The Giant Flare of 1998 August 27 from SGR 1900+14: II. Radiative Mechanism and Physical Constraints on the Source

(ABBREVIATED) The extraordinary 1998 August 27 giant flare places strong constraints on the physical properties of its source, SGR 1900+14. We make detailed comparisons of the published data with the magnetar model. The giant flare evolved through three stages, whose radiative mechanisms we address in turn. A triggering mechanism is proposed, whereby a helical distortion of the core magnetic field induces large-scale fracturing in the crust and a twisting deformation of the crust and exterior magnetic field. The envelope of the pulsating tail of the August 27 flare can be accurately fit, after ~40 s, by the contracting surface of a relativistically hot, but inhomogeneous, trapped fireball. We quantify the effects of direct neutrino-pair emission, thereby deducing a lower bound ~ 10^{32} G-cm^3 to the magnetic moment of the confining field. The radiative flux during the intermediate ~40 s of the burst appears to exceed the trapped fireball fit. The spectrum and lightcurve of this smooth tail are consistent with heating in an extended pair corona, possibly powered by continuing seismic activity in the star. We consider in detail the critical luminosity, below which a stable balance can be maintained between heating and radiative cooling in a confined, magnetized pair plasma; but above which the confined plasma runs away to local thermodynamic equilibrium. In the later pulsating tail, the best fit temperature equilibrates at a value which agrees well with the regulating effect of photon splitting. The remarkable four-peaked substructure within each 5.16-s pulse provides strong evidence for the presence of higher magnetic multipoles in SGR 1900+14. The corresponding collimation of the X-ray flux is related to radiative transport in a super-QED magnetic field.Comment: 11 July 2001, accepted for publication in the Astrophysical Journa

Comparison between S. T. radar and in situ balloon measurements

A campaign for simultaneous in situ and remote observation of both troposphere and stratosphere took place near Aire-sur-l'Adour (in southeastern France) on May 4, 1984. The aim of this campaign was a better understanding of the physics of radar echoes. The backscattered signal obtained with a stratosphere-troposphere radar both at the vertical and 15 deg. off vertical is compared with the velocity and temperature measurements made in the same region (about 10 km north of the radar site) by balloon-borne ionic anenometers and temperature sensors. In situ measurements clearly indicate that the temperature fluctuations are not always consistent with the standard turbulent theory. Nevertheless, the assumptions generally made (isotropy and turbulent field in k) and the classical formulation so derived for radar reflectivity are able to reproduce the shape of the radar return power profiles in oblique directions. Another significant result is the confirmation of the role played by the atmospheric stratification in the vertical echo power. It is important to develop these simultaneous in situ and remote experiments for a better description of the dynamical and thermal structure of the atmosphere and for a better understanding of the mechanisms governing clear-air radar reflectivity

Environment effects on triplet-triplet energy transfer in DNA

We present a quantum-chemical study of the impact of the environment on triplet exciton migration in polyA-polyT DNA sequences. Electronic couplings are estimated by combining the fragment excitation difference scheme with the polarizable continuum model. Conformational fluctuations are taken into account by considering 500 structures extracted from a classical molecular dynamics trajectory. In contrast to singlet transfer, we find that the environment effect is not strongly correlated with the coupling magnitude in vacuum, and can significantly enhance or reduce its value in individual conformations. Conformational averaging, however, leads to a net cancellation of medium effects on the overall transfer rate

Distance dependence of triplet energy transfer in water and organic solvents: A QM/MD study

The possibility to optimize optoelectronic devices, such as organic light-emitting diodes or solar cells, by exploiting the special characteristics of triplet electronic states and their migration ability is attracting increased attention. In this study, we analyze how an intervening solvent modifies the distance dependence of triplet electronic energy transfer (TEET) processes by combining molecular dynamics simulations with quantum chemical calculations of the transfer matrix elements using the Fragment Excitation Difference (FED) method. We determine the β parameter characterizing the exponential distance decay of TEET rates in a stacked perylene dimer in water, chloroform, and benzene solutions. Our results indicate that the solvent dependence of β (βvacuum = 5.14 Å-1 > βwater = 3.77 Å-1 > βchloroform = 3.61 Å-1 > βbenzene = 3.44 Å-1) can be rationalized adopting the McConnell model of superexchange, where smaller triplet energy differences between the donor and the solvent lead to smaller β constants. We also estimate the decay of hole transfer (HT) and excess electron transfer (EET) processes in the system using the Fragment Charge Difference (FCD) method and find that βTEET can be reasonably well approximated by the sum of βEET and βHT constants

Spatial and Electronic Correlations in the PE545 Light-Harvesting Complex

The recent discovery of long-lasting quantum coherence effects in photosynthetic pigment-protein complexes has challenged our view of the role that protein motions play in light-harvesting processes. Several groups have suggested that correlated fluctuations involving the pigments site energies and couplings could be at the origin of such unexpected behavior. Here we combine molecular dynamics simulations with quantum mechanics/molecular mechanics calculations to analyze the degree of correlated fluctuations in the PE545 complex of Rhodomonas sp. strain CS24. We find that correlations between the motions of the chromophores, which are significantly assisted by the water solvent, do not translate into appreciable site energy correlations but do lead to significant cross-correlations of energies and couplings. Such behavior, not observed in a recent study on the Fenna-Mathews-Olson complex, seems to provide phycobiliproteins with an additional fundamental mechanism to control quantum coherence and light-harvesting efficiency compared with chlorophyll-containing complexes

