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

Solid-phase nucleation free-energy barriers in truncated cubes: interplay of localized orientational order and facet alignment

Soft Matter ◽  
2018 ◽  
Vol 14 (11) ◽  
pp. 1996-2005 ◽  
Author(s):  
Abhishek K. Sharma ◽  
Vikram Thapar ◽  
Fernando A. Escobedo
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Simulations ◽  
Solid Phase ◽  
Orientational Order ◽  
Umbrella Sampling ◽  
Isotropic Phase ◽  
Energy Barriers ◽  
Ordered Phases ◽  
Phase Nucleation

The nucleation of ordered phases from the bulk isotropic phase of octahedron-like particles has been studied via Monte Carlo simulations and umbrella sampling.

scholarly journals Interconversion of hydrated protons at the interface between liquid water and platinum

2019 ◽  
Vol 21 (11) ◽  
pp. 5932-5940 ◽  
Author(s):  
Peter S. Rice ◽  
Yu Mao ◽  
Chenxi Guo ◽  
P. Hu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Liquid Water ◽  
Hydrogen Transfer ◽  
Umbrella Sampling ◽  
Energy Barriers ◽  
Hydrated Protons

The free energy barriers for hydrogen transfer at the H2O/Pt(111) interface calculated usingab initiomolecular dynamics and umbrella sampling.

Colloids in Brushes: The Insertion Free Energy via Monte Carlo Simulation with Umbrella Sampling

2010 ◽  
Vol 43 (7) ◽  
pp. 3511-3520 ◽  
Author(s):  
V. Ermilov ◽  
A. Lazutin ◽  
A. Halperin
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Free Energy ◽  
Umbrella Sampling

Efficient Monte Carlo sampling by direct flattening of free energy barriers

1999 ◽  
Vol 15 (3) ◽  
pp. 311-340 ◽  
Author(s):  
Gerhard Besold ◽  
Jens Risbo ◽  
Ole G. Mouritsen
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Sampling ◽  
Energy Barriers

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

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
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