Godwin, Larry (2013). Computational Mechanics Analysis of the Hidden Conformational Dynamics within a Molecular Trajectory. Masters thesis, Aston University.
Abstract
In this research, the conformational dynamics of a peptide, VPAL, is investigated. Molecular Dynamic Simulation (MD) and Computational Mechanics (CM) methods are both applied to study this dynamic behaviour of VPAL. MD was used to simulate the microscopic behaviour, while the analysis was done using CM. From the analysis and the result it is observed that, at certain time scale (140ps) the conformational dynamics of VPAL dynamics is Markovian, but as the time step reduces (Δt8 < 140ps) it becomes Non-Markovian, which is clearly described by the ε-machine constructed from the dynamics at different Δt8.
| Publication DOI: | https://doi.org/10.48780/publications.aston.ac.uk.00022277 |
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| Additional Information: | Copyright © Chattopadhyay, Amit K. 2013. Amit K Chattopadhyay asserts their moral right to be identified as the author of this thesis. This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with its author and that no quotation from the thesis and no information derived from it may be published without appropriate permission or acknowledgement. If you have discovered material in Aston Publications Explorer which is unlawful e.g. breaches copyright, (either yours or that of a third party) or any other law, including but not limited to those relating to patent, trademark, confidentiality, data protection, obscenity, defamation, libel, then please read our Takedown Policy and contact the service immediately. |
| Institution: | Aston University |
| Uncontrolled Keywords: | protein folding,peptide dynamics,conformational conformational dynamics of protein/peptides,molecular dynamic simulation (MD),computational mechanics (CM),causal states,metastable states,GROMACS,verlet algorithm,e-machine,biomolecular simulation,microscopic interactions and trajectories |
| Last Modified: | 12 Jun 2025 14:33 |
| Date Deposited: | 07 Apr 2014 10:30 |
| Completed Date: | 2013-10 |
| Authors: |
Godwin, Larry
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