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Enhancing Performance Of Ionic Liquid Property Prediction With Molecular Dynamics., Trisha H. Patel
Enhancing Performance Of Ionic Liquid Property Prediction With Molecular Dynamics., Trisha H. Patel
Electronic Theses and Dissertations
Molecular dynamics have been used to predict thermodynamic and transport properties of eight room-temperature ionic liquids. Simulation parameters including box size and van der Waals cutoffs were varied. The density, heat capacity, and self-diffusion coefficients of the ionic liquids were computed and compared to experimental data and to previously published simulations. Predicted properties were generally close to their experimentally observed values. It was determined that the prediction of ionic liquid properties via molecular dynamics simulations could be accelerated several-fold by using less stringent integration parameters and smaller simulation sizes. The properties of density and heat capacity did not change significantly …
Sum Frequency Generation Spectroscopy Of Simulated Protein Secondary Structures., Andrew J. Adams
Sum Frequency Generation Spectroscopy Of Simulated Protein Secondary Structures., Andrew J. Adams
Electronic Theses and Dissertations
Sum frequency generation (SFG) spectroscopy is an experimental technique for differentiating between various conformations and orientations of interfacial proteins. Combining a theoretical framework for SFG with molecular dynamics (MD) simulations provides a powerful tool for studying systems containing interfacial proteins with applications in cell transport, biofilms, and fermentation processes. Roeters’ method was used to calculate theoretical SFG responses for a variety of individual α-helix and β-sheet peptide secondary structures simulated using MD. Results show how the shape and locations of SFG amide I responses change with differences in hydrogen bonding patterns, peptide orientations, and SFG polarization combinations. The data presented …
Understanding Carbohydrate Recognition Mechanisms In Non-Catalytic Proteins Through Molecular Simulations, Abhishek A. Kognole
Understanding Carbohydrate Recognition Mechanisms In Non-Catalytic Proteins Through Molecular Simulations, Abhishek A. Kognole
Theses and Dissertations--Chemical and Materials Engineering
Non-catalytic protein-carbohydrate interactions are an essential element of various biological events. This dissertation presents the work on understanding carbohydrate recognition mechanisms and their physical significance in two groups of non-catalytic proteins, also called lectins, which play key roles in major applications such as cellulosic biofuel production and drug delivery pathways. A computational approach using molecular modeling, molecular dynamic simulations and free energy calculations was used to study molecular-level protein-carbohydrate and protein-protein interactions. Various microorganisms like bacteria and fungi secret multi-modular enzymes to deconstruct cellulosic biomass into fermentable sugars. The carbohydrate binding modules (CBM) are non-catalytic domains of such enzymes that …