scholarly journals Folding Pathway And Free Energy Landscape Of Villin Headpiece Subdomain HP35 Studied by String Method

2009 ◽  
Vol 96 (3) ◽  
pp. 590a-591a ◽  
Author(s):  
Wenxun Gan ◽  
Benoit Roux
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Folding Pathway ◽  
String Method ◽  
Villin Headpiece

scholarly journals SOLVATION EFFECTS ON FREE ENERGY SURFACE OF POLYALANINE

2005 ◽  
Vol 16 (09) ◽  
pp. 1489-1496 ◽  
Author(s):  
GÖKHAN GÖKOĞLU ◽  
HANDAN ARKIN ◽  
ETHEM AKTÜRK ◽  
TARIK ÇELIK
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Solvent Effects ◽  
Energy Surface ◽  
Energy Landscape ◽  
Accessible Surface Area ◽  
Free Energy Landscape ◽  
Folding Pathway ◽  
Free Energy Surface ◽  
Accessible Surface

We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway exhaustively. We have simulated and compared the system in vacuo and in solvent, and examined the changes in the free energy landscape due to the solvent effects, which are taken into account by commonly used model Accessible Surface Area.

scholarly journals Free-Energy Landscape of the Villin Headpiece in an All-Atom Force Field

Structure ◽  
2005 ◽  
Vol 13 (4) ◽  
pp. 661-668 ◽  
Author(s):  
Thomas Herges ◽  
Wolfgang Wenzel
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Villin Headpiece

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>

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