SCBMB: Ph.D. Program in Structural and Computational Biology and Molecular Biophysics at Baylor College of Medicine, Houston, TX

John W. Clark, Jr.

Rice University

Department: Electrical and Computer Engineering
Address: A224 Abercrombie Lab
6100 S. Main St. MS366
Houston, TX 77005-1892
Phone: 713-348-3597
Fax: 713-348-5686
Email: jwc@rice.edu
Web: www.ece.rice.edu/~jwc/

Education

B.S., Christian Brothers University (1962)
M.S., Case Western Reserve University (1965)
Ph.D., Case Western Reserve University (1967)

Honors

Life Fellow, Institute of Electrical and Electronics Engineers (IEEE),
"For Contributions to Modeling in Electrophysiology and Cardiopulmonary Systems", January 2005

Founding Fellow of the Biomedical Engineering Society (BMES), Biomedical Engineering Society (BMES), 2005

Founding Fellow, American Institute of Medical and Biological Engineering, presented at National Academy of Sciences, Washington, DC, 8 March 1993

Fellow, Alexander von Humboldt Foundation, Bonn, Germany. 1975
President, IEEE/Engineering in Medicine and Biology Society (EMBS) 2003

IEEE/EMBS Service Award, "For outstanding service and contributions to the EMB Society and a meritorious career in biomedical engineering education." Presented at 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’09), Minneapolis, MN 2-6 September 2009.

Houston Society for Engineering in Medicine and Biology (HSEMB) Special Award, “In recognition of outstanding service to the biomedical engineering community of Houston and for founding the Houston Society for Engineering in Medicine and Biology,” presented at 25th Annual Houston Conference on Biomedical Engineering Research, 7 February 2008.

Research Topic

Cell Modeling; Engineering in Critical Care Medicine

Research Description

In biomedical applications approximately 50% of our work is involved in the development of quantitative models of the electrophysiological behavior of cells (neurons, cardiac and smooth muscle cells, alveolar macrophages). The remainder of our work deals with large-scale (organ-level) computer modeling of the cardiovascular and pulmonary systems. Cellular projects are usually done in collaboration with life scientists, whereas organ-level projects involve collaboration with physicians and surgeons. Students engaged in these projects have the opportunity to learn about biological computation, and interact with scientists and physicians in a variety of settings from the research laboratory to critical care medicine.

