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Klauda, Jeffery

Jeffery Klauda
Associate Professor
Associate Chair and Graduate Program Director
1227A Chemical and Nuclear Engineering Building

News About This Professor


Ph.D., University of Delaware, 2003

Research Interests 

Cell membrane biophysics, thermodynamics, and molecular simulations.


Before joining the Department in Fall 2007, Dr. Klauda was an Intramural Research Training Award (IRTA) Postdoctoral Fellow in the Laboratory of Computational Biology at the National Heart, Lung and Blood Institute, National Institutes of Health (NIH). There, he studied lipid forcefield improvements and dynamical behavior of membranes, and transport of sugars through the cell membrane via proteins. His Ph.D. work mainly involved predicting the thermodynamic stability of gas hydrates and global amount of this alternate source of natural gas. The separation of molecular nitrogen and oxygen via nanoporous carbons was also a part of his doctoral work.

Current Research Projects 

Professor Klauda's research interests encompass thermodynamic modeling and molecular simulations with applications in energy, gas separation, and biomolecular systems. Thermodynamic stability of natural gas hydrates (gas encapsulated by a water crystal lattice of cavities) requires high pressures. These are commonly found in pipelines and can plug the flow of natural gas, but also exist in nature in permafrost or the seafloor.  His thermodynamic/mass transfer modeling of methane hydrates in the seafloor suggests that there are three orders of magnitude more methane in hydrated form than in conventional global reserves. These results also have huge implications for an alternate source of natural gas reserves within the U.S. to reduce dependency on foreign energy sources.

Currently, Professor Klauda's research is focused on understanding the behavior of cell membranes and how small molecules, such as sugars, cholesterol, and drugs are transported into and out of the cell. This work involves using molecular simulations to study cell membranes at an atomic level. Some of this work began at the National Institutes of Health, where he held his postdoctoral fellowship.  Dr. Klauda is currently collaborating with experimental groups to better understand membrane function and dynamics at a molecular level, including Professor John Nagle (Carnegie Mellon University), Professor Mary Roberts (Boston College), and Professor Ron Kaback (UCLA). 

Of specific interest is the cause for multi-drug antibiotic resistance in humans and the corresponding protein transport mechanism. Drug transport protein analogs, such as lactose permease, are used as initial models to understand small molecular transport in bacteria. In the future, direct transporters of antibiotics will be studied to help prevent multi-drug resistance or design better drugs.


Professor Klauda's teaching interests include:

  • Thermodynamics
  • Statistics and Design of Experiments
  • Molecular Simulation Methods

Honors and Awards 

  • 1994 Rensselaer Polytechnic Institute’s Medal of Science
  • 1998-1999 Pigford Fellowship (Dept. of Chemical Engineering at the University of Delaware)
  • 2003-2007 Intramural Research Training Award (NIH)
  • 2008 Minta Martin Award (UMD)

Professional Memberships 

  • American Institute of Chemical Engineers
  • American Chemical Society
  • Biophysical Society

Books and Chapters 

Klauda, J.B., Venable, R.M, MacKerell, A.D., and Pastor, R.W. "Considerations for Lipid Force Field Development." in Current Topics in Membranes: Computer Modeling of Membrane Bilayers. 60, 1-48 (2008).

Selected Publications 

Rogaski, B & J.B. Klauda. Membrane-binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations. J. Mol. Bio. 423, 847-861 (2012).

Klauda, J.B., V. Monje, T. Kim, and W. Im. Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains. J. Phys. Chem. B. 116, 9424-9431 (2012). Cover Article

Ezzeldin, H.M., J.B. Klauda, & S.D. Solares. Modeling of the Major Gas Vesicle Protein, GvpA: from Protein Sequence to Vesicle Wall Structure. J. Struct. Biol. 179, 18-28 (2012).

Kwon, T.K., B. Roux, SW Jo, J.B. Klauda,  A.L. Harris, & T.A. Bargiello. Molecular Dynamics Simulations of the Cx26 Hemichannel: Insights into voltage-dependent loop-gating. Biophys. J. 102, 1341-1351 (2012).

Pandit, K.R. & J.B. Klauda. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. BBA-Membranes. 1818, 1205-1210 (2012).

Lim, J.B., B. Rogaski & J.B. Klauda. Update of the Cholesterol Force Field Parameters in CHARMM. J. Phys. Chem. B. 116, 203-210 (2012).

