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Sayan Maity, Beatrix M. Bold, Jigneshkumar Dahyabhai Prajapati, Monja Sokolov, Tomáš Kubař, Marcus Elstner, and Ulrich Kleinekathöfer
"DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex"
J. Phys. Chem. Lett. 2020, 11, XXX, 8660–8667, September 29, 2020
Mila Krämer, Philipp M. Dohmen, Weiwei Xie, Daniel Holub, Anders S. Christensen, and Marcus Elstner
"Charge and Exciton Transfer Simulations Using Machine-Learned Hamiltonians"
J. Chem. Theory Comput, https://dx.doi.org/10.1021/acs.jctc.0c00246, published: June 3, 2020
Weiwei Xie, Daniel Holub, Tomáš Kubař, and Marcus Elstner
"Performance of Mixed Quantum-Classical Approaches on Modeling the Crossover from Hopping to Bandlike Charge Transport in Organic Semiconductors"
J. Chem. Theory Comput. 2020, 16, 4, 2071–2084, Publication Date: March 16, 2020
Beatrix M. Bold, Monja Sokolov, Sayan Maity, Marius Wanko, Philipp M. Dohmen, Julian J. Kranz, Ulrich Kleinekathöfer, Sebastian Höfener and Marcus Elstner
"Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes"
Phys. Chem. Chem. Phys., first published on 13 Jan 2020
Daniel Holub, Tilman Lamparter, Marcus Elstner and Natacha Gillet
"Biological Relevance of Charge Transfer Branching Pathways in Photolyases"
Phys. Chem. Chem. Phys., first published on 10 Jul 2019
Violetta Schneider, Parvesh Wadhwani, Johannes Reichert, Jochen Bürck, Marcus Elstner, Anne S. Ulrich and Tomáš Kubař
"Tetrameric Charge-Zipper Assembly of the TisB Peptide in Membranes - Computer Simulation and Experiment"
J. Phys. Chem. B 2019, 123, 1770−1779
Franziska E. Wolff, Sebastian Höfener, Marcus Elstner and Tomasz A. Wesołowski
"Origin of the Solvatochromism in Organic Fluorophores with Flexible Side Chains: A Case Study of Flugi‑2"
J. Phys. Chem. A 2019, 123, 4581−4587
Lucas Ueberricke, Daniel Holub, Julian Kranz, Frank Rominger, Marcus Elstner and Michael Masta
"Triptycene End-capped Quinoxalinophenanthrophenazines (QPPs) –Influence of Substituents and Conditions on Aggregationin the Solid State"
Chem. Eur. J. 10.1002/chem.201902002, 18 June 2019
Victor Moron, Marco Marazzi, Marius Wanko
"Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore?"
J. Chem. Theory Comput. 2019, 15, 7, 4228-4240, May 30, 2019
Daniel Holub, Tomáš Kubař, Thilo Mast, Marcus Elstner and Natacha Gillet
"What accounts for the different functions in photolyases and cryptochromes: a computational study of proton transfers to FAD"
Phys. Chem. Chem. Phys., 2019, 21, 11956-11966
Hongju Ma, Daniel Holub, Natacha Gillet, Gero Kaeser, Katharina Thoulass, Marcus Elstner, Norbert Krauß, Tilman Lamparter
"Two aspartate residues close to the lesion binding site of Agrobacterium (6‐4) photolyase are required for Mg2+ stimulation of DNA repair"
FEBS Press, first published: 31 January 2019, https://doi.org/10.1111/febs.14770
Yanan Guo, Franziska E. Wolff, Igor Schapiro, Marcus Elstner and Marco Marazzi
"Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2"
Phys.Chem.Chem.Phys., 20, 27501, first published on 11th October 2018
Sabine Reißer, Erik Strandberg, Thomas Steinbrecher, Marcus Elstner and Anne S. Ulrich
"Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid- State NMR"
J. Chem. Theory Comput. 2018, 14, 6002−6014
Milena Vujović, Mioy Huynh, Sebastian Steiner, Pablo Garcia‐Fernandez, Marcus Elstner, Qiang Cui, Maja Gruden
"Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin‐polarized DFTB3 model"
Journal of Computational Chemistry 2018, 09 October 2018, doi.org/10.1002/jcc.25614
Natacha Gillet, Marcus Elstner and Tomáš Kubař
"Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer"
The Journal of Chemical Physics 149, 072328 (2018)
Julian J. Kranz, Maximilian Kubillus, Raghunathan Ramakrishnan, O. Anatole von Lilienfeld, and Marcus Elstner
"Generalized Density-Functional Tight-Binding Repulsive Potentials from Unsupervised Machine Learning"
J. Chem. Theory Comput. 2018, 14, 2341−2352
Emil Sjulstok, Gesa Lüdemann, Tomas Kubar, Marcus Elstner, and Ilia A. Solov’yov
"Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome"
Biophysical Journal 114, 2563–2572, June 5, 2018
Marina Putzu, Frauke Gräter, Marcus Elstner and Tomáš Kubar
"On the mechanism of spontaneous thiol–disulfide exchange in proteins"
Phys. Chem. Chem. Phys., 2018, Advance Article, first published on 24 May 2018,
DOI: 10.1039/C8CP01325J
Z. Meng, T. Kubař, Y. Mu, F. Shao
"A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids"
J Chem Theory Comput 14(5):2733–2742, 2018
Nadia Elghobashi‑Meinhardt, Prasad Phatak, Ana-Nicoleta Bondar, Marcus Elstner, Jeremy C. Smith
"Catalysis of Ground State cis→ trans Isomerization of Bacteriorhodopsin’s Retinal Chromophore by a Hydrogen‑Bond Network"
The Journal of Membrane Biology (2018) 251:315–327, Published online: 8 March 2018
J. Steinmeyer, H.-K. Walter, M.A. Bichelberger, V. Schneider, T. Kubař, F. Rönicke, B. Olshausen, K. Nienhaus, G.U. Nienhaus, U. Schepers, M. Elstner, H.-A. Wagenknecht
"siRNA traffic lights: Arabino-configured 2'-anchors for fluorescent dyes are key for dual color readout in cell imaging"
Org Biomol Chem 16(20):3726–3731, 2018
S.L. Grage, S. Kara, A. Bordessa, V. Doan, F. Rizzolo, M. Putzu, T. Kubař, A.M. Papini, G. Chaume, T. Brigaud, S. Afonin, A.S. Ulrich
"Orthogonal 19F-labeling for solid-state NMR reveals the conformation and orientation of short peptaibols in membranes"
Chem Eur J 24(17):4328–4335, 2018
Van Quan Vuong, Jissy Akkarapattiakal Kuriappan, Maximilian Kubillus, Julian J. Kranz, Thilo Mast, Thomas A. Niehaus, Stephan Irle and Marcus Elstner
"Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules"
J. Chem. Theory Comput. 2018, 14, 115−125
Daniel Holub, Hongju Ma, Norbert Krauß, Tilman Lamparter, Marcus Elstner and Natacha Gillet
"Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6–4) photolyase"
Chemical Science, Accepted on 09 Dec 2017 and first published on 11 Dec 2017
H.C. Watanabe, M. Kubillus, T. Kubař, R. Stach, B. Mizaikoff, H. Ishikita
"Cation solvation with quantum chemical effects modeled by size-consistent multi-partitioning quantum mechanics/molecular mechanics method"
Phys Chem Chem Phys 19(27):17985–17997, 2017
Yusaku Hontani, Marco Marazzi, Katja Stehfest, Tilo Mathes, Ivo H. M. van Stokkum, Marcus Elstner, Peter Hegemann & John T. M. Kennis
