Prof_Kleinekathöfer

Prof. Dr. Ulrich Kleinekathöfer

Professor of Theoretical Physics
School of Science
Campus Ring 1,  28759 Bremen, Germany
Phone number
+49 421 200 3523
Email Address
ukleinekathoefer@constructor.university
Office
Research III, Room 61
Research Interests
LH2

The Computational Physics and Biophysics Group performs theoretical calculations and computational simulations including method development on a variety of molecular systems. In order to tackle the large range of dynamical processes involved, molecular dynamics simulations, electronic structure calculations and quantum dynamical simulations are performed and often coupled.

fmo

People: Prof. Ulrich Kleinekathöfer, Sayan Maity , Pooja Sarngadharan, Yannick Holtkamp

Cooperations: Marcus Elstner (Karlsruhe, Germany), Vangelis Daskalakis (Cyprus), Abhishek Singharoy (Arizona State U), Melih Sener (Urbana-Champaign)

Funding: Deutsche Forschungsgemeinschaft, EU through MSCA Doctoral Network PhotoCaM

Though light harvesting is one of the most important processes on earth, many of the molecular details of this process in plants, algae, and bacteria have yet to be elucidated. The light absorption in light-harvesting complexes is mainly performed by chlorophyll or bilin molecules. To this end, we are performing classical molecular dynamics simulations, time-dependent QM/MM,  as well as quantum chemistry calculations on light-harvesting systems. Furthermore, two strategies are followed how to use the input from the atomistic simulations to study the transfer of energy in light-harvesting systems. On the one hand, spectral densities are being determined and density matrix calculations performed. On the other hand, the time-dependent Hamiltonians are directly employed in wave-packet based Ehrenfest calculations.  On top of this, the same techniques can be employed to determine two-dimensional spectra which can be directly linked to experiment.

Selected publications:

[175]   S. Maity, V. Daskalakis, T. L. C. Jansen and U. Kleinekathöfer, Electric Field Susceptibility of Chlorophyll c Leads to Unexpected Excitation Dynamics in the Major Light-Harvesting Complex of Diatoms, J. Phys. Chem. Lett. 15, 2499–2510 (2024).

[166]   S. Maity and U. Kleinekathöfer, Recent Progress in Atomistic Modeling of Light-Harvesting Complexes: A Mini Review, Photosynth. Res. 156, 147–162 (2023).

[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).

[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).

[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).

nanopore

People: Prof. Ulrich Kleinekathöfer, Jigneshkumar Prajapati, PhD,  Abhishek Acharya

Cooperations: Prof. Mathias Winterhalter, Prof. Roland Benz and their groups

Funding: Deutsche Forschungsgemeinschaft

Previous Funding: Innovative Medicines Initiavtive “Translocation”, Marie Curie Training Program “Translocation”

Nanopores and channels are ubiquitous in biological systems. They are responsible for the transport of various ions and substrates between the different compartments of biological systems separated by membranes.  As an experimental method, electrophysiology has proven to be an important nano-analytical tool for the study of substrate transport through nanopores utilizing ion current measurements as a probe for the detection. An important example is the study of antibiotics translocation through porins such as the outer membrane protein F (OmpF) and C (OmpC). By now, numerical simulations have established themselves as an indispensable tool to decipher ion transport processes through biological as well as artificial nanopores.

Temperature dependent ion conductance in nanopores are being measured in a wide range of electrolyte concentrations in the Winterhalter and the Benz groups and compared to molecular dynamics simulations performed in our group.  It is not only the aim to understand the electrostatic and steric effects playing the major role in the channel, but also to modify the channel by mutating certain amino acids in order to fulfill some predefined properties. This way, the conductance and the selectivity for certain ion types can be engineered and one can design, for example, a molecular sieve.

Recent publications:

[174]   A. Acharya, K. Jana and U. Kleinekathöfer, Antibiotic Charge Profile Determines the Extent of L3 Dynamics in Ompf: An Expedited Passage for Molecules with a Positive Charge, J. Phys. Chem. B 127, 10 766–10 777 (2023).

[170]    J. Abellon-Ruiz, K. Jana, A. Silale, A. M. Frey, A. Baslé, M. Trost, U. Kleinekathöfer and B. van den Berg, BtuB TonB-Dependent Transporters and BtuG Surface Lipoproteins Form Stable Complexes for Vitamin B12uptake in gut Bacteroides, Nat. Commun. 14, 4714 (2023).

