Research Interests: J.W. Clark Jr.

Research centered on Computational Engineering in Biology and Medicine. The Clark Laboratory develops detailed mechanistic models of biological processes on several levels of scale: from the nano and micro levels (molecular, cellular and tissue models) to organ and body scale levels (large multiple-organ system models). Examples of cellular models include cardiac and smooth muscle cell models, which contain mechanistic descriptions of ion channels and their modulation via cell signaling systems (e.g., second messengers such as nitric oxide, cAMP and cGMP). Multiple-organ system models include cardiovascular and pulmonary systems for a variety of different species (human, canine, ovine). This work has culminated in the development of a neurally controlled human cardiopulmonary (CP) system model, which is used to study the interaction between the cardiovascular and pulmonary systems as mediated by the central nervous system (e.g., prediction of CP dynamics during the Valsalva maneuver, orthostasis, and heart failure). The Clark laboratory also develops detailed Hodgkin-Huxley-type models of individual neurons, which are further employed in neural system models, such as those describing the genesis of rhythmic breathing, feedback control of blood pressure and respiration, and quadrupedal gait (the walk, trot and gallop).

Honors and Awards:

  • 1988 Distinguished Service Award, Alliance for Engineering in Medicine and Biology; presented at the World Congress on Medical Physics and Biomedical Engineering Research.
  • 1992 Distinguished Service Award, Houston Society for Engineering in Medicine; presented at 10th Annual Houston Conference on Biomedical Engineering Research.
  • 1993 Founding Fellow, American Institute of Engineering in Medicine and Biology; award presented at the National Academy of Sciences, Washington, D.C.
  • 1999 Appointed General Chairman, Annual International Conference of the IEEE/Engineering in Medicine and Biology Society held in Houston, TX, October 23-26, 2002.
  • 2000 - 2002 IEEE/EMBS Administration Committee (AdCom); elected Representative Region 5.
  • 2000 Visiting Professor, Laboratory MECAL, University of Lyon, Lyon, France (May - July, 2000).
  • 2002 Program Co-chair, Joint EMBS-BMES Conference, Houston, TX, 23-26 October
  • 2002 President-elect IEEE EMB Society
  • 2003 President IEEE EMB Society
  • 2004 Past President IEEE EMB Society
  • 2005 Elected IEEE Fellow
  • 2005 Elected Founding Fellow of the Biomedical Engineering Society (BMES)

SELECTED PUBLICATIONS (Molecular and Cellular Modeling):

  • Schild,J.H., J.W. Clark Jr., C.C. Canavier, D.L. Kunze and M.C. Andresen, ``Afferent Synaptic Drive of Rat Medial Nucleus Tractus Solitarius Neurons: Dynamic Simulation of Graded Vesicular Mobilization, Release and non-NMDA Receptor Kinetics,'' Journal of Neurophysiology, 74: 1529-1548, 1995.
  • Butera,R.J., J.W. Clark, Jr., and J.H. Byrne, ``Dissection and Reduction of a Modeled Bursting Neuron,'' Journal of Computational Neuroscience, 3: 199-223, 1996.
  • Lindblad,D.S., 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.
  • Demir,S.S., 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.
  • Nygren,A., C. Fiset, L. Firek, J.W. Clark Jr., 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.
  • Demir,S.S., 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, J. Computational Neuroscience 9: 237-257, 2000.
  • Sun,L., 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.
  • Yang,J., J.W. Clark Jr., R.M. Bryan, and C.S. Robertson, "The myogenic response in isolated rat cerebrovascular arteries: Smooth muscle cell model," Medical Engineering Physics, 25(8): 691-709, 2003.
  • Yang, J., J.W. Clark Jr., R.M. Bryan, and C.S. Robertson, "The myogenic response in isolated rat cerebrovascular arteries: Vessel model," Medical Engineering Physics, 25(8): 711-717, 2003.
  • 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: 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.
  • Yang, J., J.W. Clark Jr., R.M. Bryan, and C.S. Robertson, "Mathematical Modeling of the Nitric Oxide/cGMP Pathways in the Vascular Smooth Muscle Cell," Amer. J. Physiology, 289: H886-H897, 2005.
  • 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.
  • 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 System 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,'' American Journal of Physiology, 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,'' Biological 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 and 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.
  • Lu, K., J.W. Clark Jr., F.H. Ghorbel,D.L. Ware, and A. Bidani,"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.
  • C. Luo, J.W. Clark Jr., A.A. DeFranceschi, 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,"Cardiovascular Engineering, 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,"Cardiovascular Engineering, 6(1): 10-29, 2006.
  • 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., Pan, T., Clark, J.W. Jr., Mawlawi, O.R.," A Motion-incorporated Reconstruction Method for Gated PET Studies,"Phys Med Biol, 51(15): 3769-83, 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.
  • 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. Cardiovascular Engineering. 7:17–31, 2007.
  • 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. (accepted for publication) 2008.
  • 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 (accepted for publication) 2008.