"Reaction dynamics of the chimeric channelrhodopsin C1C2"
Scientific Reports, Received: 8 February 2017, Accepted: 28 June 2017, Published online: 3 August 2017
Maja, Gruden, Ljubica Andjelkovic, Jissy Akkarapattiakal Kuriappan, Stepan Stepanovic, Matija Zlatar, Qiang Cui, Marcus Elstner
"Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules"
Journal of Computational Chemistry, Volume 38, Issue 25, September 30, 2017, Pages 2171–2185
First published: 24 July 2017, DOI: 10.1002/jcc.24866
Marina Putzu, Sezgin Kara, Sergii Afonin, Stephan L. Grage, Andrea Bordessa, Grégory Chaume, Thierry Brigaud, Anne S. Ulrich, Tomáš Kubař
"Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations"
Biophysical Journal, Volume 112, Issue 12, 20 June 2017, Pages 2602-2614
Julian J. Kranz, Marcus Elstner, Bálint Aradi, Thomas Frauenheim, Vitalij Lutsker, Adriel Dominguez Garcia and Thomas A. Niehaus
"Time-Dependent Extension of the Long-Range Corrected Density Functional Based Tight-Binding Method"
J. Chem. Theory Comput., 2017, 13 (4), pp 1737–1747, DOI: 10.1021/acs.jctc.6b01243, Publication Date (Web): March 8, 2017
Michal H. Kolář and Tomáš Kubař
"Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer"
J. Phys. Chem. B, Article ASAP, DOI: 10.1021/acs.jpcb.6b12109, Publication Date (Web): January 25, 2017
Mario Wolter, Marcus Elstner, Ulrich Kleinekathöfer, and Tomáš Kubař
"Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details"
J. Phys. Chem. B, 2017, 121 (3), pp 529–549, DOI: 10.1021/acs.jpcb.6b11384, Publication Date (Web): January 3, 2017
Tomáš Kubař, Marcus Elstner, Bogdan Popescu, and Ulrich Kleinekathöfer
"Polaron Effects on Charge Transport through Molecular Wires: A Multiscale Approach"
J. Chem. Theory Comput., 2017, 13 (1), pp 286–296, DOI: 10.1021/acs.jctc.6b00879, Publication Date (Web): December 1, 2016
Matías Berdakin, Martín Taccone, Kranz J. Julian, Gustavo Pino, and Cristián G. Sánchez
"Disentangling the Photophysics of DNA-Stabilized Silver Nanocluster Emitters"
J. Phys. Chem. C, 2016, 120 (42), pp 24409–24416, DOI: 10.1021/acs.jpcc.6b05363, Publication Date (Web): September 28, 2016
Natacha Gillet, Laura Berstis, Xiaojing Wu, Fruzsina Gajdos, Alexander Heck, Aurélien de la Lande, Jochen Blumberger and Marcus Elstner
"Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level"
J. Chem. Theory Comput., 2016, 12 (10), pp 4793–4805, DOI: 10.1021/acs.jctc.6b00564, Publication Date (Web): September 9, 2016
David Adrian Saez, Stefan Vogt-Geisse, Ricardo Inostroza-Rivera, Tomáš Kubař, Marcus Elstner, Alejandro Toro-Labbée and Esteban Vöhringer-Martinez
"The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate"
Phys. Chem. Chem. Phys., 2016,18, 24033-24042, DOI: 10.1039/C6CP02821G, Received 27 Apr 2016, Accepted 26 Jul 2016, First published online 27 Jul 2016
Julian J. Kranz and Marcus Elstner
"Simulation of singlet exciton diffusion in bulk organic materials"
J. Chem. Theory Comput., Just Accepted Manuscript • DOI: 10.1021/acs.jctc.6b00235 • Publication Date (Web):
19 Jul 2016
Alexander Heck, Julian J. Kranz and Marcus Elstner
"Simulation of Temperature-Dependent Charge Transport in Organic Semiconductors with Various Degrees of Disorder"
