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Special Issue "Entropies of Polymers"

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

Deadline for manuscript submissions: closed (31 December 2009)

Special Issue Editor

Guest Editor
Dr. Donald J. Jacobs (Website)

Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
Fax: +1 704 687 8197
Interests: computational physics; biological physics; protein stability; phase transitions; brownian motion

Keywords

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

Published Papers (3 papers)

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Research

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Open AccessArticle On the Structural Non-identifiability of Flexible Branched Polymers
Entropy 2009, 11(4), 907-916; doi:10.3390/e11040907
Received: 21 October 2009 / Accepted: 18 November 2009 / Published: 20 November 2009
Cited by 6 | PDF Full-text (235 KB) | HTML Full-text | XML Full-text
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 [...] 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)
Open AccessArticle Conformational Entropy of an Ideal Cross-Linking Polymer Chain
Entropy 2008, 10(3), 285-308; doi:10.3390/e10030285
Received: 8 August 2008 / Revised: 10 September 2008 / Accepted: 19 September 2008 / Published: 20 September 2008
Cited by 8 | PDF Full-text (556 KB)
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 [...] 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)

Review

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Open AccessReview Influence of Conformational Entropy on the Protein Folding Rate
Entropy 2010, 12(4), 961-982; doi:10.3390/e12040961
Received: 30 December 2009 / Revised: 15 March 2010 / Accepted: 30 March 2010 / Published: 16 April 2010
Cited by 6 | PDF Full-text (939 KB) | HTML Full-text | XML Full-text
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 [...] 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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