Gallery

Leucine Zipper

MPEG movie (1.2Mb) of a protein dimer "unzipping". The leucine zipper complex dissociates by applying adaptive potentials at both ends of the complex. The colors indicate the four heptad repeats, the structural units that are typical for coiled coil complexes, comprising seven amino acids. Leucine sidechains are depicted in spacefilling representation. This work is part of the Veni research project done by Jocelyne Vreede.

MPEG movie (7.8Mb) of a multiscale simulation of methane. The methane molecules inside the red spherical region are treated in atomistic detail. Outside this atomistic region is a layer in which the methane molecules change resolution in a smooth fashion. Outside this so-called "healing region" layer, the methane molecules are treated as coarse-grained ("united atom") spherical bodies (blue blobs); most of this large outher region is not shown. Click here to read more about the multiscale MD method.

MPEG movie (7Mb) of the formation of the signaling state of Photoactive Yellow Protein, obtained from parallel tempering simulations. The hydrogen bond network around the chromophore (yellow sticks) shifts towards Glutamic acid 46 (red sticks), followed by hydration of the chromophore binding pocket. Finally, the chromophore becomes fully exposed to solvent. This research was done by Jocelyne Vreede. Interested in reading more? Click here...

Jasper Heuft studied in a systematic manner the aqueous solvent structure around dissolved ions. This MPEG movie (60Mb!) obtained from an ab initio molecular dynamics simulation, shows the microscopic behavior of hydrochloric acid in water. Chloride ions are shown as green spheres and water molecules are represented as red (oxygen) and white (hydrogen) sticks. Four protons ride the hydrogen bonded network and jump from H₂O to H₂O. They light up as orange spheres when they temporary form a "stable" hydronium complex.

MPEG movie (6Mb) It is well-established that micelle formation proceeds via a nucleation mechanism. Recently, René Pool found that a specific soap molecule enables another mechanism for the formation of a micelle solution. This replication mechanism involves growth where the cluster changes from a spherical to an elipsoidal shape. A critical fluctuation to a dumbbell shape with a narrow neck then leads to breakup into two daughter micelles.

MPEG movie (13Mb). In this movie by Jarek Juraszek, the folding of a small protein, Trp-cage, is shown. Using transition path sampling, the extended chain of amino acids collapses.

Daniele Moroni studied the kinetics of crystal nucleation of an undercooled Lennard-Jones liquid using various path sampling methods. He obtained the rate constant and elucidated the pathways for this nucleation process. Analysis of the path ensemble revealed that crystal nucleation occurs along many different pathways, in which critical solid nuclei can be small, compact, and face-centered-cubic, but also large, less ordered, and more body- centered- cubic. The fluctuations in the cluster shape are clearly visible in this animation of a typical nucleation pathway.
This work was published as The interplay between size and structure in the critical nucleus, D. Moroni, P.R. ten Wolde and P.G. Bolhuis, in Phys. Rev. Lett. 94, 235703 (2005).

AVI movie (16Mb) of the ruthenium catalyzed hydrogen transfer of formaldehyde to methanol in an explicit solvent model. Jan-Willem Handgraaf found that during the catalytic conversion from the ketone to the corresponding alcohol the solvent molecules actively participate in the reaction. In the movie the reacting molecules are shown in ball-stick representation. Green, red, blue, cyan and white indicate ruthenium, oxygen, nitrogen, carbon and hydrogen nuclei, respectively. Hydrogen bonds are indicated by yellow dotted lines.

MPEG movie (13Mb) of water and ethene reacting to form ethanol. This reaction is acid-catalysed, so the simulation box contains an hydronium ion (purple, left of the green ethene molecule). It donates the blue proton to ethene and thereby giving it a positive charge. The positive carbon of ethene attracts the electronegative oxygen of the other purple water molecule. When the oxygen attaches to ethene, it loses one of its protons to another water molecule: Ethene is transformed into ethanol and the hydronium ion is recovered. This research was done by Titus van Erp.

AVI movie with sound (39Mb!) illustrating the high level of experimental work done in the computational chemistry group. The translation of the dialog between the first and the second scientist is: " Ah, there forms a crystal, there forms a crystal!" (1) and "it becomes solid!" (2). The Parrinello group is gratefully acknowledged for donating the equipment (i.e. the chocolate fondu fountain).