Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

Citation: Reppert, M., Kell, A., Pruitt, T., & Jankowiak, R. (2015). Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers. Journal of Chemical Physics, 142(9), 7. doi:10.1063/1.4913685The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths. A corrected lineshape function L(omega) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, omega(sp), for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers. (c) 2015 AIP Publishing LLC

Site Energies of Active and Inactive Pheophytins in the Reaction Center of Photosystem II from Chlamydomonas Reinhardtii

31 Pags. The definitive version is available at: http://pubs.acs.org/journal/jpcbfkIt is widely accepted that the primary electron acceptor in various Photosystem II (PSII) reaction centers (RCs) is pheophytin a (Pheo a) within the D1 protein (PheoD1), while PheoD2 (within the D2 protein) is photochemically inactive. The Pheo site energies, however, have remained elusive, due to inherent spectral congestion. While most researchers over the last two decades assigned the Qy-states of PheoD1 and PheoD2 bands near 678–684 nm and 668–672 nm, respectively, recent modeling [Raszewski et al. Biophys. J. 2005, 88, 986–998; Cox et al. J. Phys. Chem. B 2009, 113, 12364–12374] of the electronic structure of the PSII RC reversed the location of the active and inactive Pheos, suggesting that the mean site energy of PheoD1 is near 672 nm, whereas PheoD2 (~677.5 nm) and ChlD1 (~680 nm) have the lowest energies (i.e., the PheoD2-dominated exciton is the lowest excited state). In contrast, chemical pigment exchange experiments on isolated RCs suggested that both pheophytins have their Qy absorption maxima at 676–680 nm [Germano et al. Biochem. 2001, 40, 11472–11482; Germano et al. Biophys. J. 2004, 86, 1664–1672]. To provide more insight into the site energies of both PheoD1 and PheoD2 (including the corresponding Qx transitions, which are often claimed to be degenerate at 543 nm) and to attest that the above two assignments are most likely incorrect, we studied a large number of isolated RC preparations from spinach and wild-type Chlamydomonas reinhardtii (at different levels of intactness) as well as the Chlamydomonas reinhardtii mutant (D2-L209H), in which the active branch PheoD1 is genetically replaced with chlorophyll a (Chl a). We show that the Qx-/Qy-region site-energies of PheoD1 and PheoD2 are ~545/680 nm and ~541.5/670 nm, respectively, in good agreement with our previous assignment [Jankowiak et al. J. Phys. Chem. B 2002, 106, 8803–8814]. The latter values should be used to model excitonic structure and excitation energy transfer dynamics of the PSII RCs.Partial support to B.N. (involved in calculations) was provided by the NSF EPSCoR Grant. V.Z. (involved in writing the manuscript) acknowledges support by NSERC. R.T.S., R.P., and M.S. were involved in the design and preparation of D2-mutant and RCs. They acknowledge support from USDOE, Photosynthetic Antennae Research Center (R.T.S.), MICIN (Grant AGL2008-00377) in Spain (R.P.), and the U.S. Department of Energy’s Photosynthetic Systems Program within the Chemical Sciences, Geosciences, and Biosciences Division of the Office of Basic Energy Sciences under NREL Contract #DE-AC36-08-GO28308 (M.S.).Peer reviewe

The Injector Layout of BERLinPro

BERLinPro is an Energy Recovery Linac Project running since 2011 at the HZB in Berlin. A conceptual design report has been published in 2012 [1]. One of the key components of the project is the 100 mA superconducting RF photocathode gun under development at the HZB since 2010. Starting in 2016 the injector will go into operation, providing 6.6 MeV electrons with an emittance well below 1mm mrad and bunches shorter than 5 ps. In 2017 the 50 MeV linac will be set up and full recirculation is planned for 2018. The injector design has been finalized and is described in detail in this paper. Emphasis is further laid on beam dynamics aspects and performance simulations of two different gun cavitie

Introducing GUNLAB a compact test facility for SRF photoinjectors

Superconducting radio frequency photoelectron injectors SRF photoinjectors are promising electron sources for high brightness accelerators with high average current and short pulse duration like FELs and ERLs. For the upcoming ERL project bERLinPro we want to test and commission different SRF photoinjectors, optimize the beam performance and examine photocathode materials in an independent test facility. Therefore we designed GunLab to characterize beam parameters from the SRF photoinjectors in a compact diagnostics beamline. The main challenge of GunLab is to characterize the full six dimensional phase space as a function of drive laser and RF parameters. Here we present design and estimated performance of GunLa

BERLinPro A Compact Demonstrator ERL for High Current and Low Emittance Beams

The HZB previously BESSY was the first institution in Germany to build and operate a dedicated synchrotron light source BESSY I . About 10 years ago BESSY II, a third generation synchrotron light source, was commissioned and is very successfully running since that time. Due to its expertise in development and operation of accelerator facilities HZB is ideally suited to realize new accelerator concepts. Therefore HZB is proposing to build a demonstrator ERL facility BERLinPro that will realize high current and low emittance operation at 100 MeV. BERLinPro is intented to bring ERL technology to maturity. This paper presents an overview of the project and the key components of the facilit

Angular Scaling in Jets

We introduce a jet shape observable defined for an ensemble of jets in terms of two-particle angular correlations and a resolution parameter R. This quantity is infrared and collinear safe and can be interpreted as a scaling exponent for the angular distribution of mass inside the jet. For small R it is close to the value 2 as a consequence of the approximately scale invariant QCD dynamics. For large R it is sensitive to non-perturbative effects. We describe the use of this correlation function for tests of QCD, for studying underlying event and pile-up effects, and for tuning Monte Carlo event generators.Comment: Updated to JHEP versio

Field Emission Studies of Heat Treated Mo Substrates

Molybdenum can be used as a substrate for the bi alkali antimonide photocathodes utilized for the generation of high brightness electron beams in a superconducting radio frequency SRF photoinjector cavities. Operation at high field strength is required to obtain a low emittance beam, thus increasing the probability of field emission FE from the cathode surface. Usually, substrates are heated in situ before alkali de position to remove oxide layers from the surface. FE on Mo substrates was measured by means of a field emission scanning microscope FESM . It turned out that in situ heat treatment HT of the Mo surface significantly changes the FE behaviour by activation of new emitters. For a better understanding of the mechanism for enhanced emission after in situ heating a witness Mo sample was investigated using x ray photoelectron spectroscop

Jet Substructure Without Trees

We present an alternative approach to identifying and characterizing jet substructure. An angular correlation function is introduced that can be used to extract angular and mass scales within a jet without reference to a clustering algorithm. This procedure gives rise to a number of useful jet observables. As an application, we construct a top quark tagging algorithm that is competitive with existing methods.Comment: 22 pages, 16 figures, version accepted by JHE

Jet Dipolarity: Top Tagging with Color Flow

A new jet observable, dipolarity, is introduced that can distinguish whether a pair of subjets arises from a color singlet source. This observable is incorporated into the HEPTopTagger and is shown to improve discrimination between top jets and QCD jets for moderate to high pT.Comment: 8 pages, 6 figures (updated to JHEP version