∙ Researcher ID: I-2329-2013

Scopus Author ID: 7004179274

∙ ORCID: 0000-0002-6114-7431

Google Scholar: j2b-kXYAAAAJ

[168]   A. Acharya, I. Ghai, C. Piselli, J. D. Prajapati, R. Benz, M. Winterhalter and U. Kleinekathöfer, Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating, J. Chem. Inf. Model. (in press) (2023).

[167]   C. Piselli, V. K. Golla, R. Benz and U. Kleinekathöfer, Importance of the Lysine Cluster in the Translocation of Anions through the Pyrophosphate Specific Channel OprO, Biochim. Biophy. Acta, Biomembr. 1865, 184 086 (2023).

[166]   S. Maity and U. Kleinekathöfer, Recent Progress in Atomistic Modeling of Light-Harvesting Complexes: A Mini Review, Photosynth. Res. (in press) (2022).

[165]   R. S. Krishnan, K. Jana, A. H. Shaji, K. S. Nair, A. D. Das, D. Vikraman, H. Bajaj, U. Kleinekathöfer and K. R. Mahendran, Assembly of Transmembrane Pores from Mirror-Image Peptides, Nat. Commun. 13, 5377 (2022).

[164]   J. Wang, J. D. Prajapati, F. Gao, Y.-L. Ying, U. Kleinekathöfer, M. Winterhalter and Y.-T. Long, Identification of Single Amino Acid Chiral and Positional Isomers Using an Electrostatically Asymmetric Nanopore, J. Am. Chem. Soc. 144, 15 072–15 078 (2022).

[163]   P. Sarngadharan, S. Maity and U. Kleinekathöfer, Spectral Densities and Absorption Spectra of the Core Antenna Complex CP43 from Photosystem II, J. Chem. Phys. 156, 215 101 (2022).

[162]   A. Acharya, J. D. Prajapati and U. Kleinekathöfer, Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions, J. Phys. Chem. B 126, 3995–4008 (2022).

[161]   J. D. Prajapati, S. Pangeni, M. A. Aksoyoglu, M. Winterhalter and U. Kleinekathöfer, Changes in Salt Concentration Modify the Translocation of Neutral Molecules through a ΔCymA Nanopore in a Non-Monotonic Manner, ACS Nano 16, 7701–7712 (2022).

[160]   E. V. Shah, U. Kleinekathöfer, T. Frauenheim and D. R. Roy, Transverse Electronic Transport through Nucleobase-Pairs of a DNA Wire, Mater. Today Chem. 24, 100 834 (2022).

[159]   V. K. Golla, C. Piselli, U. Kleinekathöfer and R. Benz, Permeation of Fosfomycin through the Phosphate-Specific Channels OprP and OprO of Pseudomonas aeruginosa, J. Phys. Chem. B 126, 1388–1403 (2022).

[158]   L. Mejía, U. Kleinekathöfer and I. Franco, Coherent and Incoherent Contributions to Molecular Electron Transport, J. Chem. Phys. 156, 094 302 (2022).

[157]   K. Rajput, B. Mehta, U. Kleinekathöfer, T. Frauenheim and D. Roy, Group Three Nitride Clusters As Promising Components for Nanoelectronics, Mater. Today Chem. 23, 100 751 (2022).

[156]   A. Chrysafoudi, S. Maity, U. Kleinekathöfer and V. Daskalakis, Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study, J. Phys. Chem. Lett. 12, 9626–9633 (2021).

[155]   S. Maity, P. Sarngadharan, V. Daskalakis and U. Kleinekathöfer, Time-Dependent Atomistic Simulations of the CP29 Light-Harvesting Complex, J. Chem. Phys. 155, 055 103 (2021).

[154]   A. Acharya, J. D. Prajapati and U. Kleinekathöfer, Improved Sampling and Free Energy Estimates for Antibiotic Permeation through Bacterial Porins, J. Chem. Theory Comput. 17, 4564–4577 (2021).

[153]   S. Maity, V. Daskalakis, M. Elstner and U. Kleinekathöfer, Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-Harvesting Complex II, Phys. Chem. Chem. Phys. 23, 7407–7417 (2021).

[152]   J. D. Prajapati, U. Kleinekathöfer and M. Winterhalter, How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics, Chem. Rev. 121, 5158–5192 (2021).

[151]   S. Pangeni, J. D. Prajapati, J. Bafna, M. Nilam, W. M. Nau, U. Kleinekathöfer and M. Winterhalter, Large Peptide Permeation through a Membrane Channel: Understanding Protamine Translocation through CymA from Klebsiella Oxytoca, Angew. Chem. Int. Ed. 60, 8089–8094 (2021).

[150]   V. K. Golla, J. D. Prajapati and U. Kleinekathöfer, Millisecond-Long Simulations of Antibiotics Transport through Outer Membrane Channels, J. Chem. Theory Comput. 17, 549–559 (2021).

[149]   J. D. Prajapati and U. Kleinekathöfer, Voltage-Dependent Transport of Neutral Solutes through Nanopores: A Molecular View, J. Phys. Chem. B 124, 10 718–10 731 (2020).

[148]   E. Sancho-Vaello, D. Gil-Carton, P. François, E.-J. Bonetti, M. Kreir, K. R. Pothula, U. Kleinekathöfer and K. Zeth, The Structure of the Antimicrobial Human Cathelicidin LL-37 Shows Oligomerization and Channel Formation in the Presence of Membrane Mimics, Sci. Rep. 10, 17 356 (2020).

