Michael Crowley

Michael Crowley

Principal Scientist

Phone: 
(303) 384-6345
At NREL Since: 
2007

Dr. Michael Crowley is a principal scientist in the Biosciences Center, joining NREL in 2007 to develop a simulation and theory group. He leads the theory, modeling, and simulation efforts for biofuels research. He is the Principal Investigator for the DOE BETO project: Biochemical Process Modeling and Simulation, in which enzyme digestion, metabolic modeling, and reactor and process design are the main thrusts. He is co-PI and leads the modeling thrust of C3Bio, the Energy Frontier Research Center in which NREL is a partner with Purdue, and multiple other collaborative projects in biofuels and computational chemistry research. He and his team maintain a level of productivity that produces on the order of 15 peer-reviewed articles a year and as many presentations and are regarded internationally as the most productive and authoritative center for biofuel and biomass simulation and theory.

Mike is a developer of both CHARMM and Amber molecular dynamics software for biological macromolecular simulation and has contributed significant advances to highly-parallel high-performance scientific software for use on supercomputers. His team until recently included Antti-Pekka Hynninen who is pushing the frontier of scientific simulation using the most up-to-date computer hardware available and in preparation for future computer architectures. Mike’s group has designed and implemented new methods and algorithms specifically for biomass and biofuel related questions. He is author on over 130 peer reviewed scientific articles, has given over 200 presentations, more than 50 invited.

Mike received his B.S. in Chemistry from Fordham University, and M.S. and Ph.D. in Physical Chemistry from University of Montana in 1985 with a short period of study at University of Alberta. He had a post-doctoral fellowship was at Brandeis University with Dr. Irving Epstein. His doctoral and post-doctoral research was studying coupled chemical oscillators and coupled nonlinear differential equations and was the only study to date of non-forced coupled chemical reactions showing synchronization, locking, and chaotic behaviors. In his time as assistant professor at Penn State University, he moved to studies of semiconductor surfaces. At West Virginia University he applied the nonlinear dynamical theories to controlling chaos in chemical oscillators and flame fronts. At Carnegie Mellon University and the Pittsburgh Supercomputing Center, and at The Scripps Research Institute, with David Case and Charles Brooks, he developed highly parallel methods for simulations of bio-macromolecules.

