Browsing Science (Faculty of) by Subject "molecular dynamics"
Now showing items 1-7 of 7
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Computational Design of Protein Structure and Prediction of Ligand Binding
(University of Waterloo, 2016-08-23)Proteins perform a tremendous array of finely-tuned functions which are not only critical in living organisms, but can be used for industrial and medical purposes. The ability to rationally design these molecular machines ... -
Molecular movies and geometry reconstruction using Coulomb explosion imaging
(University of Waterloo, 2017-08-24)Coulomb explosion imaging is a technique of imaging the structure of small molecules in the gas phase and their ultrafast dynamics by inducing the rapid ionization and dissociation of the molecule into its constituent ... -
Path integral ground state approaches for the study of weakly bound clusters and confined molecules
(University of Waterloo, 2018-09-21)This thesis presents the study of weakly bound clusters in the ground state (or the zero-temperature limit) using path integral molecular dynamics. Specifically, we look individually at the quantum properties of small ... -
Path integral Langevin dynamics of complex molecular systems: from low-temperature quantum clusters to biomolecules
(University of Waterloo, 2011-08-31)This thesis presents an implementation of path integral molecular dynamics (PIMD) for sampling equilibrium and dynamical properties within the molecular modelling toolkit (MMTK) [J. Comp. Chem. 21, 79 (2000)], an open ... -
Probing the interactions that drive RNA binding and self-association of hnRNPA1 implicated in neurodegeneration
(University of Waterloo, 2024-01-17)The heteronuclear ribonucleoprotein A1 (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 has been ... -
Quantum mechanical free energy calculations using path integral molecular dynamics
(University of Waterloo, 2019-12-19)Free energy calculations are one of the most powerful tools within modern theoretical chemistry and are often used to make comparisons with experimental results. Existing free energy calculations are typically performed ... -
Understanding the dynamics and molecular interactions of the human cannabinoid receptor 1
(University of Waterloo, 2022-08-23)Cannabinoid receptor 1 (CB1), one of the most populated G-protein coupled receptors (GPCR) present within the brain, is involved in various physiological and homeostatic processes. These pathways include metabolism and ...