J. Chem. Theory Comput., Article ASAP, DOI: 10.1021/acs.jctc.6b00215, Publication Date (Web): May 25, 2016
Anders S. Christensen, Tomáš Kubař, Qiang Cui and Marcus Elstner
"Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications"
Chem. Rev., Article ASAP, DOI: 10.1021/acs.chemrev.5b00584, Publication Date (Web): April 13, 2016
Maria Ilaria Mallus, Mortaza Aghtar, Suryanarayanan Chandrasekaran, Gesa Lüdemann, Marcus Elstner and Ulrich Kleinekathöfer
"Relation between Dephasing Time and Energy Gap Fluctuations in Biomolecular Systems"
J. Phys. Chem. Lett., 2016, 7 (7), pp 1102–1108, DOI: 10.1021/acs.jpclett.6b00134, Publication Date (Web): March 07, 2016
Yanan Guo, Franziska E. Beyle, Beatrix M. Bold, Hiroshi C. Watanabe, Axel Koslowski, Walter Thiel, Peter Hegemann, Marco Marazzi, Marcus Elstner
"Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant"
Chemical Science, Received 29th January 2016, Accepted 24th February 2016,
DOI: 10.1039/c6sc00468g
Cristina García-Iriepa, Moussa Gueye, Jérémie Léonard, David Martínez-López, Pedro J. Campos, Luis Manuel Frutos, Diego Sampedro and Marco Marazzi
"A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement"
Phys. Chem. Chem. Phys., 2016, Advance Article, DOI: 10.1039/C5CP07599H, Received 09 Dec 2015, Accepted 03 Feb 2016, First published online 03 Feb 2016
A. Vogt, Y. Guo, S. P. Tsunoda, S. Kateriya, M. Elstner & P. Hegemann
"Conversion of a light-driven proton pump into a light-gated ion channel"
Scientific Reports 5, Article number: 16450 (2015), doi:10.1038/srep16450
Received: 20 April 2015, Accepted: 14 October 2015, Published online: 24 November 2015
Alexander Heck, Julian J. Kranz, Tomáš Kubař and Marcus Elstner
"Multi-Scale Approach to Non-Adiabatic Charge Transport in High-Mobility Organic Semiconductors"
J. Chem. Theory Comput., 2015, 11 (11), pp 5068–5082, DOI: 10.1021/acs.jctc.5b00719, Publication Date (Web): September 30, 2015
Van Ngo, Mauricio C. da Silva, Maximilian Kubillus, Hui Li, Benoît Roux, Marcus Elstner, Qiang Cui, Dennis R. Salahub and Sergei Yu. Noskov
"Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins"
J. Chem. Theory Comput., 2015, 11 (10), pp 4992–5001, DOI: 10.1021/acs.jctc.5b00524, Publication Date (Web): September 22, 2015
Anders S. Christensen, Marcus Elstner and Qiang Cui
"Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization"
J. Chem. Phys. 143, 084123 (2015); http://dx.doi.org/10.1063/1.4929335, Received 30 June 2015; accepted 10 August 2015; published online 28 August 2015
Yanan Guo, Tino Wolter, Tomáš Kubař, Martin Sumser, Dirk Trauner, Marcus Elstner
"Molecular Dynamics Investigation of gluazo, a Photo-Switchable Ligand for the Glutamate Receptor GluK2"
Published: August 26, 2015, DOI: 10.1371/journal.pone.0135399
Michael Gaus, Haiyun Jin, Darren Demapan, Anders S. Christensen, Puja Goyal, Marcus Elstner and Qiang Cui
"DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters"
J. Chem. Theory Comput., 2015, 11 (9), pp 4205–4219, DOI: 10.1021/acs.jctc.5b00600, Publication Date (Web): August 11, 2015
Tomáš Kubar, Kai Welke and Gerrit Groenhof
