On the relation of protein dynamics and exciton relaxation in pigment–protein complexes: An estimation of the spectral density and a theory for the calculation of optical spectra

A theory for calculating time– and frequency–domain optical spectra of pigment–protein complexes is presented using a density matrix approach. Non-Markovian effects in the exciton–vibrational coupling are included. A correlation function is deduced from the simulation of 1.6 K fluorescence line narrowing spectra of a monomer pigment–protein complex (B777), and then used to calculate fluorescence line narrowing spectra of a dimer complex (B820). A vibrational sideband of an excitonic transition is obtained, a distinct non-Markovian feature, and agrees well with experiment on B820 complexes. The theory and the above correlation function are used elsewhere to make predictions and compare with data on time–domain pump–probe spectra and frequency–domain linear absorption, circular dichroism and fluorescence spectra of Photosystem II reaction centers

Dynamical Phase Transitions for Fluxes of Mass on Finite Graphs

We study the time-averaged flux in a model of particles that randomly hop on a finite directed graph. In the limit as the number of particles and the time window go to infinity but the graph remains finite, the large-deviation rate functional of the average flux is given by a variational formulation involving paths of the density and flux. We give sufficient conditions under which the large deviations of a given time averaged flux is determined by paths that are constant in time. We then consider a class of models on a discrete ring for which it is possible to show that a better strategy is obtained producing a time-dependent path. This phenomenon, called a dynamical phase transition, is known to occur for some particle systems in the hydrodynamic scaling limit, which is thus extended to the setting of a finite graph

From large deviations to semidistances of transport and mixing: coherence analysis for finite Lagrangian data

One way to analyze complicated non-autonomous flows is through trying to understand their transport behavior. In a quantitative, set-oriented approach to transport and mixing, finite time coherent sets play an important role. These are time-parametrized families of sets with unlikely transport to and from their surroundings under small or vanishing random perturbations of the dynamics. Here we propose, as a measure of transport and mixing for purely advective (i.e., deterministic) flows, (semi)distances that arise under vanishing perturbations in the sense of large deviations. Analogously, for given finite Lagrangian trajectory data we derive a discrete-time and space semidistance that comes from the "best" approximation of the randomly perturbed process conditioned on this limited information of the deterministic flow. It can be computed as shortest path in a graph with time-dependent weights. Furthermore, we argue that coherent sets are regions of maximal farness in terms of transport and mixing, hence they occur as extremal regions on a spanning structure of the state space under this semidistance---in fact, under any distance measure arising from the physical notion of transport. Based on this notion we develop a tool to analyze the state space (or the finite trajectory data at hand) and identify coherent regions. We validate our approach on idealized prototypical examples and well-studied standard cases.Comment: J Nonlinear Sci, 201

The DLR Complex Irradiation Facility (CIF)

The DLR Institute of Space Systems in Bremen has built a new facility to study the behavior of materials under complex irradiation and to estimate their degradation in a space environment. It is named Complex Irradiation Facility (CIF). CIF allows simultaneously irradiating samples with three light sources for the simulation of the spectrum of solar electromagnetic radiation. The light sources are a solar simulator with a Xe-lamp (wavelength range 300-1200nm), a deuterium-UV-source (112-200nm), and an Argon-gas-jet-VUV-simulator. The latter allows irradiating samples with shorter wavelengths below the limitation of any window material. The VUV-simulator has been validated at the PTB (Physikalisch Technische Bundesanstalt) in Berlin by calibration that uses synchrotron radiation in the wavelength range between 40 and 400nm. Beside the different light sources CIF provides also electron and proton sources. Electrons and protons are generated in a low energy range from 1 to 10 keV with currents from 1 to 100 nA and in a higher range from 10 to 100 keV with 0.1 to 100 µA. Both particle sources can be operated simultaneously. In order to model temperature variations as appear in free space, the sample can be cooled down to liquid Nitrogen and heated up to about 450 K during irradiation. The complete facility has been manufactured in UHV-technology with metal sealing. It is free of organic compounds to avoid self-contamination. The different pumping systems achieve a final pressure of 1*1010 mbar (empty sample chamber) Besides the installed radiation sensors that control the stability of the various radiation sources and an attached mass spectrometer for analyzing the outgassing processes in the chamber, the construction of CIF allows adding other in-situ measurement systems to measure parameters that are of the user’s interest. We are currently planning to develop an in-situ measurement system in order to determine changes in the optical properties of the samples caused by irradiation. Within this paper we will show the design of CIF in more detail and discuss the performance of the various radiation sources

