Michael Domach-Chemical Engineering - Carnegie Mellon University

Michael Domach

Professor, Chemical Engineering

Office: Doherty Hall A221
Phone: 412-268-2246
Fax: 412-268-7139

Bio

Professor Mike Domach received his B.S in Chemical Engineering with Environmental Engineering and Chemistry minors from the University of Massachusetts and he obtained his Ph.D. in Chemical Engineering from Cornell University. He was the inaugural Dow Chair Recipient, Universidad Nacional del Sur, Argentina. He has served as a Senior Visiting Scientist, Bioinformatics, The Jackson Lab, Bar Harbor, ME and as a Co-Director of the NIH Training Program in Biotechnology. He is on the Editorial Board of the J. Biotechnology and was a Co-founder Automated Cell Technologies Inc, a NIST-ATP funded company. Prof. Domach wrote the textbook Introduction to Biomedical Engineering, now in its second edition. Currently, he serves as the Editor and Chief of Biotechnology Progress.

Education

Ph.D. Cornell University
B.S. Chemical Engineering, University of Massachusetts

Research

Professor Domach studies fundamental and applied aspects of cell engineering and biology. Both experimental and computational work is performed.

Vaccine Production

A collaboration with faculty at the University of Pittsburgh Medical Center and engineers at the University of Pittsburgh aims to develop improved host-plasmid platforms for producing DNA and recombinant protein vaccines.

Cellular Processes

The goal is to understand the behavior of cells in bioreactors and, thus, reactor performance in terms of biochemical reaction and control mechanisms. Current work entails developing in situ NMR and fluorescent spectroscopic methods for observing intracellular reaction processes. Coupling the experimental investigations to mathematical model development also is a key component of this work. The latter entails developing experimental designs that provide high resolution of metabolic fluxes.

Research Websites

Biomolecular engineering
Energy Science and Engineering

Highlights

  • A presentation at the August ACS Mtg (Washington DC) was selected as the Best of BIOT, and will be the subject of an upcoming WEBINAR broadcasted to industry, classrooms, and other locations.

Awards and Honors

  • Appointed Editor of Biotechnology Progress
  • Inaugural Dow Chair Holder, Universidad Nacional del Sur, Argentina, December 2007
  • Work on sensing focal adhesion in electrical sensing arrays (Biotechnol Bioeng. 87(2):138-44, 2004) was adopted for use in Chemical Biophysics: Quantitative Analysis of Cellular Systems. D.A. Beard & H. Qian, (ISBN 978 0 521 87070 2).
  • Dowd Fellowship, Carnegie Institute of Technology, 2001-2002
  • In 2000, paper voted top 20 most influential publications in 40 years of journal’s history (Domach, et al, "Computer Model for Glucose-Limited Growth of a Single Cell of E. coli B/r-A ," Biotechnol. Bioeng., v. 26, p.577, 1984.)
  • Work by Castro et al (1999) used as examples in textbook “NMR in Microbiology: Theory and Applications,” (2000) Horizon Scientific Press
  • Majewski & Domach (1990) described as first major model development in a critical review in J. Bacteriol, 2003, 185(9): 2692-2699
  • Article won first-place in national competition sponsored by the journal Envir. Progress
  • Fellow, American Institute of Biological and Medical Engineers
  • Recipient of a Presidential Young Investigator Award

Publications

Recent Publications
Selected Publications
Full Publication

Recent Publications

J.W. Meade, M.M. Ataai, and M.M. Domach.  “Use of flux pre-analysis to enable 13C tracer studies in pyruvate kinase-deficient Escherichia coli.” Biotechnology Journal, 7: 449–460, 2012.

J.T. Leppävuori, M.M. Domach, and L.T. Biegler. "Parameter Estimation in Batch Bioreactor Simulation Using Metabolic Models: Sequential Solution with Direct Sensitivities," I & EC Research. 50: 12080-12091, 2011.

Selected Publications

M.M. Domach. Introduction to Biomedical Engineering, 2nd edition (2009), Prentice Hall.

D. Cunningham. Z. Liu, N. Domagalski, R. Koepsel, M.M. Ataai, and M.M. Domach. “Pyruvate Kinase Deficient Escherichia coli Exhibits Increased Plasmid Copy Number and Cyclic AMP.” Journal of Bacteriology, 191(9): 3041-3049, 2009.

