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Jianshu Cao - One of the best experts on this subject based on the ideXlab platform.
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forster resonance energy transfer absorption and Emission Spectra in multichromophoric systems iii exact stochastic path integral evaluation
Journal of Chemical Physics, 2015Co-Authors: Jeremy Moix, Jianshu CaoAbstract:A numerically exact path integral treatment of the absorption and Emission Spectra of open quantum systems is presented that requires only the straightforward solution of a stochastic differential equation. The approach converges rapidly enabling the calculation of Spectra of large excitonic systems across the complete range of system parameters and for arbitrary bath Spectral densities. With the numerically exact absorption and Emission operators, one can also immediately compute energy transfer rates using the multi-chromophoric Forster resonant energy transfer formalism. Benchmark calculations on the Emission Spectra of two level systems are presented demonstrating the efficacy of the stochastic approach. This is followed by calculations of the energy transfer rates between two weakly coupled dimer systems as a function of temperature and system-bath coupling strength. It is shown that the recently developed hybrid cumulant expansion (see Paper II) is the only perturbative method capable of generating uniformly reliable energy transfer rates and Emission Spectra across a broad range of system parameters.
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forster resonance energy transfer absorption and Emission Spectra in multichromophoric systems i full cumulant expansions and system bath entanglement
Journal of Chemical Physics, 2015Co-Authors: Jianshu CaoAbstract:We study the Forster resonant energy transfer rate, absorption and Emission Spectra in multichromophoric systems. The multichromophoric Forster theory (MCFT) is determined from an overlap integral of generalized matrices related to the donor’s Emission and acceptor’s absorption Spectra, which are obtained via a full 2nd-order cumulant expansion technique developed in this work. We calculate the Spectra and MCFT rate for both localized and delocalized systems, and calibrate the analytical 2nd-order cumulant expansion with the exact stochastic path integral method. We present three essential findings: (i) The role of the initial entanglement between the donor and its bath is found to be crucial in both the Emission spectrum and the MCFT rate. (ii) The absorption Spectra obtained by the cumulant expansion method are nearly identical to the exact Spectra for both localized and delocalized systems, even when the system-bath coupling is far from the perturbative regime. (iii) For the Emission Spectra, the cumulant expansion can give reliable results for localized systems, but fail to provide reliable Spectra of the high-lying excited states of a delocalized system, when the system-bath coupling is large and the thermal energy is small. This paper also provides a simple golden-rule derivation of the MCFT, reviews existing methods, and motivates further developments in the subsequent papers.
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forster resonance energy transfer absorption and Emission Spectra in multichromophoric systems iii exact stochastic path integral evaluation
arXiv: Chemical Physics, 2015Co-Authors: Jeremy Moix, Jianshu CaoAbstract:A numerically exact path integral treatment of the absorption and Emission Spectra of open quantum systems is presented that requires only the straightforward solution of a stochastic differential equation. The approach converges rapidly enabling the calculation of Spectra of large excitonic systems across the complete range of system parameters and for arbitrary bath Spectral densities. With the numerically exact absorption and Emission operators one can also immediately compute energy transfer rates using the multi-chromophoric Forster resonant energy transfer formalism. Benchmark calculations on the Emission Spectra of two level systems are presented demonstrating the efficacy of the stochastic approach. This is followed by calculations of the energy transfer rates between two weakly coupled dimer systems as a function of temperature and system-bath coupling strength. It is shown that the recently developed hybrid cumulant expansion is the only perturbative method capable of generating uniformly reliable energy transfer rates and Spectra across a broad range of system parameters.
John M. Dyke - One of the best experts on this subject based on the ideXlab platform.