[147]   S. Maity, B. M. Bold, J. D. Prajapati, M. Sokolov, T. Kubař, M. Elstner and U. Kleinekathöfer, DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex, J. Phys. Chem. Lett. 11, 8660–8667 (2020).

[146]   J. Wang, J. D. Prajapati, U. Kleinekathöfer and M. Winterhalter, Dynamic Interaction of Fluoroquinolone with Magnesium Ions Monitored by Bacterial Outer Membrane Nanopores, Chem. Sci. 11, 10 344–10 353 (2020).

[145]   J. D. Prajapati, C. Mele, M. A. Aksoyoglu, M. Winterhalter and U. Kleinekathöfer, Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field, J. Chem. Inf. Model. 60, 3188–3203 (2020).

[144]   M. Madej, J. B. R. White, Z. Nowakowska, S. Rawson, C. Scavenius, J. J. Enghild, G. P. Bereta, K. Pothula, U. Kleinekathöfer, A. Baslé, N. A. Ranson, J. Potempa and B. van den Berg, Structural and Functional Insights into Oligopeptide Acquisition by the RagAB Transporter from Porphyromonas Gingivalis, Nat. Microbiol. 5, 1016–1025 (2020).

[143]   J. Cao, R. J. Cogdell, D. F. Coker, H.-G. Duan, J. Hauer, U. Kleinekathöfer, T. L. C. Jansen, T. Mančal, R. J. D. Miller, J. P. Ogilvie, V. I. Prokhorenko, T. Renger, H.-S. Tan, R. Tempelaar, M. Thorwart, E. Thyrhaug, S. Westenhoff and D. Zigmantas, Quantum Biology Revisited, Sci. Adv. 6, eaaz4888 (2020).

[142]   J. W. Vant, S.-l. J. Lahey, K. Jana, M. Shekhar, D. Sarkar, B. H. Munk, U. Kleinekathöfer, S. Mittal, C. Rowley and A. Singharoy, Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials, J. Chem. Inf. Model. 60, 2591–2604 (2020).

[141]   V. K. Golla, J. D. Prajapati, M. Joshi and U. Kleinekathöfer, Exploration of Free Energy Surfaces across a Membrane Channel Using Metadynamics and Umbrella Sampling, J. Chem. Theory Comput. 16, 2751–2765 (2020).

[140]   B. M. Bold, M. Sokolov, S. Maity, M. Wanko, P. M. Dohmen, J. J. Kranz, U. Kleinekathöfer, S. Höfener and M. 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. 22, 10 500–10 518 (2020).

[139]   A. Singharoy, C. Maffeo, K. H. Delgado-Magnero, D. J. K. Swainsbury, M. Sener, U. Kleinekathöfer, J. W. Vant, J. Nguyen, A. Hitchcock, B. Isralewitz, I. Teo, D. E. Chandler, J. E. Stone, J. C. Phillips, T. V. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten, D. P. Tieleman, C. N. Hunter, E. Tajkhorshid, A. Aksimentiev and K. Schulten, Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism, Cell 179, 1098–1111.e23 (2019).

[138]   V. Daskalakis, S. Maity, C. L. Hart, T. Stergiannakos, C. D. P. Duffy and U. Kleinekathöfer, Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II, J. Phys. Chem. B 123, 9609–9615 (2019).

[137]   V. Daskalakis, S. Papadatos and U. Kleinekathöfer, Fine Tuning of the Photosystem II Major Antenna Mobility within the Thylakoid Membrane of Higher Plants, Biochim. Biophys. Acta, Biomembr. 1861, 183 059 (2019).

[136]   S. Maity, A. Gelessus, V. Daskalakis and U. Kleinekathöfer, On a Chlorophyll-Caroteinoid Coupling in LHCII, Chem. Phys. 526, 110 439 (2019).

[135]   A. Kesireddy, K. R. Pothula, J. Lee, D. S. Patel, M. Pathania, B. van den Berg, W. Im and U. Kleinekathöfer, Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-Negative Porin, J. Phys. Chem. B 123, 5700–5708 (2019).

[134]   H. Rahman and U. Kleinekathöfer, Chebyshev Hierarchical Equations of Motion for Systems with Arbitrary Spectral Densities and Temperatures, J. Chem. Phys. 150, 244 104 (2019).

[133]   A. Atzori, G. Malloci, J. D. Prajapati, A. Basciu, A. Bosin, U. Kleinekathöfer, J. Dreier, A. V. Vargiu and P. Ruggerone, Molecular Interactions of Cephalosporins with the Deep Binding Pocket of RND-Transporter AcrB, J. Phys. Chem. B 123, 4625–4635 (2019).

[132]   H. Rahman, P. Karasch, D. A. Ryndyk, T. Frauenheim and U. Kleinekathöfer, Dephasing in a Molecular Junction Viewed from a Time-Dependent and a Time-Independent Perspective, J. Phys. Chem. C 123, 9590–9599 (2019).

[131]   S. P. Bhamidimarri, M. Zahn, J. D. Prajapati, C. Schleberger, S. Söderholm, J. Hoover, J. West, U. Kleinekathöfer, D. Bumann, M. Winterhalter and B. van den Berg, A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii, Structure 27, 268–280.e6 (2019).

[130]   V. K. Golla, E. Sans-Serramitjana, K. R. Pothula, L. Benier, J. A. Bafna, M. Winterhalter and U. Kleinekathöfer, Fosfomycin Permeation through the Outer Membrane Porin OmpF, Biophys. J. 116, 258–269 (2019).

