List of actions available to the ffeatools script.

<p>List of actions available to the ffeatools script.</p

A representation of the 5 most flexible eigenmodes of the GroEL 1GPa model.

<p>A representation of the 5 most flexible eigenmodes of the GroEL 1GPa model.</p

The eigenvalues, which correspond to positional variance, of the 20 most flexible modes found from PCA analysis of a 3<i>μ</i>s FFEA simulations of GroEL.

<p>The eigenvalues, which correspond to positional variance, of the 20 most flexible modes found from PCA analysis of a 3<i>μ</i>s FFEA simulations of GroEL.</p

The RMSD traces of the 2 different simulations of GroEL following an RMS fit to the average structure.

<p>The RMSD traces of the 2 different simulations of GroEL following an RMS fit to the average structure.</p

Diagram of the structure of data in FFEA.

<p>The same structure is used both in the “runner” and in the “tools”.</p

An electron microscopy map of GroEL (EMDB entry EMD-5403) as seen in Chimera [26](left), then converted to “.stl” using the emmaptosurf ffeatool visualised in VMD [27] (centre), and the final volumetric mesh, coarsened so that the shortest edge is 12Å visualised using the FFEA plugin for PyMOL (right).

<p>An electron microscopy map of GroEL (EMDB entry EMD-5403) as seen in Chimera [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005897#pcbi.1005897.ref026" target="_blank">26</a>](left), then converted to “.stl” using the emmaptosurf ffeatool visualised in VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005897#pcbi.1005897.ref027" target="_blank">27</a>] (centre), and the final volumetric mesh, coarsened so that the shortest edge is 12Å visualised using the FFEA plugin for PyMOL (right).</p

Weak scaling plots for a system composed of an increasing number of GroEL units matching the number of processors used, up to 248, in a large shared memory machine.

<p>a) Execution time b) Efficiency.</p

The eigenvector inner product matrices between compared trajectories.

<p><b>a)</b> is the comparison between atomistic and FFEA pseudo-atomistic PCA datasets. <b>b)</b> is the comparison between the first and second halves of the atomistic datasets.</p

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules - Fig 19

<p>a) The two soft, viscoelastic spheres before collision. b) The spheres collide and suffer a large deformation. c) The spheres bounce back as a result of the steric interactions, recover their shape, and experience negligible rotation or deflection. A movie is available in the supplementary <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005897#pcbi.1005897.s003" target="_blank">S3 File</a>.</p

Five different bead types (shown in different colours) control the interactions of the stalk of the dynein molecular motor (pink) and the microtubule track (blue).

<p>Each bead is assigned to an element of the mesh, and the forces resulting from the tabulated interaction potentials between beads are interpolated linearly onto the nodes of the elements, thus transmitting the force to the corresponding body.</p