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high level ab initio calculations on hgecl and the equilibrium geometry of the a1a state derived from franck condon analysis of the single vibronic level Emission Spectra of hgecl and dgecl
Journal of Computational Chemistry, 2009Co-Authors: Foo-tim Chau, John M. DykeAbstract:CCSD(T) and/or CASSCF/MRCI calculations have been carried out on the 1A and A1A states of HGeCl. The fully relativistic effective core potential, ECP10MDF, and associated standard valence basis sets of up to the aug-cc-pV5Z quality were employed for Ge. Contributions from core correlation and extrapolation to the complete basis set limit were included in determining the computed equilibrium geometrical parameters and relative electronic energy of these two states of HGeCl. Based on the currently, most systematic CCSD(T calculations performed in this study, the best theoretical geometrical parameters of the 1A state are re(HGe) = 1.580 ± 0.001 A, e = 93.88 ± 0.01° and re(GeCl) = 2.170 ± 0.001 A. In addition, Franck-Condon factors including allowance for anharmonicity and Duschinsky rotation between these two states of HGeCl and DGeCl were calculated employing CCSD(T) and CASSCF/MRCI potential energy functions, and were used to simulate A1A 1A SVL Emission Spectra of HGeCl and DGeCl. The iterative Franck-Condon analysis (IFCA) procedure was carried out to determine the equilibrium geometrical parameters of the A1A state of HGeCl by matching the simulated, and available experimental SVL Emission Spectra of HGeCl and DGeCl of Tackett et al., J Chem Phys 2006, 124, 124320, using the available, estimated experimental equilibrium (r) structure for the 1A state, while varying the equilibrium geometrical parameters of the A1A state systematically. Employing the derived IFCA geometry of re(HGe) = 1.590 A, re(GeCl) = 2.155 A and e(HGeCl) = 112.7° for the A1A state of HGeCl in the Spectral simulation, the simulated absorption and SVL Emission Spectra of HGeCl and DGeCl agree very well with the available experimental LIF and SVL Emission Spectra, respectively.
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franck condon simulation of the single vibronic level Emission Spectra of hsif and dsif including anharmonicity
Journal of Chemical Physics, 2004Co-Authors: Daniel K. W. Mok, Edmond P. F. Lee, Foo-tim Chau, John M. DykeAbstract:Potential energy functions (PEFs) of the X 1A′ and A 1A″ states of HSiF have been computed using the coupled-cluster single-double plus perturbative triple excitations and complete-active-space self-consistent-field multireference internally contracted configuration interaction methods, respectively, employing augmented correlation-consistent polarized-valence quadruple-zeta basis sets. For both electronic states of HSiF and DSiF, anharmonic vibrational wavefunctions and energies of all three modes have been calculated variationally with the ab initio PEFs and using Watson’s Hamiltonian for nonlinear molecules. Franck–Condon factors between the two electronic states, allowing for Duschinsky rotation, were computed using the calculated anharmonic vibrational wavefunctions. These Franck–Condon factors were used to simulate the single vibronic level (SVL) Emission Spectra recently reported by Hostutler et al. in J. Chem. Phys. 114, 10728 (2001). Excellent agreement between the simulated and observed Spectra...
Hiroshi Umakoshi - One of the best experts on this subject based on the ideXlab platform.
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lipid surrounding water molecules probed by time resolved Emission Spectra of laurdan
Langmuir, 2019Co-Authors: Nozomi Watanabe, Keishi Suga, Peter J Slotte, Thomas K M Nyholm, Hiroshi UmakoshiAbstract:The hydration states of the interfacial region of lipid bilayers were investigated on the basis of the time-resolved Emission Spectra (TRES) analysis of 6-lauroyl-2-dimethylamino naphthalene (Laurdan), a common fluorescence probe used to analyze membrane hydration. TRES derived from long and short lifetime components were extracted from samples of different lipid species: 1,2-dipalmitoyl- sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC), d- erythro- N-palmitoyl-sphingosylphosphorylcholine (PSM), and a DOPC/PSM binary bilayer system. Neither lifetime component (short or long) corresponded with the hydration properties; the short lifetime component of DOPC (1.97 ns) exhibited a peak at 440 nm, and the long lifetime components of DPPC and PSM (7.76 and 7.77 ns, respectively) exhibited peaks at the same wavelength. This similarity arose from the competition between the collisional quenching and the hydration effects of water molecules. Herein, this phenomenon was investigated using a plot of the lifetime τ and the peak position λ (τ vs λ plot), simultaneously visualizing both effects by deconvoluting the TRES. On the basis of collisional quenching theory, the distribution of the water population per lipid (water map) was generated. According to this theory, the τ vs λ plot was applied to the water map and the calculation of the number of water molecules per lipid, which is consistent with previous reports. This approach provides novel insights for the analysis of molecular hydration states using the fluorescence of Laurdan.
