184 research outputs found
A density matrix approach to photoinduced electron injection
Electron injection from an adsorbed molecule to the substrate (heterogeneous
electron transfer) is studied. One reaction coordinate is used to model this
process. The surface phonons and/or the electron-hole pairs together with the
internal degrees of freedom of the adsorbed molecule as well as possibly a
liquid surrounding the molecule provide a dissipative environment, which may
lead to dephasing, relaxation, and sometimes excitation of the relevant system.
In the process studied the adsorbed molecule is excited by a light pulse. This
is followed by an electron transfer from the excited donor state to the
quasi-continuum of the substrate. It is assumed that the substrate is a
semiconductor. The effects of dissipation on electron injection are
investigated
Coherent laser control of the current through molecular junctions
The electron tunneling through a molecular junction modeled by a single site
weakly coupled to two leads is studied in the presence of a time-dependent
external field using a master equation approach. In the case of small bias
voltages and high carrier frequencies of the external field, we observe the
phenomenon of coherent destruction of tunneling, i.e. the current through the
molecular junction vanishes completely for certain parameters of the external
field. In previous studies the tunneling within isolated and open multi-site
systems was suppressed; it is shown here that the tunneling between a single
site and electronic reservoirs, i.e. the leads, can be suppressed as well. For
larger bias voltages the current does not vanish any more since further
tunneling channels participate in the electron conduction and we also observe
photon-assisted tunneling which leads to steps in the current-voltage
characteristics. The described phenomena are demonstrated not only for
monochromatic fields but also for laser pulses and therefore could be used for
ultrafast optical switching of the current through molecular junctions.Comment: 6 pages and 4 figure
Stochastic unraveling of Redfield master equations and its application to electron transfer problems
A method for stochastic unraveling of general time-local quantum master
equations (QMEs) is proposed. The present kind of jump algorithm allows a
numerically efficient treatment of QMEs which are not in Lindblad form, i.e.
are not positive semidefinite by definition. The unraveling can be achieved by
allowing for trajectories with negative weights. Such a property is necessary,
e.g. to unravel the Redfield QME and to treat various related problems with
high numerical efficiency. The method is successfully tested on the damped
harmonic oscillator and on electron transfer models including one and two
reaction coordinates. The obtained results are compared to those from a direct
propagation of the reduced density matrix (RDM) as well as from the standard
quantum jump method. Comparison of the numerical efficiency is performed
considering both the population dynamics and the RDM in the Wigner phase space
representation.Comment: accepted in J. Chem. Phys.; 26 pages, 6 figures; the order of
authors' names on the title page correcte
Exciton scattering in light-harvesting systems of purple bacteria
Using the reduced density matrix formalism the exciton scattering in
light-harvesting systems of purple bacteria is calculated. The static disorder
(fluctuations of the site energies) as well as the dynamic disorder
(dissipation) is taken into account in this work. Circular aggregates with 18
pigments are studied to model the B850 ring of bacteriochlorophylls with LH2
complexes. It can be shown that the influence of dissipation may not be
neglected in the simulation of the time-dependent anisotropy of fluorescence.
Also an elliptical deformation of the ring could be essential
Switching the current through molecular wires
The influence of Gaussian laser pulses on the transport through molecular
wires is investigated within a tight-binding model for spinless electrons
including correlation. Motivated by the phenomenon of coherent destruction of
tunneling for monochromatic laser fields, situations are studied in which the
maximum amplitude of the electric field fulfills the conditions for the
destructive quantum effect. It is shown that, as for monochromatic laser
pulses, the average current through the wire can be suppressed. For parameters
of the model, which do not show a net current without any optical field, a
Gaussian laser pulse can establish a temporary current. In addition, the effect
of electron correlation on the current is investigated.Comment: 8 pages, 6 figure
Deciphering the Ion Selectivity of the Phosphate Specific Channel OprP from Pseudomonas Aeruginosa: A Free-Energy Molecular Dynamics Simulation Study
Influence of Static and Dynamic Disorder on the Anisotropy of Emission in the Ring Antenna Subunits of Purple Bacteria Photosynthetic Systems
Using the reduced density matrix formalism the time dependence of the exciton
scattering in light-harvesting ring systems of purple bacteria is calculated.
In contrast to the work of Kumble and Hochstrasser (J. Chem. Phys. 109 (1998)
855) static disorder (fluctuations of the site energies) as well as dynamic
disorder (dissipation) is taken into account. For the description of
dissipation we use Redfield theory in exciton eigenstates without secular
approximation. This is shown to be equivalent to the Markovian limit of Capek's
theory in local states. Circular aggregates with 18 pigments are studied to
model the B850 ring of bacteriochlorophyls within LH2 complexes. It can be
demonstrated that the dissipation is important for the time-dependent
anisotropy of the fluorescence. Smaller values of static disorder are
sufficient to produce the same decay rates in the anisotropy in comparison with
the results by Kumble and Hochstrasser
Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump
Background Efflux pumps of the Resistance-Nodulation-cell Division superfamily confer multi-drug resistance to Gram-negative bacteria. The most-studied polyspecific transporter belonging to this class is the inner-membrane trimeric antiporter AcrB of Escherichia coli. In previous studies, a functional rotation mechanism was proposed for its functioning, according to which the three monomers undergo concerted conformational changes facilitating the extrusion of substrates. However, the molecular determinants and the energetics of this mechanism still remain unknown, so its feasibility must be proven mechanistically. Methods A computational protocol able to mimic the functional rotation mechanism in AcrB was developed. By using multi-bias molecular dynamics simulations we characterized the translocation of the substrate doxorubicin driven by conformational changes of the protein. In addition, we estimated for the first time the free energy profile associated to this process. Results We provided a molecular view of the process in agreement with experimental data. Moreover, we showed that the conformational changes occurring in AcrB enable the formation of a layer of structured waters on the internal surface of the transport channel. This water layer, in turn, allows for a fairly constant hydration of the substrate, facilitating its diffusion over a smooth free energy profile. Conclusions Our findings reveal a new molecular mechanism of polyspecific transport whereby water contributes by screening potentially strong substrate-protein interactions. General significance We provided a mechanistic understanding of a fundamental process related to multi-drug transport. Our results can help rationalizing the behavior of other polyspecific transporters and designing compounds avoiding extrusion or inhibitors of efflux pumps
Comparison of two models for bridge-assisted charge transfer
Based on the reduced density matrix method, we compare two different
approaches to calculate the dynamics of the electron transfer in systems with
donor, bridge, and acceptor. In the first approach a vibrational substructure
is taken into account for each electronic state and the corresponding states
are displaced along a common reaction coordinate. In the second approach it is
assumed that vibrational relaxation is much faster than the electron transfer
and therefore the states are modeled by electronic levels only. In both
approaches the system is coupled to a bath of harmonic oscillators but the way
of relaxation is quite different. The theory is applied to the electron
transfer in with free-base porphyrin () being the donor, zinc porphyrin () being the bridge and
quinone () the acceptor. The parameters are chosen as similar as
possible for both approaches and the quality of the agreement is discussed.Comment: 12 pages including 4 figures, 1 table, 26 references. For more info
see http://eee.tu-chemnitz.de/~kili
- …