Effect of Polarization on the Opsin Shift in Rhodopsins. 2. Empirical Polarization Models for Proteins

2008 ◽  
Vol 112 (37) ◽  
pp. 11468-11478 ◽  
Author(s):  
Marius Wanko ◽  
Michael Hoffmann ◽  
Jan Frähmcke ◽  
Thomas Frauenheim ◽  
Marcus Elstner
Keyword(s):  
Opsin Shift ◽  
Polarization Models

Molecular Dynamics Using Non-Variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model

2019 ◽  
Author(s):  
Pier Paolo Poier ◽  
Louis Lagardere ◽  
Jean-Philip Piquemal ◽  
Frank Jensen
Keyword(s):  
Boundary Conditions ◽  
Periodic Boundary ◽  
Force Fields ◽  
Periodic Boundary Conditions ◽  
Computational Effort ◽  
Polarizable Force Fields ◽  
Energy Models ◽  
Capacity Model ◽  
Energy Gradient ◽  
Polarization Models

<div> <div> <div> <p>We extend the framework for polarizable force fields to include the case where the electrostatic multipoles are not determined by a variational minimization of the electrostatic energy. Such models formally require that the polarization response is calculated for all possible geometrical perturbations in order to obtain the energy gradient required for performing molecular dynamics simulations. </p><div> <div> <div> <p>By making use of a Lagrange formalism, however, this computational demanding task can be re- placed by solving a single equation similar to that for determining the electrostatic variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p><div><div><div> </div> </div> </div> <p> </p><div> <div> <div> <p>variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p> </div> </div> </div> </div> </div> </div> </div> </div> </div>

Photochemistry of a Retinal Protonated Schiff-Base Analogue Mimicking the Opsin Shift of Bacteriorhodopsin

2007 ◽  
Vol 111 (9) ◽  
pp. 2327-2334 ◽  
Author(s):  
Oshrat Bismuth ◽  
Noga Friedman ◽  
Mordechai Sheves ◽  
Sanford Ruhman
Keyword(s):  
Schiff Base ◽  
Opsin Shift

The Amplitude Compensation and Phase Compensation of Two Orthogonal Polarization Models in Optical Cavity

2017 ◽  
Vol 23 (1) ◽  
pp. 92-98
Author(s):  
陈力荣 CHEN Li-rong ◽  
李淑静 LI Shu-jing ◽  
徐忠孝 XU Zhong-xiao ◽  
王海 WANG Hai
Keyword(s):  
Optical Cavity ◽  
Orthogonal Polarization ◽  
Phase Compensation ◽  
Polarization Models ◽  
Amplitude Compensation

scholarly journals Time-resolved GRB polarization with POLAR and GBM

2019 ◽  
Vol 627 ◽  
pp. A105 ◽  
Author(s):  
J. M. Burgess ◽  
M. Kole ◽  
F. Berlato ◽  
J. Greiner ◽  
G. Vianello ◽  
...  
Keyword(s):  
Gamma Ray ◽  
Single Pulse ◽  
Current Data ◽  
Gamma Ray Bursts ◽  
Polarization Angle ◽  
Analysis Pipeline ◽  
Time Resolved ◽  
Polarization Models ◽  
Probabilistic Context ◽  
Prompt Emission

Context. Simultaneousγ-ray measurements ofγ-ray burst spectra and polarization offer a unique way to determine the underlying emission mechanism(s) in these objects, as well as probing the particle acceleration mechanism(s) that lead to the observedγ-ray emission.Aims. We examine the jointly observed data from POLAR andFermi-GBM of GRB 170114A to determine its spectral and polarization properties, and seek to understand the emission processes that generate these observations. We aim to develop an extensible and statistically sound framework for these types of measurements applicable to other instruments.Methods. We leveraged the existing3MLanalysis framework to develop a new analysis pipeline for simultaneously modeling the spectral and polarization data. We derived the proper Poisson likelihood forγ-ray polarization measurements in the presence of background. The developed framework is publicly available for similar measurements with otherγ-ray polarimeters. The data are analyzed within a Bayesian probabilistic context and the spectral data from both instruments are simultaneously modeled with a physical, numerical synchrotron code.Results. The spectral modeling of the data is consistent with a synchrotron photon model as has been found in a majority of similarly analyzed single-pulse gamma-ray bursts. The polarization results reveal a slight trend of growing polarization in time reaching values of ∼30% at the temporal peak of the emission. We also observed that the polarization angle evolves with time throughout the emission. These results suggest a synchrotron origin of the emission but further observations of many GRBs are required to verify these evolutionary trends. Furthermore, we encourage the development of time-resolved polarization models for the prompt emission of gamma-ray bursts as the current models are not predictive enough to enable a full modeling of our current data.

Combined QM/MM study of the opsin shift in bacteriorhodopsin

2001 ◽  
Vol 23 (1) ◽  
pp. 96-105 ◽  
Author(s):  
Ramkumar Rajamani ◽  
Jiali Gao
Keyword(s):  
Opsin Shift

Mechanism for the opsin shift of retinal's absorption in bacteriorhodopsin

1986 ◽  
Vol 108 (11) ◽  
pp. 3104-3105 ◽  
Author(s):  
Johan. Lugtenburg ◽  
Maria. Muradin-Szweykowska ◽  
Carola. Heeremans ◽  
Johannes A. Pardoen
Keyword(s):  
Opsin Shift

Model Systems for the Investigation of the Opsin Shift in Bacteriorhodopsin

2010 ◽  
Vol 114 (5) ◽  
pp. 2179-2188 ◽  
Author(s):  
Lars Lasogga ◽  
Wolfgang Rettig ◽  
Harald Otto ◽  
Ingrid Wallat ◽  
Julia Bricks
Keyword(s):  
Model Systems ◽  
Opsin Shift

Polarization models of young stellar objects - II. Linear and circular polarimetry of R Coronae Australis

2000 ◽  
Vol 319 (2) ◽  
pp. 337-349 ◽  
Author(s):  
Stuart Clark ◽  
Alan McCall ◽  
Antonio Chrysostomou ◽  
Tim Gledhill ◽  
Jeremy Yates ◽  
...  
Keyword(s):  
Young Stellar Objects ◽  
Stellar Objects ◽  
Polarization Models
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