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Publications

Peer-reviewed papers

46. Assigning crystallographic electron densities with free energy calculations – the case of the fluoride channel Fluc
Igor Ariz-Extreme, and Jochen S. Hub
submitted
45. Temperature-dependent atomic models of detergent micelles refined against small-angle X-ray scattering data
Miloš T. Ivanović, Linda Bruetzel, Jan Lipfert, and Jochen S. Hub
Angew. Chem. Int. Ed., accepted
44. Metastable prepores in tension-free lipid bilayers
Christina L. Ting, Neha Awasthi, Marcus Müller, and Jochen S. Hub
Phys. Rev. Lett., accepted
43. Energetics of pore formation in lipid membranes: lipid shape versus molecular interactions
Neha Awasthi and Jochen S. Hub
submitted
42. Interpreting solution X-ray scattering data using molecular simulations
Jochen S. Hub
Curr. Opin. Struct. Biol., 49, 18-26 (2018) [www] [pdf]
Access the recommendation on F1000Prime
41. Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
Roman Shevchuk and Jochen S. Hub
PLoS Comp. Biol., 13, e1005800 (2017) [www] [pdf]
40. A glycerophospholipid-specific pocket in the RVFV class II fusion protein drives target-membrane insertion
Pablo Guardado-Calvo, Kalina Atkovska, Scott A. Jeffers, Nina Grau, Marija Backovic, Jimena Pérez-Vargas, S.M. de Boer, M.A. Tortorici, Gérard Pehau-Arnaudet, Jean Lepault, Patrick England, Peter J. Rottier, Berend J. Bosch, Jochen S. Hub, Félix A. Rey
Science, 358, 663-667 (2017) [www] [pdf] [supporting info] [supporting movies]
39. Energetics and mechanism of anion permeation across formate-nitrite-transporters
Kalina Atkovska and Jochen S. Hub
Sci. Rep., 7, 12027 (2017) [www] [pdf] [supporting info]
38. Probing a continuous polar defect: A reaction coordinate for pore formation in lipid membranes
Jochen S. Hub and Neha Awasthi
J. Chem. Theory Comput., 13, 2352-2366 (2017) [www] [pdf]
37. Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly
Tiago Cordeiro, Po-chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco Blanco, Jochen S. Hub, Ramon Crehuet, Pau Bernado
Nucleic Acids Res., 45, 1501-2015 (2017) [www] [pdf] [supporting info]
36. Potential of mean force calculations of solute permeation across UT-B and AQP1: A comparison between molecular dynamics and 3D-RISM
Igor Ariz-Extreme and Jochen S. Hub
J. Phys. Chem. B, 121, 1506-1519 (2017) [www] [pdf] [supporting info]
35. Accelerating potential of mean force calculations for lipid membrane permeation: system size, reaction coordinate, solute-solute distance, and cutoffs
Naomi Nitschke, Kalina Atkovska, and Jochen S. Hub
J. Chem. Phys., 145, 125101 (2016) [www] [pdf]
34. Simulations of pore formation in lipid membranes: reaction coordinates, convergence, hysteresis, and finite-size effects
Neha Awasthi and Jochen S. Hub
J. Chem. Theory Comput., 12, 3261-3269 (2016) [www] [pdf]
33. Ultrafast anisotropic protein quake propagation after CO-photodissociation in myoglobin
Levin U.L. Brinkmann and Jochen S. Hub
Proc. Natl. Acad. Sci. USA, 113, 10565–10570 (2016) [www] [pdf] [pdf+supporting info]
32. The lipid bilayer provides a site for cortisone crystallization at high cortisone concentrations
Richard Alsop, Andree Khondker, Jochen S. Hub, and Maikel Rheinstädter
Sci. Rep., 6, 22425 (2016) [www] [pdf] [supporting info]
31. Structural properties of protein-detergent complexes from SAXS and MD simulations
Po-chia Chen and Jochen S. Hub
J. Phys. Chem. Lett., 6, 5116–5121 (2015) [www] [pdf] [supporting info]
30. Quantifying lateral inhomogeneity of cholesterol-containing membranes
Celsa Díaz-Tejada, Igor Ariz-Extreme, Neha Awasthi, and Jochen S. Hub
J. Phys. Chem. Lett., 6, 4799-4803 (2015) [www] [pdf] [supporting info]
29. Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics
Levin U.L. Brinkmann and Jochen S. Hub
J. Chem. Phys., 143, 104108 (2015) [www] [pdf]
28. MemGen: A general web server for the setup of lipid membrane simulation systems
Christopher J. Knight and Jochen S. Hub
Bioinformatics, 31, 2897-2899 (2015) [www] [pdf] [supporting info]
Please find MemGen at: http://memgen.uni-goettingen.de/
27. WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics
Christopher J. Knight and Jochen S. Hub
Nucleic Acids Res., 43, W225-W230 (2015) [www] [pdf]
Please find WAXSiS at: http://waxsis.uni-goettingen.de/
26. Interpretation of solution X-ray scattering data by explicit-solvent molecular dynamics
Po-chia Chen and Jochen S. Hub
Biophys. J., 108, 2573–2584 (2015) [pdf] [www] [supporting info] [main text and supporting info]
Related New and Notable comment by Robert Rambo and John Tainer: Biophys. J. 108:2421-2423 (2015)
Biophysical Journal Paper of the Year award. BPS on Twitter and press release.
25. Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data
Po-chia Chen and Jochen S. Hub
Biophys. J., 107, 435-447 (2014) [pdf] [www] [supporting info] [main text and supporting info]
Note: the calculations are available to everyone via the WAXSiS web server.
24. CO2 and O2 distribution in Rubisco suggests the small subunit functions as a CO2 reservoir
Michiel van Lun, Jochen S. Hub, David van der Spoel, and Inger Andersson
J. Am. Chem. Soc., 136, 3165-3171 (2014) [pdf] [www] [supporting info]
23. Thermodynamics of hydronium and hydroxide surface solvation
Jochen S. Hub, Maarten Wolf, Carl Caleman, Paul van Maaren, Gerrit Gronhof, and David van der Spoel
Chemical Science, 5, 1745-1749 (2014) [www] [pdf] [supporting info]
22. Quantifying artifacts in Ewald simulations of inhomogeneous systems with a net charge
Jochen S. Hub, Bert de Groot, Helmut Grubmüller, and Gerrit Groenhof
J. Chem. Theory Comput., 10, 381-390 (2014) [pdf] [www]
21. Local partition coefficients govern solute permeability of cholesterol-containing membranes
Florian Zocher, David van der Spoel, Peter Pohl, and Jochen S. Hub
Biophys. J., 105, 2760-2770 (2013) [pdf] [www] [pdf incl. supporting info]
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. 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]
16. 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]
15. Atomistic simulation of ion solvation in water explains surface preference of halides
Carl Caleman*, Jochen S. Hub*, 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, Maikel 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, conference reports, and manual contributions

4. GROMACS user manual, since version 5.0 [www]
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 (selected)

Interpretation of Anisotropic Solution X-ray Scattering by Means of Molecular Dynamics Simulation
Levin. U.L. Brinkmann
Master Thesis, Georg-August-University of Göttingen (2014). [Small pdf], [Large pdf],
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]

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