Innovations in Biomolecular Modeling and Simulations

0378718 - ÚOCHB 2013 RIV GB eng M - Monography Chapter
Lankaš, Filip
Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale.
Innovations in Biomolecular Modeling and Simulations. Vol. 2. Cambridge: Royal Society of Chemistry, 2012 - (Schlick, T.), s. 3-32. ISBN 978-1-84973-505-6
R&D Projects: GA MŠMT LC512
Institutional research plan: CEZ:AV0Z40550506
Keywords : DNA * multiscale modelling * coarse-grained models * molecular dynamics simulations * mechanical properties
Subject RIV: CF - Physical ; Theoretical Chemistry
http://pubs.rsc.org/en/content/chapter/bk9781849734622-00001/978-1-84973-462-2

The chapter is concerned with recent developments in the field of coarse-grained and multiscale modelling of DNA. Pseudoatom models at different scales are reviewed and critically compared. The main part is devoted to rigid base and basepair models of DNA shape and harmonic stiffness. The choice of model coordinates, inferring model parameters from unrestrained atomic-resolution molecular dynamics simulations, and the problem of locality are treated in detail. An original simulation of DNA A-tract is analyzed as an example. Anharmonic effects and alternative approaches are also discussed.
Permanent Link: http://hdl.handle.net/11104/0210124