[169]   A. Acharya, K. Jana, D. Gurvic, U. Zachariae and U. Kleinekathöfer, Fast Prediction of Antibiotic Permeability through Membrane Channels Using Brownian Dynamics, Biophys. J. 122, 2996–3007 (2023).

[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).

[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).

wire

People: Prof. Ulrich Kleinekathöfer

Cooperations: Prof. Marcus Elstner, Dr. T. Kubař, Karlsruhe Institute of Technology

The study of time-dependent effects in the transport through molecular junctions is in the focus of this research line. Two different sources of time-dependent perturbations can be considered: fluctuations resulting from surrounding liquids and external (laser) fields. Surrounding liquid molecules such as water can lead to large and fast fluctuations of the site energies of the orbitals involved in the charge transfer. Therefore, methods have to be further developed and employed to accurately and efficiently determine the charge current and noise in these cases. The fluctuations in the energies and couplings can be extracted from atomistic simulations. These parameters can then directly be used in transport calculations or first be transformed in so-called spectral densities, which in turn can be used in calculations with time-independent Hamiltonians.

Previous funding by the DFG through priority program SPP 1243 Quantum Transport at the Molecular Scale.

Selected publications:

[177]   A. Forde, S. Maity, V. M. Freixas, S. Fernandez-Alberti, A. J. Neukirch, U. Kleinekathöfer and S. Tretiak, Stabilization of Charge-Transfer Excited States in Biological Systems: A Computational Focus on the Special Pair in Photosystem II Reaction Centers, J. Phys. Chem. Lett. 15, 4142–4150 (2024).

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

[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).

[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).

spectrum

People: Prof. Ulrich Kleinekathöfer, Yannick Holtkamp

For the dynamics of quantum particles, e.g., excitons or electron, coupled to bosonic or fermionic reservoirs (or both simultaneously), a multitude of approximative theories exists. Aim is to develop and use theories which can use the information, e.g., from simulations of light-harvesting systems with as little additional approximations as possible. The methods range from the Numerical Integration of the Schrödinger Equation (NISE) over the Hierachy Equation of Motion (HEOM) approach to stochastic variants thereof. 

Selected publications:

[171]   Y. Holtkamp, M. Kowalewski, J. Jasche and U. Kleinekathöfer, Machine-Learned Correction to Ensemble-Averaged Wave Packet Dynamics, J. Chem. Phys. 159, 094 107 (2023).

[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).

[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).

[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).

[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).

see “Molecular Machine Learning”

see “PhotoCaM”

Computational Physics and Biophysics Group
Kleinekathöfer Group Sept 2023
 

August 2019

Tan Chin Tuan Exchange Fellowship, NTU Sinapore

since 2017

Full Professor of Theoretical Physics at Constructor University
(formerly known as Jacobs University Bremen)

June 2012

Research stay in the Theoretical and Computational Biophysics Group directed by Prof. Klaus Schulten at the Beckman Institute, University of Illinois at Urbana-Champaign

since   2006

Associate Professor of Theoretical Physics at Jacobs University Bremen

2004-2006

Oberassistent (senior scientist) at Technische Universität Chemnitz

July 2005

Research stay at the Beckman Institute, University of Illinois at Urbana-Champaign

2002-2003

Senior Research Fellow at the International University Bremen

June-August 2003

Research stay  at the Beckman Institute, University of Illinois at Urbana-Champaign

2002

Habilitation in Physics (Technische Universität Chemnitz)

July-August 2001

Research stay in the Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign

1997-2002

Research Assistant in the group of Prof. M. Schreiber, Technische Universität Chemnitz

1998, 2002

Research stay at the Weizmann Institute of Science, Israel, for two months each

1996-1997

Postdoctoral fellow in the group of Prof. D. Tannor in the Chemical Physics Department of the Weizmann Institute of Science

1993-1996

PhD student in the group of Prof. J. P. Toennies, Max-Planck-Institut für Strömungsforschung, Göttingen (including three one-month stays at the Pacific Lutheran University, Tacoma, USA)

1991-1993

Diploma student in the group of Prof. K. Schönhammer at the Institut für Theoretische Physik of the Universität Göttingen

1987-1993

Study of Physics at Universität Göttingen

 
  • Sayan Maity, PhD (PhD thesis)
  • Abhishek Acharya, M.Sc. (PhD thesis)
  • Kalyanashis Jana, PhD
  • Pooja Sarngadharan, M.Sc.
  • Yannick Holtkamp, M.Sc.
  • Dongyu Lyu, M.Sc.
  • Pratik Behera, M.Sc.
  • David Varas Rubio, M.Sc.