"New QM/MM implementation of the DFTB3 method in the gromacs package"
Article first published online: 4 AUG 2015, DOI: 10.1002/jcc.24029
Asif Bashir, Alexander Heck, Akimitsu Narita, Xinliang Feng, Alexei Nefedov, Michael Rohwerder, Klaus Müllen, Marcus Elstner and Christof Wöll
"Charge carrier mobilities in organic semiconductors: crystal engineering and the importance of molecular contacts"
Phys. Chem. Chem. Phys., 2015,17, 21988-21996, DOI: 10.1039/C5CP03171K, Received 02 Jun 2015, Accepted 27 Jul 2015, First published online 27 Jul 2015
Gesa Lüdemann , Ilia A. Solov’yov, Tomáš Kubař and Marcus Elstner
"Solvent Driving Force Ensures Fast Formation of a Persistent and Well-Separated Radical Pair in Plant Cryptochrome"
J. Am. Chem. Soc., 2015, 137 (3), pp 1147–1156, DOI: 10.1021/ja510550g
Pascal Friederich, Velimir Meded, Franz Symalla, Marcus Elstner and Wolfgang Wenzel
"QM/QM Approach to Model Energy Disorder in Amorphous Organic Semiconductors"
J. Chem. Theory Comput., 2015, 11 (2), pp 560–567, DOI: 10.1021/ct501023n, Publication Date (Web): January 7, 2015
Xiya Lu, Michael Gaus, Marcus Elstner and Qiang Cui
"Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications"
dx.doi.org/10.1021/jp506557r | J. Phys. Chem. B 2015, 119, 1062-1082
Maximilian Kubillus , Tomáš Kubař , Michael Gaus , Jan Řezáč , and Marcus Elstner
Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems
J. Chem. Theory Comput., 2015, 11 (1), pp 332–342, DOI: 10.1021/ct5009137, Publication Date (Web): December 9, 2014
Adam Kubas, Fruzsina Gajdos, Alexander Heck, Harald Oberhofer, Marcus Elstner and Jochen Blumberger
"Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations"
Royal Society of Chemistry, Published 22 December 2014 DOI: 10.1039/c4cp04749d
Puja Goyal , Hu-Jun Qian, Stephan Irle, Xiya Lu, Daniel Roston , Toshifumi Mori, Marcus Elstner and Qiang Cui
"Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models"
The journal of physical chemistry. B Volume: 118 Issue: 38 Pages: 11007-27 Published: 2014-Sep-25 DOI: 10.1021/jp503372v
Hiroshi C. Watanabe , Tomáš Kubar and Marcus Elstner
"Size-Consistent Multipartitioning QM/MM: A Stable and Efficient Adaptive QM/MM Method"
J. Chem. Theory Comput., Article ASAP, DOI: 10.1021/ct5005593 Publication Date (Web): September 10, 2014
Tino Wolter, Marcus Elstner, Stefan Fischer, Jeremy C. Smith and Ana-Nicoleta Bondar
“Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States”
J. Phys. Chem. B, 2015, 119 (6), pp 2229–2240, DOI: 10.1021/jp505818r, Publication Date (Web): September 7, 2014
Sabine Reißer, Erik Strandberg, Thomas Steinbrecher, Anne S. Ulrich
"3D Hydrophobic Moment Vectors as a Tool to Characterize the Surface Polarity of Amphiphilic Peptides"
DOI: http://dx.doi.org/10.1016/j.bpj.2014.04.020
Tomce Runcevski, Dr. Marina Blanco-Lomas, Dr. Marco Marazzi, Marcos Cejuela, Dr. Diego Sampedro and Prof. Robert E. Dinnebier
"Following a Photoinduced Reconstructive Phase Transformation and its Influence on the Crystal Integrity: Powder Diffraction and Theoretical Study"
Angew. Chem. Int. Ed., Article first published online: 21 MAY 2014, DOI: 10.1002/anie.201402515
Qiang Cui and Marcus Elstner