T. Zhu, C. Phalakornkule, S. Ghosh, I.E. Grossmann, R.R. Koepsel, M.M. Ataai, and M.M. Domach. "A Metabolic Network Analysis & NMR Experiment Design Program with User Interface-Driven Model Construction," Metabolic Engineering, 5(2): 74-85, 2003.

S. Ghosh, T. Zhu, I.E. Grossmann, M.M. Ataai, and M.M. Domach. "Closing the Loop Between Feasible Flux Scenario Identification for Construct Evaluation and Resolution of Realized Fluxes via NMR." 15 February 2005, 459-66, Computational Challenges in Biology Issue.

D.D. Nguyen, X. Huang, D.W. Greve, and M.M. Domach. "Fibroblast Growth and H-7 Protein Kinase Inhibitor Response Monitored in Microimpedance Sensor Arrays." Biotechnol Bioeng. 87(2): 138-44, 2004.

T. Zhu, Z. Pan, R. Koepsel, M.M. Ataai, and M.M. Domach. "Engineering of Bacillus subtilis for the Enhanced Total Synthesis of Folic Acid," Applied & Env. Microbiology. 71 (2005): 7122-7129.

C.J. Eskey, A.P. Koretsky, M.M. Domach, and R.K. Jain, "Determinants of Tumor Energy Status by 31P Nuclear Magnetic Resonance and ex vivo Tumor Perfusion," Proc. Natl. Acad. Sci. 90: 2646-2650, 1993.

M.M. Domach and M.L. Shuler, "Testing of a Potential Mechanism for E. coli Temporal Cycle Imprecision with a Structured Model," J. Theor. Biol., v.106, p.577, 1984.

Full Publications

M.M. Domach and M.L. Shuler, "Testing of a Potential Mechanism for E. coli Temporal Cycle Imprecision with a Structured Model," J. Theor. Biol., v.106, p.577, 1984.

M.M. Domach and M.L. Shuler, "A Finite Representation Model for an Asynchronous Culture of E. coli," Biotechnol. Bioeng., v. 26: p.877, 1984.

M.M. Domach, S.K. Leung, R.E. Cahn, G.G. Cocks, and M.L. Shuler, "Computer Model for Glucose-Limited Growth of a Single Cell of E. coli B/r-A ," Biotechnol. Bioeng., v. 26, p.577, 1984.

M.L. Shuler and M.M. Domach, "Mathematical Models of the Growth of Individual Cells: Tools for Testing Biochemical Mechanisms," In Foundations of Biochemical Engineering: Kinetics and Thermodynamics in Biological Systems, ACS Symp. Series, v. 207, p.93, 1983.

M.M. Domach, "Immobilized Enzyme Performance Parameter Specification," The World Biotechnology Report 1984: USA, v.24, A31-A36, 1984

M.M. Domach, "A General Dimensionless Model for the Evaluation of the Feasibility of Immobilized Enzyme Processes," Chem. Eng. J. v. 29, p.B1, 1985.

M.M. Domach, R. Armstrong, and M.S. Jhon, "Cell Mass Concentration Variance Resulting from Fluctuations in the Incoming Nutrient Concentration to a Chemostat," Bull. Math. Biol., v.47, p.337, 1985.

M.M. Domach and T.G. Gricus, "Optimization of the Retrofitting of Soluble to Immobilized Enzyme Processes," Biotechnol. Bioeng., v. 27, p.1458, 1985.

M.M. Domach and R.A. Majewski, "Consideration of the Gain, Enzymatic Capacity Utilization, and Response Time Properties of Metabolic Networks as a Function of Operating Point and Structure," Biosystems, v. 18, p.15, 1985.

M.M. Domach, "Cellular Processes, Biomolecules, and Bioprocesses," CIT Engineering News, May 1986.

R.A. Majewski and M.M. Domach, "Determining Pathway Structure-Property-Function Relationships Through Experimentation and Analytical Frameworks," Annals. N.Y. Acad. Sci., v. 506, p.106, 1987.

M.M. Domach, "Cellular System Engineering," Accent on Research, November 1988.