Education 

  • B.S. Chemistry, Fordham University, 1976

  • M.S. Physical Chemistry, University of Montana, 1980

  • Ph.D. Physical Chemistry, University of Montana, 1984

  • Postdoctoral Fellow, Brandeis University, 1985-1987

Selected Publications 

  1. Bu, L.; Himmel, M.E.; Crowley, M.F. (2015). "The Molecular Origins of Twist in Cellulose I-beta." Carbohydrate polymers (125:10); pp. 146-152.
  2. Sammond, D.W.; Yarbrough, J.M.; Mansfield, E.; Bomble, Y.J.; Hobdey, S.E.; Decker, S.R.; Taylor, L.E.; Resch, M.G.; Bozell, J.J.; Himmel, M.E.; Vinzant, T.B.; Crowley, M.F. (2014). "Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity.." Journal of Biological Chemistry (M114);
  3. Knott, B. C.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.; Stahlberg, J. "Carbohydrate-Protein Interactions that Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity." Journal of the American Chemical Society (136:24); pp. 8810-8819.
  4. Atalla, R. S.; Crowley, M. F.; Himmel, M. E.; Atalla, R. H. (2014). "Irreversible Transformations of Native Celluloses, Upon Exposure to Elevated Temperatures." Carbohydrate Polymers pp. 2-8 .
  5. Ciesielski, P.N.; Crowley, M.F.; Nimlos, M.R.; Sanders, A.W.; Wiggins, G.M.; Robichaud, D.; Donohoe, B.S.; Foust, T.D. "Biomass Particle Models with Realistic Morphology and Resolved Microstructure for Simulations of Intraparticle Transport Phenomena." Energy & Fuels (29:1); pp. 242-254.
  6. Beckham, G. T.; Stahlberg, J.; Knott, B. C.; Himmel, M. E.; Crowley, M. F.; Sandgren, M.; Sorlie, M.; Payne, C. M (2014). "Towards a Molecular-Level Theory of Carbohydrate Processivity in Glycoside Hydrolases." Current Opinion in Biotechnology (27); pp. 96-106.
  7. Hynninen, Antti-Pekka; Crowley, Michael F. "New Faster CHARMM Molecular Dynamics Engine." J. Comp. Chem. (35:406);
  8. Chen, M.; Kostylev, M.; Bomble, Y. J.; Crowley, M. F.; Himmel, M. E.; Wilson, D. B.; Brady, J.W. (2014). "Experimental and Modeling Studies of an Unusual Water-Filled Pore Structure with Possible Mechanistic Implications in Family 48 Cellulases." Journal of Physical Chemistry B (118:9); pp. 2306-2315.
  9. Knott, B. C.; Momeni, M. H.; Crowley, M. F.; Mackenzie, L. F.; Gotz, A. W.; Sandgren, M.; Withers, S. G.; Stahlberg, J.; Beckham, G. T. (2014). "Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies." Journal of the American Chemical Society (136:1); pp. 321-329.
  10. Olek, A. T.; Rayon, C.; Makowski, L.; Kim, H. R.; Ciesielski, P.; Badger, J.; Paul, L. N.; Ghosh, S.; Kihara, D.; Crowley, M. "The Structure of the Catalytic Domain of a Plant Cellulose Synthase and Its Assembly into Dimers.." The Plant Cell Online 2014 (26:7); pp. 2996-3009.
  11. Brunecky, R.; Alahuhta, M.; Xu, Q.; Donohoe, B. S.; Crowley, M. F.; Kataeva, I. A.; Yang, S. J.; Resch, M. G.; Adams, M. W. W.; Lunin, V. V.; Himmel, M. E.; Bomble, Y. J. (2014). "Response to Comment on 'Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA'." Science (344:6184); pp. 578-578.
  12. Alekozai, E. M.; GhattyVenkataKrishna, P. K.; Uberbacher, E. C; Crowley, M. F.; Smith, J. C.; Cheng, X. (2014). "Simulation Analysis of the Cellulase Cel7A Carbohydrate Binding Module on the Surface of the Cellulose I-beta." Cellulose (21:2); pp. 951-971.
  13. Brunecky, R.; Alahuhta, M.; Xu, Q.; Donohoe, B. S.; Crowley, M. F.; Kataeva, I. A.; Yang, S. J.; Resch, M. G.; Adams, M. W. W.; Lunin, V. V.; Himmel, M. E.; Bomble, Y. J. (2013). "Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA." Science (342:6165); pp. 1513-1516.
