Non-Equilibrium Isomer Distribution of the Gas-Phase Photoactive Yellow Protein Chromophore

2012 ◽  
Vol 3 (16) ◽  
pp. 2259-2263 ◽  
Author(s):  
Mitra Almasian ◽  
Josipa Grzetic ◽  
Johanne van Maurik ◽  
Jeffrey D. Steill ◽  
Giel Berden ◽  
...  
Keyword(s):  
Gas Phase ◽  
Photoactive Yellow Protein ◽  
Isomer Distribution ◽  
Non Equilibrium

Gas Phase Absorption Studies of Photoactive Yellow Protein Chromophore Derivatives

2009 ◽  
Vol 113 (34) ◽  
pp. 9442-9449 ◽  
Author(s):  
Tomás Rocha-Rinza ◽  
Ove Christiansen ◽  
Jyoti Rajput ◽  
Aravind Gopalan ◽  
Dennis B. Rahbek ◽  
...  
Keyword(s):  
Gas Phase ◽  
Photoactive Yellow Protein ◽  
Absorption Studies

scholarly journals Non-equilibrium gas-phase nitrogenation

1994 ◽  
Vol 30 (2) ◽  
pp. 571-573 ◽  
Author(s):  
S. Brennan ◽  
R. Skomski ◽  
J.M.D. Coey
Keyword(s):  
Gas Phase ◽  
Non Equilibrium

Dimerization and conformation-related free energy landscapes of dye-tagged amyloid-β12–28linked to FRET experiments

2017 ◽  
Vol 19 (14) ◽  
pp. 9470-9477 ◽  
Author(s):  
Alexander Kulesza ◽  
Steven Daly ◽  
Philippe Dugourd
Keyword(s):  
Free Energy ◽  
Electrospray Ionization ◽  
Gas Phase ◽  
Aβ Peptide ◽  
Energy Landscapes ◽  
Equilibrium Conditions ◽  
Short Peptide ◽  
Free Energy Landscapes ◽  
Non Equilibrium ◽  
Dimer Models

The free energy landscapes of Aβ-peptide dimer models under different prototype conditions support the hypothesis that the gas-phase action-FRET measurement after electrospray ionization operates under non-equilibrium conditions, with a memory of the solution conditions – even for the dimer of this relatively short peptide.

scholarly journals Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

2011 ◽  
Vol 13 (4) ◽  
pp. 1585-1589 ◽  
Author(s):  
Tomás Rocha-Rinza ◽  
Kristian Sneskov ◽  
Ove Christiansen ◽  
Ulf Ryde ◽  
Jacob Kongsted
Keyword(s):  
Gas Phase ◽  
Photoactive Yellow Protein ◽  
Coumaric Acid

Dynamic Process Modeling on Depressurization by Cooling-Controlled Condensation in a Closed Chamber

2014 ◽  
Author(s):  
Bo Zhang ◽  
Pengfei He ◽  
Chao Zhu ◽  
Zhiming Ji ◽  
Chao-Hsin Lin
Keyword(s):  
Gas Phase ◽  
Dynamic Process ◽  
Cfd Simulation ◽  
Complex Geometry ◽  
Parametric Model ◽  
Optimized Design ◽  
Internal Cooling ◽  
Closed Chamber ◽  
Parametric Effects ◽  
Non Equilibrium

It has long been realized that condensation in a chamber prefilled with condensable vapor leads to chamber depressurization, and the condensation rate can be cooling controlled. While the final state can be reasonably estimated based on the thermodynamic equilibrium, the dynamic process or rate of depressurization has not been satisfactorily modeled, which is due to the complicated coupling mechanisms of heat and mass transfer, the transient nature of non-equilibrium during the process, the complication by the co-existence of non-condensable gas (NCG) within vapor, as well as the complex geometry and material properties of chamber and cooling device involved. In this paper, we have conducted an experimental study on depressurization by steam condensation onto an internal cooling coil in a steam-prefilled closed chamber. To reveal various parametric effects on the depressurization process, a parametric model consisting of a set of coupled ordinary differential equations has been established, with some simplified assumptions including lumped heat capacity sub-models for chamber walls, cooling coils and the gas phase. To further explore the thermal non-equilibrium characteristics during the process, a simplified and transient simulation of computational fluid dynamics (CFD) is also conducted using FLUENT with user-defined function (UDF) on boundary of condensation. Both parametric and CFD models consider the existence of NCG that is pre-mixed with the vapor as impurity. By comparison with the experimental measurements, both models correctly predict the dynamic and asymptotic characteristics of depressurization with time. The CFD simulation indicates an almost instant equilibrium in pressure within the chamber and yet non-equilibrium in temperature with noticeable temperature gradients over the gas phase. The simplified parametric model provides quick and quantitative assessments of some major parametric effects (e.g., vapor purity, coolant flow rate, and vessel volume) on the rate of depressurization. The detailed mechanistic understanding, gained from proposed models, provides insights essential to the optimized design and operation of the depressurization by cooling-controlled condensation.