Selected Publications

R.J. Butera, J.W. Clark, Jr., and J.H. Byrne, ``Dissection and Reduction of a Modeled Bursting Neuron,'' Journal of Computational Neuroscience, 3: 199-223, 1996.
D.S. Lindblad, C.R. Murphey, J.W. Clark, and W.R. Giles, ``A model of the action potential and underlying membrane currents in a rabbit atrial cell,'' American Journal of Physiology, 271: H1666-H1696, 1996.
S.S. Demir, R.J. Butera, A.A. DeFranceschi, J.W. Clark, and J.H. Byrne, ``Phase Sensitivity and Entrainment in a Modeled Bursting Neuron'', Biophysical Journal, 72: 579-594, 1997.
Butera, R.J., Clark, J.W. and Byrne, J.H., ``Transient Responses of a Modeled Bursting Neuron: Analysis with Equilibrium and Averaged Nulclines,'' Biological Cybernetics, 77: 307-322, 1997.
A. Nygren, C. Fiset, L. Firek, J.W. Clark, D.S. Lindblad, R.B. Clark, and W.R. Giles, ``A Mathematical Model of An Adult Human Atrial Cell: The Role of K+ Currents in Repolarization,'' Circulation Research, 82: 63-81, 1998.
S.S. Demir, J.W. Clark and W.R. Giles, ``Parasympathetic Modulation of Sinoatrial Node Pacemaker Activity in Rabbit Heart: A Unifying Model,'' Amer. J. Physiol., 276: H2221-H2244, 1999.
Amini, B., Clark, J.W. Jr. and Canavier, C.C., ``Calcium dynamics underlying pacemaker-like and burst firing oscillations in midbrain dopaminergic neurons: A computational study,'' J. Neurophysiology, 82: 2249-2261, 1999.
Baxter, D.A., C.C. Canavier, J.W. Clark Jr. and J.H. Byrne, ``Computational Model of the Serotonergic Modulation of Sensory Neurons in Aplysia,'' J. Neurophysiology, 82: 2914-2935, 1999.
Athanasiades, A., J.W. Clark Jr., F. Ghorbel and A. Bidani, ``An Ionic Current Model for Medullary Respiratory Neurons,'' J. Computational Neuroscience 9: 237-257, 2000.
L. Sun, J-S. Fan, J.W. Clark and P.T. Palade, ``A model of the L-type Ca2+ channel in rat ventricular myocytes: Ion selectivity and inactivation mechanisms,'' J. Physiology, 529: 139-158, 2000.
Amini, B., A. Bidani, J.B. Zwischenberger, and J.W. Clark, Jr., "A model of the rat phrenic motor neuron," IEEE Trans. on Biomed. Engr., 51(7): 1103-1114, 2004.
Luo, C., J.W. Clark, J., T.A. Heming, and A. Bidani, "A simplified model for V-ATPase H+ extrusion," IEEE Trans. on Nanobioscience}, 3(4): 257-264, 2004.
Amini, B., A. Bidani, J.B. Zwischenberger, and J.W. Clark Jr., "A model of the Pacemaking Neuron of the Respiratory Central Pattern Generator," IEEE Trans. on Neural Systems and Rehabilitation Engineering, 13(2): 120-124, 2005.
Yang, J., J.W. Clark Jr., R.M. Bryan, and C.S. Robertson, "Mathematical modeling of the nitric oxide/cGMP pathway in the vascular smooth muscle cell," Amer. J. Physiol., 289: H886-H897, 2005.
Luo, C., J.W. Clark Jr., T.A. Heming, A. Bidani, "A Macrophage Cell Model for pH and Volume Regulation," J. Theoretical Biology, 238: 449-463, 2006.
SELECTED PUBLICATIONS (ORGAN SYSTEMS MODELING):
D.C. Chung, S.C. Niranjan, J.W. Clark, Jr., A.Bidani, W.E. Johnston, J.B. Zwischenberger, and D.L. Traber, ``A Dynamic Model of Ventricular Interaction and Pericardial Influence,'' Amer, J. Physiol., 272: H2942-2962, 1997.
C.H. Liu, S.C. Niranjan, J.W. Clark, Jr., K.Y. San, J.B. Zwischenberger and A. Bidani, ``Airway Mechanics, Gas Exchange and Blood Flow in a Nonlinear Model of the Human Lung,'' Journal of Applied Physiology, 84: 1447-1469, 1998.
J..W. Clark, ``The Origin of Biopotentials,'' in Medical Instrumentation: Application and Design, 3rd edition, edited by J.G. Webster, John Wiley and Sons, Inc., New York, NY Chap. 4, pp. 121-182, 1998.
C.C. Canavier, R.J. Butera, R.O. Dror, D.A. Baxter, J.W. Clark and J.H. Byrne, ``Phase Response Characteristics of Model Neurons Determine Which Patterns Are Expressed in a Ring Circuit Model of Gait Generation,'' Biological Cybernetics, 77: 367-380, 1997.
J.B. Olansen, F. Ghorbel, J.W. Clark Jr., D. Deyo, J.B. Zwischenberger and A. Bidani, ``An Automated LabVIEW-Based Data Acquisition System for Analysis of Pulmonary Function,'' J. Clinical Engineering, 23: 279-287, 1998.
R.O. Dror, C.C. Canavier, R.J. Butera, J.W. Clark and J.H. Byrne, ``A Mathematical Criterion Based on Phase Response Curves for Stability in a Ring of Coupled Oscillators,'' Biol. Cybernetics, 80: 11-23 , 1999.
C.C. Canavier, D.A. Baxter, J.W. Clark and J.H. Byrne, "Control of Multistability in Ring Circuits of Oscillators", Biological Cybernetics 80: 87-102, 1999.