C.L. Kennedy, H.R. Zanapolidou, S. Sagar, S.A. Tristram-Nagle, and M.M. Domach, "Microcalorimetry, Fractionation, and Fluorescence Study of Yeast Alcohol Dehydrogenase: Structure and Heterogeneity Implications," Biotechnol. Prog., v. 5, p.164, 1989.

R.A. Majewski and M.M. Domach, "Simple Constrained-Optimization View of Acetate Overflow in E. coli.," Biotechnol. Bioeng., v. 3, 732, 1990.

E.S. Shane, J.L. Anderson, and M.M. Domach, "Enhanced Protein Diffusion in a Solvent Gradient," I&EC Research, v. 29, p. 309, 1990.

C.L. Kennedy and M.M. Domach, "Yeast Alcohol Dehydrogenase Bound to Membranes: Surface and Microenvironment Effects on Activity and Stability," Biotechnol. Prog., v.6, p.41, 1990.

R.A Majewski and M.M. Domach, "Effect of Regulatory Mechanism on Hyperbolic Reaction Network Properties," Biotechnol. Bioeng., v.36, p.166, 1990.

R.A. Majewski and M.M. Domach, "Chemostat Cultivated E. coli at High Dilution Rate: Multiple Steady-States and Drift," Biotechnol. Bioeng., v.36, p.179, 1990.

S.L. Sagar and M.M. Domach,"Thermal Stability of Oligomeric, Reduced, and Refolded Proteins," in Protein Refolding, Chapter 5, ACS Symposium Series 470, 1991, G. Georgiou and E. De Bernardez-Clark.

A.J. Meehan, E.G. Minkley, and M.M. Domach, "Growth State Control and Dynamics of the Expression of Beta-Galactosidase Under the Control of the MicrosinB Promoter in an Isogenic Fusion," Biotechnol. Bioeng. 38: 719-726, 1991.

H.A. Zanapalidou and M.M. Domach, "Effect of Self-Associating on the Transport of Alpha-Chymotrypsin Across Microporous Membranes," Biotechnol. Prog. 7: 335-342, 1991.

M.M. Domach, "Recommendations for Cell Culture System for LifeSat Experiments," Proceedings of the LifeSat Cell Facility Workshop, Jet Propulsion Laboratory, Pasadena, CA; G. Nelson, G. Ganapathi, and M. Fong, Section 8.1, 1991.

A.J. Lipton and M.M. Domach, "Monitoring Protein Synthesis, Export, and Tryptophan Incorporation by Front-Surface Fluorescence Spectroscopy," Biotechnol. Bioeng. 39:13-19, 1992.

A.J. Meehan, A.J. Lipton, A.P. Koretsky, and M.M. Domach, "Monitoring and Characterizing Cell Suspensions by Front-Surface Fluorescence Spectroscopy and In situ 31P MRS" in Sensing in Biological Systems, Academic Press, 1991.

A.J. Meehan, C. Eskey, A.P. Koretsky, and M.M. Domach, "Cultivator for NMR Studies of Suspended Cell Cultures," Biotechnol. Bioeng. 40: 1359-1366, 1992.

C.J. Eskey, A.P. Koretsky, M.M. Domach, and R.K. Jain, "2H NMR Imaging of Tumor Blood Flow: Spatial and Temporal Heterogeneity in a Tissue-Isolated Mammary Adenocarcinoma," Cancer Research, 52: 6010-6019, 1992..

S.L. Sagar, R.R. Beitle, M.M Ataai, and M.M. Domach, "Repurification of Chymotrypsin Preparations," American Biotechnology Laboratory News, 1992.

C.J. Eskey, A.P. Koretsky, M.M. Domach, and R.K. Jain, "Determinants of Tumor Energy Status by 31P Nuclear Magnetic Resonance and ex vivo Tumor Perfusion," Proc. Natl. Acad. Sci. 90: 2646-2650, 1993.

R. Putcha and M.M. Domach, "Fluorescence Monitoring of Polycyclic Aromatic Biodegradation and Effect of Surfactants,” Envir. Prog. 12: 81-85, 1993 (first place winner of national research paper contest).

S.L. Sagar, R.R. Beitle, M.M Ataai, and M.M. Domach, "Metal-Based Affinity Separation of Alpha- and Gamma-Chymotrypsin," Bioseparation, 3: 291-296, 1993.

