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Papers by Benjamin Woiczikowski
Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als d... more Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als die angegebenen Quellen und Hilfsmittel verwendet, sowie die Satzung der Universität Karlsruhe (TH) zur Sicherung guter wissenschaftlicher Praxis beachtet habe.
The Journal of Physical Chemistry B, 2014
Charge transfer in peptides and proteins can occur on different pathways, depending on the energe... more Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult to access experimentally, different modeling strategies have been successfully applied to study these processes in the past. These can be based on a simple empirical pathway model, efficient tight binding type atomic orbital Hamiltonians or ab initio and density functional calculations. An interesting strategy, which allows an efficient calculations of charge transfer parameters, is based on a fragmentation of the system into functional units. While this works well for systems like DNA, where the charge transfer pathway is naturally divided into distinct molecular fragments, this is less obvious for charge transfer along peptide and protein backbones. In this work, we develop and access a strategy for an effective fragmentation approach, which allows one to compute electronic couplings for large systems along nanosecond time scale molecular dynamics trajectories. The new methodology is applied to a solvated peptide, for which charge transfer properties have been studied recently using an empirical pathway model. As could be expected, dynamical effects turn out to be important, which emphasizes the importance of using effective quantum approaches which allow for sufficient sampling. However, the computed rates are orders of magnitude smaller than experimentally determined, which indicates the shortcomings of present modeling approaches.
New Journal of Physics, 2010
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural flu... more Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straightforward way through time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the onsite energies along the DNA wire.
We investigate in detail the charge transport characteristics of DNA wires with various sequences... more We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and...
The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which co... more The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which combines electronic structure calculations, molecular dynamics (MD) simulations, and the formulation of an effective tight-binding model Hamiltonian. Charge transport is studied by computing transmission functions along the MD trajectories. Though G4-DNA is structurally more stable than double-stranded DNA (dsDNA), our results strongly suggest that the potential improvement of the electrical transport properties in the former is not necessarily related to an increased stability, but rather to the fact that G4 is able to explore in its conformational space a larger number of charge-transfer active conformations. This in turn is a result of the non-negligible interstrand matrix elements, which allow for additional charge transport pathways. The higher structural stability of G4 can however play an important role once the molecules are contacted by electrodes. In this case, G4 may experience ...
The Journal of Physical Chemistry B, 2011
In this report, we study the photoactivation process in Escherichia coli DNA photolyase, involvin... more In this report, we study the photoactivation process in Escherichia coli DNA photolyase, involving long-range electron transport along a conserved chain of Trp residues between the protein surface and the flavin adenine dinucleotide (FAD) cofactor. Fully coupled nonadiabatic (Ehrenfest) quantum mechanics/molecular mechanics (QM/MM) simulations allow us to follow the time evolution of charge distributions over the natural time scale of multiple charge transfer events and conduct rigorous statistical analysis. Charge transfer rates in excellent agreement with experimental data are obtained without the need for any system-specific parametrization. The simulations are shown to provide a more detailed picture of electron transfer than a classical analysis of Marcus parameters. The protein and solvent both strongly influence the localization and transport properties of a positive charge, but the directionality of the process is mainly caused by solvent polarization. The time scales of charge movement, delocalization, protein relaxation and solvent reorganization overlap and lead to nonequilibrium reaction conditions. All these contributions are explicitly considered and fully resolved in the model used and provide an intricate picture of multistep biochemical electron transfer in a flexible, heterogeneous environment.
The Journal of Physical Chemistry B, 2008
The Journal of Physical Chemistry B, 2013
The Journal of Physical Chemistry B, 2012
Physical Review Letters, 2012
Molecules in junctions often fluctuate considerably, especially when subject to the influence of ... more Molecules in junctions often fluctuate considerably, especially when subject to the influence of solvent molecules. These fluctuations in site energies and couplings can be sampled, for example, by using molecular dynamics simulations, and can lead to incoherent effects in charge transport. To this end, a popular snapshot-averaged Landauer approach is compared to a time-dependent Green's function scheme. Since sequential transport dominates in systems with rapidly varying bridges, schemes not taking the time order of conformations into account, such as the Landauer approach, are inappropriate.
The Journal of Chemical Physics, 2009
We investigate in detail the charge transport characteristics of DNA wires with various sequences... more We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics ͑MD͒ simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment ͑water, backbone, counterions͒ and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders ͑differences in base ionization potentials͒. As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. ͓J. Am. Chem. Soc. 126, 11471 ͑2004͔͒. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.
The Journal of Chemical Physics, 2010
Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als d... more Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als die angegebenen Quellen und Hilfsmittel verwendet, sowie die Satzung der Universität Karlsruhe (TH) zur Sicherung guter wissenschaftlicher Praxis beachtet habe.
Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als d... more Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als die angegebenen Quellen und Hilfsmittel verwendet, sowie die Satzung der Universität Karlsruhe (TH) zur Sicherung guter wissenschaftlicher Praxis beachtet habe.
The Journal of Physical Chemistry B, 2014
Charge transfer in peptides and proteins can occur on different pathways, depending on the energe... more Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult to access experimentally, different modeling strategies have been successfully applied to study these processes in the past. These can be based on a simple empirical pathway model, efficient tight binding type atomic orbital Hamiltonians or ab initio and density functional calculations. An interesting strategy, which allows an efficient calculations of charge transfer parameters, is based on a fragmentation of the system into functional units. While this works well for systems like DNA, where the charge transfer pathway is naturally divided into distinct molecular fragments, this is less obvious for charge transfer along peptide and protein backbones. In this work, we develop and access a strategy for an effective fragmentation approach, which allows one to compute electronic couplings for large systems along nanosecond time scale molecular dynamics trajectories. The new methodology is applied to a solvated peptide, for which charge transfer properties have been studied recently using an empirical pathway model. As could be expected, dynamical effects turn out to be important, which emphasizes the importance of using effective quantum approaches which allow for sufficient sampling. However, the computed rates are orders of magnitude smaller than experimentally determined, which indicates the shortcomings of present modeling approaches.
New Journal of Physics, 2010
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural flu... more Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straightforward way through time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the onsite energies along the DNA wire.
We investigate in detail the charge transport characteristics of DNA wires with various sequences... more We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and...
The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which co... more The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which combines electronic structure calculations, molecular dynamics (MD) simulations, and the formulation of an effective tight-binding model Hamiltonian. Charge transport is studied by computing transmission functions along the MD trajectories. Though G4-DNA is structurally more stable than double-stranded DNA (dsDNA), our results strongly suggest that the potential improvement of the electrical transport properties in the former is not necessarily related to an increased stability, but rather to the fact that G4 is able to explore in its conformational space a larger number of charge-transfer active conformations. This in turn is a result of the non-negligible interstrand matrix elements, which allow for additional charge transport pathways. The higher structural stability of G4 can however play an important role once the molecules are contacted by electrodes. In this case, G4 may experience ...
The Journal of Physical Chemistry B, 2011
In this report, we study the photoactivation process in Escherichia coli DNA photolyase, involvin... more In this report, we study the photoactivation process in Escherichia coli DNA photolyase, involving long-range electron transport along a conserved chain of Trp residues between the protein surface and the flavin adenine dinucleotide (FAD) cofactor. Fully coupled nonadiabatic (Ehrenfest) quantum mechanics/molecular mechanics (QM/MM) simulations allow us to follow the time evolution of charge distributions over the natural time scale of multiple charge transfer events and conduct rigorous statistical analysis. Charge transfer rates in excellent agreement with experimental data are obtained without the need for any system-specific parametrization. The simulations are shown to provide a more detailed picture of electron transfer than a classical analysis of Marcus parameters. The protein and solvent both strongly influence the localization and transport properties of a positive charge, but the directionality of the process is mainly caused by solvent polarization. The time scales of charge movement, delocalization, protein relaxation and solvent reorganization overlap and lead to nonequilibrium reaction conditions. All these contributions are explicitly considered and fully resolved in the model used and provide an intricate picture of multistep biochemical electron transfer in a flexible, heterogeneous environment.
The Journal of Physical Chemistry B, 2008
The Journal of Physical Chemistry B, 2013
The Journal of Physical Chemistry B, 2012
Physical Review Letters, 2012
Molecules in junctions often fluctuate considerably, especially when subject to the influence of ... more Molecules in junctions often fluctuate considerably, especially when subject to the influence of solvent molecules. These fluctuations in site energies and couplings can be sampled, for example, by using molecular dynamics simulations, and can lead to incoherent effects in charge transport. To this end, a popular snapshot-averaged Landauer approach is compared to a time-dependent Green's function scheme. Since sequential transport dominates in systems with rapidly varying bridges, schemes not taking the time order of conformations into account, such as the Landauer approach, are inappropriate.
The Journal of Chemical Physics, 2009
We investigate in detail the charge transport characteristics of DNA wires with various sequences... more We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics ͑MD͒ simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment ͑water, backbone, counterions͒ and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders ͑differences in base ionization potentials͒. As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. ͓J. Am. Chem. Soc. 126, 11471 ͑2004͔͒. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.
The Journal of Chemical Physics, 2010
Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als d... more Ich erkläre hiermit, dass ich die vorliegende Arbeit selbständig verfasst und keine anderen als die angegebenen Quellen und Hilfsmittel verwendet, sowie die Satzung der Universität Karlsruhe (TH) zur Sicherung guter wissenschaftlicher Praxis beachtet habe.