Publications

Google Scholar Profile

Book chapters 

• Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods.

• Juergen Koefinger, Bartosz Rozycki, Gerhard Hummer

• In: Bonomi M., Camilloni C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022. Humana, New York, NY (2019)

Peer-reviewed articles 

• Encoding prior knowledge in ensemble refinement

• Juergen Koefinger and Gerhard Hummer

• J. Chem. Phys.  160 (2024)

• Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions

• Max Linke, Patrick K. Quoika, Berenger Bramas, Juergen Koefinger, and Gerhard Hummer

• J. Chem. Phys.  157 (2022)

• TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes

• Marc Siggel, Sebastian Kehl, Klaus Reuter, Juergen Koefinger, and Gerhard Hummer

• J. Chem. Phys.  157 (2022)

• Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly

• Martin Voegele, Juergen Koefinger, and Gerhard Hummer

• ACS Appl. Bio Mater. (2022)

• Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

• Lukas S. Stelzl, Lisa M. Pietrek, Andrea Holla, Javier Oroz, Mateusz Sikora, Juergen Koefinger, Benjamin Schuler, Markus Zweckstetter, and Gerhard Hummer

• J. Am. Chem. Soc. Au 2 (2022)

• Empirical optimization of molecular simulation force fields by Bayesian inference

• Juergen Koefinger and Gerhard Hummer

• Europ. J. Phys. B 94 (2021)

• Solution Structure and Conformational Flexibility of a Polyketide Synthase Module

• Maja Klaus, Emanuele Rossini, Andreas Linden, Karthik S. Paithankar, Matthias Zeug, Zoya Ignatova, Henning Urlaub, Chaitan Khosla, Juergen Koefinger, Gerhard Hummer, and Martin Grininger

• J. Am. Chem. Soc. Au 1 (2021)

• Membrane fusion and drug delivery with carbon nanotube porins

• Nga T. Ho, Marc Siggel, Karen V. Camacho,  Ramachandra M. Bhaskara, Jacqueline M. Hicks, Yun-Chiao Yao, Yuliang Zhang, Juergen Koefinger, Gerhard Hummer, and  Aleksandr Noy

• Proc. Natl.  Acad. Sci. U.S.A. 118 (2021)

• MDBenchmark: a toolkit to optimize the performance of molecular dynamics simulations

• Michael Gecht, Marc Siggel, Max Linke, Gerhard Hummer, and Juergen Koefinger

• J. Chem. Phys. 153 (2020)

• Quantifying Protein-Protein Interactions in Molecular Simulations

• Alfredo Jost Lopez, Patrick K. Quoika, Max Linke, Gerhard Hummer, and Juergen Koefinger

• J. Phys. Chem. B 124 (2020)

• Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models

• Stephanie Maria Linker, Aniket Magarkar, Juergen Koefinger, Gerhard Hummer, Daniel Seeliger

• J. Chem. Theory Comput. 15 (2019)

• Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations

• Martin Voegele,  Juergen Koefinger, Gerhard Hummer

• J. Phys. Chem. B  123 (2019)

•  Efficient ensemble refinement via reweighting

• Juergen Koefinger, Lukas S. Stelzl,  Klaus Reuter, Cesar Allande, Katrin Reichel, Gerhard Hummer

• J. Chem. Theory and Comput. 15 (2019)

• CADISHI: Fast CAlculation of DIStance HIstograms on CPUs and GPUs

• Klaus Reuter and  Juergen Koefinger

• Comput. Phys. Commun. 236 (2019)

• Precision DEER Distances from Spin-Label Ensemble Refinement

• Katrin Reichel, Lukas S. Stelzl,  Juergen Koefinger, Gerhard Hummer

• J. Phys. Chem. Letters 9 (2018)

• Molecular dynamics simulations of carbon nanotube porins in lipid bilayers

• Martin Voegele, Juergen Koefinger, and Gerhard Hummer

• Faraday Discuss. 209 (2018)

• Hydrodynamics of diffusion in lipid membrane simulations

• Martin Voegele, Juergen Koefinger, and Gerhard Hummer

• Phys. Rev. Lett. 120  (2018) 

