Dr. Ir. Bernd Ensing

Van 't Hoff Institute for Molecular Sciences
University of Amsterdam
Science Park 904
1098 XH Amsterdam

room: C2.238
phone: (+31) 20 525 5067
b.ensinguva.nl

Publications

  1. Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (φ, ψ) space.
    Zhiwei Liu, Bernd Ensing, and Preston B. Moore
    J. Chem. Theory. Comput. 7 (2011), 402 - 419 DOI: 10.1021/ct100395n
  2. A Reply to the Comment by M. Praprotnik et al.
    Steven O. Nielsen, Preston B. Moore, Bernd Ensing
    Phys. Rev. Lett. 107 (2011), 099802 DOI: 10.1103/PhysRevLett.107.099802
  3. Recent progress in multiscale molecular dynamics simulation of soft matter.
    Steven O. Nielsen, Rosa E. Bulo, Preston B. Moore, Bernd Ensing
    Invited Perspective and cover article Phys. Chem. Chem. Phys. 12 (2010), 12401 - 12412 DOI: 10.1039/c004111d
  4. Adaptive multiscale molecular dynamics of macromolecular fluids.
    Steven O. Nielsen, Preston B. Moore, and Bernd Ensing
    Phys. Rev. Lett. 105 (2010), 237802 DOI: 10.1103/PhysRevLett.105.237802
  5. Smooth capping of short-range repulsive forces in hybrid atomistic/coarse-grain molecular dynamics simulation.
    Bernd Ensing
    Proceedings of Multiscale Materials Modeling in press (2010)
  6. Non-linear reaction coordinate analysis in the reweighted path ensemble.
    Wolfgang Lechner, Jutta Rogal, Jarek Juraszek, Bernd Ensing, and Peter Bolhuis
    J. Chem. Phys. 133 (2010), 174110 DOI: 10.1063/1.3491818
  7. The reweighted path ensemble.
    Jutta Rogal, Wolfgang Lechner, Jarek Juraszek, Bernd Ensing, and Peter Bolhuis
    J. Chem. Phys. 133 (2010), 174109 DOI: 10.1063/1.3491817
  8. Multiscale molecular dynamics and the reverse mapping problem.
    Bernd Ensing and Steven O. Nielsen
    Book chapter in Trends in Computational Nanomechanics (Challenges and Advances in Computational Chemistry and Physics, Volume 9) edited by T. Dumitrica (Springer, 2010), p. 25 - 60 DOI: 10.1007/978-1-4020-9785-0_2
  9. Hydrolysis of cisplatin - a first-principles metadyamics study
    Justin Kai-Chi Lau and Bernd Ensing
    Phys. Chem. Chem. Phys. 12 (2010) 10348 - 10355 , DOI: 10.1039/b918301a
  10. A simple coarse-grained model for self-assembling silk-like protein fibers
    Marieke Schor, Bernd Ensing, and Peter G. Bolhuis
    Faraday Discuss. 144 (2010), 127 - 141, DOI: 10.1039/b901608b
  11. Toward a Practical Method for Adaptive QM/MM Simulations
    Rosa E. Bulo, Bernd Ensing, Jetze Sikkema, and Lucas Visscher
    J. Chem. Theory Comput. 5 (2009), 2212 - 2221, DOI: 10.1021/ct900148e
  12. Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics.
    Bernd Ensing, Steven O. Nielsen, Preston B. Moore, Michael L. Klein, and Michele Parrinello
    J. Chem. Theory Comput. 3 (2007), 1100 - 1105, DOI: 10.1021/ct600323n
  13. Proton shuttles and phosphatase activity in soluble epoxide hydrolase.
    Marco De Vivo, Bernd Ensing, Matteo Dal Peraro, German A. Gomez, David W. Christianson, and Michael L. Klein
    J. Am. Chem. Soc. 129 (2007) 387-394 DOI: 10.1021/ja066150c
  14. Coarse grained-to-atomistic mapping algorithm: a tool for multiscale simulations.
    Steven O. Nielsen, Bernd Ensing, Preston B. Moore, and Michael L. Klein
    Book chapter in Multiscale Simulation Methods for Nanomaterials, R. B. Ross and S. Mohanty, Editors. 2007, John Wiley & Sons, Inc., Hoboken, NJ, USA DOI: 10.1002/9780470191675.ch5
  15. Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents.
    Ekta Khurana, Steven O. Nielsen, Bernd Ensing, and Michael L. Klein
    J. Phys. Chem. B 110 (2006), 18965-18972 DOI: 10.1021/jp057471y
  16. Formamide hydrolysis in alkaline aqueous solution: Insights from ab-initio metadynamics calculations.
    Jochen Blumberger, Bernd Ensing, and Michael L. Klein
    Communication in Angewandte Chemie Int. Edit. 45 (2006), 2893-2897 DOI: 10.1002/anie.200600283
  17. Metadynamics as a tool for exploring the free energy landscape of chemical reactions.
    Bernd Ensing, Marco De Vivo, Zhiwei Liu, Preston Moore, and Michael L. Klein
