Biological Kinetics Modeling

1992 ◽  
pp. 177-189
Author(s):  
J. C. Todd ◽  
S. K. Bhattacharya ◽  
V. J. Law
Keyword(s):  
Kinetics Modeling ◽  
Biological Kinetics

scholarly journals The Dynamics of Subunit Rotation in a Eukaryotic Ribosome

Biophysica ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 204-221
Author(s):  
Frederico Campos Freitas ◽  
Gabriele Fuchs ◽  
Ronaldo Junio de Oliveira ◽  
Paul Charles Whitford
Keyword(s):  
Free Energy ◽  
Large Scale ◽  
Small Subunit ◽  
Free Energy Barrier ◽  
Temperature Dependent ◽  
Molecular Flexibility ◽  
Subunit Rotation ◽  
Biological Kinetics ◽  
Rate Limiting ◽  
Reversible Rotation

Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ∼1 MDa) undergoes spontaneous and reversible rotation events (∼8∘). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.

Chemical kinetics modeling and LES combustion model effects on a perfectly premixed burner

2009 ◽  
Vol 337 (6-7) ◽  
pp. 318-328 ◽  
Author(s):  
Guillaume Albouze ◽  
Thierry Poinsot ◽  
Laurent Gicquel
Keyword(s):  
Chemical Kinetics ◽  
Combustion Model ◽  
Kinetics Modeling

Dehydration of S tevia   rebaudiana  Bertoni Leaves: Kinetics, Modeling and Energy Features

2014 ◽  
Vol 39 (5) ◽  
pp. 508-520 ◽  
Author(s):  
Roberto Lemus-Mondaca ◽  
Antonio Vega-Gálvez ◽  
Nelson O. Moraga ◽  
Sebastián Astudillo
Keyword(s):  
Kinetics Modeling

On kinetics modeling of vibrational energy exchange with application to the nozzle flow problem

1997 ◽  
Author(s):  
John Gilmore ◽  
Surendra Sharma ◽  
Deepak Bose ◽  
Graham Candler ◽  
John Gilmore ◽  
...  
Keyword(s):  
Energy Exchange ◽  
Flow Problem ◽  
Vibrational Energy ◽  
Nozzle Flow ◽  
Kinetics Modeling

Studies on the Salting Step of Tunisian Kaddid Meat: Experimental Kinetics, Modeling and Quality

2011 ◽  
Vol 5 (5) ◽  
pp. 1882-1895 ◽  
Author(s):  
Meriem Chabbouh ◽  
Sami Ben Hadj Ahmed ◽  
Abdelhamid Farhat ◽  
Ali Sahli ◽  
Sihem Bellagha
Keyword(s):  
Kinetics Modeling ◽  
Experimental Kinetics
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