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Past Events

Events which have already happened.

Talk- Dillion Fox (from Jun 11, 2018 11:00 AM to Jun 11, 2018 12:30 PM)
Structural Modeling of the Intrinsically Disordered Reflectin Protein
No talk (from Jun 04, 2018 11:00 AM to Jun 04, 2018 12:05 PM)
 
No talk (from May 28, 2018 11:00 AM to May 28, 2018 12:00 PM)
 
Talk- Maxim Lavrentovich (Guest speaker) (from May 21, 2018 11:00 AM to May 21, 2018 12:30 PM)
 
Talk- Sunny Hwang (from May 14, 2018 11:00 AM to May 14, 2018 12:30 PM)
Protein-mediated transport of mercuric ions across the bacterial inner membrane
Talk- Michelle Aranha (from May 07, 2018 11:00 AM to May 07, 2018 12:30 PM)
Metal oxide nanoparticle – lipid bilayer interactions and vaccine development against Group A streptococcus In this talk, I will discuss the preliminary results from two topics: 1) metal oxide - lipid bilayer interactions and 2) vaccine development against Group A streptococcus (GAS) using a combination of computational, statistical and experimental approaches. Metal oxide - lipid bilayer interactions: In this study, we have assessed the effects of a metal oxide nanoparticle namely titanium dioxide (TiO 2 ) on unsaturated bilayers composed of uncharged DOPC lipids and negatively charged DOPG lipids. TiO 2 is a transition metal oxide and finds applications in pigments, additives, catalysts and construction materials. However, some experimental studies have uncovered the potential cytotoxic effects of transition metal oxide nanoparticles which include changes in cell morphology, mitochondrial functions, membrane leakage, necrosis and apoptosis. With their extensive use in a wide array of applications it has become of vital importance to understand their potential cytotoxic effect to design them for safe applications. Molecular dynamics (MD) simulations can help shed some light on the nature of the interaction when the metal oxide nanoparticle first encounters the cell membrane. For instance, in the case of DOPC, we have found a localized decrease in the bilayer thickness on account of a compression of head groups together rather than any perturbation of the tail groups, a depletion in the hydration layer of the DOPC leaflet at the point of contact with the nanoparticle and a slowdown in diffusion of lipids after it comes in contact with nanoparticle. Through our atomistic MD study, we have assessed the effect on structural and dynamical properties of both DOPC and DOPG bilayers. These preliminary studies may pave the way for a more detailed study into the differential interactions of various other metal oxide nanoparticles with mixed lipid bilayers. Vaccine development against (GAS): This study will demonstrate how the use of combined computational, statistical and experimental approaches can exploit the structural similarities of the N -terminal region of M proteins of the more than 200 strains of GAS bacteria to predict the M peptides that will evoke cross-opsonic antibodies against heterologous strains of GAS. We have used homology modeling to predict the N - terminal structures of M proteins of 21 strains belonging to a sequence -based cluster. Unsupervised learning on structure-based features and supervised learning employing regression were used to detect relatedness among different M peptides as well as to identify any peptide structure - activity relationship. Clusters of related M peptides identified by these methods were used to select a few M peptides to incorporate into the first vaccine construct.
Talk- Konstantinos Vogiatzis (Guest speaker) (from Apr 30, 2018 11:00 AM to Apr 30, 2018 12:30 PM)
 
Journal Club (from Apr 25, 2018 11:00 AM to Apr 25, 2018 12:00 PM)
Led by Quentin Johnson & Jeremy Smith
No Talk (from Apr 23, 2018 11:00 AM to Apr 23, 2018 12:30 PM)
 
Journal Club (from Apr 18, 2018 11:00 AM to Apr 18, 2018 12:10 PM)
Led by Utsab Shrestha & Loukas Petridis
Talk- Julie Mitchell (from Apr 16, 2018 11:00 AM to Apr 16, 2018 12:30 PM)
 
Journal Club (from Apr 11, 2018 11:00 AM to Apr 11, 2018 12:00 PM)
Led by Yead Jewel & Jeremy Smith
Talk- Ada Sedova (from Apr 09, 2018 11:00 AM to Apr 09, 2018 12:30 PM)
Ab initio simulations of nucleic acid oligonucleotides and building blocks using the Oak Ridge Leadership Computing Facility (OLCF) Supercomputers.
Journal Club (from Apr 04, 2018 11:00 AM to Apr 04, 2018 12:00 PM)
Led by Adam Green & Jerry Parks
Talk- Adam Green (from Apr 02, 2018 11:00 AM to Apr 02, 2018 12:30 PM)
 
Journal Club (from Mar 28, 2018 11:00 AM to Mar 28, 2018 12:00 PM)
Led by Deepa Davarjan & Jerry Parks
Talk- Hong Guo (from Mar 26, 2018 11:00 AM to Mar 26, 2018 12:30 PM)
Computer Simulation and Analysis of Proteins: from Study of One Protein at a Time to Analysis of One Million Proteins All Together
Journal Club (from Mar 21, 2018 11:05 AM to Mar 21, 2018 12:05 PM)
Led by John Eblen & Jeremy Smith
Talk- Tongye Shen (from Mar 19, 2018 11:00 AM to Mar 19, 2018 12:30 PM)
Fantastic molecular motions and how to capture them
No Journal Club-Spring Break (from Mar 14, 2018 11:00 AM to Mar 14, 2018 12:00 PM)
 
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