[129]   H. Rahman and U. Kleinekathöfer, Non-Equilibrium Green’s Function Transport Theory for Molecular Junctions with General Molecule-Lead Coupling and Temperatures, J. Chem. Phys. 149, 234 108 (2018).

[128]   C. J. F. Solano, J. D. Prajapati, K. R. Pothula and U. Kleinekathöfer, Brownian Dynamics Approach Including Explicit Atoms for Studying Ion Permeation and Substrate Translocation across Nanopores, J. Chem. Theory Comput. 14, 6701–6713 (2018).

[127]   M. I. Mallus, Y. Shakya, J. D. Prajapati and U. Kleinekathöfer, Environmental Effects on the Dynamics in the Light-Harvesting Complexes LH2 and LH3 Based on Molecular Simulations, Chem. Phys. 515, 141–151 (2018).

[126]   J. Lee, K. R. Pothula, U. Kleinekathöfer and W. Im, Simulation Study of OccK5 Functional Properties in Pseudomonas aeruginosa Outer Membranes, J. Phys. Chem. B 122, 8185–8192 (2018).

[125]   N. Abdali, F. Younas, S. Mafakheri, K. R. Pothula, U. Kleinekathöfer, A. Tauch and R. Benz, Identification and Characterization of Smallest Pore-Forming Protein in the Cell Wall of Pathogenic Corynebacterium urealyticum DSM 7109, BMC Biochem. 19, 3 (2018).

[124]   A. Aunkham, M. Zahn, A. Kesireddy, K. R. Pothula, A. Schulte, A. Baslé, U. Kleinekathöfer, W. Suginta and B. van den Berg, Structural Basis for Chitin Acquisition by Marine Vibrio Species, Nat. Commun. 9, 220 (2018).

[123]   A. V. Vargiu, V. K. Ramaswamy, I. Malvacio, G. Malloci, U. Kleinekathöfer and P. Ruggerone, Water-Mediated Interactions Enable Smooth Substrate Transport in a Bacterial Efflux Pump, Biochim. Biophys. Acta, Gen. Subj. 1862, 836–845 (2018).

[122]   J. D. Prajapati, C. J. F. Solano, M. Winterhalter and U. Kleinekathöfer, Enrofloxacin Permeation Pathways across the Porin OmpC, J. Phys. Chem. B 122, 1417–1426 (2018).

[121]   J. Abellón-Ruiz, S. S. Kaptan, A. Baslé, B. Claudi, D. Bumann, U. Kleinekathöfer and B. van den Berg, Structural Basis for Maintenance of Bacterial Outer Membrane Lipid Asymmetry, Nat. Microbiol. 2, 1616–1623 (2017).

[120]   J. D. Prajapati, C. J. F. Solano, M. Winterhalter and U. Kleinekathöfer, Characterization of Ciprofloxacin Permeation Pathways across the Porin OmpC Using Metadynamics and a String Method, J. Chem. Theory Comput. 13, 4553–4566 (2017).

[119]   S. Ganguly, A. Kesireddy, I. Bárcena-Uribarri, U. Kleinekathöfer and R. Benz, Conversion of OprO into an OprP-like Channel by Exchanging Key Residues in the Channel Constriction, Biophys. J. 113, 829–834 (2017).

[118]   M. I. Mallus, M. Schallwig and U. Kleinekathöfer, Relation between Vibrational Dephasing Time and Energy Gap Fluctuations, J. Phys. Chem. B 121, 6471–6478 (2017).

[117]   K. R. Pothula, N. N. Dhanasekar, U. Lamichhane, F. Younas, D. Pletzer, R. Benz, M. Winterhalter and U. Kleinekathöfer, Single Residue Acts As Gate in OccK Channels, J. Phys. Chem. B 121, 2614–2621 (2017).

[116]   M. Aghtar, U. Kleinekathöfer, C. Curutchet and B. Mennucci, Impact Of Electronic Fluctuations And Their Description On The Exciton Dynamics In The Light-Harvesting Complex PE545, J. Phys. Chem. B 121, 1330–1339 (2017).

[115]   A. J. Glenwright, K. R. Pothula, S. P. Bhamidimarri, D. S. Chorev, A. Baslé, S. J. Firbank, H. Zheng, C. V. Robinson, M. Winterhalter, U. Kleinekathöfer, D. N. Bolam and B. van den Berg, Structural Basis for Nutrient Acquisition by Dominant Members of the Human Gut Microbiota, Nature 541, 407–411 (2017).

[114]   M. Wolter, M. Elstner, U. Kleinekathöfer and T. 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 121, 529–549 (2017).

[113]   U. Kleinekathöfer, Simulation des Transports durch Außenmembrankanäle, BIOspektrum 23, 28–31 (2017).

[112]   T. Kubař, M. Elstner, B. Popescu and U. Kleinekathöfer, Polaron Effects on Charge Transport through Molecular Wires: A Multi-Scale Approach, J. Chem. Theory Comput. 13, 286–296 (2017).

[111]   S. Chandrasekaran, K. R. Pothula and U. Kleinekathöfer, Protein Arrangement Effects on the Exciton Dynamics in the PE555 Complex, J. Phys. Chem. B 121, 3228–3236 (2017).

[110]   C. J. F. Solano, K. R. Pothula, J. D. Prajapati, P. M. De Biase, S. Y. Noskov and U. Kleinekathöfer, BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms, J. Chem. Theory Comput. 12, 2401–2417 (2016).