scholarly journals Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore

2016 ◽  
Vol 18 (39) ◽  
pp. 27476-27485 ◽  
Author(s):  
Francisco F. García-Prieto ◽  
Aurora Muñoz-Losa ◽  
M. Luz Sánchez ◽  
M. Elena Martín ◽  
Manuel A. Aguilar
Keyword(s):  
Methyl Ester ◽  
Gas Phase ◽  
Environmental Effects ◽  
Solvent Effects ◽  
Water Solution ◽  
Acid Methyl Ester ◽  
Photoactive Yellow Protein ◽  
Coumaric Acid ◽  
Acid Methyl

Environmental effects on the deactivation channels of the PYP chromophore in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level.

scholarly journals Non-equilibrium interplay between gas-particle partitioning and multiphase chemical reactions of semi-volatile compounds: mechanistic insights and practical implications for atmospheric modeling of PAHs

2020 ◽  
Author(s):  
Jake Wilson ◽  
Ulrich Pöschl ◽  
Manabu Shiraiwa ◽  
Thomas Berkemeier
Keyword(s):  
Mass Transport ◽  
Gas Phase ◽  
Chemical Reactions ◽  
Rate Coefficient ◽  
Chemical Transport ◽  
Atmospheric Modeling ◽  
Time Step ◽  
Transport Models ◽  
Chemical Transport Models ◽  
Non Equilibrium

Abstract. Polycyclic aromatic hydrocarbons (PAHs) are carcinogenic air pollutants. The dispersion of PAHs in the atmosphere is influenced by gas-particle partitioning and chemical loss. These processes are closely interlinked and may occur at vastly differing timescales, which complicates their mathematical description in chemical transport models. Here, we use a kinetic model that explicitly resolves mass transport and chemical reactions in the gas and particle phases to describe and explore the dynamic and non-equilibrium interplay of gas-particle partitioning and chemical losses of PAHs on soot particles. We define the equilibration timescale τeq of gas-particle partitioning as the e-folding time for relaxation of the system to the partitioning equilibrium. We find this metric to span seconds to hours depending on temperature, particle surface area and the type of PAH. The equilibration time can be approximated using a time-independent equation τeq ≈ 1/(kdes + kads), which depends on the desorption rate coefficient kdes and adsorption rate coefficient kads, both of which can be calculated from experimentally-accessible parameters. The model reveals two regimes in which different physical processes control the equilibration timescale: a desorption-controlled and an adsorption-controlled regime. In a case study with the PAH pyrene, we illustrate how chemical loss can perturb the equilibrium particulate fraction at typical atmospheric concentrations of O3 and OH. For the surface reaction with O3, the perturbation is significant and increases with the gas-phase concentration of O3. Conversely, perturbations are smaller for reaction with the OH radical, which reacts with PAHs on both the surface of particles and in the gas phase. Global and regional chemical transport models typically approximate gas-particle partitioning with instantaneous equilibration approaches. We highlight scenarios in which these approximations deviate from the explicit-coupled treatment of gas-particle partitioning and chemistry presented in this study. We find that the discrepancy between solutions depends on the operator-splitting time step and the choice of time step can help to minimize the discrepancy. The findings and techniques presented in this work are not only relevant for PAHs, but can also be applied to other semi-volatile substances that undergo chemical reactions and mass transport between the gas and particle phase.

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