Dr. Michael L. Klein

 

Michael Klein

Dean, College of Science and Technology

Laura H.Carnell Professor of Science

B.Sc, University of Bristol, UK (1961)
Ph.D., University of Bristol, UK (1964)

OFFICE
Bio Life Science Building

Rm. 106


MAILING ADDRESS

Department of Chemistry
Beury Hall 130
1901 N. 13th Street
Philadelphia, PA 19122


PHONE

office: 215-204-4212
fax: 215-204-1532

lab: 215-204-1927

email: mlklein@temple.edu

RESEARCH GROUP

https://icms.cst.temple.edu/

 

Theory / Simulation / Modeling

Appointments

2009-Director, Temple Institute for Computational Molecular Science

2009-Carnell Professor, College of Science & Technology, Temple University

1994-2009 Director, Penn Center for Molecular Modeling

1993-2009 Director, Laboratory for Research on the Structure of Matter

1993-2009 Hepburn Professor of Physical Science, University of Pennsylvania

1987- Professor of Chemistry, University of Pennsylvania

1968-87 Associate, Senior, & Principal Research Officer,

Chemistry Division, NRCC, Ottawa, Canada

Awards and Honors

2009 National Academy of Sciences

2008 American Chemical Society – Peter Debye Award in Physical Chemistry

2008 University of Oxford –  Hinshelwood Lecturer

2008 Honorary Fellow, Chemical Research Society of India

2006 Chemical Research Society of India – CNR Rao Award

2005 Honorary Fellow, Indian Academy of Sciences – Bangalore

2005 Honorary Member, Materials Research Society of India

2004 European Physical Society, CECAM Prize for Computational Science

2004 Associate of TWAS, Academy of Sciences of the Developing World

2003 Fellow, Royal Society of London

2003 Fellow, American Academy of Arts & Sciences

2003 Fellow, Institute of Physics UK

2003 Schlumberger Professor, Universities of Oxford & Cambridge, UK

1999 American Physical Society, Aneesur Rahman Prize Computational Physics

1998 American Chemical Society, Philadelphia Section Award

1998 Linnett Professorship, University of Cambridge, UK

1998 Honorary Fellow Sydney Sussex College, Cambridge, UK

1997 Miller Professorship, University of California, Berkeley

1996 Alexander von Humboldt Award, Max-Planck-Institute, Stuttgart

1993 Hepburn Professor of Physical Science, University of Pennsylvania

1991-93 William Smith Professor of Chemistry, University of Pennsylvania

1991 Fellow American Physical Society

1989 Guggenheim Fellow

1988 Néel Professor, École Normale Supérieure, Lyon, France

1985 Fellow Commoner, Trinity College Cambridge, UK

1984 Fellow Royal Society of Canada 
 
 
 
 
 

Publications: 570 papers and 4 books (Edited); Hirsch Index, h=74 

Reports:

Cyberinfrastructure NSF Blue Ribbon Panel (2001-2003; D. Atkins, Chair)

www.communitytechnology.org/nsf_ci_report/ 

Chemistry at the Centre International Review UK Chemical Sciences (2002; G. Whitesides, Chair)

http://www.rsc.org/pdf/lap/whitesides.pdf

New Science for a Sustainable & Secure Energy Future (2008; BESAC sub-committee report)

http://www.er.doe.gov/bes/reports/files/NSSSEF_rpt.pdf 

Chemistry for the Next Decade International Review UK Chemical Research (2009; M.L. Klein, Chair)

http://www.rsc.org/images/ChemistryIR2009_tcm18-210865.pdf

see also: http://www.rsc.org/Education/EiC/issues/2009July/Endpoint.asp 
 
 

Selected Publications

“Quantum character of a proton in a hydrogen bond” M.E. Tuckerman,  D. Marx, M.L. Klein, M. Parrinello, Science 275, 817-820 (1997).

“Assessment of all-atom potentials for modeling membranes: MD simulations of solid & liquid alkanes and crystals of phospholipid fragments” D.J. Tobias, K. Tu, M.L. Klein, J. Chem Phys. 94, 1482-1502 (1997).

“Molecular dynamics simulation of a synthetic ion channel” Q. Zhong, Q. Jiang, P.B. Moore, D.M. Newns, M.L. Klein, Biophys J. 74, 3-10 (1998).