[109]   M. I. Mallus, M. Aghtar, S. Chandrasekaran, G. Lüdemann, M. Elstner and U. Kleinekathöfer, Relation between Dephasing Time and Energy Gap Fluctuations in Biomolecular Systems, J. Phys. Chem. Lett. 7, 1102–1108 (2016).

[108]   B. Popescu, H. Rahman and U. Kleinekathöfer, Chebyshev Expansion Applied to Dissipative Quantum Systems, J. Phys. Chem. A 120, 3270–3277 (2016).

[107]   K. R. Pothula, C. J. Solano and U. Kleinekathöfer, Simulations of Outer Membrane Channels and Their Permeability, Biochim. Biophys. Acta, Biomembr. 1858, 1760–1771 (2016).

[106]   S. P. Bhamidimarri, J. D. Prajapati, B. van den Berg, M. Winterhalter and U. Kleinekathöfer, Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example, Biophys. J. 110, 600–611 (2016).

[105]   M. Aghtar and U. Kleinekathöfer, Environmental Coupling and Population Dynamics in the PE545 Light-Harvesting Complex, J. Lumin. 169, 406–409 (2016).

[104]   R. Benz, M. D. Jones, F. Younas, E. Maier, N. Modi, R. Mentele, F. Lottspeich, U. Kleinekathöfer and J. Smit, OmpW of Caulobacter crescentus Functions As an Outer Membrane Channel for Cations, PLoS One 10, e0143 557 (2015).

[103]   N. Modi, S. Ganguly, I. Bárcena-Uribarri, R. Benz, B. van den Berg and U. Kleinekathöfer, Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa, Biophys. J. 109, 1429–1438 (2015).

[102]   S. Chandrasekaran, M. Aghtar, S. Valleau, A. Aspuru-Guzik and U. Kleinekathöfer, Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins, J. Phys. Chem. B 119, 9995–10 004 (2015).

[101]   B. van den Berg, P. S. Bhamidimarri, D. J. Prajapati, U. Kleinekathöfer and M. Winterhalter, Outer-Membrane Translocation of Bulky Small Molecules by Passive Diffusion, Proc. Natl. Acad. Sci. USA 112, E2991–E2999 (2015).

[100]   B. Popescu, H. Rahman and U. Kleinekathöfer, Using the Chebyshev Expansion in Quantum Transport Calculations, J. Chem. Phys. 142, 154103 (2015).

[99]    K. R. Pothula and U. Kleinekathöfer, Theoretical Analysis of Ion Conductance and Gating Transitions in the OpdK (OccK1) Channel, Analyst 140, 4855–4864 (2015).

[98]    J. M. A. Blair, V. N. Bavro, V. Ricci, N. Modi, P. Cacciotto, U. Kleinekathöfer, P. Ruggerone, A. V. Vargiu, A. J. Baylay, H. E. Smith, Y. Brandon, D. Galloway and L. J. V. Piddock, AcrB Drug-Binding Pocket Substitution Confers Clinically Relevant Resistance and Altered Substrate Specificity, Proc. Natl. Acad. Sci. USA 112, 3511–3516 (2015).

[97]    C. P. van der Vegte, J. D. Prajapati, U. Kleinekathöfer, J. Knoester and T. L. C. Jansen, Atomistic Modeling of Two-Dimensional Electronic Spectra and Excited State Dynamics for a Light Harvesting 2 Complex, J. Phys. Chem. B 119, 1302–1313 (2015).

[96]    R. Schulz, A. V. Vargiu, P. Ruggerone and U. Kleinekathöfer, Computational Study of Correlated Domain Motions in the AcrB Efflux Transporter, BioMed Res. Int. 2015, 487 298 (2015).

[95]    N. Modi, I. Bárcena-Uribarri, M. Bains, R. Benz, R. E. W. Hancock and U. Kleinekathöfer, Tuning the Affinity of Anion Binding Sites in Porin Channels with Negatively Charged Residues: Molecular Details for OprP, ACS Chem. Biol. 10, 441–451 (2015).

[94]    M. Aghtar, J. Strümpfer, C. Olbrich, K. Schulten and U. Kleinekathöfer, Different Types of Vibrations Interacting with Electronic Excitations in Phycoerythrin 545 and Fenna-Matthews-Olson Antenna Systems, J. Phys. Chem. Lett. 5, 3131–3137 (2014).

[93]    J. Lu, N. Modi and U. Kleinekathöfer, Simulation of Ion Transport through an N-Acetylneuraminic Acid-Inducible Membrane Channel: From Understanding to Engineering, J. Phys. Chem. B 117, 15 966–15 975 (2013).

[92]    N. Abdali, E. Barth, A. Norouzy, R. Schulz, W. M. Nau, U. Kleinekathöfer, A. Tauch and R. Benz, Corynebacterium Jeikeium Jk0268 constitutes for the 40 amino Acid Long PorACj, Which Forms a Homooligomeric and Anion-selective Cell Wall Channel, PLoS One 8, e75 651 (2013).

[91]    K. R. Mahendran, R. Schulz, H. Weingart, U. Kleinekathöfer and M. Winterhalter, The Permeability Barrier: Passive and Active Drug Passage Across Membranes, in Bacterial Membranes: Structural and Molecular Biology, edited by H. Remaut and R. Fronzes (Caister Academic Press, 2013).

