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Entropy
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Entropies of Polymers
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Entropies of Polymers

A special issue of Entropy (ISSN 1099-4300).

Deadline for manuscript submissions: closed (31 December 2009) | Viewed by 33678

Special Issue Editor

Dr. Donald J. Jacobs

E-Mail Website
Guest Editor
Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
Interests: statistical physics; biophysics; intelligent algorithms; adaptive control; inverse problems; optimization; simulation, computational modeling; multiscale modeling; data analytics; stochastic processes; extreme statistics; data reduction; machine learning
Special Issues, Collections and Topics in MDPI journals

Keywords

  • computational physics
  • biological physics
  • protein stability
  • phase transitions
  • Brownian motion

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Published Papers (3 papers)

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10 pages, 235 KiB  
Article
On the Structural Non-identifiability of Flexible Branched Polymers
by Koh-hei Nitta
Entropy 2009, 11(4), 907-916; https://doi.org/10.3390/e11040907 - 20 Nov 2009
Cited by 10 | Viewed by 11482
Abstract
The dynamics and statics of flexible polymer chains are based on their conformational entropy, resulting in the properties of isolated polymer chains with any branching potentially being characterized by Gaussian chain models. According to the graph-theoretical approach, the dynamics and statics of Gaussian [...] Read more.
The dynamics and statics of flexible polymer chains are based on their conformational entropy, resulting in the properties of isolated polymer chains with any branching potentially being characterized by Gaussian chain models. According to the graph-theoretical approach, the dynamics and statics of Gaussian chains can be expressed as a set of eigenvalues of their Laplacian matrix. As such, the existence of Laplacian cospectral trees allows the structural nonidentifiability of any branched flexible polymer. Full article
(This article belongs to the Special Issue Entropies of Polymers)
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24 pages, 556 KiB  
Article
Conformational Entropy of an Ideal Cross-Linking Polymer Chain
by Oleg K. Vorov, Dennis R. Livesay and Donald J. Jacobs
Entropy 2008, 10(3), 285-308; https://doi.org/10.3390/e10030285 - 20 Sep 2008
Cited by 25 | Viewed by 10591
Abstract
We present a novel analytical method to calculate conformational entropy of ideal cross-linking polymers from the configuration integral by employing a Mayer series expansion. Mayer-functions describing chemical bonds within the chain and for cross-links are sharply peaked over the temperature range of interest, [...] Read more.
We present a novel analytical method to calculate conformational entropy of ideal cross-linking polymers from the configuration integral by employing a Mayer series expansion. Mayer-functions describing chemical bonds within the chain and for cross-links are sharply peaked over the temperature range of interest, and, are well approximated as statistically weighted Dirac delta-functions that enforce distance constraints. All geometrical deformations consistent with a set of distance constraints are integrated over. Exact results for a contiguous series of connected loops are employed to substantiate the validity of a previous phenomenological distance constraint model that describes protein thermodynamics successfully based on network rigidity. Full article
(This article belongs to the Special Issue Entropies of Polymers)
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Review

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22 pages, 939 KiB  
Review
Influence of Conformational Entropy on the Protein Folding Rate
by Oxana V. Galzitskaya
Entropy 2010, 12(4), 961-982; https://doi.org/10.3390/e12040961 - 16 Apr 2010
Cited by 10 | Viewed by 10399
Abstract
One of the most important questions in molecular biology is what determines folding pathways: native structure or protein sequence. There are many proteins that have similar structures but very different sequences, and a relevant question is whether such proteins have similar or different [...] Read more.
One of the most important questions in molecular biology is what determines folding pathways: native structure or protein sequence. There are many proteins that have similar structures but very different sequences, and a relevant question is whether such proteins have similar or different folding mechanisms. To explain the differences in folding rates of various proteins, the search for the factors affecting the protein folding process goes on. Here, based on known experimental data, and using theoretical modeling of protein folding based on a capillarity model, we demonstrate that the relation between the average conformational entropy and the average energy of contacts per residue, that is the entropy capacity, will determine the possibility of the given chain to fold to a particular topology. The difference in the folding rate for proteins sharing more ball-like and less ball-like folds is the result of differences in the conformational entropy due to a larger surface of the boundary between folded and unfolded phases in the transition state for proteins with a more ball-like fold. The result is in agreement with the experimental folding rates for 67 proteins. Proteins with high or low side chain entropy would have extended unfolded regions and would require some additional agents for complete folding. Such proteins are common in nature, and their structural properties are of biological importance. Full article
(This article belongs to the Special Issue Entropies of Polymers)
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