  14. McCann, M.; Mahdi, A.; Rakesh, A.; Bozell, J.; Carpita, N.; Chapple, C.; Crowley, M. (2015). "Tailoring Biomass for Biochemical, Chemical or Thermochemical Catalytic Conversion." The FASEB Journal 29 (no. 1 Supplement); pp. 485-488.
  15. Lin, Y.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.; Chu, J. W (2013). "Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures." Journal of Physical Chemistry B (117:37); pp. 10750-10758.
  16. Taylor, C. B.; Payne, C. M.; Himmel, M. E.; Crowley, M. F.; McCabe, C.; Beckham, G. T. (2013). "Binding Site Dynamics and Aromatic-Carbohydrate Interactions in Processive and Non-Processive Family 7 Glycoside Hydrolases." Journal of Physical Chemistry B (117:17); pp. 4924-4933.
  17. Payne, C. M; Resch, M. G.; Chen, L.; Crowley, M. F.; Himmel, M. E.; Taylor, L. E.; Sandgren, M.; Stahlberg, J.; Stals, I.; Tan, Z.; Beckham, G. T. (2013). "Glycosylated Linkers in Multimodular Lignocellulose-Degrading Enzymes Dynamically Bind to Cellulose." Proceedings of the National Academy of Sciences of the United States of America (110:36); pp. 14646-14651.
  18. GhattyVenkataKrishna, P. K.; Alekozai, E. M.; Beckham, G. T.; Schulz, R.; Crowley, M. F.; Uberbacher, E. C.; Cheng, X. (2013). "Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity." Biophysical Journal (104:4); pp. 904-912.
  19. Bu, L.; Crowley, M. F.; Himmel, M. E.; Beckham, G. T. (2013). "Computational Investigation of pH Dependence on Loop Flexibility and Catalytic Function in Glycoside Hydrolases." Journal of Biological Chemistry (288:17); pp. 12175-12186.
  20. Wu, M.; Beckham, G. T.; Larsson, A. M.; Ishida, T.; Kim, S.; Payne, C. M.; Himmel, M. E.; Crowley, M. F.; Horn, S. J.; Westereng, B.; Igarashi, K.; Samejima, M.; Stahlberg, J.; Eijsink, V. G. H.; Sandgren, M. (2013). "Crystal Structure and Computational Characterization of the Lytic Polysaccharide Monooxygenase GH61D from the Basidiomycota Fungus Phanerochaete chrysosporium." Journal of Biological Chemistry (288:18); pp. 12828-12839.
  21. Vermaas, J. V.; Payne, C. M.; Crowley, M. F.; Beckham, G. T. (2013). "Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases." Biophysical Journal (104:2); pp. 113-113.
  22. Wu, M.; Bu, L.; Vuong, T. V.; Wilson, D. B.; Crowley, M. F.; Sandgren, M.; Stahlberg, J.; Beckham, G. T.; Hansson, H. (2013). "Loop Motions Important to Product Expulsion in the Thermobifida fusca Glycoside Hydrolase Family 6 Cellobiohydrolase from Structural and Computational Studies." Journal of Biological Chemistry (288:46); pp. 33107-33117.
  23. Ciesielski, P.N.; J.F. Matthews; M.P. Tucker; G.T. Beckham; M.F. Crowley; M.E. Himmel; B.S. Donohoe (2013). "3D Electton Tomography of Pretreated Biomass Informs Atomic Modeling of Cellulose Microfibrils.." Acs Nano (7:9); pp. 8011-8019.
  24. Payne, C. M.; Jiang, W.; Shirts, M. R.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T (2013). "Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy." Journal of the American Chemical Society (135:50); pp. 18831-18839.
  25. Matthews, J. F.; Himmel, M. E.; Crowley, M. F. (2012). "Conversion of Cellulose I-alpha to I-beta v ia a High Temperature Intermediate (I-HT) and Other Cellulose Phase Transformations." Cellulose (19:1); pp. 297-306.
  26. Bu, L.; Nimlos, M. R.; Shirts, M. R.; Stahlberg, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T. (2012). "Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes." Journal of Biological Chemistry (287:29); pp. 24807-24813.
