial: Back to fundamentals: Anatomy-based physiological bioengineering. Ann Biomed Eng 28: 701-703, 2000.

Bassingthwaighte JB. Editorial: Renewing the Annals: Dreams for the next stages. Ann Biomed Eng 28: 483, 2000.

Bassingthwaighte JB and Katz JL. Editorial: A symposium issue: Biomechanics. Ann Biomed Eng 29: 1033, 2001.

Bassingthwaighte JB. Editorial: ABME: On-line submission, on-line review. Ann Biomed Eng 29: 359, 2001.

Bassingthwaighte JB. Editorial: New leadership for the Annals. Ann Biomed Eng 29: 455, 2001.

Bassingthwaighte JB. Proteins, cells, organs: hierarchical structuring in modeling biological systems. Proceedings of the Second Joint EMBS/BMES Conference, Houston, TX, USA: October 23-26, 2002 . IEEE, 2002, p. 2176-2177.

Nebeker F, Geselowitz M, Arzbaecher R, Babb A, Bailey J, Dunn R, Bassingthwaighte J, Chato J, Chien S, Colton C, Eden M, Fung YC, Geddes L, Greatbatch W, Jaron D, Johns RJ, Katz JL, Mates R, Merrill E, Peppas N, Rataer B, Reid JM, Sachs M, Schwan H, Tirrell M, Valentianzzi M, and Welkowitz W. Voices of Experience. Interviews by Frederik Nebeker and Michael Geselowitz. IEEE Eng Med Biol Mag 21: 48-89, 2002.

Bassingthwaighte JB. Annals of Biomedical Engineering: A Historical Review. The Biomedical Engineering Society: An Historical Perspective , edited by Paul H. Fagette J and Patricia I Horner. Landower, MD: Biomedical Engineering Society, 2004, p. 87-90.

Bassingthwaighte JB. James Bassingthwaighte, President 1977-1978. The Biomedical Engineering Society: An Historical Perspective , edited by Paul H. Fagette J and Patricia I Horner. Landower, MD: Biomedical Engineering Society, 2004, p. 23-25.

Coatrieux J-L and Bassingthwaighte JB. Special Issue on the Physiome and Beyond. Proc IEEE 94: 671-677, 2006.

Conferences

Bassingthwaighte JB and Vinnakota K. The Physiome Project: How Integrative systems approaches can aid target selection. Eur Fed Pharmaceut Sci Satellite Keynote Lecture 16, 2002.

Bassingthwaighte JB, Vinnakota K, Lambeth MJ, and Kushmerick MJ. Modeling the energy metabolism of cardiac myocytes. Proc Jap Soc Electrocardiology 2002.

Bassingthwaighte JB. Analysis of the cardiome. Symposium on Phenotyping: Mouse cardiovascular function and development 13, 2002.

Bassingthwaighte JB. Fractal lessons from the heart: Scaling and multicausality in physiological systems. Arthur S. Iberall Distinguished Lecture on Life and the Sciences of Complexity. University of Connecticut 2004.


Comments or Questions?

[This page was last modified 06Jul12, 3:08 pm.]

Model development and archiving support at physiome.org provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.