“Molecular dynamics study of the LS3 voltage-gated ion channel” Q. Zhong, P.B. Moore, D.M. Newns, M.L. Klein, FEBS Lett. 427, 267-270 (1998).

“Molecular dynamics simulations of the influenza a virus M2 ion channel in a membrane-mimetic environment” Q. Zhong, T. Husslein, D. Newns, M L. Klein, FEBS Letters 434, 265-271 (1998).

“Molecular dynamics simulation of a synthetic four-α-helix bundle that binds the anesthetic halothane” L.A. Davis, M.L. Klein, D. Scharf, FEBS Lett. 455, 332-338 (1999).

“Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a Gold(111) surface” M. Tarek, K. Tu, M.L. Klein, D.J. Tobias, Biophys. J. 77, 964-972 (1999).

“Molecular dynamics study of lipid-DNA complexes” S. Bandyopadhyay, M. Tarek and M.L. Klein, J. Phys. Chem. B 103, 10075-10080 (1999).

“Molecular dynamics simulation of four-a-helix bundles that bind the anesthetic halothane” L.A. Davies, Q. Zhong, M.L. Klein, D. Scharf, FEBS Letters 478, 61-66 (2000).

“Two possible conducting states of the influenza a virus M2 ion channel” Q. Zhong, D.M. Newns, P. Pattnaik, J.D. Lear, M.L. Klein, FEBS Letters 473, 195-198 (2000).

“Molecular dynamics study of structure and gating of low molecular weight ion channels” D.M. Newns, Q. Zhong, P. B. Moore, T. Husslein, P. Pattnaik, M.L. Klein, Parallel Computing 26, 965-976 (2000).

“Water on the move” M.L. Klein, Science 291, 2106 (2001).

“Electrostatic interactions in a neutral model phospholipid bilayer with highly unsaturated alkyl chains by molecular dynamics simulations” L. Saiz, M.L. Klein, J. Chem. Phys. 116, 3052-3057 (2002).

“Histidine protonation in aqueous solution via constrained Car-Parrinello molecular dynamics” I. Ivanov, M.L. Klein, J. Am. Chem. Soc.  124, 13380-13381 (2002).

“Influence of anesthetic and nonimmobilizer molecules on the physical properties of a polyunsaturated lipid bilayer” L. Koubi, L. Saiz, M. Tarek, D. Scharf, M.L. Klein, J. Phys. Chem. B. 107, 14500-14508 (2003).

“Characterization of the dizinc analogue of the synthetic diiron protein DF1 using ab initio and hybrid quantum/classical molecular dynamics simulations” A. Magistrato, W.F. DeGrado, A. Laio, U. Rothlisberger, J. VandeVondele, M.L. Klein, J. Phys. Chem. B 107, 4182-4188 (2003).

“Probing the configurational space of a metalloprotein core: An ab initio molecular dynamics study of Duo Ferro 1 Binuclear Zn Cofactor” G.A. Papoian, W. F. DeGrado, M.L. Klein, J. Am. Chem. Soc. 125, 560-569 (2003).

“Transmembrane peptide-induced lipid sorting and mechanism of Lx-to-inverted phase transition using coarse grain molecular dynamics” S.O. Nielsen, C.F. Lopez, I. Ivanov, P.B. Moore, J.C. Shelley, M.L. Klein Biophys. J. 87, 2107-2115 (2004).

“Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers” R.J. Doerksen, B. Chen, D.Liu, G.N. Tew, W.F. DeGrado, M.L. Klein, Chem. Eur. J. 10, 5008-5016 (2004).

“Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model” G. Srinivas, M.L. Klein, Nanotechnology 15, 1289-1295 (2004).

“Hydrogen bonding structure and dynamics of water at the dimyristoylphosphatidylcholine lipid bilayer surface from a molecular dynamics simulation” C.F. Lopez, S.O. Nielsen, M.L. Klein, P.B. Moore, J. Phys. Chem. B. 108, 6603-6610 (2004).

“Understanding nature's design for a nanosyringe” C. F. Lopez, S. O. Nielsen, P. B. Moore, M.L. Klein, Proc. Natl. Acad. Sci. USA 101, 4431-4434 (2004)

“Membrane bound hydraphiles facilitate cation translocation” G. Srinivas, C.F. Lopez, M.L. Klein, J. Phys. Chem. B. 108, 4231-4235 (2004).

