Heuristic-based energy landscape paving for the circular packing problem with performance constraints of equilibrium

2015 ◽  
Vol 431 ◽  
pp. 166-174 ◽  
Author(s):  
Jingfa Liu ◽  
Yucong Jiang ◽  
Gang Li ◽  
Yu Xue ◽  
Zhaoxia Liu ◽  
...  
Keyword(s):  
Energy Landscape ◽  
Packing Problem ◽  
Performance Constraints ◽  
Circular Packing ◽  
Energy Landscape Paving

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

2013 ◽  
Vol 88 (5) ◽  
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

A beam search algorithm for the circular packing problem

2009 ◽  
Vol 36 (5) ◽  
pp. 1513-1528 ◽  
Author(s):  
Hakim Akeb ◽  
Mhand Hifi ◽  
Rym M’Hallah
Keyword(s):  
Search Algorithm ◽  
Packing Problem ◽  
Beam Search ◽  
Circular Packing

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

2006 ◽  
Vol 05 (03) ◽  
pp. 587-594 ◽  
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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