Movie Gallery
All movies and images were made with VMD.
To view these videos, you need a media player such as QuickTime, RealPlayer, Windows Media Player or VLC. Please note that that some file extensions are incompatible with certain media players (for example, Windows Media Player will not read files with the extension .mov or .mp4, and VLC will not play .mov files). If you are having problems viewing the videos with one player, try another. Quicktime will play all of the videos in this gallery. VLC is available for free at http://www.videolan.org/vlc.
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Folding of the villin headpiece (.mpg, 10.4M) (YouTube version) Trajectory showing the folding of WT villin headpiece in a six microsecond MD simulation. (more info) (request) |
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Flexible fitting of the ribosome into a 6.7-A map (.mpg, 5.4M) This movie illustrates the flexible fitting of the ribosome into a cryo-EM map using MDFF. (more info) (request) |
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Equilibration of
a water droplet on a hydrophobic annealed surface (.mpg, 10.9M) (YouTube version) The movie shows the dynamics of a drop composed of 2000 water molecules on top of an annealed silica slab. The initial configuration corresponds to a water disc of 3 nanometers (nm) height and 6 nm diameter placed on top of an annealed silica slab of 11.4 nm x 11.4 nm x 2.0 nm dimension. The system was equilibrated for 2 nanoseconds of molecular dynamics simulation. (more info) (request) |
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View of ribosome. (.mpg, 5.0M) This movie shows an equilibration of the ribosome. (A more complete movie is available here.) (more info) (request) |
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Forced
unfolding of titin Z1Z2 (.mpg, 2.9M) This movie shows the forced unfolding of titin Z1Z2. A force of 750pN was applied to the C-terminus of Z2 while the N-terminus of Z1 was held fixed. As the structure unravels, we find that intramolecular beta-strands are broken in sequential fashion. (more info) (request) |
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Forced
unfolding of the titin Z1Z2-telethonin complex (.mpg, 6.7M) This movie shows the forced unfolding of the titin Z1Z2-telethonin complex. A force of 1200pN was applied to both titin Z2 termini, resulting in the detachment of the Z2 domain from telethonin via separation of intermolecular beta strands, followed by the subsequent unraveling of the Ig domain. (more info) (request) |
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Alpha-hemolysin (.mpg, 4.0M) (YouTube version) This movie shows alpha-hemolysin assembled with a lipid bilayer. (more info) (request) |
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Translocation of DNA (.mpg, 3.9M) (YouTube version) This movie shows the electrophoretically-driven translocation of a 58-nucleotide DNA strand through the transmembrane pore of alpha-hemolysin. (more info) (request) |
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Ion permeation through alpha-hemolysin
(.mpg, 2.9M) (YouTube version) This movie shows induced by a 240mV bias currents of K+ and Cl- ions through the transmembrane pore of alpha-hemolysin. (more info) (request) |
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Water channels in cell membranes (.mpg, 13.1M) (YouTube version) This is our water permeation movie for the 2003 Nobel prize in Chemistry! (movie details) (more info) (request) |
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Confining DNA (.mpg, 4.2M) This movie illustrates a molecular dynamics simulation of poly(dA11) strand in a shrinking pore. (more info) (request) |
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Stretching DNA (.mpg, 4.4M) This movie illustrates the stretching of a poly(dA11) strand by a constant force applied to its 5' (bottom) end. (more info) (request) |
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Opening simulation of LacI-DNA complex (.mov, 2.4M) Forces are applied to the ends of the protein-bound DNA segments in order to mimic the opening of the lac repressor in vivo and in experiment. The color scale of the elastic rod model of DNA corresponds to the energy stored along the loop (red showing high density of elastic energy, and blue, low energy density). (more info) (request) |
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The lock opening in LacI (.mp4, 3.0M) Opening of the lock of LacI, where three groups of interacting residues keep lacI in the ''V'' configuration when wrestling the DNA loop. (more info) (request) |
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Stretching the anthrax
toxin-receptor complex (.mpg, 4.2M) This moving shows stretching the receptor CMG2 away from the anthrax toxin protein PA under neutral conditions. (more info) (request) |
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Stretching FN-III-1 (.mpg, 2.2M) Stretching the extra-cellular matrix protein fibronectin type III1 module. (more info) (request) |
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Sugar permeation through LacY (.mpg, 2.8M) Lactose is induced through LacY by SMD. The kink of helix I (in pink) facilitate smooth sugar passage. Lactose undergoes a rotation passing the central binding cavity. (more info) (request) |
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Ion-SWNT Terahertz Oscillator (.mpg, 395k) A potassium ion interacts with a 16 Angstroms carbon nanotube. The ion induces a strong dielectric response in the nanotube wall that can be described by a self-consistent tight-binding method. (more info) (request) |
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DNA forced through small nanopore (.mpg, 3.8M) A high electric field forced dsDNA through a 2.0 nm diameter pore that is impermeable at smaller fields. The 6.5 V bias deformed the DNA helix, shifting one of the strands relative to the multiscale by approximately one nucleotide, while preserving the hydrogen bonds between strands. (more info) (request) |
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Determining voltage threshold for
translocation of dsDNA (.mpg, 13.3M) This video is from a simulation done to establish the threshold field required to drive dsDNA through a 2.0 nanometer diameter pore. Here, a 3.9 V path caused the partial unzipping of the DNA strands prior to reaching the center of the membrane. (more info) (request) |
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Ionic Conduction through Silica Nanopore (.mpg, 7.2M) (YouTube version) This movie illustrate the conduction of KCL through a silica nanopore. The nanopore has 1 nm radius, KCL is in solution and under 1 V bias (more info) (request) |
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Simulation of an empty viral capsid. (.mpg, 15.4M) The empty capsid of Satellite Tobacco Mosaic Virus was simulated for 10 ns. Although the complete virus is very stable, the empty capsid collapses: a pronounced instability develops on the surface. If you are having problems viewing this video, please try using QuickTime. (more info) (request) |
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Simulation of the complete virus. (.mpg, 21.6M) The complete Satellite Tobacco Mosaic Virus was simulated (1 million atoms for 14 ns). The virus is very stable, however its compounds exhibit considerable motion in an asymmetric fashion. If you are having problems viewing this video, please try using QuickTime. (more info) (request) |
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Translocation of a polypeptide helix
through SecY (.mpg, 3.1M) (YouTube version) Viewed from the cytoplasmic side of the membrane, SecY is shown opening for a polypeptide helix as it is pulled across the channel. The helix, shown in blue, forces open the pore ring (transparent yellow) and displaces the plug of SecY (red), thus completing a protein translocation event. (more info) (request) |
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K+ permeation through Kv1.2 channel (.mpg, 1.6M) The movie shows simulation of K+ conduction through Kv1.2 under a voltage bias. The conduction occurs via the knock-on mechanism as suggested by Hodgkin and Keynes about 50 years ago. (more info) (request) |
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