Measurements of Penetration and Detoxification of PS II Herbicides in Whole Leaves by a Fluorometric Method

The effect of herbicides that inhibit the photosynthetic electron transport at the photosystem II acceptor side has been analyzed in whole plants by using a fluorometric method. The data reported indicate that the apparent variable fluorescence of the induction curve normalized to the control value provides reliable information about the penetration rate and metabolic detoxification of PS II herbicides in whole plants

Sustainability of the Slovenian Pension System: An Analysis with an Overlapping-generations General Equilibrium Model

The article presents an analysis of welfare effects in Slovenia, an analysis of macroeconomic effects of the Slovenian pension reform and an analysis of effects of the pension fund deficit on sustainability of Slovenian public finances with a dynamic OLG general equilibrium model. It has been established that while young generations and new generations will lose from the pension reform, even complete implementation of the reform might not be sufficient to compensate unfavourable demographic developments. The level of expected deficit of the PAYG-financed state pension fund seems to be most worrying. Financing the pension system with VAT revenues as an extreme case could result in more sustainable public finances, since GDP and welfare levels ought to increase, yet this might be infeasible to implement politically, given that the generations of voters would have their welfare decreased. In addition, the present pension system is intransparent and tremendously complicated and should primarily be made more comprehensible to the public.general equilibrium models, macroeconomic effects, OLG-GE, PAYG, pension system, sustainability of public finances, Slovenia, welfare analysis

Toda Soliton Limits on General Backgrounds

AbstractStarting from an arbitrary background solution of the Toda lattice, we study limits ofN-soliton solutions on this given background asNtends to infinity. This yields a new class of solutions of the Toda lattice. Simultaneously, we solve an inverse spectral problem for one dimensional Jacobi operators–we explicitly construct Jacobi operators whose spectrum contains a given (countable, bounded) set of eigenvalues and whose absolutely continuous spectrum coincides with that of a given background operator

Modeling of photosynthetic light-harvesting: From structure to function

AbstractIn order to bridge the gap between the crystal structure of photosynthetic pigment-protein complexes and the data gathered in optical experiments, two essential problems need to be solved. On one hand, theories of optical spectra and excitation energy transfer have to be developed that take into account the pigment-pigment (excitonic) and the pigment-protein (exciton-vibrational) coupling on an equal footing. On the other hand, the parameters entering these theories need to be calculated from the structural data. Good agreement between simulations and experimental data then allows to draw conclusions on structure-function relationships of these complexes and to make predictions. In the development of theory, a delicate question is how to describe the interplay between the quantum dynamics of excitons and the dephasing of coherences by the coupling of excitons to protein vibrations. Quantum mechanic coherences are utilized for efficient light harvesting. In the reaction centers of purple bacteria an energy sink is created by a coherent coupling of exciton states to intermolecular charge transfer states. The dephasing of coherences can be monitored, e.g., by the temperature dependent shift of optical lines. In the Fenna-Matthews-Olson protein, which acts as an excitation energy wire between the outer chlorosome antenna and the reaction center complex, an energy funnel for efficient light-harvesting is formed by the pigment-protein coupling. The protein shifts the local transition energies of the pigments, the so-called site energies in a specific way, such that pigments facing the reaction center are redshifted with respect to those on the chlorosome side. In the light-harvesting complex of higher plants an excitation energy funnel is created by the use of two different types of chlorophyll (Chl) pigments, Chla and Chlb and by the pigment-protein coupling that creates an energy sink at Chla 610 located in the stromal layer at the periphery of the complex. The close contact between Chla and Chlb gives rise to ultrafast subpicosecond exciton transfer, whereas dynamic localization effects are inferred to lead to long ps relaxation times between the majority of Chla pigments