Highly motivated and interested undergraduate and graduate students as well as postdoctoral candidates, who feel their research interests are particularly aligned with the main research areas of the group, are encouraged to contact Prof. Ulrich Kleinekathöfer.

Potential postdoctoral candidates can also apply for fellowship from organizations such as the Alexander von Humboldt Foundation or the EU  Marie Skłodowska-Curie Actions Postdoctoral program.

.............................................................................................................................................................

Two PhD positions in Computational (Bio)Physics/Chemistry

Two PhD positions on Computational (Bio)Physics/Chemistry and on the Dynamics of Open Quantum Systems are available in the group of Prof. Ulrich Kleinekathoefer at Constructor University Bremen, Germany https://constructor.university/comp_phys

One position is focused on multi-scale modeling of charge  transfer in heme-containing complexes. The respective research will involve a combination of quantum and molecular dynamics simulations as  well as  electronic structure calculations  with some similarities to earlier work on charge and excitation energy transfer also using non-adiabatic methods (see https://constructor.university/comp_phys).

The second project  focuses on the dynamics in open quantum systems applied, e.g., to the time propagation of excitons and charges in biological systems such as light-harvesting complexes but with possible connections to quantum computing.

The Computational Physics and Biophysics Group led by Prof. Ulrich Kleinekathoefer is located at Constructor University Bremen,  a private, state-accredited, English-language research university. The research group focuses on modeling dynamical processes in (bio)molecular systems using quantum and classical approaches and especially combinations thereof. Molecular simulations of light-harvesting complexes and membrane proteins are at the center of the research. For more details see https://constructor.university/comp_phys

The successful candidates should hold a master degree in theoretical (bio)physics or theoretical (bio)chemistry. Solid knowledge in the theory of molecular systems and statistical mechanics  as well as skills in molecular dynamics simulations are highly desirable especially for the first position. Proficiency in programming would be beneficial. A good command of English is essential, both as the local working language and because of our international collaborations.

The PhD positions are available immediately and applications will be considered until the positions are filled. Applicants should submit a CV, a brief
statement of research interests, and the names of two referees by e-mail to Prof. Ulrich Kleinekathoefer at
ukleinekathoefer(at)constructor.university
 

(in order of their disappearance)

Sehrish Jamal, M.Sc., DAAD PhD exchange student
Jigneshkumar Prajapati, PhD (PhD thesis)
Vinaya Kumar Golla, M.Sc.(PhD thesis)
Anusha Kesireddy, PhD (PhD thesis)
Hasan Rahman, PhD (PhD thesis)
Manas Sanjay Joshi, M. Sc.
Salvatore Cubisino (guest)
Yannick M. Holtkamp, B.Sc.
Karunakar Reddy Pothula, PhD (PhD thesis)
Jing Lu, M.Sc.
Kristians Cernevics, M. Sc. (guest)
Dr. Shreyas Kaptan
Dr. Carlos José Fernández Solano
Maria Ilaria Mallus, PhD (PhD thesis)
Dr. Fabio Grassi
Suryanarayanan Chandrasekaran, PhD (PhD thesis)
Dr. Bogdan Popescu (PhD thesis)
Dr. Mortaza Aghtar (PhD thesis)
Dr. Niraj Modi (PhD thesis)
Dr. Jörg Liebers (PhD thesis)
Dr. Robert Schulz (PhD thesis)
Dr. Carsten Olbrich (PhD thesis)
Dr. Soroosh Pezeshki (PhD thesis)
Lisa Moevius, M.Sc.
Atef Fadl Amin, PhD
Dr. Guangqi Li (PhD thesis)
Ciprian Padurariu, M.Sc.
Dr. Markus Schröder (PhD thesis)
Dipl.-Phys. Sven Welack (Diploma thesis)
Dr. Alexey Novikov (PhD thesis)
Dr. Ivan Kondov (PhD thesis)

Publications
 

[182]   Y. M. Holtkamp, E. Godinez-Ramirez and U. Kleinekathöfer, Spectral Densities, Structured Noise and Ensemble Averaging within Open Quantum Dynamics, J. Chem. Phys 161, 134 101 (2024).

[181]   V. Daskalakis, S. Maity and U. Kleinekathöfer, An Unexpected Water Channel in the Light-Harvesting Complex of a Diatom: Implications for the Switch between Light Harvesting and Photoprotection, ACS Phys. Chem. Au (in press) (2024).