• Rotational diffusion depends on box size in molecular dynamics simulations

• Max Linke,  Juergen Koefinger, and Gerhard Hummer

• J. Phys. Chem. Lett.  9 (2018)

• Fully anisotropic rotational diffusion tensor from molecular dynamics simulations

• Max Linke,  Juergen Koefinger, and Gerhard Hummer

• J. Phys. Chem. B  122 (2018)

• Carbon nanotubes mediate fusion of lipid vesicles

• Ramachandran M. Bhaskara, Stephanie Linker, Martin Voegele, Juergen Koefinger, and Gerhard Hummer

• ACS Nano 12 (2017)

• Bayesian ensemble refinement by replica simulations and reweighting

• Gerhard Hummer and Juergen Koefinger

• J. Chem. Phys. 143 (2015)

• Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation

• Thomas RM Barends, Lutz Foucar, Albert Ardevol, Karol Nass, Andrew Aquila, Sabine Botha, R Bruce Doak, Konstantin Falahati, Elisabeth Hartmann, Mario Hilpert, Marcel Heinz, Matthias C Hoffmann, Juergen Koefinger, Jason E Koglin, Gabriela Kovacsova, Mengning Liang, Despina Milathianaki, Henrik T Lemke, Jochen Reinstein, Christopher M Roome, Robert L Shoeman, Garth J Williams, Irene Burghardt, Gerhard Hummer, Sébastien Boutet, Ilme Schlichting

• Science 350 (2015)

• Solution Structure of the Atg1 Complex: Implications for the Architecture of the Phagophore Assembly Site

• Juergen Koefinger, Michael J. Ragusa, Il-Hyung Lee, Gerhard Hummer, and James H. Hurley

• Structure 23 (2015)

• Atomic-resolution structural information from scattering experiments on macromolecules in solution

• Juergen Koefinger and Gerhard Hummer

• Phys. Rev. E 87 (2013)

• Phase transition and interpore correlations of water in nanopore membranes

• Georg Menzl, Juergen Koefinger, and Christoph Dellago

• Phys. Rev. Lett. 109 (2012)

• Single-file water in nanopores

• Juergen Koefinger, Gerhard Hummer, and Christoph Dellago

• Phys. Chem. Chem. Phys. 13 (2011)

• Microscopic properties of nanopore water from its time-dependent dielectric response

• Juergen Koefinger and Christoph Dellago

• Phys. Rev. B 82 (2010)

• Single-file water as a one-dimensional Ising model

• Juergen Koefinger and Christoph Dellago

• New J. Phys. 12 (2010)

• Orientational relaxation and dielectric response of nanopore water

• Juergen Koefinger and Christoph Dellago

• Phys. Rev. Lett. 103 (2009)

• A one-dimensional dipole lattice model for water in narrow nanopores

• Juergen Koefinger, Gerhard Hummer, and Christoph Dellago

• J. Chem. Phys. 130 (2009)

• The statistics of electric field fluctuations in liquid water

• Bernhard Reischl, Juergen Koefinger, and Christoph Dellago

• Mol. Phys. 107 (2009)

• Macroscopically ordered water in nanopores

• Juergen Koefinger, Gerhard Hummer, and Christoph Dellago

• Proc. Natl. Acad. Sci. 105 (2008)

• Biasing the center of charge in molecular dynamics simulations with empirical valence bond models: free energetics of an excess proton in a water

• Juergen Koefinger and Christoph Dellago

• J. Phys. Chem. B 112 (2007)

• Phase behaviour of a symmetrical binary fluid mixture

• Juergen Koefinger, Nigel B. Wilding, and Gerhard Kahl

• J. Chem. Phys. 125 (2006)

• Phase behaviour of a symmetrical binary mixture in a field

• Juergen Koefinger, Gerhard Kahl, and Nigel B. Wilding

• Europhys. Lett. 75 (2006)

• Modell colloid-polymer mixtures in porous matrices: density functional versus

• integral equation

• Mathias Schmitt, Elisabeth Schoell-Paschinger, Juergen Koefinger, Gerhard Kahl

• J. Phys.: Cond. Matt. 14 (2002)