Monte Carlo Energy Landscape Paving and Basin Paving simulation of RNA T-loop hairpin

We propose a hybrid algorithm, which combines the features of the energy landscape paving (ELP) and Monte Carlo Minimization (MCM) methods. We have tested its performance in studying the low-energy conformations of the heptapeptide deltorphin.

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A COMBINATION OF REPLICA EXCHANGE MONTE CARLO AND ENERGY LANDSCAPE PAVING ALGORITHMS TO INCREASE THE EFFECTIVENESS OF CONFORMATIONAL SAMPLING

International Journal of Modern Physics C ◽

10.1142/s0129183104006352 ◽

2004 ◽

Vol 15 (07) ◽

pp. 933-937 ◽

Cited By ~ 1

Author(s):

HANDAN ARKIN

Keyword(s):

Monte Carlo ◽

Hybrid Algorithm ◽

Energy Landscape ◽

Monte Carlo Sampling ◽

Replica Exchange ◽

Conformational Sampling ◽

Sampling Techniques ◽

Replica Exchange Monte Carlo ◽

Energy Landscape Paving ◽

Low Energy Conformations

A combination of replica exchange Monte Carlo sampling techniques and energy landscape paving approach is presented. This hybrid algorithm combines the features of the energy landscape paving (ELP) and replica exchange methods (REM). I have tested its performance in studying the low-energy conformations of the benchmark peptide Met-enkephalin.

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Insight into the unwrapping of the dinucleosome

Soft Matter ◽

10.1039/d0sm00161a ◽

2020 ◽

Vol 16 (20) ◽

pp. 4806-4813

Author(s):

Fatemeh Khodabandeh ◽

Hashem Fatemi ◽

Farshid Mohammad-Rafiee

Keyword(s):

Monte Carlo Simulation ◽

Monte Carlo ◽

Energy Landscape ◽

Dynamical Features ◽

Insight Into

The energy landscape and configurations of dinucleosome in different unwrapped states are studied. The dynamical Monte-Carlo simulation demonstrates dynamical features such as the unwrapping force for partial/full wrapping processes.

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Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins

Physical Review E ◽

10.1103/physreve.88.052704 ◽

2013 ◽

Vol 88 (5) ◽

Cited By ~ 2

Author(s):

Jingfa Liu ◽

Beibei Song ◽

Zhaoxia Liu ◽

Weibo Huang ◽

Yuanyuan Sun ◽

...

Keyword(s):

Lattice Model ◽

Energy Landscape ◽

Face Centered Cubic ◽

Face Centered ◽

Energy Landscape Paving

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Global Optimization by Energy Landscape Paving

Physical Review Letters ◽

10.1103/physrevlett.88.068105 ◽

2002 ◽

Vol 88 (6) ◽

Cited By ~ 154

Author(s):

Ulrich H. E. Hansmann ◽

Luc T. Wille

Keyword(s):

Global Optimization ◽

Energy Landscape ◽

Energy Landscape Paving

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STUDIES OF FINDING LOW ENERGY CONFIGURATIONS IN OFF-LATTICE PROTEIN MODELS

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633606002453 ◽

2006 ◽

Vol 05 (03) ◽

pp. 587-594 ◽

Cited By ~ 11

Author(s):

JINGFA LIU ◽

WENQI HUANG

Keyword(s):

Lower Energy ◽

Gradient Descent ◽

Energy Landscape ◽

Three Dimensional ◽

Ground States ◽

Low Energy ◽

Protein Models ◽

Energy Configurations ◽

Energy Landscape Paving ◽

Lattice Protein Models

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

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