Spectral properties of molecular oligomers. A non-Markovian quantum state diffusion approach

Absorption spectra of small molecular aggregates (oligomers) are considered. The dipole-dipole interaction between the monomers leads to shifts of the oligomer spectra with respect to the monomer absorption. The line-shapes of monomer as well as oligomer absorption depend strongly on the coupling to vibrational modes. Using a recently developed approach [Roden et. al, PRL 103, 058301] we investigate the length dependence of spectra of one-dimensional aggregates for various values of the interaction strength between the monomers. It is demonstrated, that the present approach is well suited to describe the occurrence of the J- and H-bands

Suppression of quantum oscillations and the dependence on site energies in electronic excitation transfer in the Fenna-Matthews-Olson trimer

Energy transfer in the photosynthetic complex of the Green Sulfur Bacteria known as the Fenna-Matthews-Olson (FMO) complex is studied theoretically taking all three subunits (monomers) of the FMO trimer and the recently found eighth bacteriochlorophyll (BChl) molecule into account. We find that in all considered cases there is very little transfer between the monomers. Since it is believed that the eighth BChl is located near the main light harvesting antenna we look at the differences in transfer between the situation when BChl 8 is initially excited and the usually considered case when BChl 1 or 6 is initially excited. We find strong differences in the transfer dynamics, both qualitatively and quantitatively. When the excited state dynamics is initialized at site eight of the FMO complex, we see a slow exponential-like decay of the excitation. This is in contrast to the oscillations and a relatively fast transfer that occurs when only seven sites or initialization at sites 1 and 6 is considered. Additionally we show that differences in the values of the electronic transition energies found in the literature lead to a large difference in the transfer dynamics

Non-Markovian quantum state diffusion for absorption spectra of molecular aggregates

In many molecular systems one encounters the situation where electronic excitations couple to a quasi-continuum of phonon modes. That continuum may be highly structured e.g. due to some weakly damped high frequency modes. To handle such a situation, an approach combining the non-Markovian quantum state diffusion (NMQSD) description of open quantum systems with an efficient but abstract approximation was recently applied to calculate energy transfer and absorption spectra of molecular aggregates [Roden, Eisfeld, Wolff, Strunz, PRL 103 (2009) 058301]. To explore the validity of the used approximation for such complicated systems, in the present work we compare the calculated (approximative) absorption spectra with exact results. These are obtained from the method of pseudomodes, which we show to be capable of determining the exact spectra for small aggregates and a few pseudomodes. It turns out that in the cases considered, the results of the two approaches mostly agree quite well. The advantages and disadvantages of the two approaches are discussed

Cervarix™: a vaccine for the prevention of HPV 16, 18-associated cervical cancer

Cervical cancer continues to be the second largest cause of cancer deaths in women worldwide. Persistent infection with high-risk types of human papillomavirus (HPV) is a necessary cause of cervical cancer. Thus, prophylactic vaccination against HPV is an attractive strategy to prevent cervical cancer. Current strategies for the development of safe and effective preventive vaccines are based on the induction of neutralizing antibodies against the major capsid protein, L1 of HPV. Cervarix™ is one of the preventive HPV vaccines that has been approved in the Europe and Australia and is currently under review by the US Food and Drug Administration. Cervarix is composed of HPV16 and HPV18 L1 virus-like particles (VLPs) formulated in ASO4 adjuvant. Vaccination with Cervarix has been shown to protect women against a high proportion of precursor lesions of cervical cancer caused by these two HPV types. This review explores the various features of this new vaccine candidate and discusses the future directions in the field of HPV vaccine development

Testing Autonomous Robot Control Software Using Procedural Content Generation

We present a novel approach for reducing manual effort when testing autonomous robot control algorithms. We use procedural content generation, as developed for the film and video game industries, to create a diverse range of test situations. We execute these in the Player/Stage robot simulator and automatically rate them for their safety significance using an event-based scoring system. Situations exhibiting dangerous behaviour will score highly, and are thus flagged for the attention of a safety engineer. This process removes the time-consuming tasks of hand-crafting and monitoring situations while testing an autonomous robot control algorithm. We present a case study of the proposed approach – we generated 500 randomised situations, and our prototype tool simulated and rated them. We have analysed the three highest rated situations in depth, and this analysis revealed weaknesses in the smoothed nearness-diagram control algorithm

Tectonic synthesis of the Olympic Mountains segment of the Cascadia wedge, using two-dimensional thermal and kinematic modeling of thermochronological ages

A fully coupled two-dimensional kinematic and thermal model of a steady state accretionary wedge, constrained by an extensive data set of fission track and (U-Th)/He ages for apatite and zircon, is here used to investigate the development of the Olympic Mountains segment of the Cascadia accretionary wedge. The model has two main free parameters: ε_(max), the maximum rate of erosion for a generic erosion function operating at the top of the wedge, and α, the distribution of sedimentary accretion into the wedge. The best fit values for ε_(max) and α and their confidence limits are determined through an iterative search of parameter space. This study represents the first time that such inversion methods have been used to quantify the thermal-kinematic evolution of an accretionary wedge. Our results suggest that horizontal transport plays an important role in the exhumation trajectories experienced by material passing through the Cascadia wedge. At a 95% confidence interval, 80 to 100% of the sedimentary sequence from the subducting Juan de Fuca Plate has been accreted at the front of the wedge offshore of the Olympics over the past 14 m.y. This frontally accreted material must then traverse the entire width of the wedge prior to its eventual exposure in the Olympic forearc high. Assessed in this two-dimensional framework, the fission track and (U-Th)/He age data sets from the Olympic Mountains are all best fit by ε_(max) of 0.9–1.0 mm yr^(−1), despite variation in the timescales relevant to the three chronometers. This result supports the hypothesis that the Olympic Mountains segment of the Cascadia accretionary wedge has been in a flux steady-state since ∼14 Ma. The demonstration of a flux balance across the Cascadia margin also suggests that margin-parallel transport has not had a significant role in driving uplift of the Olympic Mountains

