Workshop material

The movie shows two peptides that are fragments of the Alzheimer Precursor Protein (APP). Using metadynamics to accelerate the formation of hydrophobic/hydrophilic interactions between them, they aggregate and form the typical beta sheet structure (which is shown as arrows in the movie), which is characteristic for amyloid fibrils. So the shown process could be the very first step of amyloid fibril formation.

The visualization has been done with VMD using its internal Tachion ray-tracer and MovieMaker plugin. Then the saved frames have been assembled in the movie using mencoder.

Data from Ute Roehrig – Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics – Molecular Modeling Group (Lausanne, Switzerland)

This movie is the logical continuation of the preceiding one. It shows a fragments of the Alzheimer Precursor Protein (APP) that aggregates to other 15 more that already form an amyloid fibril.

The visualization has been done with VMD using its internal Tachion ray-tracer and MovieMaker plugin. Then the saved frames have been assembled in the movie using mencoder.

Data from Ute Roehrig – Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics – Molecular Modeling Group (Lausanne, Switzerland)

The movie shows the phase transition that a RbCl crystal incurs under pressure. The visualization of the results of the Molecular Dynamics simulation show the elementary cell change from cubic cell centered to octahedral.

The visualization has been done with STM4. A post processing step was needed to overcome a STM4 limitation (4 frames are generated for each time step). Then the movie has been assembled from the frames using mencoder.

Data from Stefano Leoni – Max-Planck-Institute for Chemical Physics of Solids (Dresden, Germany)

This movie show the same phase transition without polyhedra. I use this and the above movies to teach the importance of simplifying representations in chemistry.

The work that started the request for a nice visualization is:

Branduardi D., Gervasio F. L., and Parrinello M. From A to B in free energy space J. Chem. Phys. 126, 054103 (2007) (10 pages)

The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.

The two charts on the left show the original visualizations contained in the article. On the left the trajectory computed by a standard method. On the right the result of the novel algorithm.

The energy landscape is parametrized by the two angles Φ and Ψ. The tubes show three trajectories computed by the new algorithm. The tube diameter and color show the error.

The visualization has been done with STM4. A postprocessing step, using ImageMagick, was done to smooth the image and add the logo.

Data from Davide Branduardi – Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus (Lugano, Switzerland)

But if you want to see how to close the presentation of the scientific results, see this movie. To understand it you need a little background:

1. Davide Branduardi works in the group of Prof. Michele Parrinello
2. Prof. Michele Parrinello is from Sicily
3. Sicily was called Trinacria
4. Trinacria si represented by a head with three (Tri means three) legs