Laboratory of Molecular & Thermodynamic Modeling

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Invited Talks


  1. “Binding of a Curvature-sensing Peptide to Model Organelle Membranes of Yeast”, Biological Membranes and Membrane Proteins, Telluride, CO (2015)
  2. “Molecular Simulations of Hydrotropes, Lipid Membranes and a Peripheral Membrane Protein” West Virginia University, Morgantown, WV (2015).
  3. “Developing Quantum Mechanically-based Force Field Parameters from Gas Hydrates to Biology”, AIChE Annual Meeting, Prof. Sandler Symposium (2015)
  4. "Lipid Force Fields: Current Approaches to Force Field Development and their Accuracy” 2nd Molecular Simulations Summer School. University of Calgary (2014).
  5. “Simulations of Cell Membranes: Developing Accurate Lipid Force Fields and Probing Conformational Changes in Membrane Transporters” University of Maryland, Biophysics Program (2014).
  6. “Probing Small Molecule Self-assembly, Lipid Membranes and Membrane-associated Proteins” Lehigh University, Department of Chemical and Biomolecular Engineering (2014).
  7. “Molecular Modeling of Biomolecules: How can GPUs Advance Research?” GPU Summit, University of Maryland, Institute for Advanced Computing (2014).
  8. “Interpreting Experimental Studies of Self-Assembly and Transmembrane Proteins with Molecular Simulation”, National Institute of Standards and Technology, Gaithersburg, MD, Software and Systems Division (2014).
  9. “Probing the Transport Cycle of Secondary Active Transporters with Atomistic Simulations” Computational Modeling Workshop and Mini-Symposium. University of Chicago (2014).
  10. “Lipid Bilayer Simulations: Force fields, Simulation and Analysis” Computational Modeling Workshop and Mini-Symposium. University of Chicago (2014).
  11. “Molecular Simulations of Pore-forming Membranes and Membrane-associated Proteins” Rensselaer Polytechnic Institute, Department of Chemical and Biological Engineering (2014).
  12. “Mechanisms for a novel pore-forming lipid and lipid binding to a peripheral membrane protein” Workshop on Molecular Simulations of Biophysics and Biochemistry. RIKEN AICS in Kobe, Japan (2013).
  13. “Simulations of Biomembranes: Importance of Lipid Diversity and Structural Changes of Membrane Transport Proteins” 3rd International Conference on Molecular Simulation (ICMS). Kobe, Japan (2013).
  14. “Force Field Development and Molecular Simulations of Model Lipid Membranes” Satellite Meeting of ICMS2013. Nagoya University, Japan (2013).
  15. Modeling Lipid Bilayer and Microsecond Simulations of a Peripheral Membrane Protein”, Biological Membranes and Membrane Proteins, Snowmass, CO (2013).
  16. “E. coli Plasma Membrane Modeling and Membrane-associated Transport Proteins”, University of Maryland, Department of Bioengineering (2013).
  17. “Modeling Plasma Membranes and Proteins that Transport Small Molecules and Membrane Components”, Georgia Institute of Technology, Department of Chemical and Biomolecular Engineering (2013).
  18. “Modeling Plasma Membranes and Proteins that Transport Small Molecules and Membrane Components”, Temple University, Institute for Computational Molecular Science (2013).
  19. “Simulation Studies on Biological Membranes with High Performance Computing” Enabling Discovery with HPC, Baltimore, MD (2012).
  20. “All-atom Molecular Simulations to Probe Structure and Dynamics of Bacterial Membranes and Membrane-associated Proteins”, NIST Center for Neutron Research (2012).
  21. “Modeling Bacterial Membrane Structure to Membrane Protein Dynamics at an Atomic Level”, Univeristy of Virginia, Department of Chemical Engineering (2011).
  22. “Diversity of Lipids in Organisms and their Organelles: Is this Required to Accurately Model Real Membranes?”, Biological Membranes and Membrane Proteins, Snowmass, CO (2011).
  23. “Molecular simulations of certain model human membranes and secondary active transport proteins” National Institutes of Health, NHLBI, Laboratory of Computational Biology (2011).
  24. “Molecular Modeling of Cellular Membranes and Associated Proteins”, University of Maryland, Special Joint ChBE/Chemistry & Biochemistry Seminar (2011).
  25. "Multi-scale Modeling of Gas Hydrates Reserves in the Seafloor Sediment", Petroleum Institute, Department of Chemical Engineering, Abu Dhabi, UAE (2011).
  26. “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).
  27. “Gas Hydrates: A Significant but Relatively Untapped Alternate Source of Natural Gas”, National Capitol Section of AIChE, College Park, MD (2009).
  28. “Understanding the Structure and Dynamics of Biomembranes and Their Components”, National Taiwan University, Department of Chemical Engineering, Taipei (2009).
