List of works by Ulrich Kleinekathöfer

A Monte Carlo method for propagating multi-dimensional wave packets

A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii

scientific article published on 13 December 2018

A density matrix approach to photoinduced electron injection

A time-dependent modified Redfield theory for absorption spectra applied to light-harvesting systems

Absorption spectra for a model light-harvesting system using non-Markovian theories

AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity.

scientific article

Atomistic Modeling of Two-Dimensional Electronic Spectra and Excited-State Dynamics for a Light Harvesting 2 Complex

article

BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms.

scientific article published on 18 April 2016

Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

scientific article published on 17 January 2020

Brownian Dynamics Approach Including Explicit Atoms for Studying Ion Permeation and Substrate Translocation across Nanopores

BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides

Calculation of absorption spectra for light-harvesting systems using non-Markovian approaches as well as modified Redfield theory

article by Markus Schröder et al published 28 February 2006 in Journal of Chemical Physics

Characterization of Ciprofloxacin Permeation Pathways across the Porin OmpC Using Metadynamics and a String Method

scientific article published on 17 August 2017

Chebyshev Expansion Applied to Dissipative Quantum Systems

scientific article published on 4 February 2016

Chebyshev hierarchical equations of motion for systems with arbitrary spectral densities and temperatures

scientific article published on 01 June 2019

Coherent control of the spin current through a quantum dot

Coherent destruction of the current through molecular wires using short laser pulses

Coherent laser control of the current through molecular junctions

article by G.-Q Li et al published July 2007 in Europhysics Letters

Coherent-state path integral approach to the damped harmonic oscillator

Comparing the temperature-dependent conductance of the two structurally similar E. coli porins OmpC and OmpF.

scientific article published on May 2010

Computational modeling of ion transport through nanopores

article

Computational study of correlated domain motions in the AcrB efflux transporter.

scientific article published on 5 January 2015

Conversion of OprO into an OprP-like Channel by Exchanging Key Residues in the Channel Constriction

scientific article published in August 2017

Corynebacterium jeikeium jk0268 constitutes for the 40 amino acid long PorACj, which forms a homooligomeric and anion-selective cell wall channel

scientific article

DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex

scientific article published on 29 September 2020

DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations

scientific article

Density matrix theory for reductive electron transfer in DNA

article published in 2006

Different Types of Vibrations Interacting with Electronic Excitations in Phycoerythrin 545 and Fenna-Matthews-Olson Antenna Systems

scientific article published on 2 September 2014

Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations

scientific article

Effect of the F610A mutation on substrate extrusion in the AcrB transporter: explanation and rationale by molecular dynamics simulations.

scientific article

Efficiency of different numerical methods for solving Redfield equations

Enrofloxacin Permeation Pathways across the Porin OmpC.

scientific article published on 6 January 2018

Environmental coupling and population dynamics in the PE545 light-harvesting complex

Exciton scattering in light-harvesting systems of purple bacteria

article by Pavel Heřman et al published December 2001 in Journal of Luminescence

Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study

article

Exploration of Free Energy Surfaces Across a Membrane Channel Using Metadynamics and Umbrella Sampling

scientific article published on 13 March 2020

Femtosecond laser pulse control of electron transfer processes

article published in 2002

Fine tuning of the photosystem II major antenna mobility within the thylakoid membrane of higher plants

scientific article published on 10 September 2019

Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials

scientific article published on 30 March 2020

Fosfomycin Permeation through the Outer Membrane Porin OmpF

scientific article published on 08 December 2018

From Atomistic Modeling to Electronic Properties of Light-Harvesting Systems

From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex

scientific article

Functional rotation of the transporter AcrB: insights into drug extrusion from simulations

scientific article (publication date: June 2010)

Generalized Heitler-London theory for H 3 : a comparison of the surface integral method with perturbation theory

scholarly article in European Physical Journal D, vol. 18 no. 1, January 2002

Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109.

scientific article published on 9 May 2018

Impact of Electronic Fluctuations and Their Description on the Exciton Dynamics in the Light-Harvesting Complex PE545.

scientific article published on 23 January 2017

Improved Sampling and Free Energy Estimates for Antibiotic Permeation through Bacterial Porins

scientific article published on 17 June 2021

Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins.

scientific article published on 23 July 2015

Influence of static and dynamic disorder on the anisotropy of emission in the ring antenna subunits of purple bacteria photosynthetic systems

scholarly article by Pavel Heřman et al published January 2002 in Chemical Physics

Juxtaposing density matrix and classical path-based wave packet dynamics

scientific article

Laser-Assisted Electron Transport in Nanoscale Devices

Laser-driven molecular wires studied by a non-Markovian density matrix approach

article published in 2006

Line defects in quasi-one-dimensional systems: Orthogonality exponents and electron density

scientific article published on 01 August 1993

Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details.

scientific article published on 3 January 2017

Millisecond-Long Simulations of Antibiotics Transport through Outer Membrane Channels

scientific article published on 30 December 2020

Modeling charge transport in DNA using multi-scale methods

Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-Negative Porin

scientific article published on 01 July 2019

Modeling of light-harvesting in purple bacteria using a time-dependent Hamiltonian approach