[90]    B. Popescu and U. Kleinekathöfer, Treatment of Time-Dependent Effects in Molecular Junctions, phys. stat. sol. (b) 250, 2288–2297 (2013), special issue ’Quantum Transport at the Molecular Scale’.

[89]    T. Kubař, R. Gutiérrez, U. Kleinekathöfer, G. Cuniberti and M. Elstner, Modeling Charge Transport in DNA Using Multi-Scale Methods, phys. stat. sol. (b) 250, 2277–2287 (2013), special issue ’Quantum transport at the molecular scale’.

[88]    N. Modi, I. Bárcena-Uribarri, M. Bains, R. Benz, R. E. W. Hancock and U. Kleinekathöfer, Role of the Central Arginine R133 Towards the Ion Selectivity of the Phosphate Specific Channel OprP: Effects of Charge and Solvation, Biochemistry 52, 5522–5532 (2013).

[87]    M. Aghtar, J. Strümpfer, C. Olbrich, K. Schulten and U. Kleinekathöfer, The FMO Complex in a Glycerol-Water Mixture, J. Phys. Chem. B 117, 7157–7163 (2013).

[86]    N. Modi, R. Benz, R. E. W. Hancock and U. Kleinekathöfer, Modeling the Ion Selectivity of the Phosphate Specific Channel OprP, J. Phys. Chem. Lett. 3, 3639–3645 (2012).

[85]    P. R. Singh, I. Bárcena-Uribarri, N. Modi, U. Kleinekathöfer, R. Benz, M. Winterhalter and K. R. Mahendran, Pulling Peptides Across Nanochannels: Resolving Peptide Binding and Translocation Through the Hetero-oligomeric Channel from Nocardia Farcinica, ACS Nano 6, 10 699–10 707 (2012).

[84]    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, 176 802 (2012).

[83]    M. Namboodiri, J. Liebers, U. Kleinekathöfer and A. Materny, Selective Probing of Vibrational Hot States in Bromine Using Time-Resolved Coherent Anti-Stokes Raman Scattering, J. Phys. Chem. A 116, 11 341–11 346 (2012).

[82]    N. Modi, M. Winterhalter and U. Kleinekathöfer, Feature Article: Computational Modeling of Ion Transport Through Nanopores, Nanoscale 4, 6166–6180 (2012).

[81]    M. Aghtar, J. Liebers, J. Strümpfer, K. Schulten and U. Kleinekathöfer, Juxtaposing Density Matrix and Classical Path-Based Wave Packet Dynamics, J. Chem. Phys. 136, 214 101 (2012).

[80]    L. Mühlbacher and U. Kleinekathöfer, Preparational Effects on the Excitation Energy Transfer in the FMO Complex, J. Phys. Chem. B 116, 3900–3906 (2012).

[79]    C. Olbrich and U. Kleinekathöfer, From Atomistic Modeling to Electronic Properties of Light-Harvesting Systems, in Quantum Efficiency in Complex Systems, Part II: from Molecular Aggregates to Organic Solar Cells, edited by U. Würfel, M. Thorwart and E. R. Weber, vol.  85 of Semiconductors and Semimetals, 83–114 (Academic Press, 2011).

[78]    N. Modi, P. R. Singh, K. R. Mahendran, R. Schulz, M. Winterhalter and U. Kleinekathöfer, Probing the Transport of Ionic Liquids in Aqueous Solution Through Nanopores, J. Phys. Chem. Lett. 2, 2331–2336 (2011).

[77]    C. Olbrich, J. Strümpfer, K. Schulten and U. Kleinekathöfer, Theory and Simulation of the Environmental Effects on FMO Electronic Transitions, J. Phys. Chem. Lett. 2, 1771–1776 (2011).

[76]    A. V. Vargiu, F. Collu, R. Schulz, K. M. Pos, M. Zacharias, U. Kleinekathöfer and P. Ruggerone, Effects of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations, J. Am. Chem. Soc. 133, 10 704–10 707 (2011).

[75]    C. Olbrich, T. L. C. Jansen, J. Liebers, M. Aghtar, J. Strümpfer, K. Schulten, J. Knoester and U. Kleinekathöfer, From Atomistic Modeling to Excitation Dynamics and Two-Dimensional Spectra of the FMO Light-Harvesting Complex, J. Phys. Chem. B 115, 8609–8621 (2011).

[74]    U. Kleinekathöfer, B. Isralewitz, M. Dittrich and K. Schulten, Domain Motion of Individual F1-ATPase β-subunits During Unbiased Molecular Dynamics Simulations, J. Phys. Chem. A 115, 7267–7274 (2011).

[73]    R. Schulz, A. V. Vargiu, P. Ruggerone and U. Kleinekathöfer, The Role of Water During the Extrusion of Substrates by the Efflux Transporter AcrB, J. Phys. Chem. B 115, 8278–8287 (2011).

[72]    C. Olbrich, J. Strümpfer, K. Schulten and U. Kleinekathöfer, Quest for Spatially Correlated Fluctuations in the FMO Light-Harvesting Complex, J. Phys. Chem. B 115, 758–764 (2011).

[71]    C. Wagner, C. Olbrich, H. Brutzer, M. Salomo, U. Kleinekathöfer, U. F. Keyser and F. Kremer, TmHU Induced DNA Condensation As Studied with an Optical Tweezers Assisted Force Clamp, J. Biol. Phys. 37, 117–131 (2011).

