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Elastic energy and phase structure in a continuous spin Ising chain with applications to chiral homopolymers
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2011 (English)In: Physical Review E - Statistical, Nonlinear and Soft Matter Physics, ISSN 1539-3755, Vol. 83, no 1, 011126- p.Article in journal (Refereed) Published
Abstract [en]

We present a numerical Monte Carlo analysis of the phase structure in a continuous spin Ising chain that describes chiral homopolymers. We find that depending on the value of the Metropolis temperature, the model displays the three known nontrivial phases of polymers: At low temperatures the model is in a collapsed phase, at medium temperatures it is in a random walk phase, and at high temperatures it enters the self-avoiding random walk phase. By investigating the temperature dependence of the specific energy we confirm that the transition between the collapsed phase and the random walk phase is a phase transition, while the random walk phase and self-avoiding random walk phase are separated from each other by a crossover transition. We propose that the model can be applied to characterize the statistical properties of protein folding. For this we compare the predictions of the model to a phenomenological elastic energy formula, proposed by J. Lei and K. Huang [e-print arXiv:1002.5013; Europhys. Lett. 88, 68004 (2009)] to describe folded proteins.

Place, publisher, year, edition, pages
2011. Vol. 83, no 1, 011126- p.
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-147775DOI: 10.1103/PhysRevE.83.011126ISI: 000286761300003OAI: oai:DiVA.org:uu-147775DiVA: diva2:400980
Available from: 2011-03-01 Created: 2011-02-28 Last updated: 2012-08-01Bibliographically approved
In thesis
1. Bending, Twisting and Turning: Protein Modeling and Visualization from a Gauge-Invariance Viewpoint
Open this publication in new window or tab >>Bending, Twisting and Turning: Protein Modeling and Visualization from a Gauge-Invariance Viewpoint
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proteins in nature fold to one dominant native structure. Despite being a heavily studied field, predicting the native structure from the amino acid sequence and modeling the folding process can still be considered unsolved problems. In this thesis I present a new approach to this problem with methods borrowed from theoretical physics. In the first part I show how it is possible to use a discrete Frenet frame to define the discrete curvature and torsion of the main chain of the protein. This method is then extended to the side chains as well. In particular I show how to use the discrete Frenet frame to produce a statistical distribution of angles that works in similar fashion as the commonly used Ramachandran plot and side chain rotamers. The discrete Frenet frame displays a gauge symmetry, in the choice of basis vectors on the normal plane, that is reminiscent of features of Abelian-Higgs theory. In the second part of the thesis I show how this similarity with Abelian-Higgs theory can be translated into an effective energy for a protein. The loops of the proteins are shown to correspond to solitons so that the whole protein can be constructed by gluing together any number of solitons. I present results of simulating proteins by minimizing the energy, starting from a real line or straight helix, where the correct native fold is attained. Finally the model is shown to display the same phase structure as real proteins.

 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 68 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 921
Keyword
protein folding, discrete frenet frame, solitons, protein visualization
National Category
Physical Sciences
Research subject
Physics and Astronomy specializing in Theoretical Physics
Identifiers
urn:nbn:se:uu:diva-172358 (URN)978-91-554-8338-8 (ISBN)
Public defence
2012-05-25, Å80101, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2012-05-04 Created: 2012-04-05 Last updated: 2012-08-01Bibliographically approved

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