  27. Sammond, D. W.; Payne, C. M.; Brunecky, R.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T. (2012). "Cellulase Linkers Are Optimized Based on Domain Type and Function: Insights from Sequence Analysis, Biophysical Measurements, and Molecular Simulation." PLoS One (7:11); pp. e48615-e48615.
  28. Matthews, J. F.; Beckham, G. T.; Bergenstrahle, M.; Brady, J. W.; Himmel, M. E.; Crowley, M. F. (2012). "Comparison of Cellulose Ib Simulations with Three Carbohydrate Force Fields." Journal of Chemical Theory and Computation (8:2); pp. 735-748.
  29. Taylor, C. B.; Talib, M. F.; McCabe, C.; Bu, L.; Adney, W. S.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T. (2012). "Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-Binding Module." Journal of Biological Chemistry (287:5); pp. 3147-3155.
  30. Nimlos, M. R.; Beckham, G. T.; Matthews, J. F.; Bu, L.; Himmel, M. E.; Crowley, M. F. (2012). "Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-Binding Module on Cellulose." Journal of Biological Chemistry (287:24); pp. 20603-20612.
  31. Bu, L.; Beckham, G. T.; Shirts, M. R.; Nimlos, M. R.; Adney, W. S.; Himmel, M. E.; Crowley, M. F. (2011). "Probing Carbohydrate Product Expulsion from a Processive Cellulase with Multiple Absolute Binding Free Energy Methods." Journal of Biological Chemistry (286:20); pp. 18161-18169.
  32. Beckham, G. T.; Bomble, Y. J.; Bayer, E. A.; Himmel, M. E.; Crowley, M. F. (2011). "Applications of Computational Science for Understanding Enzymatic Deconstruction of Cellulose." Current Opinion in Biotechnology (22:2); pp. 231-238.
  33. Tavagnacco, L.; Mason, P. E.; Schnupf, U.; Pitici, F.; Zhong, L. H.; Himmel, M. E.; Crowley, M. F.; Cesaro, A.; Brady, J. W. (2011). "Sugar-Binding Sites on the Surface of the Carbohydrate-Binding Module of CBH I from Trichoderma reesei." Carbohydrate Research (346:6); pp. 839-846.
  34. Payne, C. M.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T. (2011). "Decrystallization of Oligosaccharides from the Cellulose 1 beta Surface with Molecular Simulation." Journal of Physical Chemistry Letters (2 :13); pp. 1546-1550.
  35. Lin, Y.; Silvestre-Ryan, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G.T.; Chu, J. W. (2011). "Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft." Journal of the American Chemical Society (133:41); pp. 16617-16624.
  36. Beckham, G. T.; Matthews, J. F.; Peters, B.; Bomble, Y. J.; Himmel, M. E.; Crowley, M. F. (2011). "Molecular-Level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common Cellulose Polymorphs." Journal of Physical Chemistry B (115:14); pp. 4118-4127.
  37. Matthews, J. F.; Bergenstrahle, M.; Beckham, G. T.; Himmel, M. E.; Nimlos, M. R.; Brady, J. W.; Crowley, M. F. (2011). "High-Temperature Behavior of Cellulose I." Journal of Physical Chemistry B (115:10); pp. 2155-2166.
  38. Bomble, Y. J.; Beckham, G. T.; Matthews, J. F.; Nimlos, M. R.; Himmel, M. E.; Crowley, M. F. (2011). "Modeling the Self Assembly of the Cellulosome Enzyme Complex." Journal of Biological Chemistry (286:7); pp. 5614-5623.
  39. Beckham, G. T.; Crowley, M. F. (2011). "Examination of the alpha-Chitin Structure and Decrystallization Thermodynamics at the Nanoscale." Journal of Physical Chemistry B (115:15); pp. 4516-4522.
  40. Hynninen, A.-P.; Matthews, J.F.; Beckham, G.T.; Crowley, M.F.; Nimlos, M.R. (2011). "Coarse-grain Model for Glucose, Cellobiose, and Cellotetraose in Water." J. Chem. Theory and Comp. (7:7); pp. 2137-2150.
  41. Petridis, L.; Xu, J. ; Crowley, M. F.; Smith, J. C.; Cheng, X. (2010). "Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes." American Chemical Society (Washington, D.C.:3); p. 55. Accessed February 10, 2015: https://www.nrel.gov/energysciences/73.
