scholarly journals Driven Adaptive-Bias Scheme: A Hybrid Free Energy Method for Biomolecular Systems with Complex Energy Landscapes

2014 ◽  
Vol 106 (2) ◽  
pp. 640a
Author(s):  
Mahmoud Moradi ◽  
Emad Tajkhorshid
Keyword(s):  
Free Energy ◽  
Energy Method ◽  
Energy Landscapes ◽  
Complex Energy ◽  
Biomolecular Systems

scholarly journals Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path

2008 ◽  
Vol 95 (6) ◽  
pp. 2692-2701 ◽  
Author(s):  
Gregg Lois ◽  
Jerzy Blawzdziewicz ◽  
Corey S. O’Hern
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Reaction Path ◽  
Energy Landscapes ◽  
Complex Energy ◽  
Energy Reaction

scholarly journals Sonifying Stochastic Walks on Biomolecular Energy Landscapes

2018 ◽  
Author(s):  
Robert E. Arbon ◽  
Alex J. Jones ◽  
Lars A. Bratholm ◽  
Tom Mitchell ◽  
David R. Glowacki
Keyword(s):  
Free Energy ◽  
Markov Models ◽  
Dynamic Properties ◽  
Energy Landscape ◽  
Visual Display ◽  
Free Energy Landscape ◽  
Auditory Display ◽  
Energy Landscapes ◽  
Biomolecular Systems ◽  
Relative Free Energy

Translating the complex, multi-dimensional data produced by simulations of biomolecules into an intelligible form is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams. This allows for concurrent visual display of the physical configuration of a biomolecule and auditory display of characteristics of the corresponding free energy landscape. The resulting sonification provides information about the relative free energy features of a given configuration including its stability.

scholarly journals Distributions of experimental protein structures on coarse-grained free energy landscapes

2015 ◽  
Vol 143 (24) ◽  
pp. 243153 ◽  
Author(s):  
Kannan Sankar ◽  
Jie Liu ◽  
Yuan Wang ◽  
Robert L. Jernigan
Keyword(s):  
Free Energy ◽  
Protein Structures ◽  
Coarse Grained ◽  
Energy Landscapes ◽  
Free Energy Landscapes
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