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

Optimized Multifidelity Machine Learning for Quantum Chemistry

Machine learning (ML) provides access to fast and accurate quantum chemistry (QC) calculations for various properties of interest such as excitation energies. It is often the case that high accuracy in prediction using an ML model, demands a large and costly training set. Various solutions and procedures have been presented to reduce this cost. These include methods such as $\Delta$-ML, hierarchical-ML, and multifidelity machine learning (MFML). MFML combines various $\Delta$-ML like sub-models for various fidelities according to a fixed scheme derived from the sparse grid combination technique. In this work we implement an optimization procedure to combine multifidelity models in a flexible scheme resulting in optimized MFML (o-MFML) that provides superior prediction capabilities. This hyper-parameter optimization is carried out on a holdout validation set of the property of interest. This work benchmarks the o-MFML method in predicting the atomization energies on the QM7b dataset, and again in the prediction of excitation energies for three molecules of growing size. The results indicate that o-MFML is a strong methodological improvement over MFML and provides lower error of prediction. Even in cases of poor data distributions and lack of clear hierarchies among the fidelities, which were previously identified as issues for multifidelity methods, the o-MFML provides advantage to the prediction of quantum chemical properties.Comment: SI not include

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

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

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