[70]    C. Olbrich, J. Liebers and U. Kleinekathöfer, Modeling of Light-Harvesting in Purple Bacteria Using a Time-Dependent Hamiltonian Approach, phys. stat. sol. (b) 248, 393–398 (2011).

[69]    U. Kleinekathöfer, Trendbericht: Quantendynamik Komplexer Systeme, Nachrichten aus der Chemie 58, 334–336 (2010).

[68]    K. R. Mahendran, P. R. Singh, J. Arning, S. Stolte, U. Kleinekathöfer and M. Winterhalter, Permeation Through Nanochannels: Revealing Fast Kinetics, J. Phys.: Condens. Matter 22, 454 131 (2010).

[67]    C. Olbrich and U. Kleinekathöfer, Time-Dependent Atomistic View on the Electronic Relaxation in Light-Harvesting System II, J. Phys. Chem. B 114, 12 427–12 437 (2010).

[66]    G.-Q. Li and U. Kleinekathöfer, Optimal Control of Shot Noise and Fano Factor by External Fields, Eur. Phys. J. B 76, 309–319 (2010).

[65]    C. Padurariu, A. F. Amin and U. Kleinekathöfer, Laser-Assisted Electron Transport in Nanoscale Devices, in Nonlinear Dynamics of Nanosystems, edited by G. Radons, B. Rumpf and H. G. Schuster, 369–406 (Wiley-VCH, 2010).

[64]    R. Schulz, A. V. Vargiu, F. Collu, U. Kleinekathöfer and P. Ruggerone, Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations, PLoS Comput. Biol. 6, e1000 806 (2010).

[63]    I. Biro, S. Pezeshki, H. Weingart, M. Winterhalter and U. Kleinekathöfer, Comparing the Temperature-Dependent Conductance of the Two Structurally Similar E. coli Porins OmpC and OmpF, Biophys. J. 98, 1830–1839 (2010).

[62]    J. Liebers, A. Scaria, A. Materny and U. Kleinekathöfer, Probing the Vibrational Dynamics of High-lying Electronic States Using Pump-degenerate Four-wave Mixing, Phys. Chem. Chem. Phys. 12, 1351–1356 (2010).

[61]    S. Pezeshki, C. Chimerel, A. Bessenov, M. Winterhalter and U. Kleinekathöfer, Understanding Ion Conductance on a Molecular Level: An All-Atom Modeling of the Bacterial Porin OmpF, Biophys. J. 97, 1898–1906 (2009).

[60]    T. Kubař, U. Kleinekathöfer and M. Elstner, Solvent Fluctuations Drive the Hole Transfer in DNA: A Mixed Quantum-Classical Study, J. Phys. Chem. B 113, 13 107–13 117 (2009).

[59]    J. Liebers, A. Scaria, A. Materny and U. Kleinekathöfer, Ultrafast Vibrational Dynamics in Higher Electronic Excited States of Iodine, J. Raman Spectros. 40, 822–827 (2009).

[58]    U. Kleinekathöfer, Time-Local Quantum Master Equations and Their Applications to Dissipative Dynamics and Molecular Wires, in Energy Flow Dynamics in Biomaterial Systems, edited by I. Burghardt, V. May, D. A. Micha and E. Bittner, vol.  93 of Springer Series in Chemical Physics, 339–361 (Springer, 2009).

[57]    R. Schulz and U. Kleinekathöfer, Transitions Between Closed and Open Conformations of TolC: The Effects of Ions in Simulations, Biophys. J. 96, 3116–3125 (2009).

[56]    A. F. Amin, G.-Q. Li, A. H. Phillips and U. Kleinekathöfer, Coherent Control of the Spin Current Through a Quantum Dot, Eur. Phys. J. B 68, 103–109 (2009).

[55]    A. Scaria, J. Liebers, U. Kleinekathöfer and A. Materny, Probing the Contributions of Hot Vibrational States Using Pump-degenerate Four-wave Mixing, Chem. Phys. Lett. 470, 39–43 (2009).

[54]    G.-Q. Li, M. Schreiber and U. Kleinekathöfer, Suppressing the Current Through Molecular Wires: Comparison of Two Mechanisms, New J. Phys. 10, 085 005 (2008).

[53]    C. Chimerel, L. Movileanu, S. Pezeshki, M. Winterhalter and U. Kleinekathöfer, Transport at the Nanoscale: Temperature Dependence of Ion Conductance, Eur. Biophys. J. 38, 121–125 (2008).

[52]    G.-Q. Li, S. Welack, M. Schreiber and U. Kleinekathöfer, Tailoring Current Flow Patterns Through Molecular Wires Using Shaped Optical Pulses, Phys. Rev. B 77, 075 321–1–5 (2008).

[51]    G.-Q. Li, M. Schreiber and U. Kleinekathöfer, Time-dependent Suppression of Current Through Molecular Junctions, phys. stat. sol. (b) 245, 2720–2724 (2008).

[50]    G.-Q. Li, U. Kleinekathöfer and M. Schreiber, Treatment of Laser-field Effects on a Molecular Wire and Its Coupling to the Leads, J. Lumin. 128, 1078–1080 (2008).

[49]    J. Liebers, U. Kleinekathöfer and V. May, Sequences of Ultrafast Non-resonant Multiphoton Transitions in a Three-electronic Level Molecule, Chem. Phys. 347, 229–242 (2008).

[48]    S. Pezeshki, M. Schreiber and U. Kleinekathöfer, Shaping Femtosecond Coherent Anti-stokes Raman Spectra Using Optimal Control Theory, Phys. Chem. Chem. Phys. 10, 2058–2066 (2008).

