Response to “Comment on ‘Communication: Benzene dimer–-The free energy landscape’” [J. Chem. Phys. 140, 227101 (2014)]

2014 ◽  
Vol 140 (22) ◽  
pp. 227102 ◽  
Author(s):  
Anil Kumar Tummanapelli ◽  
Sukumaran Vasudevan
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Chem Phys ◽  
Free Energy Landscape ◽  
Benzene Dimer

scholarly journals Comment on “Communication: Benzene dimer—The free energy landscape” [J. Chem. Phys. 139, 201102 (2013)]

2014 ◽  
Vol 140 (22) ◽  
pp. 227101 ◽  
Author(s):  
Ad van der Avoird ◽  
Rafał Podeszwa ◽  
Bernd Ensing ◽  
Krzysztof Szalewicz
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Chem Phys ◽  
Free Energy Landscape ◽  
Benzene Dimer

Communication: Benzene dimer—The free energy landscape

2013 ◽  
Vol 139 (20) ◽  
pp. 201102 ◽  
Author(s):  
Anil Kumar Tummanapelli ◽  
Sukumaran Vasudevan
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Benzene Dimer

Reply to the ‘Comment on “Topography of the Free Energy Landscape on the Claisen–Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step”’ by N. D. Coutinho, H. G. Machado, V. H. Carvalho-Silva and W. A. da Silva, Phys. Chem. Chem. Phys., 2021, 23, 6738

2021 ◽  
Vol 23 (38) ◽  
pp. 22202-22206
Author(s):  
Nayara Dantas Coutinho ◽  
Hugo Gontijo Machado ◽  
Valter Henrique Carvalho-Silva ◽  
Wender Alves da Silva
Keyword(s):  
Free Energy ◽  
Temperature Effect ◽  
Energy Landscape ◽  
Chem Phys ◽  
Free Energy Landscape ◽  
Hybrid Treatment ◽  
Limiting Step ◽  
Rate Controlling Step ◽  
Phys Chem Chem Phys

New calculations improved by explicit-implicit hybrid treatment ensure that the overall iKIE > 1 does not exclude step R4 as a limiting-step and that the debate about the infallibility of the generalization of step R5 as RCS is reasonable.

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>

The Perturbed Free Energy Landscape: Linking Ligand Binding to Biomolecular Folding

ChemBioChem ◽  
2020 ◽  
Author(s):  
fareed aboul-ela ◽  
Abdallah S Abdelsatter ◽  
Youssef Mansour
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Energy Landscape ◽  
Free Energy Landscape
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