O’Connor, J.W & J.B. Klauda.  Lipid Membranes with a Majority of Cholesterol: Applications to the Ocular Lens and Aquaporin 0.  J. Phys. Chem. B.  115, 6455-5464 (2011).

Bandyopadhyay, A.A. &  J.B. Klauda. Gas Hydrate Structure and Pressure Predictions based on an Updated Fugacity-based Model with the PSRK Equation of State. I&EC Research. 50, 148-157 (2011).

Lim, J.B. & J.B. Klauda. Branching at the Iso- and Anteiso- Positions in Complex Chlamydia Membranes: A Molecular Dynamics Study. BBA-Membranes. 1808, 323-331 (2011).

Song, K.C., P.W. Livanec, J.B. Klauda, K. Kuczera, R.C. Dunn, & W. Im. Orientation of Fluorescent Lipid Analog BODIPY-PC to Probe Lipid Membrane Properties: Insights from Molecular Dynamics Simulations. J. Phys. Chem. B. 115, 6157-5165 (2011).

Klauda, J. B., R. M. Venable, J. A. Freites, J. W. O'Connor, C. Mondragon-Ramirez, I. Vorobyov, D. J. Tobias, A. D. MacKerell, & R. W. Pastor. Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types. J. Phys. Chem. B. 114, 7830-7843 (2010).

Jo, S.H., H. Rui, J.B. Lim, J.B. Klauda, & W. Im. Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies. J. Phys. Chem. B. 114, 13342-13348 (2010).

Rogaski, B., J.B. Lim, & J.B. Klauda. Sterol binding and membrane lipid attachment to the Osh4 protein of yeast.  J. Phys. Chem. B.  114, 13562-13573 (2010).

Pendse, P.Y., B.R. Brooks & J.B. Klauda. Probing the Periplasmic-open State of Lactose Permease in Response to Sugar Binding and Proton Translocation. JMB. 404, 506-521 (2010). Cover Article

Jo, S.H., J.B. Lim, J.B. Klauda, & W. Im. CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes. Biophys. J. 97, 50-58 (2009).

Singh, R.P., B.R. Brooks, & J.B. Klauda. Binding and Release of Cholesterol in the Osh4 Protein of Yeast. Proteins: Structure, Function, and Bioinformatics. 75, 468-477 (2009).

Klauda, J.B., M.F. Roberts, and A.G. Redfield, B.R. Brooks, & R.W. Pastor. Rotation of Lipids in Membranes: MD Simulation, 31P Spin-Lattice Relaxation, and Rigid-Body Dynamics.  Biophys. J. 94 , 3074-3083 (2008).

Klauda, J.B.  & B.R. Brooks. CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes. J. Chem. Theory Comp. 4, 107-115 (2008).

Klauda, J.B., N.V. Eldho, K. Gawrisch, B.R. Brooks, & R.W. Pastor. Collective and Noncollective Models of NMR Relaxation in Lipid Vesicles and Multilayers. J. Phys. Chem. B. 112, 5924 (2008).

Miller, T., R.P. Singh, J.B. Klauda, M. Hodošček, B.R. Brooks, & H.L. Woodcock III.  CHARMMing: A New, Flexible, Web-based front-end to CHARMM. J. Chem. Info. Mod.  48, 1920-1929 (2008).

Klauda, J.B. & B.R. Brooks.  Sugar Binding in Lactose Permease: Anomeric State of a Disaccharide Influences Binding Structure.  J Mol. Biol. 367, 1523-1534 (2007).

Klauda, J.B., X. Wu, R.W. Pastor, & B.R. Brooks.  Long-range Lennard-Jones and Electrostatic Interactions in Interfaces: Application of the Isotropic Periodic Sum Method.  J. Phys. Chem. B. 111, 4393-43400 (2007).

Klauda, J.B., B.R. Brooks, & R.W. Pastor.  Dynamical Motions of Lipids and a Finite Size Effect in Simulations of Bilayers.  J. Chem. Phys. 125, 144710 (2006).

Klauda, J.B., N. Kučerka, B.R. Brooks, R.W. Pastor, & J.F. Nagle. Simulation-based Methods for Interpreting X-ray Data from Lipid Bilayers. Biophys. J. 90, 2796-2807 (2006).

