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Lipid Bilayer Molecular Dynamics
Participating group members: Fuchang Yin, Hao
Wang, Patrick Coppock
Watch a 20 Mbyte quicktime
animation of the reconstruction of the bilayer ribbon edge!
(10 ps/frame, made from a Gromacs molecular dynamics trajectory
using VMD and GraphicConverter)
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As lipid bilayers form the basis of all biological membranes, their
physical properties influence many aspects of cell biology. Because
bilayers are generally tough and resistant to tearing, their edges
are typically unstable – a patch of bilayer will typically get rid
of its edges by merging with other patches or by curving around to
form an unbroken vesicle. The unstable edge may be an important
player, however, in transient processes like membrane pore formation
and bilayer fusion. We are simulating bilayer ribbons of the
phospholipid DMPC in water to investigate the structure, energetics,
and dynamics of the bilayer edge. We use the molecular dynamics code
Gromacs , which we run in
parallel on our Linux cluster . For a starting configuration, the
bilayer edge was created by removing a strip of lipids from a
continuous bilayer (coordinates obtained from the Tieleman group
website at
the University of Calgary) and filling the space with water. This
leaves a region of unfavorable contact (at the left and right edges
of the cross-sectional view shown below) between the lipids'
hydrophobic tails (grey) and the surrounding water (not shown):
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Over the course of several nanoseconds of simulation time, the
structure evolves as the lipid's hydrophilic headgroups (red)
migrate around the edge to eliminate this unfavorable contact:
We have analyzed the structure, dynamics, and energetics
of this reconstructed DMPC bilayer edge and published our findings in
the Biophysical Journal.
Recently, we have been exploring the equilibrium distribution of lipids with different
tail lengths near the bilayer edge, first
using a coarse-grained model, and more recently (as in the snapshot below, in which blue represents DMPC and
red represents DDPC) through atomistic simulations in the semi-grand canonical ensemble. For more on mixed-lipid
systems, see here.
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