  29. “Predicting the Locations and Amounts of Seafloor Methane Hydrates”, Central Geological Survey of Taiwan, Taipei (2009).
  30. “Structure and Dynamics of Lipids, Model Cellular Membranes, and Membrane Proteins”, University of Kansas, Center for Bioinformatics, Lawrence (2008)
  31. “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).
  32. “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).
  33. "Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of Kentucky, Lexington (2007).
  34. “Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of Pennsylvania, Philadelphia (2007).
  35. “Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of South Carolina, Columbia (2007).
  36. “Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?” University of Maryland, College Park (2007).
  37. “Structure of Lipid Membranes and Improving the Head Group Force Field” eChemInfo, Philadelphia (2005).
  38. “Phase Behavior of Gas Hydrates and Global Predictions for Methane Hydrate Seafloor Reserves” The University of Melbourne–Department of Chemical & Biomolecular Engineering (2003).

Conference Presentations (Speaker)


  1.  “Probing the Dependence of pH on Sugar Binding and Protein Structure in a Polysaccharide Lyase.” Biophysical Society (2015).
  2. “Probing the Toxicity of Ethanol to Biological Membranes with Application to Biofuels Production.” AIChE Annual Meeting (2014)
  3. “CHARMM-Compatible Lipid Parameters for Ceramides and United Atom Chains” AIChE Annual Meeting (2013).
  4. “Developing CHARMM-compatible Lipid Parameters for Ceramides and United Atom Chains” Biophysical Society (2013).
  5. “Lipid Diversity: Is It Important in Modeling Organism and Organelle Membranes?” AIChE Annual Meeting (2012).
  6. “Osh4 Membrane Binding Through Molecular Dynamics” Biophysical Society (2012).
  7. “Atomic-level Simulations to Probe Conformational Changes of Secondary Active Transport Proteins” Biophysical Society (2012).
  8. “Quantification of Sugar Binding Affinity and Study of Proton Translocation in Lactose Permease of Escherichia ColiAIChE Annual Spring Meeting (2011).
  9. “Extending the CHARMM Force Field to Sphingolipids and Lipids with Polyunsaturated Chains” AIChE Annual Meeting (2011)
  10. “New all-atom method to probe unknown conformations and substrate transport of secondary active membrane transport proteins” ACS National Spring Meeting (2011).
  11. “Gas hydrates: Where and how much is trapped in this alternative source of natural gas” ACS National Spring Meeting (2011).
  12. “Molecular simulations of model bacterial and ocular lens lipid membranes with the CHARMM36 force field” ACS National Spring Meeting (2011).
  13. “Refining and Testing CHARMM Lipid Parameters for Biologically Important Membranes” Biophysical Society (2011).
  14.  “A Modified Lipid Force Field for CHARMM: Development and Application to Single-Celled Organism Membranes” Biophysical Society (2010).
  15. “Improving the lipid force field of CHARMM: A quantum mechanical and experimental approach” AIChE Annual Meeting (2009).
  16. “Improving the lipid force field of CHARMM: A quantum mechanical and experimental approach” ACS National Fall Meeting (2009).
  17. "An Atomic-level Model for the Periplasmic Open State of Lactose Permease” Biophysical Society (2009).
  18. “Binding and Release of Cholesterol in the Osh4 Protein of Yeast” AIChE Annual Meeting (2008).
  19. “Binding and Release of Cholesterol in the Osh4 Protein of Yeast” ACS National Fall Meeting (2008).
  20. “Determining the Outward-Facing Structure and Sugar Binding in Lactose Permease of E. coliAIChE Annual Meeting (2007).
  21. “Long-range Lennard-Jones and Electrostatic Interactions in Interfaces: Application and Development of the Isotropic Periodic Sum Method” AIChE Annual Meeting (2007).
  22. “Structural Changes in Lactose Permease and How Sugar-Type Effects Binding Structure” Biophysical Society (2007).
  23. “Dynamical Motions of Lipids and a Finite Size Effect of Bilayers” AIChE Annual Meeting (2006).
  24. “Disaccharide Binding in Lactose Permease of E. coli: Sugar Structure Influences Binding” AIChE Annual Meeting (2006).
  25. “Lactose Permease-Sugar Interactions: The Anomeric State of a Disaccharide Determines its Binding Structure” Symposium of Protein Society (2006).
  26. “Importance of Including Long-range Interactions in Simulations of Biologically Relevant 2D Surfaces” AIChE Annual Meeting (2005).
  27. “Structure and Dynamics of Lipid Membranes: How can Simulations Aid Experiments?” AIChE Annual Meeting (2005).
  28. “Refining the Structure of Lipid Bilayers with Insight from Molecular Dynamics Simulations” ACS National Fall Meeting (2005).