"Density functional tight binding: values of semi-empirical methods in an ab initio era"
Phys. Chem. Chem. Phys., 2014, Advance Article, DOI: 10.1039/C4CP00908H, First published online 13 May 2014
Marcus Elstner and Gotthard Seifert
"Density functional tight binding"
Phil.Trans.R.Soc. A 372:20120483, 2014
Tino Wolter, Thomas Steinbrecher, Dirk Trauner, Marcus Elstner
"Ligand Photo-Isomerization Triggers Conformational Changes in iGluR2 Ligand Binding Domain"
PLOS one, Published: April 08, 2014, DOI: 10.1371/journal.pone.0092716
Alexander Heck, P. Benjamin Woiczikowski, Tomáš Kubař, Kai Welke, Thomas Niehaus, Bernd Giese, Spiros Skourtis, Marcus Elstner and Thomas B. Steinbrecher
"Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals"
J. Phys. Chem. B, Article ASAP, DOI: 10.1021/jp408907g, Publication Date (Web): March 21, 2014
Jonas Wietek, J. Simon Wiegert, Nona Adeishvili, Franziska Schneider, Hiroshi Watanabe, Satoshi P. Tsunoda, Arend Vogt, Marcus Elstner, Thomas G. Oertner, Peter Hegemann
Conversion of Channelrhodopsin into a Light-Gated Chloride Channel
Science 25 April 2014: Vol. 344 no. 6182 pp. 409-412 DOI: 10.1126/science.1249375
Michael Gaus , Xiya Lu , Marcus Elstner , and Qiang Cui
"Parameterization of DFTB3/3OB for Sulfur and Phosphorus for chemical and biological applications"
J. Chem. Theory Comput., 2014, 10 (4), pp 1518–1537 DOI: 10.1021/ct401002w, Publication Date (Web): March 12, 2014
Oleg Babii, Dr. Sergii Afonin, Dr. Marina Berditsch, Sabine Reiβer, Dr. Pavel K. Mykhailiuk, Dr. Vladimir S. Kubyshkin, Dr. Thomas Steinbrecher, Prof. Anne S. Ulrich and Prof. Igor V. Komarov
"Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics"
Article first published online: 19 FEB 2014, DOI: 10.1002/anie.201310019
Adam Kubas, Felix Hoffmann, Alexander Heck, Harald Oberhofer, Marcus Elstner and Jochen Blumberger
"Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations"
J. Chem. Phys. 140, 104105 (2014)
Michael Gaus, Qiang Cui, Marcus Elstner
"Density functional tight binding: application to organic and biological molecules"
WIREs Comput Mol Sci 2014, 4:49–61. doi: 10.1002/wcms.1156
Oliver P. Ernst, David T. Lodowski, Marcus Elstner, Peter Hegemann, Leonid S. Brown and Hideki Kandori
"Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms"
Chem. Rev., 2014, 114 (1), pp 126–163, DOI: 10.1021/cr4003769
Tino Wolter, Kai Welke, Prasad Phatak, Ana-Nicoleta Bondar and Marcus Elstner
"Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation"
Phys. Chem. Chem. Phys., 2013,15, 12582-12590
Mario Wolter, Marcus Elstner, and Tomáš Kubař
"Charge transport in desolvated DNA"
J. Chem. Phys. 139, 125102 (2013)
Gesa Lüdemann, P. Benjamin Woiczikowski, Tomáš Kubar, Marcus Elstner, and Thomas B. Steinbrecher
"Charge Transfer in E. coli DNA Photolyase: Understanding Polarization and Stabilization Effects via QM/MM Simulations"
Journal of Physical Chemistry B (2013) DOI: 10.1021/ jp406319b
Tomáš Kubar, Rafael Gutiérrez, Ulrich Kleinekathöfer, Gianaurelio Cuniberti, Marcus Elstner
"Modeling charge transport in DNA using multi-scale methods"
physica status solidi (b) (2013) DOI: 10.1002/pssb.201349148