Klauda, J.B., B.R. Brooks, A.D. MacKerell, R.M. Venable, & R.W. Pastor.  An Ab Initio Study on the Torsional Surface of Alkanes and its Effect on Molecular Simulations of Alkanes and DPPC Bilayers.  J.  Phys. Chem. B. 109, 5300-5311 (2005).

Klauda, J.B., R.W. Pastor, & B.R. Brooks. Adjacent Gauche Stabilization in Linear Alkanes: Implications for Lipid/Polymer Models. J. Phys. Chem. B. 109, 15684-15686 (2005).

Klauda, J. B. & S.I. Sandler.  Global Distribution of Methane Hydrate in Ocean Sediment. Energy & Fuels. 19, 469-470 (2005).

Jiang, J., J.B. Klauda, & S.I. Sandler. Hierarchical Modeling N2 Adsorption on the Outer Surface of and within a C60 Crystal: From Quantum Mechanics to Molecular Simulation. J. Phys. Chem. B. 109, 4731-4737 (2005).

Arora, G., J.B. Klauda, & S.I. Sandler. A Comparative Study of Nitrogen Physisorption on Different C70 Crystal Structures Using an Ab Initio Based Potential. J. Phys. Chem. B. 109, 17267-17273 (2005).

Jiang, J., J.B. Klauda, & S.I. Sandler. Hierarchical Modeling Gas Adsorption in the C168 Schwarzite: From Quantum Mechanics to Molecular Simulation. J. Phys. Chem. B. 108, 9852-9860 (2004).

Klauda, J.B., J. Jiang, & S.I. Sandler. An Ab Initio Study on the Effect of Carbon Surface Curvature and Ring Structure on N2(O2)-Carbon Intermolecular Potentials.  J. Phys. Chem. B.  108, 9842-9851 (2004).

Klauda, J.B., S.L. Garrison, G.  Arora, J. Jiang, & S.I. Sandler.  HM-IE: A Quantum Chemical Hybrid Method for Accurate Interaction Energies.  J. Phys. Chem. A. 108, 107-112 (2004).

Klauda, J. B. & S.I. Sandler. Predictions of Gas Hydrate Phase Equilibria and Amounts in Natural Sediment Porous Media. Marine Petroleum Geology. 20, 459-470 (2003).

Jiang, J., J.B. Klauda, & S.I. Sandler. Monte Carlo Simulation of O2 and N2 Adsorption in Nanoporous Carbon (C168 Schwarzite). Langmuir. 19, 3512-3518 (2003). Cover Article

Klauda, J. B. & S.I. Sandler.  Phase Behavior of Clathrate Hydrates: A Model for Single and Multiple Gas Component Hydrates. Chem. Eng. Sci. 58, 27-41 (2003).

Klauda, J. B. & S.I. Sandler.  Ab Initio Intermolecular Potentials for Gas Hydrates and Their Predictions. J. Phys. Chem. B. 106, 5722-5732 (2002).

Klauda, J. B. & S.I. Sandler.  Modeling Gas Hydrate Phase Equilibria in Laboratory and Natural Porous Media. Ind. Eng. Chem. Res. 40, 4197-4208 (2001).

Klauda, J. B. & S.I. Sandler.  A Fugacity Model for Gas Hydrate Phase Equilibria. Ind. Eng. Chem. Res. 39, 3377-3386 (2000).

Selected Presentations 

“All-atom Molecular Simulations to Probe Structure and Dynamics of Bacterial Membranes and Membrane-associated Proteins”, NIST Center for Neutron Research (2012).

“Modeling Bacterial Membrane Structure to Membrane Protein Dynamics at an Atomic Level”, Univeristy of Virginia, Department of Chemical Engineering (2011).

“Diversity of Lipids in Organisms and their Organelles: Is this Required to Accurately Model Real Membranes?”, Biological Membranes and Membrane Proteins, Snowmass, CO (2011).

“Molecular simulations of certain model human membranes and secondary active transport proteins” National Institutes of Health, NHLBI, Laboratory of Computational Biology (2011).

“Molecular Modeling of Cellular Membranes and Associated Proteins”, University of Maryland, Special Joint ChBE/Chemistry & Biochemistry Seminar (2011).