Niranjan, S.C., Bidani, A., Ghorbel, F., Zwischenberger, J.B. and Clark Jr., J.W., ``Analysis of Inspiratory Waveforms on Pulmonary Blood Flow and Gas Exchange During Mechanical Ventilation,'' Computers in Biomedical Research, 32: 355-390, 1999.
D.A. Baxter, H.A. Lechner, C.C. Canavier, R.J. Butera, A.A. DeFranceschi, J.W. Clark, and J.H. Byrne, ``Coexisting Stable Oscillatory States in Single Cell and Multi cellular Neuronal Oscillators,'' in Oscillations in Neural Systems, D.S. Levine V.R. Brown, and V.T. Shirley, eds., L. Erlbaum Associates, Mahwah, NJ, 51-77, 1999.
Olansen, J.B., Clark, J.W., Khoury, D., Ghorbel, F. and Bidani, A., ``A closed-loop model of the canine cardiovascular system that includes ventricular interaction,'' Computers in Biomedical Research, 33: 260-295, 2000.
Athanasiades, A., F. Ghorbel, J.W. Clark Jr., S.C. Niranjan, J.Olansen, J.B. Zwischenberger, and A. Bidani, `` Energy Analysis of a Nonlinear Model of the Normal Human Lung,'' J. Biological Systems 8: 115-139, 2000.
J.B. Olansen, F. Ghorbel, J.W. Clark Jr. and A. Bidani, ``Using Virtual Instrumentation to Develop a Modern Biomedical Engineering Laboratory,'' International J. Engineering Education, 16: 244-254, 2000.
Lu, K., Clark, J.W., Ghorbel, F., D. Ware and Bidani, A.,"A Human Cardiopulmonary System Model Applied to the Analysis of the Valsalva Maneuver," Amer. J. Physiol., 281: H2661-H2679, 2001.
Lu, K., J.W. Clark Jr., F.H. Ghorbel, D.L. Ware, J.B. Zwischenberger, and A. Bidani, "Whole-body gas exchange in human predicted by a cardiopulmonary model," Cardiovascular Engineering, 3: 1-19, 2003.
Lu, K., J.W. Clark Jr., F.H. Ghorbel, C.S. Robertson, D.L. Ware, J.B. Zwischenberger, and A. Bidani, "Cerebral autoregulation and gas exchange studied with a human cardiopulmonary model," Amer. J. Physiol.,286: H584-H601, 2004.
Luo, C., J.W. Clark, C.C. Canavier, D.A. Baxter and J.H. Byrne, "Multimodal behavior in a four neuron ring circuit: Mode switching," IEEE Trans. on Biomed. Engr.,51(2): 205-218, 2004.
Ha, R.R., J. Qian , D.L. Ware, J.B. Zwischenberger, A. Bidani, and J.W. Clark Jr., "An integrative cardiovascular model of the standing and reclining sheep," J. Cardiovascular Engr., 5(2): 53-76, 2005
Ha, R.R., D. Wang, J.B. Zwischenberger and J.W. Clark Jr.,"Hemodynamic Analysis and Design of a Paracorporeal Artificial Lung Device," J. Cardiovascular Engineering, 6(1), 11-30, 2006.
Luo, C., D. L. Ware, J. B. Zwischenberger and J. W. Clark Jr., “Using a Human Cardiopulmonary Model to Study and Predict Normal and Diseased Ventricular Mechanics, Septal Interaction, and Atrio-Ventricular Blood Flow Patterns,” J. Cardiovasc. Engr. 7:17–31, 2007.
Luo, C., D. L. Ware, J. B. Zwischenberger and J. W. Clark Jr., “A Mechanical Model of the Human Heart Relating Septal Function to Myocardial Work and Energy, J. Cardiovascular Engineering 8(3):174-184, 2008.
D. Ramachandran, C. Luo, T.S. Ma and J.W. Clark, Jr., Using a Human Cardiovascular-Respiratory System Model to Characterize Cardiac Tamponade and Pulsus Paradoxus, J. Theoretical Biology and Medical Modeling (accepted for publication) 2009.
SELECTED PUBLICATIONS (MEDICAL IMAGE PROCESSING):
Yue,Y. M.M. Croitoru, A. Bidani, J.B. Zwischenberger, and J.W. Clark, Jr., "Nonlinear Multiscale Wavelet Diffusion for Speckle Suppression and Edge Enhancement in Ultrasound Images," IEEE Trans. Medical Imaging 25(3): 297-311, 2006
Qiao,F., T. Pan, J.W Clark Jr. and O.R. Mawlawi, "A Motion-incorporated Reconstruction Method for Gated PET Studies," Phys. Med. Biol. 51: 3769–3783, 2006.
Qiao F, T. Pan, J.W. Clark Jr and O.R. Mawlawi, “Joint Model of Motion and Anatomy for PET image Reconstruction,” Med. Physics, 34(12):4626-4639, 2007.
Qiao F, T. Pan, J.W. Clark Jr and O.R. Mawlawi, "Region of Interest Motion Compensation for PET Image Reconstruction,” Phys. Med. Biol. 52(10): 2675-89, 2007.
Chang , G., T. Pan, J.W. Clark Jr and O.R. Mawlawi, "Optimization of Super-resolution Processing Using Incomplete Image Sets in PET Imaging," Med. Phys. 35(12):5748-5757, 2008
Yue, Y., J.W. Clark Jr. and D. Khoury, “Speckle Tracking in Intracardiac Echocardiography for the Assessment of Myocardial Deformation,” IEEE Trans. on Biomed. Engr. 56(2):416-425, 2009.
Chang, G., T. Pan, F. Qiao, J.W. Clark Jr and O.R. Mawlawi, "Comparison Between Two Super-resolution Implementations in PET Imaging," Med. Phys. 36(4):1370-1383, 2009

Lab Members

Lab Photos

Last edited on: August 05, 2009