  29. “Lipid Bilayers: Structural and Dynamical Properties with an Improved Forcefield Fit to Ab Initio Quantum Mechanics” Biophysical Society (2005).
  30. “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).
  31. “A Self-guided Langevin Dynamic Study of ?-Hairpin Folding with Explicit Solvent: Computational Efficiency and Folding Pathways” AIChE Annual Meeting (2004).
  32. “A Quantum Chemical Hybrid Method (HM-IE) for Calculating Interaction Energies Used to Develop Accurate Intermolecular Potentials” AIChE Annual Meeting (2003).
  33. Ab Initio Intermolecular Potentials of Absorbents in Nanoporous Carbon Schwartzite Structures” AIChE Annual Meeting (2002).
  34. “Phase Behavior of Clathrate Hydrates: A Model for Single and Multiple Gas Component Hydrates” AIChE Annual Meeting (2002).
  35. “Intermolecular Potentials for Gas-Hydrates Obtained from Ab Initio Quantum Mechanics” ACS National Fall Meeting (2002).
  36. “Predictions of Gas Hydrate Phase Equilibria in Laboratory and Natural Sediment Porous Media” AIChE Annual Meeting (2001).

Conference Presentations (Mentored)


  1. Konas, R.M., J.L. Daristotle, N.B. Harbor & J.B. Klauda. “How does Ethanol Affect the Stability of Simple Model Yeast Membranes?” Biophysical Society (2015).
  2. Kang, H. & J.B. Klauda. “Molecular Dynamics Simulations of Sphingomyelin-Cholesterol Bilayers.” Biophysical Society (2015).
  3. Boughter, C.T, V. Monje-Galvan‡ & J.B. Klauda. “Influence of Cholesterol on Phospholipid Bilayer Dynamics.” Biophysical Society (2015).
  4. Zhuang, X. & J.B. Klauda. “Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease.”  Biophysical Society (2015).
  5. Khakbaz, P. & J.B. Klauda. “Investigating Lipid Phase Changes from Liquid Crystalline to Ripple to Gel Phases with All-atom Molecular Dynamics Simulations.” Biophysical Society (2015).
  6. Monje-Galvan, V.  & J.B. Klauda. “Membrane Binding of the Osh4 Curvature-Sensing Peptide” Biophysical Society (2015).
  7. Monje-Galvan, V.  & J.B. Klauda. “Binding Studies of a Saccharomyces Cerevisiae Peripheral Protein Osh4” ACS Spring National Meeting (2015).
  8. Zhuang, X. & J.B. Klauda. “Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease.”  ACS Spring National Meeting (2015).
  9. Khakbaz, P. & J.B. Klauda. “Investigating Lipid Phase Changes from Liquid Crystalline to Ripple to Gel Phases with All-atom Molecular Dynamics Simulations.” ACS Spring National Meeting (2015).
  10. Zhuang, X. & J.B. Klauda. “Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease.”  Delaware Membrane Protein Symposium (2015).
  11. Monje-Galvan, V.  & J.B. Klauda. “Membrane Binding of the Osh4 Curvature-Sensing Peptide” Delaware Membrane Protein Symposium (2015).
  12. Monje, V  & J.B. Klauda. “Molecular dynamics of yeast membrane models and binding of the ALPS-like motif” Computational/Theory Washington/Baltimore Symposium at NIH (2014).
  13. Khakbaz, P. & J.B. Klauda. “Studying Conformational Changes of Mhp1 Using All-atom Simulations.” Computational/Theory Washington/Baltimore Symposium at NIH (2014).
  14. Zhuang, X. J.R. Makover & J.B. Klauda. “Investigating the accuracy of C36 for lipid at various temperatures.”  Computational/Theory Washington/Baltimore Symposium at NIH (2014).
  15. Khakbaz, P. & J.B. Klauda. “Studying Conformational Changes of Mhp1 using Unbiased All-atom Molecular Simulations.” AIChE Annual Meeting (2014).
  16. Zhuang, X. & J.B. Klauda. “Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease.”  AIChE Annual Meeting (2014).
  17. Monje-Galvan, V.  & J.B. Klauda. “Membrane Binding of the Osh4 Curvature-Sensing Peptide” Quitel Conference in Ecuador (2014).
  18. Zhuang, X. J.R. Makover & J.B. Klauda. “Temperature Dependence of Bilayer Structural Properties Studied with Molecular Dynamics Simulations” Biophysical Society (2014).
  19. Khakbaz, P. & J.B. Klauda. “Studying Conformational Changes of Mhp1 using Unbiased All-atom Molecular Simulations” Biophysical Society (2014).
  20. Monje, V. & J.B. Klauda. “Molecular Dynamics of Yeast Membranes & Preliminary studies of ALPS-motif binding mechanism” Biophysical Society (2014).