[47]    U. Kleinekathöfer, Decomposition of Spectral Densities: Application to Dissipative Dynamics, Spectra and Molecular Wires, in Dynamics of Open Quantum Systems, edited by K. H. Hughes, 20–24 (CCP6, 2007).

[46]    G.-Q. Li, M. Schreiber and U. Kleinekathöfer, Coherent Laser Control of the Current Through Molecular Junctions, EPL 79, 27 006–1–6 (2007).

[45]    M. Schröder, M. Schreiber and U. Kleinekathöfer, Reduced Dynamics of Coupled Harmonic and Anharmonic Oscillators Using Higher-order Perturbation Theory, J. Chem. Phys. 126, 114 102–1–10 (2007).

[44]    M. Schröder, M. Schreiber and U. Kleinekathöfer, A Time-dependent Modified Redfield Theory for Absorption Spectra Applied to Light-harvesting Systems, J. Lumin. 125, 126–132 (2007).

[43]    U. Kleinekathöfer, G.-Q. Li, S. Welack and M. Schreiber, Coherent Destruction of the Current Through Molecular Wires Using Short Laser Pulses, phys. stat. sol. (b) 243, 3775–3781 (2006).

[42]    U. Kleinekathöfer, G.-Q. Li, S. Welack and M. Schreiber, Switching the Current Through Model Molecular Wires with Gaussian Laser Pulses, Europhys. Lett. 75, 139–145 (2006).

[41]    S. Welack, U. Kleinekathöfer and M. Schreiber, Laser-driven Molecular Wires Studied by a Non-Markovian Density Matrix Approach, J. Lumin. 119 & 120, 462–467 (2006).

[40]    U. Kleinekathöfer, G.-Q. Li and M. Schreiber, Density Matrix Theory for Reductive Electron Transfer in DNA, J. Lumin. 119 & 120, 91–95 (2006).

[39]    S. Welack, M. Schreiber and U. Kleinekathöfer, The Influence of Ultra-fast Laser Pulses on Electron Transfer in Molecular Wires Studied by a Non-Markovian Density Matrix Approach, J. Chem. Phys. 124, 044 712–1–9 (2006).

[38]    M. Schröder, U. Kleinekathöfer and M. Schreiber, Calculation of Absorption Spectra for Light-harvesting Systems Using Non-Markovian Approaches As Well As Modified Redfield Theory, J. Chem. Phys. 124, 084 903–1–14 (2006).

[37]    U. Kleinekathöfer, M. Schröder and M. Schreiber, Absorption Spectra for a Model Light-harvesting System Using Non-Markovian Theories, J. Lumin. 112, 461–464 (2005).

[36]    U. Kleinekathöfer, Non-Markovian Theories Based on the Decomposition of the Spectral Density, J. Chem. Phys. 121, 2505 (2004).

[35]    M. Schröder and U. Kleinekathöfer, Monte Carlo Method for Propagating Multi-dimensional Wave Packets, phys. stat. sol. (b) 241, 2157–2167 (2004).

[34]    A. Novikov, U. Kleinekathöfer and M. Schreiber, Coherent-state Path Integral Approach to the Damped Harmonic Oscillator, J. Phys. A: Math. Gen. 37, 3019–3040 (2004).

[33]    M. Schreiber, I. Barvík, P. Heřman, I. Kondov and U. Kleinekathöfer, Non-Markovian Effects in the Anisotropy of Fluorescence in LH2 Units, J. Lumin. 108, 137–141 (2004).

[32]    A. Novikov, U. Kleinekathöfer and M. Schreiber, The Mapping Approach in the Path Integral Formalism Applied to Curve-crossing Systems, Chem. Phys. 296, 149–158 (2004).

[31]    U. Kleinekathöfer, I. Barvík, P. Heřman, I. Kondov and M. Schreiber, Memory Effects in the Fluorescence Depolarization Dynamics Studied Within the B850 Ring of Purple Bacteria, J. Phys. Chem. B 107, 14 094–14 102 (2003).

[30]    I. Kondov, U. Kleinekathöfer and M. Schreiber, Stochastic Unraveling of Redfield Master Equations and Its Application to Electron Transfer Problems, J. Chem. Phys. 119, 6635–6646 (2003).

[29]    M. Schreiber, I. Kondov and U. Kleinekathöfer, Numerical Simulation of Electron Transfer Rates in Betaine-30, Nonlin. Opt. 29, 595–601 (2002).

[28]    I. Barvík, I. Kondov, P. Heřman, M. Schreiber and U. Kleinekathöfer, Femtosecond Dynamics in the Anisotropy of Emission in LH2 Units, Nonlin. Opt. 29, 167–172 (2002).

[27]    U. Kleinekathöfer, I. Kondov and M. Schreiber, Stochastic Unraveling of Time-local Quantum Master Equations Beyond the Lindblad Class, Phys. Rev. E 66, 037 701 (2002).

[26]    T. Mančal, U. Kleinekathöfer and V. May, Femtosecond Laser Pulse Control of Electron Transfer, J. Chem. Phys. 117, 636–646 (2002).

[25]    V. Čápek and U. Kleinekathöfer, On Homogeneous Generalized Master Equations, J. Phys. A: Math. Gen. 35, 5521–5524 (2002).

[24]    A. Damjanović, I. Kosztin, U. Kleinekathöfer and K. Schulten, Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics, Quantum Chemistry and Polaron Model Study, Phys. Rev. E 65, 031 919 (2002).