S.L. Sagar, H.A. Zanapolidou, and M.M. Domach, "Protein Biophysical Chemistry and Biochemistry Effects on Membrane Transport and Immobilization," Bioseparation, 4: 75-182, 1994.

C.J. Eskey, N. Wolmark, C.L. McDowell, M.M. Domach, and R.K. Jain, "Residence Time Distribution in Tumors," Journal National Cancer Society, 86: 293-297, 1994.

J. Lee, A. Goel, M.M. Ataai, and M.M. Domach, "Flux Adaptations in Citrate Synthase-Deficient E. coli," Annals. NY Academy of Science, 745: 35-59, 1994.

S.A. Buchannan, S.M. Melnik, C. Tancin, P. Whitmore, W. Bennett, and M.M. Domach, "An Evaluation of the Book-Keeper Assessment of Mass Deacidification Process," 1995, Library of Congress and Government Printing Office.

R.L. Auger, A.M. Jacobson, and M.M. Domach, "Determination of Naphthalene Partitioning in Nonionic Surfactant Micelles by Aqueous Phase Fluorescence Quenching," Env. Sci. & Technol. 29: 1273-1278, 1995.

R.L. Auger, A.M. Jacobson, and M.M. Domach, “Effect of Nonionic Surfactant Addition on Bacterial Metabolism of Naphthalene: Assessment of Toxicity and Overflow Metabolism Potential," J. Hazardous Materials, 43: p.263, 1995.

C.D. Castro, A.J. Meehan, and M.M. Domach, "Polyphosphate & Catabolite Responses of Chemostat-Cultivated S. cerevisiae After Alkalinization: Observation Enabled with in situ 31P NMR," Applied & Env. Microbiology, 61: 4448-4453, 1995.

C. Vierheller, A. Goel, M.M. Domach and M.M. Ataai, "Sustained and Constitutive High Levels of Protein Production in Continuous Cultures of B. subtilis," Biotechnol. Bioeng. 47: 520-525, 1995.

A. Goel, J. Lee, M.M. Domach, and M.M Ataai. "Suppressed Acid Formation by Cofeeding Glucose and Citrate in Bacillus Cultures: Emergence of Pyruvate Kinase as a Potential Metabolic Engineering Site," Biotechnol. Prog., 11: 380-386, 1995.

M.M. Domach. Review of "The Theory of the Chemostat; Dynamics of Microbial Competition," J. Am. Chem. Soc. 117: 11616-11618, 1995.

S.L. Sagar and M.M. Domach, "Using Differential Scanning Calorimetry to Elucidate Metal-Protein Binding Modalities in Alpha- and Gamma-Chymotrypsin," Bioseparations, 5: 289-294, 1995.

Z. Yang, M.M. Domach, R. Auger, F. Yang, and A.J. Russell, "Polyethylene Glycol-Induced Stabilization of Subtilisin," Enzym. Microbiol. Technol. 18: 82-89, 1996.

A. Goel, J. Lee, M.M. Domach, and M.M Ataai. "Coordination of Glycolysis and TCA Cycle Reaction Networks: Citrate-Glucose Metabolism Eliminates Acids and Reveals Potential Metabolic Engineering Strategies," Annals. N.Y. Acad. Sci. 782: 1-16, 1996.

J.W. Lee, A. Goel, M.M. Ataai, and M.M. Domach, “Supply-Side Analysis of Growth of B. subtilis on Glucose-Citrate Medium: Feasible Network Alternatives and Yield Optimality," Applied and Env. Microbiol. 63: 710-718, 1997..

J.P. Goff, D.S. Shields, J.E. Bush, et al, “Kinetics of the First Division of CD34+Lin- Cells: Manual Compared to Continuous Automated Observation and the Influence of Cytokines,” Blood 90 (10): 2109-2109, 1997.

J.E. Bush, M.M. Domach, P.A. DiMilla, et al, “Fission Time Histograms of Small Numbers of CD34+LIN- And CD34+LIN+ Cells by a Novel Tissue Culturing Device Cells,” Exptl. Hematology, 25 (8): 274-274, 1997.

J.E. Bush, P.A. DiMilla, and M.M Domach, “Cell Motility and Morphology of Primitive Hematopoietic Cells.” Molec. Biol. Cell. 9: 728, 1998.