  21. Monje, V., & J.B. Klauda. “Simulation studies on organelle-specific yeast membrane models and amphipathic lipid packing sensor (ALPS) motif binding mechanism” AIChE Annual Meeting (2013).
  22. Monje, V., T. Kim, W. Im, & J.B. Klauda. “Improved CHARMM Force Field for Polyunsaturated Fatty Acid Chains, A Study on DAPC Membranes” Biophysical Society (2013).
  23. Pendse, P.Y. & J.B. Klauda. “Investigation of the Proton Translocation Mechanism in Lactose Permease of E. Coli by a Hybrid QM/MM Approach.” AIChE Annual Meeting (2012).
  24. Pendse, P.Y. & J.B. Klauda. “Study of Ligand Binding Thermodynamics and Proton Translocation in Lactose Permease of Escherichia Coli.” ACS Spring National Meeting (2012).
  25. Pandit, K. & J.B. Klauda. “In Silico Model Escherichia Coli Membranes: Simulating a Lipid with a Cyclopropane Ring.” AIChE Annual Meeting (2011).
  26. Noon, M.S. J.B. Lim, A.D.. MacKerell Jr., J.B. Klauda. “Structure Prediction and Simulations of the Major Outer Membrane Protein of Chlamydia.” Biophsyical Society (2011).
  27. Rogaski, B. & J.B. Klauda. “Phosphoplipid Binding and Membrane Attachment of the Osh4 Protein.” Biophsyical Society (2011).
  28. Pandit, K. & J.B. Klauda. “In Silico Model Escherichia Coli Membranes: Simulating a Lipid with a Cyclopropane Ring.” Biophsyical Society (2011).
  29. Pendse, P.Y & J.B. Klauda. “Mechanistic and Thermodyanmic Insights into the Transport Cycle of Lactose Permease.” Biophsyical Society (2011).
  30. Villanueva, D.Y. & J.B. Klauda. “Lipid Bilayers of Ester-modified Lipids.” Biophsyical Society (2011).
  31. Rogaski, B. & J.B. Klauda. “Phosphoplipid Binding and Membrane Attachment of the Osh4 Protein.” ACS Spring National Meeting (2011).
  32. Pendse, P.Y. & J.B. Klauda. “Quantification of binding affinity in lactose permease of E. coli to understand the anomeric binding phenomenon.” ACS Spring National Meeting (2011).
  33. Pendse, P.Y. & J.B. Klauda. “Binding Free Energy Calculations to Understand the Mechanism of Sugar Binding to Lactose Permease of E. Coli.” AIChE Annual Meeting (2010).
  34. Rogaski, B. & J.B. Klauda. “PIP Binding and Membrane Attachment of a Protein Involved in Intracellular Transport of Sterols.” AIChE Annual Meeting (2010).
  35. Pendse, P.Y., B.R. Brooks, & J.B. Klauda. “An Atomic-level Model for the Periplasmic Open State of Lactose Permease.” Chemistry and Biology Interface Symposium, Baltimore (2010).
  36. Rogaski, B. & J.B. Klauda. “Binding of A Natural Sterol to the Osh4 Protein of Yeast and Membrane Attachment.” Chemistry and Biology Interface Symposium, Baltimore (2010).
  37. Noon, M.S. & J.B. Klauda. “Structure Prediction of the Major Outer Membrane Protein of Chlamydia.” Chemistry and Biology Interface Symposium, Baltimore (2010).
  38. Lim, J.B. & J.B. Klauda. “Branching at the Iso- and Anteiso- Positions in Complex Chlamydia Membranes: A Molecular Dynamics Study.” Chemistry and Biology Interface Symposium, Baltimore (2010).
  39. Rogaski, B. & J.B. Klauda. “Binding of a Natural Sterol to the Osh4 Protein of Yeast and Membrane Attachment.” Biophysical Society (2010).
  40. Pendse, P.Y., B.R. Brooks, & J.B. Klauda. “An Atomic-level Model for the Periplasmic Open State of Lactose Permease.” Biophysical Society (2010).
  41. Lim, J.B. & J.B. Klauda “Molecular Dynamics Simulations of Complex Mixed Lipid Bilayers to Model Yeast Membranes” ACS National Fall Meeting (2009).
  42. Pendse, P. & J.B. Klauda “Structural Changes and Quantification of Ligand Affinity in Lactose Permease of Escherichia coli.” ACS National Fall Meeting (2009).
  43. Lim, J.B., S. Jo, W. Im, & J.B. Klauda “Molecular Dynamics Simulations of Complex Mixed Lipid Bilayers to Model Yeast Membranes” Chemistry and Biology Interface Symposium, Baltimore (2009).
  44. Pendse, P. & J.B. Klauda “Structural Changes and Sugar Binding in Lactose Permease of E. coliChemistry and Biology Interface Symposium, Baltimore (2009).