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 10 of 10 for “"GROMACS"”.
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Simulation studies of slow dynamics of hydration water in lysozyme : hydration level dependence and comparison with experiment using new time domain analysis
… of Molecular Dynamics (MD) simulations using the GROMACS® package has been performed in this thesis. It is used to mimic and simulate the hydration water in Lysozyme with three different hydration levels (h = 0.3, 0.45 and 0.6). In this thesis, GROMACS is used in an innovative way, because it is …
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Optimizing xylitol production: a molecular and experimental study of xylose reductase in Candida tropicalis
… molecular dynamics simulations using GROMACS and the pHbuilder tool are employed. By analyzing the enzyme’s stability and structural dynamics across different pH levels, this research aims to improve xylitol yield while minimizing environmental impact. The findings contribute to …
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Application of molecular mechanics polarization to fragment based drug design.
… After some performing some MD simulations in GROMACs we found that GPUs were an improved option and thus continued the simulation work with ACEMD which allowed multiple GPUs in tandem. After running the MD simulations for 200ns with atomic charges generated from the polarization the results we …
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Investigating Lipase Stability in Hydrophobic Solvent at Extreme Temperatures: A Molecular Dynamics Study of Candida Antarctica Lipase B in Polydimethylsiloxane
… of a PDMS force field to enable use with the GROMACS software and were subsequently combined with the CHARMM36 biomolecular force field. Validation of the force field adaptions showed excellent agreement with the experimental results and the original force field validation. MD simulations of …
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Stability Study of Engineered Ferritin Nano-vaccines by Combined Molecular simulation and Experiments
… this project, experiments and MD simulations on Gromacs were used to examine the hydrophobic, thermal, and pH stability of four genetically altered human heavy-chain ferritins (C1, C2, C3, and C4). By working on this project, we can determine how the mutation will impact the HFns' stability …
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BUILDING A MODEL TO SIMULATE PROTEIN AGGREGATION AT ATOMISTIC DETAIL.
… models into one and perform MD simulations using GROMACS. The method was developed using a short peptide derived from the Transthyretin protein. The first attempt was to coarse grain the representation of the TTR peptide mapping a single bead per residue on the Cα. However, such simplified …
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Molecular-level modelling of complex liquid interfaces
… developed for measuring the contact angle for GROMACS coordinate files which, whilst producing efficient results for uniform spreading, is generally than the more traditional method. However for non-uniform spreading it could be argued that the traditional method is less reliable. Analysis of a …
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Biophysical and computational insights into the stability of RhoB and its cancer-associated variants
… region in Cdc42 spectra. MD simulations with GROMACS were employed to complement the experimental NMR dynamics and biophysical data collected on RhoB. The simulations were applied to predict how different Rho family proteins (RhoB, Cdc42 and RhoA) begin to unfold in silico. MD simulation …
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How life uses sound to reorganise matter: The role of anharmonic phonon exchange in enzyme catalysis
… prepared MalL crystals, then digitised into the Gromacs software package and energy minimised in a simulated water bath to approximate the vibrational modes of the in vivo configuration. I obtain the substrate molecule's harmonic frequencies and anharmonic shifts via molecular dynamics performed …
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A single AKH neuropeptide activating three different fly AKH-receptors: an insecticide study via computational methods
Flies are a widely distributed pest insect that poses a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic …