Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 46 for “"Molecular dynamic simulations"”.
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Structure and Property of Polymers and Biopolymers from Molecular Dynamic Simulations
… important to determine their functions. Molecular dynamics (MD) simulations have a unique advantage to explore the structure and property of polymers and biopolymers from the molecular level. In the dissertation, MD simulations were conducted to study the mechanisms of various biological …
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Small Molecules as Amyloid Inhibitors: Molecular Dynamic Simulations with Human Islet Amyloid Polypeptide (IAPP)
… features that impede IAPP aggregation, molecular dynamics (MD) simulations were performed on a model fragment of IAPP(20-29) in the presence of morin, quercetin, dihydroquercetin, epicatechin, and myricetin. Contacts between Phe23 residues are critical to oligomer formation, and …
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Using Unnatural Amino Acids and Nonnative Cofactors for Metalloprotein Design and Engineering
… enzyme in a modular and accumulative fashion. Molecular dynamic simulations indicate that these changes may be due to the steric effects of the linker arms inside the protein cavity. The realization that the covalent anchors exert effects through interaction with substrates entering the pocket …
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Ligand Binding and Structural Dynamics in C-Type Cytochromes
The first molecular dynamic simulations of the interaction of cyt c and yeast bc1 complex are described. Contrary to results from crystallographic studies, the simulations reveal multiple dynamic hydrogen bonds and salt bridges in the cyt c-c 1 interface. A novel structural change in cyt c is also …
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Modeling of Therapeutic Drugs, Polymers, and Self-Assembling Peptides
… materials. In particular, we conducted atomistic molecular dynamics simulations to study systems in three main areas: A) small drugs and therapeutic polymers, B) therapeutic peptides, and C) materials based on self-assembled peptides. A) We designed and investigated antivirals based on …
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Understanding Heterogeneous Nucleation Mechanisms in Polyolefins
… uncertainty in the measured kinetics and thermodynamics of nucleation. Molecular simulations have recently showed promise to investigate the nano time- and length- scales associated with nucleation, but remain unverified with real materials. This thesis advances the way that heterogeneous …
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Chemogenomic approaches to drug design : docking-based virtual screening of nematode GPCRs for potential anthelmintic agents
… identity with the template. Explicit membrane molecular dynamic simulations were used to optimize and refine the helices of the model over 100 ns. The homology model was of acceptable quality.
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Synthesis and modification of pamam dendrimers as histone replacement molecules
… dendrimer-DNA compaction using linear dichroism, dynamic light scattering and competitive binding of ethidium. Experiments designed to investigate modified dendrimer-lipid interactions are also discussed and the results of these are compared to molecular dynamic simulations. The synthesis of novel …
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Transport studies in graphene-based materials and structures
… in graphene-based systems. We employ the molecular dynamic simulations to study the thermal transport in graphene nanoribbons (GNRs) exhibiting various properties, including chirality dependent thermal conductivity, thermal rectification in asymmetric GNRs, defects and isotopic engineering …
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Polyurea aerogels: From nanoscopic to macroscopic properties
… for the formation of these nanoparticles through Molecular Dynamic simulations is suggested"--Abstract, page iv.
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Design and characterization of zeolite membranes for fluid separation
… of all the composite membranes investigated. Molecular simulation methods were used to gain an understanding of how hydrocarbon molecules behave both within the pores and on the surfaces of silicalite-1, mordenite and LTA zeolites. Molecular dynamic simulations were used to investigate the …
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Biophysical Characterization of the Interaction between the Universal Stress G4LZI3 protein and Schistosoma mansoni Hsp60 Substrate Binding Domain
… the interaction between the two proteins. Molecular dynamic simulations were implemented in the present study chosen based on their robustness and effectiveness in interpreting binding conformational changes between the protein and its ligand. MD simulations analysis done in the study …
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Biophysical investigations of the interaction between substrate binding domain of Hsp40 and the RING finger domain of Retinoblastoma Binding Protein 6
… between these two proteins. In this study molecular dynamic simulations were used to confirm the interaction between the proteins and associated binding parameters. This was followed by the recombinant expression of the proteins within two difference expression vectors and E. coli bacterial …
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Direct energy landscape sampling of the homogeneous nucleation and crystal growth of a model liquid
… process over long timescales with molecular dynamic simulations have met major obstacles because of the temporal constraints of molecular dynamics. Herein, we circumvent this temporal limitation by using an improved metadynamics method based on the adaptive basin-climbing algorithm …
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INTEGRATION OF QUANTUM-MECHANICAL AND MOLECULAR DOCKING APPROACHES IN GLOBAL METHODS FOR METABOLISM PREDICTION OF XENOBIOTICS
… ligand-based approaches alone. Then, docking and molecular dynamic simulations were carried out using the bonded model within the MCPB.py approach, to efficiently parametrize the porphyrin ring. Then classification models were built using both ligand and structure-based information, provided by …
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Developments in the Theory of X-ray Absorption and Compton Scattering.
… Green’s function (RSGF) approach coupled with molecular dynamic simulations to create a representation of a disordered system. Thermal disorder has the effect of smearing the high momentum umklapp peak in the case of Be and Li. I find good agreement with experimental results and, to a good …
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Light-induced transformations in biomembranes
… The partition coefficient calculated from molecular dynamic simulations agrees with experimental data obtained with size-exclusion chromatography. Then, we implement the approach of vesicle electrodeformation in order to assess the increase in the membrane area, which is observed as a …
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Multiscale Mechanics of Graphene Oxide and Graphene Based Composite Films
… possess high strength in the gigapascal range. Molecular Dynamic simulations showed that the transition in the failure behavior from interplanar fracture to intraplanar fracture was responsible for the huge strength discrepancy between nanometer scale GO and bulk GO papers. Additionally, the …
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Theoretical Studies of Protein-Protein Interactions
… methods, e.g. First Passage Processes method, to Molecular Dynamics and Brownian Dynamics simulations. We first gain insights into the structure of the ERK2-EtsΔ138 complex. We find that in the lowest energy complex F120 residue of EtsΔ138 occupies ψ2 hydrophobic pocket of the FRS of ERK2 and that …
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BIOPHYSICAL STUDIES OF THE MECHANISM OF CERAMIDE CHANNEL DESTABLIZATION BY BCL-XL IN APOPTOSIS AND THE USE OF RECTIFICATION TO PROBE THE STRUCTURE AND DYNAMICS OF A NOVEL ESCHERICHIA COLI CHANNEL
… outer membrane permeability assay, and molecular dynamic simulations. Interestingly, the hydrophobic groove serves to inhibit another channel former, Bax. We found that the binding sites for Bax and ceramide on Bcl-xL are distinct but overlapping. We used that fact to generate mutants …
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