Laboratory of Molecular & Thermodynamic Modeling

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Images & Movies


Molecular Modeling


Timescales for molecular modeling of different simulation methods


Lipid Membranes

72 DPPC lipid bilayer fully hydrated at 323K simulated with the NPAT ensemble and PME/LRC. Water in blue spheres, Carbon silver, ends of aliphatic chain in yellow

288 DPPC lipid bilayer fully hydrated at 323K simulated with the NPAH ensemble and PME/LRC. Water omitted for clarity






72 DPPC lipid bilayer fully hydrated at 323K simulated with the NPAT ensemble and cutoffs. Unphysical freezing of chains to a ripple phase

Chain Order/Disorder of a DPPC Bilayer





Lipid Bilayer Movie: Dynamics of a fluid bilayer



Lactose Permease



a) LacY (purple) embedded in membrane b) Two domain structure (blue/green) of LacY with a water filled lumen (red spheres)




Sugar escaping the binding pocket and LacY's response a) top view b) side view. The intracellular loop covers the opening in response to sugar movement.


Lactose Permease Movie: Sugar Escape


Cholesterol/Sterol Transport Protein of Yeast (Osh4)



Cholesterol within the binding pocket of Osh4.


Gas Hydrates


Our volume estimate of CH4 at STP entrapped in hydrates in the seafloor. This modeling assumes that methane originates from seafloor organic carbon.

Gas hydrates (white) in the seafloor (blackish brown)