Dissecting the nature of exciton interactions in ethyne-linked tetraarylporphyrin arrays

We investigate how electronic energy transfer in a series of three ethyne-linked Zinc- and free base-tetraarylporphyrin dimers is tuned by the type of linker and by substitution on the porphyrin rings. We use TD-DFT combined with a recently developed fully polarizable QM/MM/PCM method. This allows us to dissect the bridge-mediated contributions to energy transfer in terms of superexchange (through-bond) interactions and Coulomb (through space) terms mediated by the polarizability of the bridge. We explore the effects of the substituents and of the bridge-chromophore mutual orientation on these contributions. We find that bridge-mediated superexchange contributions largely boost energy transfer between the porphyrin units. When the effect of the solvent is also considered through PCM, we find good agreement with the through-bond versus through-space contributions determined experimentally, thus indicating the need to properly include both solvent and bridge effects in the study of energy transfer in bridged molecular dyads

Toward a unified modeling of environment and bridge-mediated contributions to electronic energy transfer: A fully polarizable QM/MM/PCM approach

Recent studies have unveiled the similar nature of solvent (screening) effects and bridge-mediated contributions to electronic energy transfer, both related to the bridge/solvent polarizability properties. Here, we exploit the similarity of such contributions to develop a fully polarizable mixed QM/discrete/continuum model aimed at studying electronic energy transfer processes in supramolecular systems. In the model, the definition of the three regions is completely flexible and allows us to explore the possibility to describe bridge-mediated contributions by using a polarizable MM description of the linker. In addition, we show that the classical MMPol description of the bridge can be complemented either with an analogous atomistic or with a continuum description of the solvent. Advantages and drawbacks of the model are finally presented and discussed with respect to the system under study

Can Förster Theory Describe Stereoselective Energy Transfer Dynamics in a Protein-Ligand Complex?

Förster resonance energy transfer (FRET) reactions involving ligands and aromatic amino acids can substantially impact the fluorescence properties of a protein-ligand complex, an impact intimately related to the corresponding binding mode. Structural characterization of such binding events in terms of intermolecular distances can be done through the well-known R-6 distance-dependent Förster rate expression. However, such interpretation suffers from uncertainties underlying Förster theory in the description of the electronic coupling that promotes FRET, mostly related to the dipole-dipole orientation factor, dielectric screening effects and deviations from the ideal dipole approximation. Here, we investigate how Förster approximations impact the prediction of energy transfer dynamics in the complex between flurbiprofen and human serum albumin (HSA), as well as a model flurbiprofen-Trp dyad, in which recent observations of enantioselective fluorescence quenching has been ascribed to energy transfer from flurbiprofen to Trp. To this aim, we combine classical molecular dynamics simulations with polarizable quantum mechanics/molecular mechanics (QM/MM) calculations that allow overcoming Förster approximations. On the basis of our results, we discuss the potential of structure-based simulations in the characterization of drug-binding events through fluorescence techniques. Overall, we find an excellent agreement among theory and experiment both in terms of enantioselectivity and FRET times, thus strongly supporting the reliability of the binding modes proposed for the (S)- and (R)- enantiomers of flurbiprofen. In particular, we show that the dynamic quenching arises from a small fraction of drug bound to the secondary site of HSA at the interface between subdomains IIA and IIB, whereas the enantioselectivity arises from the larger flexibility of the (S)-flurbiprofen enantiomer in the binding pocket

Theoretical characterization of the spectral density of the water-soluble chlorophyll-binding protein from combined quantum mechanics/molecular mechanics molecular dynamics simulations

Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042−4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called 'geometry mismatch' problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis

How abasic sites impact hole transfer dynamics in GC-rich DNA sequences

Changes in DNA charge transfer properties upon the creation of apurinic and apyrimidinic sites have been used to monitor DNA repair processes, given that such lesions generally reduce charge transfer yields. However, because these lesions translate into distinct intra and extrahelical conformations depending on the nature of the unpaired base and its DNA context, it is unclear the actual impact of such diverse conformations on charge transfer. Here we combine classical molecular dynamics, quantum/molecular mechanics (QM/MM) calculations, and kinetic Monte Carlo simulations to investigate the impact of abasic sites on the structure and hole transfer (HT) properties of DNA. We consider both apurinic and apyrimidinic sites in polyG and polyGC sequences and find that most situations lead to intrahelical conformations where HT rates are significantly slowed down due to the energetic disorder induced by the abasic void. In contrast, the presence of an unpaired C flanked by C bases leads to an extrahelical conformation where stacking among G sites is reduced, leading to an attenuation of electronic couplings and a destabilization of hole states. Interestingly, this leads to an asymmetric HT behavior, given that the 5′ to 3′ transfer along the G strand is slowed down by one order of magnitude while the opposite 3′ to 5′ transfer remains similar to that estimated for the reference polyG sequence. Our simulations thus suggest that electrochemical monitoring of the DNA repair process following changes in charge transfer properties can miss repair events linked to abasic sites adopting extrahelical conformations