W. Li, S. A. Edwards, L. Lu, T. Kubar, S. P. Patil, H. Grubmüller, G. Groenhof, F. Gräter
"Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene"
ChemPhysChem 2013, 14 (12), 2687–2697
T. Kubar and M. Elstner
"A hybrid approach to simulation of electron transfer in complex molecular systems"
J. R. Soc. Interface 2013, 10, 20130415
T. Kubar , Z. Bodrog , M. Gaus , Chr. Köhler , B. Aradi , Th. Frauenheim , and M. Elstner
"Parametrization of the SCC-DFTB Method for Halogens"
J. Chem. Theory Comput., 2013, 9 (7), pp 2939–2949
T. Kubar and M. Elstner
"Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA"
Phys. Chem. Chem. Phys., 2013, 15, 5794-5813
Osama K. Abou-Zied, Najla Al-Lawatia, Marcus Elstner and Thomas B. Steinbrecher
"Binding of Hydroxyquinoline Probes to Human Serum Albumin: Combining Molecular Modeling and Forster’s Resonance Energy Transfer Spectroscopy to Understand Flexible Ligand Binding"
J. Phys. Chem. B 2013, 117, 1062 - 1074
Tino Wolter, Thomas Steinbrecher, Marcus Elstner
"Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors"
PLoS ONE 8(3): e58774. doi:10.1371/journal.pone.0058774, Published: March 25, 2013
Nir Goldman, Sriram Goverapet Srinivasan, Sebastian Hamel, Laurence E. Fried, Michael Gaus and Marcus Elstner
"Determination of a Density Functional Tight Binding Model with an Extended Basis Set and Three-Body Repulsion for Carbon under Extreme Pressures and Temperatures"
J. Phys. Chem. C, 2013, 117 (15), pp 7885–7894
K. Welke, H. C. Watanabe, T. Wolter, M. Gaus and M. Elstner
"QM/MM Simulations of Vibrational Spectra in Bacteriorhodopsin and Channelrhodopsin-2"
Phys. Chem. Chem. Phys., 2013, DOI: 10.1039/C3CP44181D, Link to article
H.C. Watanabe, K. Welke, D.J. Sindhikara, P. Hegemann and M. Elstner
"Towards an understanding of channelrhodopsin function: Simulations lead to novel insights of channel mechanism"
H. C. Watanabe, M. Elstner and T. Steinbrecher
"Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics"
J. Comp. Chem., 2013, 34, 3, 198-205, Link to article
T. Steinbrecher and M. Elstner
"QM and QM/MM Simulations of Proteins"
Biomolecular Simulations : Methods and Protocols; Methods in Molecular Biology, 924, 2012, Link
M. Gaus , A. Goez , and M. Elstner
"Parametrization and Benchmark of DFTB3 for Organic Molecules"
J. Chem. Theory Comput., 2012, Link to article
S. Kaminski, M. Gaus and M. Elstner
"Improved Electronic Properties from 3rd Order SCC-DFTB with Cost Efficient Post-SCF Extensions"
J. Phys. Chem. A, 2012, Link to article
B. Popescu, P. B. Woiczikowski, M. Elstner, and U. Kleinekathöfer
"Time-Dependent View of Sequential Transport through Molecules with Rapidly Fluctuating Bridges"
Phys. Rev. Lett. 109, 176802 (2012), Link to article
T. Steinbrecher, S. Prock, J. Reichert, P. Wadhwani, B. Zimpfer, J. Bürck, M. Berditsch, M. Elstner and A. S. Ulrich
"Peptide-Lipid Interactions of the Stress-Response Peptide TisB That Induces Bacterial Persistence"
Biophys. J., 2012, 103, 7, 1460-1469, Link to article
G. Hou, X. Zhu, M. Elstner and Q. Cui
"A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions"
J. Chem. Theory Comput., 2012, 8 (11), pp 4293–4304, Link to article