Absence of Quantum Oscillations and Dependence on Site Energies in Electronic Excitation Transfer in the Fenna–Matthews–Olson Trimer

Energy transfer in the photosynthetic Fenna–Matthews–Olson (FMO) complex of green sulfur bacteria is studied numerically taking all three subunits (monomers) of the FMO trimer and the recently found eighth bacteriochlorophyll (BChl) molecule into account. The coupling to the non-Markovian environment is treated with a master equation derived from non-Markovian quantum state diffusion. When the excited-state dynamics is initialized at site eight, which is believed to play an important role in receiving excitation from the main light harvesting antenna, we see a slow exponential-like decay of the excitation. This is in contrast to the oscillations and a relatively fast transfer that usually occurs when initialization at sites 1 or 6 is considered. We show that different sets of electronic transition energies can lead to large differences in the transfer dynamics and may cause additional suppression or enhancement of oscillations.Chemistry and Chemical Biolog

Influence of Complex Exciton-Phonon Coupling on Optical Absorption and Energy Transfer of Quantum Aggregates

We present a theory that efficiently describes the quantum dynamics of an electronic excitation that is coupled to a continuous, highly structured phonon environment. Based on a stochastic approach to non-Markovian open quantum systems, we develop a dynamical framework that allows us to handle realistic systems where a fully quantum treatment is desired yet the usual approximation schemes fail. The capability of the method is demonstrated by calculating spectra and energy transfer dynamics of mesoscopic molecular aggregates, elucidating the transition from fully coherent to incoherent transfer

MiRP1 forms IKr potassium channels with HERG and is associated with cardiac arrhythmia.

A novel potassium channel gene has been cloned, characterized, and associated with cardiac arrhythmia. The gene encodes MinK-related peptide 1 (MiRP1), a small integral membrane subunit that assembles with HERG, a pore-forming protein, to alter its function. Unlike channels formed only with HERG, mixed complexes resemble native cardiac IKr channels in their gating, unitary conductance, regulation by potassium, and distinctive biphasic inhibition by the class III antiarrhythmic E-4031. Three missense mutations associated with long QT syndrome and ventricular fibrillation are identified in the gene for MiRP1. Mutants form channels that open slowly and close rapidly, thereby diminishing potassium currents. One variant, associated with clarithromycin-induced arrhythmia, increases channel blockade by the antibiotic. A mechanism for acquired arrhythmia is revealed: genetically based reduction in potassium currents that remains clinically silent until combined with additional stressors

Reliability of histopathologic diagnosis of fibrotic interstitial lung disease: an international collaborative standardization project

Malaltia pulmonar intersticial; Fibrosi pulmonar; Pneumònia intersticial habitualEnfermedad pulmonar intersticial; Fibrosis pulmonar; Neumonía intersticial habitualInterstitial lung disease; Pulmonary fibrosis; Usual interstitial pneumoniaBackground Current interstitial lung disease (ILD) diagnostic guidelines assess criteria across clinical, radiologic and pathologic domains. Significant interobserver variation in histopathologic evaluation has previously been shown but the specific source of these discrepancies is poorly documented. We sought to document specific areas of difficulty and develop improved criteria that would reduce overall interobserver variation. Methods Using an internet-based approach, we reviewed selected images of specific diagnostic features of ILD histopathology and whole slide images of fibrotic ILD. After an initial round of review, we confirmed the presence of interobserver variation among our group. We then developed refined criteria and reviewed a second set of cases. Results The initial round reproduced the existing literature on interobserver variation in diagnosis of ILD. Cases which were pre-selected as inconsistent with usual interstitial pneumonia/idiopathic pulmonary fibrosis (UIP/IPF) were confirmed as such by multi-observer review. Cases which were thought to be in the spectrum of chronic fibrotic ILD for which UIP/IPF were in the differential showed marked variation in nearly all aspects of ILD evaluation including extent of inflammation and extent and pattern of fibrosis. A proposed set of more explicit criteria had only modest effects on this outcome. While we were only modestly successful in reducing interobserver variation, we did identify specific reasons that current histopathologic criteria of fibrotic ILD are not well defined in practice. Conclusions Any additional classification scheme must address interobserver variation in histopathologic diagnosis of fibrotic ILD order to remain clinically relevant. Improvements to tissue-based diagnostics may require substantial resources such as larger datasets or novel technologies to improve reproducibility. Benchmarks should be established for expected outcomes among clinically defined subgroups as a quality metric.This research did not receive any specific grant from funding agencies in the public, commercial or not-for-profit sectors