J.E. Bush, P.A. DiMilla P, M.M Domach, et al, “Motility and Morphology of Individual Primitive Hematopoietic Cells Cultured In Media with Different Cytokine Combinations. Expt. Hematology, 26 (8): 193, 1998.

A. Goel, J. Lee, M.M. Domach, M.M. Ataai, “Metabolic Fluxes, Pools, and Enzyme Measurements Suggest a Tighter Coupling of the Energetics and Biosynthetic Reactions is Associated with Reduced Pyruvate Kinase Flux, Biotech. Bioeng. 64(2): 129-134, 1999.

C.D. Castro, A.P. Koretsky, and M.M. Domach, "Design Trade-Offs in In Situ Chemostat NMR, Biotech. Prog. 15: 185-195, 1999.

C.D. Castro, A.P. Koretsky, and M.M. Domach, "NMR-Observed Phosphate Trafficking & Polyphosphate Dynamics in Wild-Type and vph1-1 Mutant S. cerevisae," Biotech. Prog. 15 (1): 65-73, 1999.

J-H Kim, M.M. Domach, R.D. Tilton, “Pyrene Solubilization in Octaethylene Glycol Monododecyl Ether Micelles,” Colloids and Surfaces, 150: 55-68, 1999.

J.H. Kim, M.M. Domach, and R.D. Tilton, “Pyrene Solubilization Capacity in Octaethylene Glycol Monododecyl Ether (C12E8) Micelles,” Colloids and Surfaces A-Physicochemical and Engineering Aspects, 150 (1-3): 55-68, 1999.

J-H Kim, M.M. Domach, R.D. Tilton, “Pyrene Micropartitioning and Solubilization by SDS Complexes with Polyethylene Gycol,” J. Phys. Chem. B, 103: 10582-90, 1999.

M.M. Domach, "Recent Advances in Analytical Methods," J. Biotechnology, 71: 229-232, 1999.

J.S. Greenberger, J.P. Goff, J. Bush, A. Bahnson, D. Koebler, H. Athanassiou, M.M. Domach, and R.K. Houck. “Expansion of Hemapoietic Stem Cells In Vitro as a Model System for Human Tissue Engineering.” Clinics in Plastic Surgery, 26 (4): 569-578, 1999.

C. Phalakornkule, B. Fry, R. Koepsel, M.M. Ataai, and M.M Domach. “13C NMR Evidence for Pyruvate Kinase Flux Attenuation Underlying Suppressed Acid Formation in B. subtilis,” Biotech. Prog. 16: 169-175, 2000.

S. Lee, C. Phalakornkule, M.M. Domach, and I.E. Grossmann. “Recursive MILP Model for Finding All the Alternate Optima in LP Models for Metabolic Networks,” Computers in Chemical Engineering, 24: 711-716, 2000.

B. Fry, T. Zhu, R.R. Koepsel, C. Phalakornkule. M.M Domach, M.M. Ataai, “Characterization of Growth and Acid Formation in a Bacillus subtilis Pyruvate Kinase Mutant,” Applied and Environmental Microbiology, 66: 4025-4050, 2001.

C. Phalakornkule, T. Zhu, S. Lee, R. Koepsel, M.M. Ataai, I.E. Grossmann, and M.M. Domach, “A MILP-Based Flux Alternative Generation & NMR Experimental Design Strategy for Metabolic Engineering,” Metabolic Engineering, 3: 124-137, 2001

Zhu T., Phalakornkule C., Koepsel R.R., Domach M.M., and M.M. Ataai. “Cell Growth and By-Product Formation in a Pyruvate Kinase Mutant of E. coli,” Biotechnol. Prog. 17: 624-628, 2001.

Lee, J., Goel, A., Ataai, M.M., and Domach, M.M. “Flux Regulation Patterns and Energy Audit of E. coli B/r and K-12,” J. Microbiol. Biotechnol. 12(2): 258-267, 2002.

T. Zhu, R. Koepsel, M.M. Domach, and M.M. Ataai. “Metabolic Engineering of Folic Acid Production.” ACS Symposium Series 862, Fermentation Biotechnology, Chapter 12, 207-218, 2003 (ed. B.C. Saha).

T. Zhu, R.R. Koepsel, C. Phalakornkule, M.M. Ataai, I.E. Grossmann, and M.M. Domach. “A Metabolic Network Analysis & NMR Experiment Design Program With User Interface-Driven Model Construction,” Metabolic Engineering, 5(2): 74-85, 2003.