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Lipid-Surrounding Water Molecules Probed by Time-Resolved Emission Spectra of Laurdan
2019Co-Authors: Nozomi Watanabe, Keishi Suga, Peter J Slotte, Thomas K M Nyholm, Hiroshi UmakoshiAbstract:The hydration states of the interfacial region of lipid bilayers were investigated on the basis of the time-resolved Emission Spectra (TRES) analysis of 6-lauroyl-2-dimethylamino naphthalene (Laurdan), a common fluorescence probe used to analyze membrane hydration. TRES derived from long and short lifetime components were extracted from samples of different lipid species: 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), d-erythro-N-palmitoyl-sphingosylphosphorylcholine (PSM), and a DOPC/PSM binary bilayer system. Neither lifetime component (short or long) corresponded with the hydration properties; the short lifetime component of DOPC (1.97 ns) exhibited a peak at 440 nm, and the long lifetime components of DPPC and PSM (7.76 and 7.77 ns, respectively) exhibited peaks at the same wavelength. This similarity arose from the competition between the collisional quenching and the hydration effects of water molecules. Herein, this phenomenon was investigated using a plot of the lifetime τ and the peak position λ (τ vs λ plot), simultaneously visualizing both effects by deconvoluting the TRES. On the basis of collisional quenching theory, the distribution of the water population per lipid (water map) was generated. According to this theory, the τ vs λ plot was applied to the water map and the calculation of the number of water molecules per lipid, which is consistent with previous reports. This approach provides novel insights for the analysis of molecular hydration states using the fluorescence of Laurdan
R D Preece - One of the best experts on this subject based on the ideXlab platform.
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the sharpness of gamma ray burst prompt Emission Spectra
Astronomy and Astrophysics, 2015Co-Authors: Hendrik Van Eerten, J Greiner, Reem Sari, Narayana P Bhat, Andreas Von Kienlin, W S Paciesas, R D PreeceAbstract:Context. We study the sharpness of the time-resolved prompt Emission Spectra of gamma-ray bursts (GRBs) observed by the Gammaray Burst Monitor (GBM) on board the Fermi Gamma-ray Space Telescope. Aims. We aim to obtain a measure of the curvature of time-resolved Spectra that can be compared directly to theory. This tests the ability of models such as synchrotron Emission to explain the peaks or breaks of GBM prompt Emission Spectra. Methods. We take the burst sample from the official Fermi GBM GRB time-resolved Spectral catalog. We re-fit all Spectra with a measured peak or break energy in the catalog best-fit models in various energy ranges, which cover the curvature around the Spectral peak or break, resulting in a total of 1113 Spectra being analyzed. We compute the sharpness angles under the peak or break of the triangle constructed under the model fit curves and compare them to the values obtained from various representative Emission models: blackbody, single-electron synchrotron, synchrotron Emission from a Maxwellian or power-law electron distribution. Results. We find that 35% of the time-resolved Spectra are inconsistent with the single-electron synchrotron function, and 91% are inconsistent with the Maxwellian synchrotron function. The single temperature, single Emission time, and location blackbody function is found to be sharper than all the Spectra. No general evolutionary trend of the sharpness angle is observed, neither per burst nor for the whole population. It is found that the limiting case, a single temperature Maxwellian synchrotron function, can only contribute up to 58 +23 −18 % of the peak flux. Conclusions. Our results show that even the sharpest but non-realistic case, the single-electron synchrotron function, cannot explain a large fraction of the observed GRB prompt Spectra. Because any combination of physically possible synchrotron Spectra added together will always further broaden the spectrum, Emission mechanisms other than optically thin synchrotron radiation are likely required in a full explanation of the Spectral peaks or breaks of the GRB prompt Emission phase.