  42. Beckham, G. T.; Matthews, J. F.; Bomble, Y. J.; Bu, L.; Adney, W. S.; Himmel, M. E.; Nimlos, M. R.; Crowley, M. F. (2010). "Identification of Amino Acids Responsible for Processivity in a Family 1 Carbohydrate-Binding Module from Fungal Cellulase." Journal of Physical Chemistry B (114:3); pp. 1447-1453.
  43. Bomble, Y. J.; Crowley, M. F.; Xu, Q.; Himmel, M. E. (2010). "Modeling the Cellulosome Using Multiscale Methods,,Computational Modeling in Lignocellulosic Biofuel Production." American Chemical Society p. 75. Accessed February 10, 2015: https://www.nrel.gov/energysciences/98.
  44. Beckham, G. T.; Bomble, Y. J.; Matthews, J. F.; Taylor, C. B.; Resh, M. G.; Yarbrough, J. M.; Decker, S. R.; Bu, L.; Zhao, X.; McCabe, C.; Wohlert, J.; Bergenstrahle, M.; Brady, J. W.; Adney, W. S.; Himmel, M. E.; Crowley, M. F (2010). "O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase is a Flexible, Disordered Protein." Biophysical Journal (99:11); pp. 3773-3781.
  45. Crowley, M. F. ; Williamson, M. J. ; Walker, R. C. (2009). "CHAMBER: Comprehensive Support for CHARMM Force Fields Within the AMBER Software." International Journal of Quantum Chemistry (109:15); pp. 3767-3772.
  46. Bu, L.; Beckham, G. T.; Crowley, M. F.; Chang, C. H.; Matthews, J. F.; Bomble, Y. J.; Adney, W. S.; Himmel, M. E.; Nimlos, M. R. (2009). "Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface is Altered by Hydrolyzed Glycosidic Bonds." Journal of Physical Chemistry B (113:31); pp. 10994-11002.
  47. Zhong, L.; Matthews, J. F.; Hansen, P. I.; Crowley, M. F.; Cleary, J. M.; Walker, R. C.; Nimlos, M. R.; Brooks, C. L. III; Adney, W. S.; Himmel, M. E.; Brady, J. W. (2009). "Computational Simulations of the Trichoderma reesei Cellobiohydrolase I Acting on Microcrystalline Cellulose I..beta..: The Enzyme-Substrate Complex." Carbohydrate Research (344:15); pp. 1984-1992.
  48. Xu, J.; Crowley, M. F.; Smith, J. C. (2009). "Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin  Complexation from Computer Simulation." Protein Science (18:5); pp. 949-959.
  49. Ding, S. Y.; Xi, Q.; Crowley, M.; Zeng, Y.; Nimlos, M.; Lamed, R.; Bayer, E. A.; Himmel, M. E. (2008). "Biophysical Perspective on the Cellulosome: New Opportunities for Biomass Conversion." Current Opinion in Biotechnology (19:3); pp. 218-227.
  50. Zhong, L.; Matthews, J. F.; Crowley, M. F.; Rignall, T.; Talon, C.; Cleary, J. M.; Walker, R. C.; McCabe, C.; Nimlos, M. R.; Brooks, C. L. III; Himmel, M. E.; Brady, J. W. (2008). "Interactions of the Complete Cellobiohydrolase I from Trichodera reesei with Microcrystalline Cellulose I-Beta." Cellulose (15:2); pp. 261-273.
  51. Crowley, M. F.; Uberbacher, E. C.; Brooks III, C. L.; Walker, R.C.; Nimlos, M. R.; Himmel, M. E. (2008). "Developing Improved MD Codes for Understanding Processive Cellulases." Journal of Physics: Conference Series (125:7);
  52. Nimlos, M. R.; Adney, W. S.; Himmel, M. E.; Brady, J. W.; Matthews, J. F.; Crowley, M. F.; Cleary, J. M.; Walker, R. C.; Zhong, L. "Family 1 Carbohydrate Binding Modules Show Induced Fit Interaction with the Cellulose Substrate."
  53. Nimlos, M. R.; Matthews, J. F.; Crowley, M. F.; Walker, R. C.; Chukkapalli, G.; Brady, J. W.; Adney, W. S.; Cleary, J. M.; Zhong, L.; Himmel, M. E. (2007). "Molecular Modeling Suggests Induced Fit of Family I Carbohydrate-Binding Modules with a Broken-Chain Cellulose Surface." Protein Engineering, Design & Selection (20:4); pp. 179-187.