“Effect of the pore region of a transmembrane ion channel on the physical properties of a simple membrane” L. Saiz, S. Bandyopadhyay, M.L. Klein, J. Phys. Chem. B. 108, 2608-2613 (2004).

 “The transmembrane domain of the acetylcholine receptor: Insights from simulations on synthetic peptide models” L. Saiz, M.L. Klein, Biophys. J. 88, 959-970 (2005).

“Concentration effects of volatile anesthetics on the properties of model membrane: a coarse grain approach” M. Pickholz, L. Saiz, M.L. Klein, Biophys. J. 88, 1524-1534 (2005).

 “Structure and dynamics of model pore insertion into a membrane” C.F. Lopez, S.O. Nielsen, B. Ensing, P.B. Moore, M.L. Klein, Biophysical J. 88, 3083-3094 (2005).

“Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics” I. Ivanov, M.L. Klein, J. Am. Chem. Soc. 127, 4010-4020 (2005). 

“Molecular dynamics simulations of surfactant self-organization at a solid-liquid interface” G. Srinivas, S.O. Nielsen, P. B. Moore, M.L. Klein, J. Am. Chem. Soc. 128, 848-853 (2006).

“Ab initio calculations of intramolecular parameters for a class of arylamide polymers” S. Vemparala, I. Ivanov, V. Pophristic, K. Spiegel, M.L. Klein, J. Comput. Chem. 27, 693-700 (2006).

“Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics and classical molecular dynamics study” V. Pophristic, S. Vemparala, I. Ivanov, Z. Liu, M.L. Klein, W.F. DeGrado, J. Phys. Chem. B 110, 3517-3526 (2006).

“Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics” I. Ivanov, S. Vemparala, V. Pophristic, K. Kuroda, W.F. DeGrado, J. A. McCammon, M.L. Klein, J. Am. Chem. Soc. 128, 1778-1779 (2006).

“Role of aromatic localisation in the gating process of a potassium channel” C. Domene, S. Vemparala, M.L. Klein, C. Venien-Bryan, D.A. Doyle, Biophys. J. 90, L01-L03 (2006).

“Metadynamics as a tool for exploring free energy landscapes of chemical reactions” B. Ensing, M. De Vivo, Z. Liu, P. Moore and M.L. Klein, Acc. Chem. Res. 39, 73-81 (2006).

“Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics” C.F. Lopez, S.O. Nielsen, G. Srinivas, W.F. DeGrado, M.L. Klein, J. Chem. Theory and Comput. 2, 649-655 (2006).

“Shrinkage of a rapidly growing tumor by drug-loaded polymersomes: ph-triggered release through copolymer degradation” F. Ahmed, R. I. Pakunlu, G. Srinivas, A. Brannan, F. Bates, M.L. Klein, T. Minko, D.E. Discher, Molecular Pharmaceutics 3, 340-350 (2006).

“Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents” E. Khurana, S. O. Nielsen, B. Ensing, M.L. Klein, J. Phys. Chem. B 110, 18965-18972 (2006).

“Exploring the gating mechanism in the ClC chloride channel via metadynamics” F.L. Gervasio, M. Parrinello, M. Ceccarelli, M.L. Klein, J. Mol. Biol. 361, 390-398 (2006).

“Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles” S. Vemparala, L. Saiz, R.G. Eckenhoff , M.L. Klein, Biophys J. BioFAST , (2006).

“Relative pK(a) values from first-principles molecular dynamics: the case of histidine deprotonation” I. Ivanov, B. Chen, S. Raugei, and M.L. Klein, J. Phys. Chem B 110, 6365-6371 (2006).

“Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study” E. Khurana, S.O. Nielsen and M.L. Klein, J. Phys. Chem. B 110, 22136-22142 (2006).

“Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein” J. Blumberger, M L. Klein, J. Am. Chem. Soc. , ASAP article (2006).

“Polarization effects and charge transfer in the KcsA potassium channel” D. Bucher, S. Raugei, L. Guidoni, M. DalPeraro, U. Rothlisberger, P. Carloni, M.L. Klein, Biophys. Chem. 124, 292-301 (2006).

