Simulation Study of Free-Energy Barriers in the Wetting Transition of an Oily Fluid on a Rough Surface with Reentrant Geometry

Langmuir ◽  
2012 ◽  
Vol 28 (46) ◽  
pp. 16080-16090 ◽  
Author(s):  
Elizabeth S. Savoy ◽  
Fernando A. Escobedo
Keyword(s):  
Free Energy ◽  
Rough Surface ◽  
Simulation Study ◽  
Wetting Transition ◽  
Energy Barriers

Calculation of the free energy barriers in the oligomerisation of Ab

10.2741/3104 ◽  
2008 ◽  
Vol Volume (13) ◽  
pp. 5614 ◽  
Author(s):  
Mookyung Cheon
Keyword(s):  
Free Energy ◽  
Energy Barriers

Microscopic mechanisms of initial oxidation of Si(100): Reaction pathways and free-energy barriers

2012 ◽  
Vol 85 (20) ◽  
Author(s):  
Kenichi Koizumi ◽  
Mauro Boero ◽  
Yasuteru Shigeta ◽  
Atsushi Oshiyama
Keyword(s):  
Free Energy ◽  
Reaction Pathways ◽  
Energy Barriers ◽  
Initial Oxidation

scholarly journals Cavity hydration dynamics in cytochrome c oxidase and functional implications

2017 ◽  
Vol 114 (42) ◽  
pp. E8830-E8836 ◽  
Author(s):  
Chang Yun Son ◽  
Arun Yethiraj ◽  
Qiang Cui
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Transmembrane Protein ◽  
Wetting Transition ◽  
Protonation State ◽  
Hydration Level ◽  
Level Change ◽  
Dynamics Simulations

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport.

Nucleation free-energy barriers with Hybrid Monte-Carlo/Umbrella Sampling

2014 ◽  
Vol 16 (45) ◽  
pp. 24913-24919 ◽  
Author(s):  
M. A. Gonzalez ◽  
E. Sanz ◽  
C. McBride ◽  
J. L. F. Abascal ◽  
C. Vega ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Umbrella Sampling ◽  
Energy Barriers ◽  
Hybrid Monte Carlo
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