scholarly journals The computation of free energy of TIP4P water using expanded ensemble method

2003 ◽  
Vol 52 (9) ◽  
pp. 2342
Author(s):  
Sheng Zheng-Mao ◽  
Luo Jun-Wei
Keyword(s):  
Free Energy ◽  
Ensemble Method ◽  
Expanded Ensemble

Determination of Free Energy from Chemical Potentials: Application of the Expanded Ensemble Method

1996 ◽  
Vol 18 (1-2) ◽  
pp. 43-58 ◽  
Author(s):  
A. P. Lyubartsev ◽  
A. Laaksonen ◽  
P. N. Vorontsov-velyaminov
Keyword(s):  
Free Energy ◽  
Ensemble Method ◽  
Chemical Potentials ◽  
Expanded Ensemble

New version of Monte Carlo expanded ensemble method for precise calculations of free energy difference

2006 ◽  
Vol 32 (6) ◽  
pp. 437-442 ◽  
Author(s):  
S. V. Burov ◽  
P. N. Vorontsov-Velyaminov ◽  
E. M. Piotrovskaya
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Energy Difference ◽  
Ensemble Method ◽  
Free Energy Difference ◽  
Expanded Ensemble

Free Energy Calculations by Expanded Ensemble Method for Lattice and Continuous Polymers

1996 ◽  
Vol 100 (4) ◽  
pp. 1153-1158 ◽  
Author(s):  
P. N. Vorontsov-Velyaminov ◽  
A. V. Broukhno ◽  
T. V. Kuznetsova ◽  
A. P. Lyubartsev
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Ensemble Method ◽  
Energy Calculations ◽  
Expanded Ensemble

scholarly journals Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method

Membranes ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 974
Author(s):  
Seungho Choe
Keyword(s):  
Drug Delivery ◽  
Free Energy ◽  
Cell Penetrating Peptides ◽  
Model Membrane ◽  
Model Membranes ◽  
Ensemble Method ◽  
Sampling Techniques ◽  
Path Sampling ◽  
Transport Mechanisms ◽  
Cell Penetrating

Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of the most powerful and flexible path sampling techniques, can be helpful to reveal translocation paths and free energy barriers along those paths. Within the WE approach we show how Arg9 (nona-arginine) and Tat interact with a DOPC/DOPG(4:1) model membrane, and we present free energy (or potential mean of forces, PMFs) profiles of penetration, although a translocation across the membrane has not been observed in the current simulations. Two different compositions of lipid molecules were also tried and compared. Our approach can be applied to any CPPs interacting with various model membranes, and it will provide useful information regarding the transport mechanisms of CPPs.

scholarly journals Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

2016 ◽  
Vol 473 (12) ◽  
pp. 1651-1662 ◽  
Author(s):  
Shinji Iida ◽  
Haruki Nakamura ◽  
Junichi Higo
Keyword(s):  
Free Energy ◽  
Room Temperature ◽  
Dimensional Space ◽  
Energy Landscape ◽  
Complex Structure ◽  
Complex Form ◽  
Ensemble Methods ◽  
Ensemble Method ◽  
Free Energy Landscape ◽  
Conformational Sampling

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein–protein or protein–ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks.

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