We investigate the interaction between light and molecular systems modelled as quantum emitters coupled to a multitude of vibrational modes via a Holstein-type interaction. We follow a quantum Langevin equations approach that allows for analytical derivations of absorption and fluorescence profiles of molecules driven by classical fields or coupled to quantized optical modes. We retrieve analytical expressions for the modification of the radiative emission branching ratio in the Purcell regime and for the asymmetric cavity transmission associated with dissipative cross-talk between upper and lower polaritons in the strong coupling regime. We also characterize the Förster resonance energy transfer process between donor-acceptor molecules mediated by the vacuum or by a cavity mode.PACS numbers: 05.60.Gg, 37.30.+i, 81.05.Fb Recent experimental progress [1] has shown that the Purcell enhancement of the zero-phonon line of a single molecule can strongly alter the branching ratio of spontaneous emission between the line of interest and additional Stokes lines thus turning the molecule into an ideal quantum emitter. At the mesoscopic level, experiments in the collective strong coupling regime of organic molecules with cavities or delocalized plasmonic modes have shown important light-induced modifications of material properties. Experimental and theoretical endeavors go into the direction of charge and energy transport enhancement [2-6], Förster resonance energy transfer (FRET) enhancement [7][8][9][10][11], modified chemical reactivity [12][13][14][15][16], polariton dynamics [17,18] etc. Oftentimes however, experiments rely on theoretical models developed for standard cavity quantum electrodynamics (cavity QED) [19][20][21] with two-level systems where one distinguishes between i) the Purcell regime, characterized by modifications of the spontaneous emission rates and ii) the strong coupling regime leading to the occurrence of hybrid light-matter states referred to as polaritons. Recent theoretical efforts aim at covering this gap by solving a generalized light-electronic-vibrations problem modeled as a Holstein-Tavis-Cummings Hamiltonian. Investigations aim at providing an understanding of the vibrationally induced cavity polariton asymmetry [18,22], vibrationally dressed polaritons [23], dark vibronic polaritons [24,25], developing a cavity Born-Oppenheimer theory [26,27] or deriving relevant simplified models for large scale numerics in the mesoscopic limit [28].We provide here an alternative path based on solving the Holstein-Tavis-Cummings dynamics at the level of operators rather than states. The basic model considers a molecular box (see Fig. 1(b)) comprised of an internal electronic transition coupled to any number of vibrational modes. Radiative decay and vibrational relaxation are included as stochastic source terms in a set of coupled standard quantum Langevin equations [29][30][31][32][33] for vibrational and polaron operators (similarly applied in optomechanical systems [34][35][36]). The method is nu...

Molecules constitute compact hybrid quantum optical systems that can interface photons, electronic degrees of freedom, localized mechanical vibrations, and phonons. In particular, the strong vibronic interaction between electrons and nuclear motion in a molecule resembles the optomechanical radiation pressure Hamiltonian. While molecular vibrations are often in the ground state even at elevated temperatures, one still needs to get a handle on decoherence channels associated with phonons before an efficient quantum optical network based on optovibrational interactions in solid-state molecular systems could be realized. As a step towards a better understanding of decoherence in phononic environments, we take here an open quantum system approach to the nonequilibrium dynamics of guest molecules embedded in a crystal, identifying regimes of Markovian versus non-Markovian vibrational relaxation. A stochastic treatment, based on quantum Langevin equations, predicts collective vibron-vibron dynamics that resembles processes of sub-and super-radiance for radiative transitions. This in turn leads to the possibility of decoupling intramolecular vibrations from the phononic bath, allowing for enhanced coherence times of collective vibrations. For molecular polaritonics in strongly confined geometries, we also show that the imprint of optovibrational couplings onto the emerging output field results in effective polariton cross-talk rates for finite bath occupancies.

The rate of energy transfer in donor-acceptor systems can be manipulated via the common interaction with the confined electromagnetic modes of a micro-cavity. We analyze the competition between the near-field short range dipole-dipole energy exchange processes and the cavity mediated long-range interactions in a simplified model consisting of effective two-level quantum emitters that could be relevant for molecules in experiments under cryogenic conditions. We find that free-space collective incoherent interactions, typically associated with sub- and superradiance, can modify the traditional resonant energy transfer scaling with distance. The same holds true for cavity-mediated collective incoherent interactions in a weak-coupling but strong-cooperativity regime. In the strong coupling regime, we elucidate the effect of pumping into cavity polaritons and analytically identify an optimal energy flow regime characterized by equal donor/acceptor Hopfield coefficients in the middle polariton. Finally we quantify the build-up of quantum correlations in the donor-acceptor system via the two-qubit concurrence as a measure of entanglement.

The EC number system for the classification of enzymes uses different criteria such as reaction pattern, the nature of the substrate, the type of transferred groups or the type of acceptor group. These criteria are used with different emphasis for the various enzyme classes and thus do not contribute much to an understanding of the mechanisms of enzyme catalyzed reactions. To explore the reasons for bonds being broken in enzyme catalyzed metabolic reactions, we calculated physicochemical effects for the bonds reacting in the substrate of these enzymatic reactions. These descriptors allow the definition of similarities within these reactions and thus can serve as a method for the classification of enzyme reactions. To foster an understanding of the investigations performed here, we compare the similarities found on the basis of the physicochemical effects with the EC number classification. To allow a reasonable comparison we selected enzymatic reactions where the EC number system is largely built on criteria based on the reaction mechanism. This is true for hydrolysis reactions, falling into the domain of the EC class 3 (EC 3.b.c.d). The comparison is made by a Kohonen neural network based on an unsupervised learning algorithm. For these hydrolysis reactions, the similarity analysis on physicochemical effects produces results that are, by and large, similar to the EC number. However, this similarity analysis reveals finer details of the enzymatic reactions and thus can provide a better basis for the mechanistic comparison of enzymes.

The Biochemical Pathways Wall Chart (http://www.expasy.org/tools/pathways/ref.1) has been converted into a molecule and reaction database. Major features of this database are that each molecule is represented by lists of all atoms and bonds (as connection tables), and in the reactions the reaction centre, the atoms and bonds directly involved in the bond rearrangement process, are marked. The information in the database has been enriched by a set of diverse 3D structure conformations generated by the programs CORINA and ROTATE. The web-based structure and reaction retrieval system C@ROL provides a wide range of search methods to mine this rich database. The database is accessible at http://www2.chemie.uni-erlangen.de/services/biopath/index.html and http://www.mol-net.de/databases/biopath.html .

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We discuss Floquet engineering of dissipative molecular systems through periodic driving of an infrared-active vibrational transition, either directly or via a cavity mode. Following a polaron quantum Langevin equation approach, we derive correlation functions and stationary quantities showing strongly modified optical response of the infrared-dressed molecule. The coherent excitation of molecular vibrational modes in combination with the modulation of electronic degrees of freedom due to vibronic coupling can lead to both enhanced vibronic coherence and control over vibrational sideband amplitudes. The additional coupling to an infrared cavity allows for the controlled suppression of undesired sidebands, an effect stemming from the Purcell enhancement of vibrational relaxation rates.