X. Huang, D.D Nguyen, D.W. Greve, and M.M. Domach. “Impedance Based Biosensor Array for Monitoring Mammalian Cell Behavior," IEEE Sensors Journal, 5(3): 304-309, 2003.

D.D Nguyen, X. Huang X, D.W. Greve, and M.M. Domach. “Fibroblast Growth and H-7 Protein Kinase Inhibitor Response Monitored in Microimpedance Sensor Arrays,” Biotechnol Bioeng. 87(2):138-44, 2004.

X. Huang, D.D. Nguyen, D.W. Greve, and M.M. Domach. “Simulation of Microelectrode Impedance Changes due to Cell Growth,” IEEE Sensors Journal, 4(5): 576-583, 2004.

S. Ghosh, T. Zhu, I.E. Grossmann, M.M. Ataai, and M.M. Domach. “Closing the Loop Between Feasible Flux Scenario Identification For Construct Evaluation & Resolution of Realized Fluxes via NMR,” Computers & Chemical Engineering, 29: 459-466, 2005. Appeared in special issue with intent to pose and describe systems analysis problems presented by biological systems.

T. Zhu, Z. Pan, R. Koepsel, M.M. Ataai, and M.M. Domach. “Engineering of Bacillus subtilis for the Enhanced Total Synthesis of Folic Acid,” Appld. Env. Microbiol. 71(11): 7122-7129, 2005.

N. Domalgalski and M.M. Domach. “Basics of Molecular Biology,” In the CRC Handbook of Biomedical Engineering (2006). MMD is also section editor who solicited and edited other contributions.

S. Ghosh, I.E. Grossmann, M.M. Ataai, and M.M. Domach. “A Three-Level Problem-Centric Strategy for Selecting NMR Precursors and Analytes.” Metabolic Engineering, 8: 491-507, 2006.

Z. Pan, R. Koepsel, M.M. Domach, and M.M. Ataai. “Regulating Expression of Pyruvate Kinase In Bacillus Subtilis for Control of Growth Rate And Formation of Acidic Byproducts.” Biotech. Prog. Sep-Oct; 22(5):1451-5, 2006.

D. Cunningham. Z. Liu, N. Domagalski, R. Koepsel, M.M. Ataai, and M.M. Domach. “Pyruvate Kinase Deficient Escherichia coli Exhibits Increased Plasmid Copy Number and Cyclic AMP.” J. Bacteriol. 191(9): 3041-3049, 2009.

D.S Cunningham, R. Koepsel, M. Ataai, and M.M Domach. “Factors Affecting Plasmid Production in Escherichia coli from a Resource Allocation Standpoint.” Microbial Cell Factories, 8(27): 1 – 17, 2009.

Z. Pan, D.S. Cunningham, T. Zhu, K. Ye, R. R. Koepsel, M.M. Domach, M.M. Ataai. “Enhanced Recombinant Protein Production in Pyruvate Kinase Mutant of Bacillus subtilis.” Appl Microbiol Biotechnol.  85:1769–1778, 2009.

M.M. Domach and L.W. Walker. “Stabilizing Biomacromolecules in Nontoxic Nano-structured Materials.” Journal of the Association for Laboratory Automation 15 136-144 (2010).

J.T. Leppävuori, M.M. Domach, and L.T. Biegler. "Parameter Estimation in Batch Bioreactor Simulation Using Metabolic Models: Sequential Solution with Direct Sensitivities," I & EC Research. 50: 12080-12091, 2011.

J.W. Meade, M.M. Ataai, and M.M. Domach.  “Use of flux pre-analysis to enable 13C tracer studies in pyruvate kinase-deficient Escherichia coli.” Biotechnology Journal, 7: 449–460, 2012.

R. Travedi, J.W. Meade, P. Bartlow, S. Khan, M.M. Ataai, and M.M. Domach.  “High Plasmid Yield in E. coli DH5? Through the inc Mutations” (submitted).

J.W. Meade, P. Bartlow, R. Travedi, S. Khan, M.M. Ataai, and M.M. Domach.  “Proteomic Contrast of Stationary and Exponential E. coli DH5? Hosting High Copy Numbers of Plasmids” (submitted).