Modeling the Ion Selectivity of the Phosphate Specific Channel OprP

article

Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB

scientific article published on 28 May 2019

Non-Markovian effects in the anisotropy of fluorescence in LH2 units

Non-Markovian theories based on a decomposition of the spectral density

scientific article

Non-equilibrium Green’s function transport theory for molecular junctions with general molecule-lead coupling and temperatures

scientific article published on 21 December 2018

OmpW of Caulobacter crescentus Functions as an Outer Membrane Channel for Cations

scientific article published on 25 November 2015

On homogeneous generalized master equations

article published in 2002

Optimal control of shot noise and Fano factor by external fields

Outer-membrane translocation of bulky small molecules by passive diffusion

scientific article published on 26 May 2015

Permeation of Fosfomycin through the Phosphate-Specific Channels OprP and OprO of Pseudomonas aeruginosa

scientific article published on 9 February 2022

Permeation through nanochannels: revealing fast kinetics

article published in 2010

Perturbative treatment of intercenter coupling in the framework of Redfield theory

article published in 2001

Polaron Effects on Charge Transport through Molecular Wires: A Multiscale Approach.

scientific article

Preparational Effects on the Excitation Energy Transfer in the FMO Complex

Probing the Transport of Ionic Liquids in Aqueous Solution through Nanopores

article

Probing the contributions of hot vibrational states using pump-degenerate four-wave mixing

article

Probing the vibrational dynamics of high-lying electronic states using pump-degenerate four-wave mixing

article

Protein Arrangement Effects on the Exciton Dynamics in the PE555 Complex.

scientific article published on 7 September 2016

Pulling Peptides across Nanochannels: Resolving Peptide Binding and Translocation through the Hetero-oligomeric Channel from Nocardia farcinica

article by Pratik Raj Singh et al published 12 November 2012 in ACS Nano

Quantum biology revisited

scientific article published on 03 April 2020

Quest for spatially correlated fluctuations in the FMO light-harvesting complex

scientific article published on 10 December 2010

Reduced dynamics of coupled harmonic and anharmonic oscillators using higher-order perturbation theory.

scientific article published in March 2007

Relation between Dephasing Time and Energy Gap Fluctuations in Biomolecular Systems.

scientific article published on 7 March 2016

Relation between Vibrational Dephasing Time and Energy Gap Fluctuations

scientific article published on 18 June 2017

Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example

scientific article

Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation

scientific article

Role of water during the extrusion of substrates by the efflux transporter AcrB.

scientific article

Selective probing of vibrational hot states in bromine using time-resolved coherent anti-Stokes Raman scattering

scientific article

Sequences of ultrafast non-resonant multiphoton transitions in a three-electronic level molecule

Shaping femtosecond coherent anti-Stokes Raman spectra using optimal control theory

scientific article

Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes

Simulation des Transports durch Außenmembrankanäle

Simulation of ion transport through an N-acetylneuraminic acid-inducible membrane channel: from understanding to engineering

scientific article

Simulations of outer membrane channels and their permeability

scientific article published on 22 December 2015

Single Residue Acts as Gate in OccK Channels

scientific article

Solvent fluctuations drive the hole transfer in DNA: a mixed quantum-classical study

scientific article published in October 2009

Stochastic unraveling of Redfield master equations and its application to electron transfer problems

Stochastic unraveling of time-local quantum master equations beyond the Lindblad class

Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II

scientific article published on 01 November 2019

Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis

scientific article published on 11 May 2020

Structural basis for chitin acquisition by marine Vibrio species

scientific article published on 15 January 2018

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

scientific article published on 16 October 2017

Structural basis for nutrient acquisition by dominant members of the human gut microbiota

scientific article

Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa

scientific article

Suppressing the current through molecular wires: comparison of two mechanisms

Switching the current through model molecular wires with Gaussian laser pulses

article

Tailoring current flow patterns through molecular wires using shaped optical pulses

scholarly article in Physical Review B, vol. 77 no. 7, February 2008

The FMO complex in a glycerol-water mixture

scientific article published on 06 June 2013

The influence of ultrafast laser pulses on electron transfer in molecular wires studied by a non-Markovian density-matrix approach

scientific article

The mapping approach in the path integral formalism applied to curve-crossing systems

article by Alexey Novikov et al published January 2004 in Chemical Physics

The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics

scientific article published on 15 October 2020

Theoretical analysis of ion conductance and gating transitions in the OpdK (OccK1) channel

article

Theoretische Chemie 2009

article

Theory and Simulation of the Environmental Effects on FMO Electronic Transitions

scientific article

Three-body exchange energies in H3 and He3 calculated by the surface integral method

article published in 2000

Time-Dependent Atomistic View on the Electronic Relaxation in Light-Harvesting System II

article by Carsten Olbrich & Ulrich Kleinekathöfer published 30 September 2010 in Journal of Physical Chemistry

Time-Dependent View of Sequential Transport through Molecules with Rapidly Fluctuating Bridges

scientific article published in Physical Review Letters

Time-Local Quantum Master Equations and their Applications to Dissipative Dynamics and Molecular Wires

article

Time-dependent suppression of current through molecular junctions

Transitions between closed and open conformations of TolC: the effects of ions in simulations

scientific article published on April 2009

Transport at the nanoscale: temperature dependence of ion conductance.

scientific article

Treatment of laser-field effects on a molecular wire and its coupling to the leads

Treatment of time-dependent effects in molecular junctions

Tuning the affinity of anion binding sites in porin channels with negatively charged residues: molecular details for OprP.

scientific article

Ultrafast vibrational dynamics in higher electronic excited states of iodine

article

Understanding ion conductance on a molecular level: an all-atom modeling of the bacterial porin OmpF.

scientific article published on October 2009

Using the Chebychev expansion in quantum transport calculations

scientific article published on April 2015

Voltage-Dependent Transport of Neutral Solutes through Nanopores: A Molecular View

scientific article published on 11 November 2020

Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump

scientific article

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