title: Modelling biomacromolecular assemblies with continuum mechanics.
abstract: We have developed a continuum mechanical description of proteins using a finite element algorithm which has been generalized to include thermal fluctuations and which is therefore known as fluctuating finite element analysis (FFEA). Whereas conventional molecular dynamics (MD) simulations provide a trajectory in which each individual atomic position fluctuates, a FFEA trajectory shows how the overall shape of the protein changes due to thermal agitation. We describe the theoretical background to FFEA, its relationship to more established biomolecular modelling methods and provide examples of its application to the mesoscale biomolecular dynamics of the molecular motor dynein.
authors: *School of Physics and Astronomy, University of Leeds, Leeds, West Yorkshire, LS2 9JT, U.K.
authors: Benjamin
authors: B
authors: Hanson
authors: *School of Physics and Astronomy, University of Leeds, Leeds, West Yorkshire, LS2 9JT, U.K.
authors: Robin
authors: R
authors: Richardson
authors: †Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield, South Yorkshire, S3 7RH, U.K.
authors: Robin
authors: R
authors: Oliver
authors: ‡School of Mathematics, University of Leeds, Leeds, West Yorkshire, LS2 9JT, U.K.
authors: Daniel J
authors: DJ
authors: Read
authors: ‡School of Mathematics, University of Leeds, Leeds, West Yorkshire, LS2 9JT, U.K.
authors: Oliver
authors: O
authors: Harlen
authors: *School of Physics and Astronomy, University of Leeds, Leeds, West Yorkshire, LS2 9JT, U.K.
authors: Sarah
authors: S
authors: Harris
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004398:Dyneins / Q000737:chemistry* / Q000378:metabolism; D020342:Finite Element Analysis; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation
chemical_list: D004398:Dyneins