“Proton shuttles and phosphatase activity in soluble epoxide hydrolase” M. De Vivo, B. Ensing, M. Dal Peraro, G.A. Gomez, D.W. Christianson, M.L. Klein, J. Am. Chem. Soc. 129, 387-394 (2007).

“Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations” M. Dal Peraro, K. Spiegel, G. Lamoureux, M. De Vivo, W.F. DeGrado, M.L. Klein, J. Struct. Biol. 157, 444-453 (2007).

“Role of zinc content on the catalytic efficiency of b1 metallo β-lactamases” M. Dal Peraro, A. J. Vila, P. Carloni, M.L. Klein, J. Am. Chem. Soc. 129, 2808-2816 (2007).

“Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants” W. Shinoda, R. DeVane, M.L. Klein, Mol. Sim. 33, 27-36 (2007).

“A stable water chain in the hydrophobic pore of the amtb ammonium transporter” G. Lamoureux, M.L. Klein, S. Bernèche, Biophys. J. 92, L82-L84 (2007).

Emerging applications of polymersomes in delivery: From molecular dynamics to shrinkage of tumors,” Discher DE, Ortiz V, Srinivas G, et al. Progress in Polymer Science 32 (8-9): 838-857 (2007)

 “Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance,” Spiegel K, Magistrato A, Carloni P, et al. Journal of Phys. Chem.B 111 (41): 11873-11876 (2007)

Large-scale molecular dynamics simulations of self-assembling systems,” Klein ML, Shinoda W 
Science 321(5890): 798-800 (2008)

 “Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement” J.R. Calhoun, W. Liu, K. Spiegel, M. DalPeraro, M.L. Klein, K.G. Valentine, A.J. Wand, W.F. DeGrado, Structure 16, 210-215 (2008).

“Probing the structure of DNA carbon nanotube hybrids with molecular dynamics” R.R. Johnson, A.T. Johnson, M.L. Klein, Nano Letters 8, 69-75 (2008).

“Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure” K. Spiegel, A. Magistrato, P. Maurer, P. Ruggerone, U. Rothlisberger, P. Carloni, J. Reedijk, M.L. Klein, J Computational Chemistry 29, 38-49 (2008).

 “Coarse-grained molecular modeling of non-ionic surfactant self-assembly,”  
Shinoda W, DeVane R, Klein ML Soft Matter 4 (12): 2454-2462 (2008)

Probing Peptide Nanotube Self-Assembly at a Liquid-Liquid Interface with Coarse-Grained Molecular Dynamics,” Khurana E, DeVane RH, Kohlmeyer A, et al. Nano Letters 8 (11): 3626-3630 (2008)

Embedded cholesterol in the nicotinic acetylcholine receptor,” Brannigan G, Henin J, Law R, et al. Proceedings National Academy of Sciences USA 105 (38): 14418-14423 (2008)

Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism,” De Vivo M, Dal Peraro M, Klein ML Journal of the American Chemical Society 130 (33): 10955-10962 (2008)

X-ray diffraction and computation yield the structure of alkanethiols on gold(111),”  
Cossaro A, Mazzarello R, Rousseau R, et al. Science 321 (5891): 943-946 (2008)

Conformational changes and gating at the selectivity filter of potassium channels,” Domene C, Klein ML, Branduardi D, et al. Journal of the American Chemical Society 130 (29): 9474-9480 (2008)

United-Atom Acyl Chains For CHARMM Phospholipids,” Henin J, Shinoda W, Klein ML Journal of Physical Chemistry B 112 (23): 7008-7015 (2008)

The role of conformation in ion permeation in a K+ channel,” Domene C, Vemparala S, Furini S, et al. Journal of the American Chemical Society 130 (11): 3389-3398 (2008)

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement,” Calhoun JR, Liu W, Spiegel K, et al. Structure 16 (2): 210-215 (2008)

Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics,”  
Johnson RR, Johnson ATC, Klein ML Nano Letters 8 (1): 69-75 (2008)

Identification of a fluorescent general anesthetic, 1-aminoanthracene,” Butts CA, Xi J, Brannigan G, et al. Proceedings National Academy of Sciences USA  106 (16): 6501-6506 (2009)