[180]   A. Acharya, P. K. Behera and U. Kleinekathöfer, Molecular Mechanism of Ciprofloxacin Translocation through the Major Diffusion Channels of the ESKAPE Pathogens Klebsiella Pneumoniae and Enterobacter Cloacae, J. Phys. Chem. B 128, 8376–8387 (2024).

[179]   M. Sokolov, D. S. Hoffmann, P. M. Dohmen, M. Krämer, S. Höfener, U. Kleinekathöfer and M. Elstner, Non-Adiabatic Molecular Dynamics Simulations Provide New Insights into the Exciton Transfer in the Fenna–Matthews–Olson Complex, Phys. Chem. Chem. Phys. 26, 19 469–19 496 (2024).

[178]   P. Sarngadharan, Y. Holtkamp and U. Kleinekathöfer, Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex, J. Phys. Chem. B 128, 5201–5217 (2024).

[177]   A. Forde, S. Maity, V. M. Freixas, S. Fernandez-Alberti, A. J. Neukirch, U. Kleinekathöfer and S. Tretiak, Stabilization of Charge-Transfer Excited States in Biological Systems: A Computational Focus on the Special Pair in Photosystem II Reaction Centers, J. Phys. Chem. Lett. 15, 4142–4150 (2024).

[176]   V. Vinod, U. Kleinekathöfer and P. Zaspel, Optimized Multifidelity Machine Learning for Quantum Chemistry, Mach. Learn.: Sci. Technol. 5, 015 054 (2024).

[175]   S. Maity, V. Daskalakis, T. L. C. Jansen and U. Kleinekathöfer, Electric Field Susceptibility of Chlorophyll c Leads to Unexpected Excitation Dynamics in the Major Light-Harvesting Complex of Diatoms, J. Phys. Chem. Lett. 15, 2499–2510 (2024).

[174]   A. Acharya, K. Jana and U. Kleinekathöfer, Antibiotic Charge Profile Determines the Extent of L3 Dynamics in Ompf: An Expedited Passage for Molecules with a Positive Charge, J. Phys. Chem. B 127, 10 766–10 777 (2023).

[173]   V. Vinod, S. Maity, P. Zaspel and U. Kleinekathöfer, Multifidelity Machine Learning for Molecular Excitation Energies, J. Chem. Theory Comput. 19, 7658–7670 (2023).

[172]   J. P. Götze, S. Maity and U. Kleinekathöfer, Incoherent Energy Transfer between the Baseplate and FMO Protein Explored at Ideal Geometries, J. Phys. Chem. B 127, 7829–7838 (2023).

[171]   Y. Holtkamp, M. Kowalewski, J. Jasche and U. Kleinekathöfer, Machine-Learned Correction to Ensemble-Averaged Wave Packet Dynamics, J. Chem. Phys. 159, 094 107 (2023).

[170]    J. Abellon-Ruiz, K. Jana, A. Silale, A. M. Frey, A. Baslé, M. Trost, U. Kleinekathöfer and B. van den Berg, BtuB TonB-Dependent Transporters and BtuG Surface Lipoproteins Form Stable Complexes for Vitamin B12  Uptake in Gut Bacteroides, Nat. Commun. 14, 4714 (2023).

[169]   A. Acharya, K. Jana, D. Gurvic, U. Zachariae and U. Kleinekathöfer, Fast Prediction of Antibiotic Permeability through Membrane Channels Using Brownian Dynamics, Biophys. J. 122, 2996–3007 (2023).

[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. 63, 910–927 (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. 156, 147–162 (2023).

[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).

Teaching

Prof. Kleinekathöfer is mainly involved in the Physics and Data Science  undergraduate program as well as some additional undergraduate programs.

Courses which he taught so far (partially together with colleagues) include but are not limited to Computational Physics, Electrodynamics, Statistical Physics, Numerical Software Lab, Physical Chemistry & Molecular Simulations, Statistical and Advanced Quantum Mechanics, …
For more details and current courses, have a look at CampusNet and for teaching material at Moodle (login required).

Concerning B.Sc. and M.Sc. thesis projects, please do not hesitate to contact Prof. Ulrich Kleinekathöfer or any of his group members.

Conferences

Over the last years, the Computational Physics and Biophysics Group was involved in organizing several workshops and conferences.

prof_kleinekathoefer_conferences