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Three-dimensional director-field predictions of viral DNA packing arrangements

Klug, W. S. and Feldmann, M. T. and Ortiz, M. (2005) Three-dimensional director-field predictions of viral DNA packing arrangements. Computational Mechanics, 35 (2). pp. 146-152. ISSN 0178-7675. https://resolver.caltech.edu/CaltechAUTHORS:20170408-154613814

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Abstract

In this work we develop a discrete director-field model for coarse-grained description of packing arrangements of DNA within bacteriophage virus heads. This computational lattice model allows us to explore the complex energy landscape of fully three-dimensional configurations of packaged DNA. By minimizing the system’s free energy by means of the simulated annealing and the conjugate gradient methods, we make predictions about favorable packing conformations. In particular we show that the planar-wrapped inverse spool conformation is stable everywhere inside a virus except in a central core region, where the DNA tends to buckle out of the spooling plane.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1007/s00466-004-0613-xDOIArticle
https://rdcu.be/bOBFjPublisherFree ReadCube access
ORCID:
AuthorORCID
Ortiz, M.0000-0001-5877-4824
Additional Information:© Springer-Verlag 2004. Received: 5 April 2004 / Accepted: 8 July 2004 / Published online: 22 September 2004.
Group:GALCIT
Subject Keywords:Viral DNA; Packaging; Energy minimization; Numerical optimization
Issue or Number:2
Record Number:CaltechAUTHORS:20170408-154613814
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170408-154613814
Official Citation:Klug, W., Feldmann, M. & Ortiz, M. Computational Mechanics (2005) 35: 146. doi:10.1007/s00466-004-0613-x
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:76063
Collection:CaltechAUTHORS
Deposited By: 1Science Import
Deposited On:19 May 2017 22:13
Last Modified:24 Feb 2020 10:30

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