Gallery
- 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...
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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).
