Universal and Accessible Entropy Estimation Using a Compression Algorithm

Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug design. Current techniques suffer from being model specific, requiring abundant computation resources and simulation at c...

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Veröffentlicht in:Physical review letters Jg. 123; H. 17; S. 1
Hauptverfasser: Avinery, Ram, Kornreich, Micha, Beck, Roy
Format: Journal Article
Sprache:Englisch
Veröffentlicht: College Park American Physical Society 25.10.2019
Schlagworte:
Algorithms
Complex systems
Complexity
Computer simulation
Entropy
Molecular dynamics
Proteins
Variations
ISSN:0031-9007, 1079-7114, 1079-7114
Online-Zugang:Volltext
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Zusammenfassung:Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug design. Current techniques suffer from being model specific, requiring abundant computation resources and simulation at conditions far from the studied realization. Here, we present a universal scheme to calculate entropy using lossless-compression algorithms and validate it on simulated systems of increasing complexity. Our results show accurate entropy values compared to benchmark calculations while being computationally effective. In molecular-dynamics simulations of protein folding, we exhibit unmatched detection capability of the folded states by measuring previously undetectable entropy fluctuations along the simulation timeline. Such entropy evaluation opens a new window onto the dynamics of complex systems and allows efficient free-energy calculations.
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ISSN:0031-9007
1079-7114
1079-7114
DOI:10.1103/PhysRevLett.123.178102