Publications

Peer-reviewed papers

22. Local micro-partition coefficients govern solute permeability of cholesterol-containing membranes
Florian Zocher, Christian L. Wennberg, David van der Spoel, Peter Pohl, and Jochen S. Hub
submitted
22. Why the water droplet surface is acidic
Jochen S. Hub, Maarten Wolf, Carl Caleman, Paul van Maaren, Gerrit Gronhof, and David van der Spoel
submitted
21. Artifacts in non-neutral simulation systems using Ewald sum electrostatics
Jochen S. Hub, Bert de Groot, Helmut Grubmüller, and Gerrit Gronhof
submitted
20. Organic molecules on the surface of water droplets - an energetic perspective
Jochen S. Hub, Carl Caleman, and David van der Spoel
Phys. Chem. Chem. Phys., 14, 9537-9545 (2012) [pdf] [www] [supporting info]
19. Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes
Christian L. Wennberg, David van der Spoel, and Jochen S. Hub
J. Am. Chem. Soc. 134, 5351–5361 (2012) [pdf] [www] [supporting info]
18. Partial least squares functional mode analysis: application to membrane proteins Aqy1 and CLC-ec1
Tatyana Krivobokova, Rodolfo Briones, Jochen S. Hub, Axel Munk, and Bert L. de Groot
Biophys. J. 103, 786-796 (2012) [pdf] [www] [supporting info]
17. Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin
Erik Malmerberg, Zaid Omran, Jochen S. Hub, Xuewen Li, Gergely Katona, Sebastian Westenhoff, Linda Johansson, Magnus Andersson, Marco Cammarata, Michael Wulff, David van der Spoel, Jan Davidsson, Alexandre Specht, Richard Neutze
Biophys. J. 101, 1245-1353 (2011) [pdf] [www] [supporting info]
16. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, and David van der Spoel
J. Chem. Theory Comput. 8, 61-74 (2012) [pdf] [www] [supporting info PDF] [supporting info ZIP]
15. Atomistic simulation of ion solvation in water explains surface preference of halides
Jochen S. Hub, Carl Caleman, Paul J. van Maaren, and David van der Spoel
Proc. Natl. Acac. Sci. USA 108, 6838-6842 (2011) [pdf] [www] [supporting info]
14. Comment on “Molecular selectivity in aquaporin channels studied by the 3D-RISM theory”
Jochen S. Hub and Bert L. de Groot
J. Phys. Chem. B, 115, 8364-8366 (2011) [pdf] [www]
13. Voltage-regulated water flux through aquaporin channels in silico
Jochen S. Hub, Camilo Aponte-Santamaría, Helmut Grubmüller, and Bert L. de Groot
Biophys. J. 99(12), L97-L99 (2010) [pdf] [www] [supporting info]
12. g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates
Jochen S. Hub, Bert L. de Groot, and David van der Spoel
J. Chem. Theory Comput., 6(12), 3713-3720 (2010) [pdf] [www]
11. Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes
Jochen S. Hub, Fritz K. Winkler, Mike Merrick, and Bert L. de Groot
J. Am. Chem. Soc. 132, 13251-13263 (2010) [pdf] [www] [supporting info]
10. Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin
Camilo Aponte-Santamaría, Jochen S. Hub, and Bert L. de Groot
Phys Chem Chem Phys 12, 10246-10254 (2010) [pdf] [www]
9. Quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulations
Jochen S. Hub, Marcus B. Kubitzki, and Bert L. de Groot
PLoS Comp Biol 6(5), e1000774 (2010) [pdf] [supporting info] [www]
8. Detection of functional modes in protein dynamics
Jochen S. Hub and Bert L. de Groot
PLoS Comp Biol 5(8), e1000480 (2009) [pdf] [supporting info] [www]
7. g_permute: Permutation-reduced phase space density compaction
Friedemann Reinhard, Oliver F. Lange, Jochen S. Hub, Jürgen Haas, and Helmut Grubmüller
Comp Phys Comm 180, 455-458 (2009) [pdf] [www]
6. Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels
Guillem Portella, Jochen S. Hub, Martin S. Vesper, and Bert L. de Groot
Biopyhs J 95, 2275-2282 (2008) [pdf] [www]
5. Mechanism of selectivity in aquaporins and aquaglyceroporins
Jochen S. Hub and Bert L. de Groot
Proc. Natl. Acad. Sci. USA 105:1198-1203 (2008) [pdf] [supporting info] [www]
4. Is TEA an Inhibitor for human Aquaporin-1?
Jochen S. Hub, E. Matthias Müller, Helmut Grubmüller, and Bert L. de Groot
Pflügers Arch 456:663-669 (2008) [pdf] [www]
3. Short range order and collective dynamics of DMPC bilayers. A comparison between molecular dynamics simulations, x-ray, and neutron scattering experiments
Jochen S. Hub, Tim Salditt, Meikel C. Rheinstädter, and Bert L. de Groot
Biophys J 93, 3156-3168 (2007) [pdf] [www]
2. Does CO2 permeate through Aquaporin-1?
Jochen S. Hub and Bert L. de Groot
Biophys J 91, 842-848 (2006) [pdf] [www]
1. Molecular Anatomy of a Trafficking Organelle
S. Takamori, M. Holt, K. Stenius, E. A. Lemke, M. Grønborg, D. Riedel, H. Urlaub, S. Schenck, B. Brügger, P. Ringler, S.A. Müller, B. Rammner, F. Gräter, J.S. Hub, B.L. De Groot, G. Mieskes, Y. Moriyama, J. Klingauf, H. Grubmüller, J. Heuser, F. Wieland, and R. Jahn
Cell 127, 831-846 (2006) [www]