"Multi-scale Modeling of Gas Hydrates Reserves in the Seafloor Sediment", Petroleum Institute, Department of Chemical Engineering, Abu Dhabi, UAE (2011).

“Model Biomembranes of Single-Celled Organisms and a Protein that Controls Substrate Transport in E. coli”, Advanced Materials Research, Central Michigan University, Mt. Pleasant, MI (2010).

“Gas Hydrates: A Significant but Relatively Untapped Alternate Source of Natural Gas”, National Capitol Section of AIChE, College Park, MD (2009).

“Understanding the Structure and Dynamics of Biomembranes and Their Components”, National Taiwan University, Department of Chemical Engineering, Taipei (2009).

“Predicting the Locations and Amounts of Seafloor Methane Hydrates”, Central Geological Survey of Taiwan, Taipei (2009).

“Structure and Dynamics of Lipids, Model Cellular Membranes, and Membrane Proteins”, University of Kansas, Center for Bioinformatics, Lawrence (2008)

“Improving the Lipid Force Field from ab Initio Methods and the Sugar Transporter of E. coli” mini-Carbohydate Symposium, National Institutes of Health, Bethesda (2008).

“Pure Lipid Membranes and Active Transport of Sugars Through the Cytoplasmic Membrane via Lactose Permease” Biological Membranes: Emerging Challenges at the Interface between Theory, Computer Simulation, and Experiment, Park City, UT (2007).

"Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of Kentucky, Lexington (2007).

“Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of Pennsylvania, Philadelphia (2007).

“Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of South Carolina, Columbia (2007).

“Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of Maryland, College Park (2007).

“Structure of Lipid Membranes and Improving the Head Group Force Field” eChemInfo, Philadelphia (2005).

“Phase Behavior of Gas Hydrates and Global Predictions for Methane Hydrate Seafloor Reserves” The University of Melbourne–Department of Chemical & Biomolecular Engineering (2003).

“Osh4 Membrane Binding Through Molecular Dynamics” Biophysical Society (2012).

“Atomic-level Simulations to Probe Conformational Changes of Secondary Active Transport Proteins” Biophysical Society (2012).

“Quantification of Sugar Binding Affinity and Study of Proton Translocation in Lactose Permease of Escherichia ColiAIChE Annual Spring Meeting (2011).

“Extending the CHARMM Force Field to Sphingolipids and Lipids with Polyunsaturated Chains” AIChE Annual Meeting (2011)

“New all-atom method to probe unknown conformations and substrate transport of secondary active membrane transport proteins” ACS National Spring Meeting (2011).

“Gas hydrates: Where and how much is trapped in this alternative source of natural gas” ACS National Spring Meeting (2011).

“Molecular simulations of model bacterial and ocular lens lipid membranes with the CHARMM36 force field” ACS National Spring Meeting (2011).

“Refining and Testing CHARMM Lipid Parameters for Biologically Important Membranes” Biophysical Society (2011).

 “A Modified Lipid Force Field for CHARMM: Development and Application to Single-Celled Organism Membranes” Biophysical Society (2010).

“Improving the lipid force field of CHARMM: A quantum mechanical and experimental approach” AIChE Annual Meeting (2009).

“Improving the lipid force field of CHARMM: A quantum mechanical and experimental approach” ACS National Fall Meeting (2009).

"An Atomic-level Model for the Periplasmic Open State of Lactose Permease” Biophysical Society (2009).

“Binding and Release of Cholesterol in the Osh4 Protein of Yeast” AIChE Annual Meeting (2008).

“Binding and Release of Cholesterol in the Osh4 Protein of Yeast” ACS National Fall Meeting (2008).

“Determining the Outward-Facing Structure and Sugar Binding in Lactose Permease of E. coliAIChE Annual Meeting (2007).

“Long-range Lennard-Jones and Electrostatic Interactions in Interfaces: Application and Development of the Isotropic Periodic Sum Method” AIChE Annual Meeting (2007).

“Structural Changes in Lactose Permease and How Sugar-Type Effects Binding Structure” Biophysical Society (2007).

“Dynamical Motions of Lipids and a Finite Size Effect of Bilayers” AIChE Annual Meeting (2006).

“Disaccharide Binding in Lactose Permease of E. coli: Sugar Structure Influences Binding” AIChE Annual Meeting (2006).

“Lactose Permease-Sugar Interactions: The Anomeric State of a Disaccharide Determines its Binding Structure” Symposium of Protein Society (2006).

