Cool Images
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Gas Hydrates
Initial Research in the Lab (extending from Dr. Klauda's Ph.D. work) was on Gas Hydrate research. Using thermodynamic and mass transfer modeling, estimates in location and amounts of methane in gas hydrate form were made. At the time (2005), this was found to be an order of magnitude or higher than conventional reserves (Energy & Fuels. vol 19: p459)
Figure 7 from Energy & Fuels. vol 19: p459.
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Cell Membrane Modeling
- E. Coli's Inner Membrane: Modeling the lipid diversity in cellular membranes has been a key focus in the lab. One of the first studies was on the inner membrane of E. coli with its unique cyclopropane-containing lipids.
Coordinates from BBA-Biomemb. 1818: p1205. with cylopropane in blue. - Modified Lipids and Pore Formation: Lipids have been chemical altered to potentially change the permeability of a membrane. Ester-modified lipids by placing this group in the acyl chain was shown to develop pores that are large enough for water and ions to permeate.
Coordinates from Langmuir. 29: p14196. with ions in yellow, water in blue and ester-modified lipids in red. - Modeling Ethanol Production in Cells: We have been modeling chemical and fuels production in single-celled organisms using molecular simulation. The damage to the cell be chemical production can be due to membrane cell distruction or increased leakage. The following image is of ethanol at 12 mol%.
Coordinates from J. Phys. Chem B. 119: p13134. with ethanol in orange and lipids other colors. - Modeling Stratum Corneum (SC) of Skin: We have been modeling the SC to probe the structure and resistance of this skin layer to drug permeation. Ceramides in the SC can form a dual bilayer with a sandwiched fluid in the middle to form the long and short periodicity phases seen in experiment. We aim to use this model to investigate dermal delivery.
Coordinates from to be published work. - Modeling Leaflet Asymmetry in Yeast Plasma Membrane: Many cellular membranes naturally have leaflet composition asymmetry, but the ability to model this has only been reachable recently. In this image we are modeling the asymmetry of the yeast plasma membrane with its inositol-containing ceramides in the outer leaflet.
Coordinates from to be published work.
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Protein Modeling
- Lactose Permease: This integral membrane protein is classified as a secondary active transporter (SAT) that can transport lactose across the cell membrane coupled to the proton transport in a symport mechanism. We have studied this protein's binding and structural changes as a simple model for this class of SAT proteins.
Coordinates from J. Mol. Bio. 367: p1523. with sugar in green. - Oxysterol Binding Proteins: These proteins are involved in lipid exchange within the cell and form membrane contact sites to faciliate this exchange. We study the Osh4 protein in yeast to model this lipid exchange.
Coordinates from J. Mol. Bio. 423: p847. - Plexin: Plexin proteins are important group of transmembrane receptors that are involved in growth of neurons, bones, but also associated with growth diseases like cancer. Our initial work in collaboration with Dr. Berger at U. Virigina focused on understanding the dimerization of these proteins in the transmembrane and juxtamembrane region for Plexin A3.
Coordinates from Biochem. 55: p4928. - semi-SWEET Transporters: In addition to LacY we have also simulated the SWEET transporters that dimerize in transporting monosaccharids across the bilayer. We have been able to use unbiased MD simulations to probe the transport cycle of this uniporter.
Coordinates from J. Mol. Bio. 430: p3337.
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Educational
- Time/Length Scale Diagram: In modelling one must always consider the time/length scales attainable with different methods. Below is a simple figure that illustrates this.