Book chapters and conference reports

3. A Decade of Debate: Significance of CO2 Permeation through Membrane Channels still Controversial
Bert L. de Groot and Jochen S. Hub
ChemPhysChem 12, 1021-1022 (2011) [pdf] [www]
2. Dynamics and Energetics of Permeation through Aquaporins. What do we learn from Molecular Dynamics Simulations?
Jochen S. Hub, Helmut Grubmüller, and Bert L. de Groot
Handbook of Experimental Pharmacology. Aquaporins. vol. 190, Springer 2009 [pdf] [www]
1. Dynamics and criticality of correlated electrons and quantum gases
C. Lavalle, M. Rigol, J. Hub, and A. Muramatsu
"High Performance Computing in Science and Engineering '04" (Springer - 2004) [www]

Theses

Selectivity, Regulation, and Inhibition of Aquaporin Channels. A Molecular Dynamics Study
Jochen S. Hub
Dissertation, Georg-August-University of Göttingen, Germany (2008). Published online
Spin- and density correlations in the one-dimensional t-J model from quantum-monte-carlo simulations
Jochen Hub
Diploma thesis, University of Stuttgart, German, [pdf], [ps.gz]

Invited conference talks

2. Ammonia, carbon dioxide, and water permeability of the Rh50 channel and lipid membranes from MD simulations , International Workshop on Epithelial Transport 2010, Strobl, Austria
1. Understanding channel selectivity from potentials of mean force, Gromacs Workshop 2008, Göttingen, Germany [pdf]

Invited seminar talks

4. Channels, motion, water droplets. What do we learn from MD simulation?
Seminar of the Collaborative Research Centre 860, Georg-August-University of Göttingen, Germany, January 2011
3. From Crystal Structure to Channel Permeability. Computational Studies of Rhesus and Aquaporin Channels
Institute Nationale de la Transfusion Sanguine, Paris, January 2011
2. Channels, motion, water droplets. What do we learn from MD simulation?
Seminar of the Max-Planck-Institute for Biophysics, Frankfurt, Germany, January 2011
1. From channel structure to solute permeability. What do we learn from MD simulations?
Simbios Talk, Stanford University, February 2010

Please note: This website is part of the personal CV of Jochen S. Hub.