“Importance of Including Long-range Interactions in Simulations of Biologically Relevant 2D Surfaces” AIChE Annual Meeting (2005).

“Structure and Dynamics of Lipid Membranes: How can Simulations Aid Experiments?” AIChE Annual Meeting (2005).

“Refining the Structure of Lipid Bilayers with Insight from Molecular Dynamics Simulations” ACS National Fall Meeting (2005).

“Lipid Bilayers: Structural and Dynamical Properties with an Improved Forcefield Fit to Ab Initio Quantum Mechanics” Biophysical Society (2005).

“An Ab Initio Study on the Torsional Surface of Alkanes and its Effect on Molecular Simulations of Alkanes and DPPC Bilayers” AIChE Annual Meeting (2004).

“A Self-guided Langevin Dynamic Study of ?-Hairpin Folding with Explicit Solvent: Computational Efficiency and Folding Pathways” AIChE Annual Meeting (2004).

“A Quantum Chemical Hybrid Method (HM-IE) for Calculating Interaction Energies Used to Develop Accurate Intermolecular Potentials” AIChE Annual Meeting (2003).

Ab Initio Intermolecular Potentials of Absorbents in Nanoporous Carbon Schwartzite Structures” AIChE Annual Meeting (2002).

“Phase Behavior of Clathrate Hydrates: A Model for Single and Multiple Gas Component Hydrates” AIChE Annual Meeting (2002).

“Intermolecular Potentials for Gas-Hydrates Obtained from Ab Initio Quantum Mechanics” ACS National Fall Meeting (2002).

“Predictions of Gas Hydrate Phase Equilibria in Laboratory and Natural Sediment Porous Media” AIChE Annual Meeting (2001).

Related News 

Klauda Named PROMISE Outstanding Faculty Mentor
Professor honored for efforts to increase student diversity in STEM majors. September 17, 2015

Boughter, Gastfriend, Piekarz Win 2014 Undergraduate Research Awards
Students recognized for work on metabolic engineering, nanoparticle synthesis. May 8, 2015

Monje-Galvan Presents Work on Molecular Dynamics Simulations of Protein Binding
Trip to conference supported by Chemical Society of Washington travel award. March 30, 2015

Klauda, Sriram Promoted
ChBE professors elevated to rank of Associate Professor with tenure. June 2, 2014

ChBE Undergrads Heading to DuPont for SCI Internships
"Exceptional" sophomore and junior chosen from nationwide field of applicants. April 11, 2014

2013-2014 ChBE Undergraduate Awards
Exceptional students recognized at annual ceremony. April 10, 2014

Liu Wins NSF CAREER Award
New ceramic membrane could improve conversion of natural gas into chemicals and fuels. December 12, 2013

2012-2013 ChBE Undergraduate Awards
Exceptional students recognized at annual ceremony. April 10, 2013

Klauda Earns NSF CAREER Award
Grant supports use of advanced simulations to study protein transport in cell membranes. August 27, 2012

ChBE Graduate Research Awards Announced
Winners will represent department in college-level competition. April 27, 2012

2011-2012 ChBE Undergraduate Awards
Exceptional students recognized by the Department, Clark School, and professional societies. April 20, 2012

Pendse Wins Travel Award
Chemical Society of Washington helps fund grad student's trip to American Chemical Society's annual meeting. April 19, 2012

Villanueva Presents at ACC Conference
ChBE sophomore selected for her work on cell membranes. May 5, 2011

Breger, Pendse Win at GRID
ChBE grad students win health, modeling divisions of university-wide research showcase. April 18, 2011

Pendse and Klauda’s Protein Research on Cover of Journal of Molecular Biology
New simulations could lay groundwork for understanding antibiotic resistance. November 22, 2010

Pendse, Emdadi Take 2nd and 3rd Place at ResearchFest 2010
ChBE students recognized for work in transport, dispersion polymerization. February 22, 2010

2008-2009 ChBE Undergraduate Awards
Students recognized at annual Clark School event. May 1, 2009

Lim Wins Best Poster Award
Undergraduate presented results of cholesterol study at Bioscience Day. November 15, 2008

ChBE Welcomes 3 New Faculty
Klauda, Wang arrive Fall 2007; Sriram Spring 2008. August 28, 2007