Laboratory of Molecular & Thermodynamic Modeling

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Peer-Reviewed Articles


    2015

  1. Kang, H & J.B. Klauda. Molecular Dynamics Simulations of Palmitoyloleoyl-phosphatidylglycerol Bilayers. Molecular Simulation. 41: 948-954 (2015).
  2. Park, S., A.H. Beaven, J.B. Klauda and W. Im. How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? J. Chem. Theor. Comp. 11: 3466-3477 (2015).
  3. Khakbaz, P. and J.B. Klauda. Probing the Importance of Lipid Diversity in Cell Membranes via Molecular Simulation. Chem. Phys. Lipids. 192: 12-22 (2015). Invited
  4. Konas, R.M., J.L. Daristotle, N.B. Harbor, and J.B. Klauda. Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations. J. Phys. Chem. B. 119: 13134-13141 (2015).
  5. Qi, Y., X. Cheng, J. Lee, J. Vermaas, T.V. Pogorelov, E. Tajkhorshid, S. Park, J.B. Klauda, and Wonpil Im. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophys. J. 109: 2012-2022 (2015).
  6. Monje-Galvan, V. and J.B. Klauda. Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties. Biochem. 54: 6852-6861 (2015).
  7. Wu, E., Y. Qi, S. Park, S.S. Mallajosyula, A.D. MacKerell, Jr., J.B. Klauda, and W. Im. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophys. J. 109: 2090-2100 (2015).
  8. MacDermaid, C.M., H.K. Kashyap, R.H. DeVane, W. Shinoda, J.B. Klauda, M.L. Klein, and G. Fiorin. Molecular Dynamics Simulations of Cholesterol-rich Membranes using a Coarse-grained Force Field for Cyclic Alkanes. J. Chem. Phys.  143, 243144 (2015).
  9. 2014

  10. Lee, S., A. Tran, M. Allsopp, J.B. Lim, J. Hénin, & J.B. Klauda. CHARMM36 United-Atom Chain Model for Lipids and Surfactants. J. Phys. Chem. B. 118: 547-556 (2014).
  11. Jeong, J.C., S. Jo, E.L. Wu, Y. Qi, V. Monje, M.S. Yeom, L. Gorenstein, F. Chen, J.B. Klauda, & W. Im. ST-analyzer: A Web-based User Interface for Simulation Trajectory Analysis. Journal of Comp. Chem. 35: 957-963 (2014).
  12. Wu, E.L., Y. Qi, K.C. Song, J.B. Klauda, & W. Im. Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms. J. Phys. Chem. B. 118: 4315-4325 (2014).
  13. Wu, E.L., P.J. Fleming, M.S. Yeom, G. Widmalm, J.B. Klauda, K.G. Fleming & W. Im. E. coli Outer Membrane and Interactions with OmpLA.  Biophysical J. 106: 2493-2502 (2014).  Cover Article
  14. Subramanian, D. J.B. Klauda, and M.A. Anisimov. Mesoscale Phenomena in Ternary Solutions of Tertiary Butyl Alcohol, Water, and Propylene Oxide. J. Phys. Chem. B. 118: 5994-6006 (2014).
  15. Venable, R.M., A.J. Sodt, B. Rogaski, H. Rui, E. Hatcher, A.D. MacKerell, Jr., R.W. Pastor, and J.B. Klauda. CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature. Biophysical J. 107: 1885-1895 (2014).
  16. Wu, E., X. Cheng, S. Jo, H. Rui, K.C. Song, E.M. Dávila-Contreras, Y. Qi, J. Lee, V. Monje-Galvan, R.M. Venable, J.B. Klauda, and W. Im. CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations. J. of Comp. Chem. 35: 1997-2004 (2014).
  17. Zhuang, X., J.R. Makover, W. Im, & J.B. Klauda. A Systematic Molecular Dynamics Simulation Study of Temperature Dependent Bilayer Structural Properties. BBA-Biomemb. 1838: 2520-2529 (2014).
  18. Kern, N.R, H.S. Lee, E.L. Wu, K. Vanommeslaeghe, A.D MacKerell, Jr., J.B. Klauda, S. Jo, and W. Im. Lipid-Linked Oligosaccharides in Membranes Sample Conformations that Facilitate Binding to Oligosaccharyltransferase. Biophys. J. 107: 1885-1895 (2014).
  19. 2013

  20. Subramanian, D., J.B. Klauda, J. Leys, and M.A. Anisimov. Thermodynamic Anomalies and Structural Fluctuations in Aqueous Solutions of Tertiary Butyl Alcohol. Herald of St. Petersburg University (Вестник СПбГУ) 4, 140-153 (2013).
  21. Cheng, X., S.H. Jo, J.B. Klauda, and W. Im. CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems. Journal of Chemical Information and Modeling. 53, 2171-2180 (2013).
  22. Wu, E.L., O. Engström, S. Jo, D, Stuhlsatz, MS Yeom, J.B. Klauda, G. Widmalm, and W. Im. Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics. Biophys. J. 105, 1444-1455 (2013).
  23. Villanueva, D.Y., J.B. Lim, and J.B. Klauda. Influence of Ester-modified Lipids on Bilayer Structure. Langmuir. 29, 14196-14203 (2013).
  24. Subramanian, D., C.T. Boughter, J.B. Klauda, B. Hammouda, and M.A. Anisimov. Mesoscale inhomogeneities in aqueous solutions of small amphiphilic molecules. Faraday Discuss. 167: 217-238 (2013).

    2012-2000

  25. Rogaski, B and J.B. Klauda. Membrane-binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations. J. Mol. Bio. 423, 847-861 (2012).
  26. 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
  27. Ezzeldin, H.M., J.B. Klauda, and 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).
  28. 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).
  29. 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).
  30. 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).
  31. 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).
  32. 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).
  33. 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).
  34. 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).
  35. 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).
  36. 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).
  37. 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).
  38. 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
  39. 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).
  40. 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).
  41. 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).
  42. Klauda, J.B.  & B.R. Brooks. CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes. J. Chem. Theory Comp. 4, 107-115 (2008).
  43. 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).
  44. 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).
  45. 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).
  46. 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).
  47. 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).
  48. 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).
  49. 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).
  50. 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).
  51. Klauda, J. B. & S.I. Sandler.  Global Distribution of Methane Hydrate in Ocean Sediment. Energy & Fuels. 19, 469-470 (2005).
  52. 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).
  53. 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).
  54. 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).
  55. 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).
  56. 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).
  57. 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).
  58. 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
  59. 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).
  60. Klauda, J. B. & S.I. Sandler.  Ab Initio Intermolecular Potentials for Gas Hydrates and Their Predictions. J. Phys. Chem. B. 106, 5722-5732 (2002).
  61. 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).
  62. Klauda, J. B. & S.I. Sandler.  A Fugacity Model for Gas Hydrate Phase Equilibria. Ind. Eng. Chem. Res. 39, 3377-3386 (2000).