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the sharpness of gamma ray burst prompt Emission Spectra
arXiv: High Energy Astrophysical Phenomena, 2015Co-Authors: Hendrik Van Eerten, J Greiner, Reem Sari, Narayana P Bhat, Andreas Von Kienlin, W S Paciesas, R D PreeceAbstract:We aim to obtain a measure of the curvature of time-resolved Spectra that can be compared directly to theory. This tests the ability of models such as synchrotron Emission to explain the peaks or breaks of GBM prompt Emission Spectra. We take the burst sample from the official Fermi GBM GRB time-resolved Spectral catalog. We re-fit all Spectra with a measured peak or break energy in the catalog best-fit models in various energy ranges, which cover the curvature around the Spectral peak or break, resulting in a total of 1,113 Spectra being analysed. We compute the sharpness angles under the peak or break of the triangle constructed under the model fit curves and compare to the values obtained from various representative Emission models: blackbody, single-electron synchrotron, synchrotron Emission from a Maxwellian or power-law electron distribution. We find that 35% of the time-resolved Spectra are inconsistent with the single-electron synchrotron function, and 91% are inconsistent with the Maxwellian synchrotron function. The single temperature, single Emission time and location blackbody function is found to be sharper than all the Spectra. No general evolutionary trend of the sharpness angle is observed, neither per burst nor for the whole population. It is found that the limiting case, a single temperature Maxwellian synchrotron function, can only contribute up to $58^{+23}_{-18}$% of the peak flux. Our results show that even the sharpest but non-realistic case, the single-electron synchrotron function, cannot explain a large fraction of the observed GRB prompt Spectra. Because of the fact that any combination of physically possible synchrotron Spectra added together will always further broaden the spectrum, Emission mechanisms other than optically thin synchrotron radiation are likely required in a full explanation of the Spectral peaks or breaks of the GRB prompt Emission phase.
Eliza M R Kempton - One of the best experts on this subject based on the ideXlab platform.
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a significant increase in detection of high resolution Emission Spectra using a three dimensional atmospheric model of a hot jupiter
The Astronomical Journal, 2020Co-Authors: Hayley Beltz, Emily Rauscher, M Brogi, Eliza M R KemptonAbstract:High resolution spectroscopy has opened the way for new, detailed study of exoplanet atmospheres. There is evidence that this technique can be sensitive to the complex, three-dimensional (3D) atmospheric structure of these planets. In this work, we perform cross correlation analysis on high resolution (R~100,000) CRIRES/VLT Emission Spectra of the Hot Jupiter HD 209458b. We generate template Emission Spectra from a 3D atmospheric circulation model of the planet, accounting for temperature structure and atmospheric motions---winds and planetary rotation---missed by Spectra calculated from one-dimensional models. In this first-of-its-kind analysis, we find that using template Spectra generated from a 3D model produces a more significant detection (6.9 sigma) of the planet's signal than any of the hundreds of one-dimensional models we tested (maximum of 5.1 sigma). We recover the planet's thermal Emission, its orbital motion, and the presence of CO in its atmosphere at high significance. Additionally, we analyzed the relative influences of 3D temperature and chemical structures in this improved detection, including the contributions from CO and H2O, as well as the role of atmospheric Doppler signatures from winds and rotation. This work shows that the Hot Jupiter's 3D atmospheric structure has a first-order influence on its Emission Spectra at high resolution and motivates the use of multi-dimensional atmospheric models in high-resolution Spectral analysis.
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constraining hot jupiter atmospheric structure and dynamics through doppler shifted Emission Spectra
The Astrophysical Journal, 2017Co-Authors: Jisheng Zhang, Eliza M R Kempton, Emily RauscherAbstract:We present a coupled 3-D atmospheric dynamics and radiative transfer model to predict the disk-integrated thermal Emission Spectra of transiting exoplanets in edge-on orbits. We calculate Spectra at high resolution to examine the extent to which high-resolution Emission Spectra are influenced by 3-D atmospheric dynamics and planetary rotation, and to determine whether and how we can constrain thermal structures and atmospheric dynamics through high-resolution spectroscopy. This study represents the first time that the line-of-sight geometry and resulting Doppler shifts from winds and rotation have been treated self-consistently in an Emission spectrum radiative transfer model, which allow us to assess the impact of the velocity field on thermal Emission Spectra. We apply our model to predict Emission Spectra as a function of orbital phase for three hot Jupiters, HD 209458b, WASP-43b and HD 189733b. We find net Doppler shifts in modeled Spectra due to a combination of winds and rotation at a level of 1-3 km/s. These Doppler signatures vary in a quasi-sinusoidal pattern over the course of the planets' orbits as the hot spots approach and recede from the observer's viewpoint. We predict that WASP-43b produces the largest Doppler shift due to its fast rotation rate. We find that the net Doppler shift in an exoplanet's disk-integrated thermal Emission spectrum results from a complex combination of winds, rotation, and thermal structure. However, we offer a simple method that estimates the magnitude of equatorial wind speeds in hot Jupiters through measurements of net Doppler shifts and lower resolution thermal phase curves.