Movie Gallery:
Hydrophobic Hydration of Xenon | ||
| The movie captures 5 picoseconds of a
molecular dynamics simulation of a hydrophobic Xenon particle dissolved in liquid water
at 275 K and ambient pressure conditions.
Shown are the water molecules in the hydration shell, as well as the fluctuating hydrogen bond
network. Note the volatility of the hydrogen bond network, and the preferential straddling geometry
adopted by the first shell water molecules, trying to keep the
hydrogen bond network intact. The position of the "camera" is
rotating around the hydrophobic particle and moving with
the freely diffusing Xenon particle.
Scientific Information: D. Paschek, J. Chem. Phys. 120, 10605-10617 (2004). (PDF) |
Folding of the AK-peptide | ||
|
Replica Exchange Molecular Dynamics Simulation of the unbiased folding
of the 21 residue AK-peptide in an explicit water solvent. The water
molecules have been removed for display purposes. The movie
depicts the conformational search of
one single replica (out of 40)
within about 6 ns of simulation time. The total movie
shows 8 ns of simulation time. Scientific Information: D. Paschek, S. Gnanakaran, A.E. García, Proc. Natl. Acad. Sci. USA 102, 6765-6770 (2005). (PDF) |
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Folding of Trp-cage | ||
|
Replica Exchange Molecular Dynamics Simulation of the unbiased folding
of a Trp-cage miniprotein in an explicit water solvent. The water
molecules have been removed for display purposes. The movie
depicts the conformational search of
one single replica (out of 50), repeatedly reaching the native folded
structure within about 1 microsecond of simulation time. Scientific Information: R. Day, D. Paschek, A.E. García, Proteins: Structure, Function and Bioinformatics 78, 1889-1899 (2010). (PDF) |
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Simulation of Trp-cage solvated by water | ||
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Molecular Dynamics simulation
of a Trp-cage miniprotein in an explicit water solvent. The movie spans a total of five picoseconds
shows the short-time dynamics of the folded state of Trp-cage in a water environment. The flickering yellow bonds indicate intermolecular
hydrogen bonds, forming a transient 3-dimensional hydrogen bond network.
Scientific Information: D. Paschek, H. Nymeyer, A.E. García, J. Struct. Biol. (Special Issue: Advances in molecular dynamics simulations) 157, 524-533 (2007). (PDF) |
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Diffusion of a Hydrogen Atom in Water | ||
| The movie captures 5 picoseconds of a molecular dynamics simulation of a metastable "hydrophobic" hydrogen atom dissolved in liquid water at 300 K and ambient pressure conditions. Shown is the fluctuating hydrogen bond network of water embedding the H-particle. The oxygen atoms of the water molecules represent the vertices of the network. Note that the small H particle is quickly exploring the accessible free volume left over by the water molecules. The "open" water network structure permits the H-particle to adopt a diffusion coefficient being about three to four times larger than the diffusion coefficient of water itself. | ||