    Acc. Chem. Res. 39 (2006), 73-81 DOI: 10.1021/ar040198i
  18. Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels.
    Bernd Ensing and Michael L. Klein
    Cover article in Proc. Natl. Acad. Sci., USA 102 (2005), 6755-6759 DOI: 10.1073/pnas.0408094102
  19. A recipe for the computation of the free energy barrier and lowest free energy path of concerted reactions.
    Bernd Ensing, Alessandro Laio, Michele Parrinello and Michael L. Klein
    J. Phys. Chem. B 109 (2005), 6676-6687 DOI: 10.1021/jp045571i
  20. Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study.
    Steve O. Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B. Moore, and Michael L. Klein
    Cover article in Biophys. J. 88 (2005), 3822-3828 DOI: 10.1529/biophysj.104.057703
  21. Structure and dynamics of model pore insertion into a membrane.
    Carlos F. Lopez, Steve O. Nielsen, Bernd Ensing, Preston B. Moore, and Michael L. Klein
    Cover article in Biophys. J. 88 (2005), 3083-3094 DOI: 10.1529/biophysj.104.053769
  22. Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle.
    Marco De Vivo, Bernd Ensing, and Michael L. Klein
    Communication in J. Am. Chem. Soc. 127 (2004), 11226-11227 DOI: 10.1021/ja053049j
  23. A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.
    Bernd Ensing, Alessandro Laio, Francesco L. Gervasio, Michele Parrinello, and Michael L. Klein
    Communication in J. Am. Chem. Soc. 126 (2004), 9492-9493 DOI: 10.1021/ja048285t
  24. Methane to methanol oxidation by the hydrated iron(IV)oxo species in aqueous solution; a combined DFT and Car-Parrinello molecular dynamics study.
    Bernd Ensing, Francesco Buda, Michiel C.M. Gribnau, and Evert Jan Baerends
    J. Am. Chem. Soc. 126 (2004), 4355-4365 DOI: 10.1021/ja038865a
  25. O-2 evolution in the Fenton reaction.
    Francesco Buda, Bernd Ensing, Michiel C.M. Gribnau, and Evert Jan Baerends
    Chem.Eur. J. 9 (2003), 3436-3444 DOI: 10.1002/chem.200204444
  26. Fenton-like chemistry in water: Oxidation catalysis by Fe(III) and H2O2.
    Bernd Ensing, Francesco Buda, and Evert Jan Baerends
    J. Phys. Chem. A. 107 (2003), 5722-5731 DOI: 10.1021/jp0267149
  27. Reaction path sampling of the reaction between iron(II) and hydrogen peroxide in aqueous solution.
    Bernd Ensing and Evert Jan Baerends
    J. Phys. Chem. A. 106 (2002), 7902-7910 DOI: 10.1021/jp025833l
  28. A Car-Parrinello study of the formation of oxidizing intermediates from Fentons reagent in aqueous solution.
    Bernd Ensing, Francesco Buda, Peter E. Bloechl, and Evert Jan Baerends
    Phys. Chem. Chem. Phys. 4 (2002), 3619-3627 DOI: 10.1039/b201864k
  29. Chemical involvement of solvent water molecules in elementary steps of the Fenton oxidation reaction.
    Bernd Ensing, Francesco Buda, Peter E. Bloechl, and Evert Jan Baerends
    Communication in Angewandte Chemie Int. Edit., 40 (2001), 2893-2895 DOI: 10.1002/1521-3757(20010803)113:15<2977::AID-ANGE2977>3.0.CO;2-Q
  30. DFT study of the active intermediate in the Fenton reaction.
    Francesco Buda, Bernd Ensing, Michiel C.M. Gribnau, and Evert Jan Baerends
    Chem. Eur. J. 7 (2001), 2775-2783 DOI: 10.1002/1521-3765(20010702)7:13<2775::AID-CHEM2775>3.0.CO;2-6
  31. Solvation effects on the SN2 reaction between CH3Cl and Cl- in water.
    Bernd Ensing, Evert Jan Meijer, Peter E. Bloechl, and Evert Jan Baerends
    J. Phys. Chem. A, 105 (2001), 3300-3310 DOI: 10.1021/jp003468x
  32. Comparison of the accurate Kohn-Sham solution with the generalized gradient approximations (GGAs) for the SN2 reaction F- + CH3F -> FCH3 + F-: A qualitative rule to predict success or failure of GGAs.
    Oleg V. Gritsenko, Bernd Ensing, Pieter R.T. Schipper, and Evert Jan Baerends
    J. Phys. Chem. A 104 (2000), 8558-8565 DOI: 10.1021/jp001061m
  33. A combined molecular dynamics-ab initio study of hydrogen molecule adsorption on ideal, relaxed and temperature-reconstructed MgO (111) surfaces.
    Micael Baudin, Kersti Hermansson, Bernd Ensing, Maria Alfredsson, and Mark Wojcik
    J. Chem. Phys. 109 (1998), 7515-7521 DOI: 10.1063/1.477409