[23]    T. Sachse and U. Kleinekathöfer, Generalized Heitler-London Theory for H3: A Comparison of the Surface Integral Method with Perturbation Theory, Eur. Phys. J. D 18, 61–68 (2002).

[22]    P. Heřman, U. Kleinekathöfer, I. Barvík and M. Schreiber, Influence of Static and Dynamic Disorder on the Anisotropy of Emission in the Ring Antenna Subunits of Purple Bacteria Photosynthetic Systems, Chem. Phys. 275, 1–13 (2002).

[21]    P. Heřman, U. Kleinekathöfer, I. Barvík and M. Schreiber, Exciton Scattering in Light-harvesting Systems of Purple Bacteria, J. Lumin. 94&95, 447–450 (2001).

[20]    M. Schreiber, I. Kondov and U. Kleinekathöfer, A Density Matrix Approach to Photoinduced Electron Injection, J. Lumin. 94&95, 471–474 (2001).

[19]    U. Kleinekathöfer, I. Kondov and M. Schreiber, Perturbative Treatment of Intercenter Coupling in the Framework of Redfield Theory, Chem. Phys. 268, 121–130 (2001).

[18]    I. Kondov, U. Kleinekathöfer and M. Schreiber, Efficiency of Different Numerical Methods for Solving Redfield Equations, J. Chem. Phys. 114, 1497–1504 (2001).

[17]    U. Kleinekathöfer, Ground State Potentials for Alkaline Earth-Helium Diatoms Calculated by the Surface Integral Method, Chem. Phys. Lett. 324, 403–410 (2000).

[16]    D. Kilin, U. Kleinekathöfer and M. Schreiber, Electron Transfer in Porphyrin Complexes in Different Solutions, J. Phys. Chem. A 104, 5413–5421 (2000).

[15]    M. Schreiber, I. Kondov and U. Kleinekathöfer, Different Direct Integrators for Redfield Equations Applied to Electron Transfer Dynamics, J. Mol. Liq. 86, 77–84 (2000).

[14]    U. Kleinekathöfer, T. I. Sachse, K. T. Tang, J. P. Toennies and C. L. Yiu, Three-body Exchange Energies in H3 and He3 Calculated by the Surface Integral Method, J. Chem. Phys. 113, 948–956 (2000).

[13]    U. Kleinekathöfer, M. Lewerenz and M. Mladenović, Long Range Binding in Alkali-Helium Pairs, Phys. Rev. Lett. 83, 4717–4720 (1999).

[12]    M. Nest, U. Kleinekathöfer, M. Schreiber and P. Saalfrank, The Mapped Fourier Method for Scattering Problems, Chem. Phys. Lett. 313, 665–669 (1999).

[11]    M. Schreiber, D. Kilin and U. Kleinekathöfer, Comparison of Two Models for Bridge-assisted Charge Transfer, J. Lumin. 83&84, 235–240 (1999).

[10]    U. Kleinekathöfer and D. J. Tannor, Extension of the Mapped Fourier Method to Time-dependent Problems, Phys. Rev. E 60, 4926–4933 (1999).

[9]    U. Kleinekathöfer, K. T. Tang, J. P. Toennies and C. L. Yiu, The Generalized Heitler-London Theory for H3 Potential Energy Surfaces, J. Chem. Phys. 111, 3377–3386 (1999).

[8]    M. Schreiber, D. Kilin and U. Kleinekathöfer, Photo-induced Intermolecular Charge Transfer in Porphyrin Complexes, in Excitonic Processes in Condensed Matter, edited by R. T. Williams and W. M. Yen, 99–104 (The Electrochemical Society, 1998).

[7]    U. Kleinekathöfer, S. H. Patil, K. T. Tang and J. P. Toennies, A Boundary Condition Determined Wave Function for the H2 Molecule, vol.  72, 1361–1375 (1998).

[6]    U. Kleinekathöfer, K. T. Tang, J. P. Toennies and C. L. Yiu, Van Der Waals Potentials of He2, Ne2 and Ar2 with the Exchange Energy Calculated by the Surface Integral Method, J. Chem. Phys. 107, 9502–9513 (1997).

[5]    U. Kleinekathöfer, S. H. Patil, K. T. Tang and J. P. Toennies, A Boundary Condition Determined Wave Function for the Ground State of Helium and Isoelectronic Ions, Phys. Rev. A 54, 2840–2849 (1996).

[4]    C. Johann, U. Kleinekathöfer, K. T. Tang and J. P. Toennies, Generalized Heitler-London Theory with Exchange Energy by the Surface Integral Method: An Application to the Alkali-Metal Dimer Cations, Chem. Phys. Lett. 257, 651–657 (1996).

[3]    U. Kleinekathöfer, K. T. Tang, J. P. Toennies and C. L. Yiu, Potentials for Some Rare Gas and Alkali-Helium Systems Calculated from the Surface Integral Method, Chem. Phys. Lett. 249, 257–263 (1996).

[2]    U. Kleinekathöfer, K. T. Tang, J. P. Toennies and C. L. Yiu, Angular Momentum Coupling in the Exchange Energy of Multielectron Systems, J. Chem. Phys. 103, 6617–6630 (1995).

[1]    U. Kleinekathöfer, Line Defects in Quasi-one-dimensional Systems: Orthogonality Exponents and Electron Density, Phys. Rev. B 48, 4816–4822 (1993).