Initial Response of the Potassium Channel Voltage Sensor to a Transmembrane Potential,” Treptow W, Tarek M, Klein ML Journal of the American Chemical Society 131 (6): 2107- (2009)

Evaluation of Electronic Coupling in Transition-Metal Systems Using DFT: Application to the Hexa-Aquo Ferric-Ferrous Redox Couple,” Migliore A, Sit PHL, Klein ML J. Chemical Theory and Computation 5 (2): 307-323 (2009)

Free Energy Landscape of a DNA-Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics,” Johnson RR, Kohlmeyer A, Johnson ATC, et al. Nano Letters 9 (2): 537-541(2009)

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus,” Khurana E, Dal Peraro M, DeVane R, et al. Proceedings National Academy of Sciences USA  106 (4): 1069-1074 (2009) 

"Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations," L. Delemotte, M. Tareka, M. L. Klein, C. Amaral, and W. Treptow Proc. Natl. Acad. Sci., 115, 6109-6114 (2011)

"Morphologies of Charged Diblock Copolymers Simulated with a Neutral Coarse-Grained Model," D. A. Pantano, M. L. Klein, D. E. Discher, and P. B. Moore J. Phys. Chem. B, 115, 4689-4695 (2011)

"Exploring the reorientation of benzene in an ionic liquid via molecular dynamics: Effect of temperature and solvent effective charge on the slow dynamics," Y. Yasaka, M. L. Klein, M. Nakahara, N. Matubayasi, J. Chem. Phys., 134, 191101 (2011).

"Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2," J. Wang, C. Ma, G. Fiorin, V. Carnevale, T. Wang, F. Hu, R. A. Lamb, L. H. Pinto, M. Hong, M. L. Klein, W. F. DeGrado J. Am. Chem. Soc., 133(32), 12834-12841 (2011)

"Coarse-grained force field for ionic surfactants," W. Shinoda, R. DeVane, M. L. Klein Soft Matter, 7, 6178-6186 (2011).

"Raft registration across bilayers in a molecularly detailed model," D. A. Pantano, P. B. Moore, M. L. Klein, D. E. Discher Soft Matter, 7, 8182-8191 (2011).

"Hydrogen evolution from formic acid in an ionic liquid solvent: A mechanistic study by ab initio molecular dynamics," B. L. Bhargava, Y. Yasaka, M. L. Klein, J. Phys.Chem.B., 115, 14136 (2011).

"Nanoscale Organization in Aqueous Dicationic Ionic Liquid Solutions," B. L. Bhargava, Michael L. Klein J. Phys. Chem. B, 115(35), 10439-10446 (2011)

"Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations," V. Carnevale; W. Treptow; M. L. Klein J. Phys. Chem. Lett., 2 (19), 2504-2508 (2011

"Curvature, Rigidity, and Pattern Formation in Functional Polymer Micelles and Vesicles from Dynamic Visualization to Molecular Simulation," S. M. Loverde, D. A. Pantano, D. A. Christian, A. Mahmud, M. L. Klein, D. E. Discher Curr. Opin. Solid State Mater. Sci., 15, 277-284 (2011).

"Nanoparticle Shape Improves Delivery: Rational Coarse Grain Molecular Dynamics (rCG-MD) of Taxol in Worm-Like PEG-PCL Micelles," S. M. Loverde, M. L. Klein, D. E. Discher Adv. Mater., Early View, (2011)

"Micellization studied by GPU-accelerated coarse-grained molecular dynamics," B. G. Levine, D. N. LeBard, R. H. DeVane, W. Shinoda, A. Kohlmeyer, M. L. Klein, J. Chem. Theor. Comput., ASAP Article (2011).

"Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration," D. N. LeBard, B. G. Levine, R. H. DeVane, W. Shinoda, M. L. Klein, Chem. Phys. Lett., In Press (2011).

"Surfactant concentration effects on micellar properties," A. Jusufi, D. N. LeBard, B. G. Levine, and M. L. Klein J. Phys. Chem. B, ASAP Article (2011).

"Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing units," D. N. LeBard, B. G. Levine, P. Mertmann, S. A. Barr, A. Jusufi, S. Sanders, M. L. Klein, A. Z. Panagiotopoulos, Soft Matter, Advance Article, (2011).