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You searched for +publisher:"University of Notre Dame" +contributor:("Professor S. Alex Kandel, Committee Member"). One record found.

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University of Notre Dame

1. Christopher Joseph Fennell. Development of Molecular Dynamics Techniques for the Study of Water and Biochemical Systems</h1>.

Degree: Chemistry and Biochemistry, 2006, University of Notre Dame

This dissertation comprises a body of research in the field of classical molecular simulations, with particular emphasis placed on the proper depiction of water. It is arranged such that the techniques and models are first developed and tested before being applied and compared with experimental results. Accordingly, the first chapter starts by introducing the technique of molecular dynamics and discussing technical considerations needed to correctly perform molecular simulations. The second chapter builds on these consideration aspects by discussing correction techniques for handling long-ranged electrostatic interactions. Particular focus is placed on the damped shifted force (SF) technique, and it is shown to be nearly equivalent to the Ewald summation in simulations of condensed phases. Since the SF technique is pairwise, it scales as O(N) and lacks periodicity artifacts. This technique is extended to include point-multipoles, and optimal damping parameters are determined to ensure proper depiction of the dielectric behavior of molecular systems. The third chapter applies the above techniques and focuses on water model development, specifically the single-point soft sticky dipole (SSD) model. In order to better depict water with SSD in computer simulations, it needed to be reparametrized, resulting in SSD/RF and SSD/E, new variants optimized for simulations with and without a reaction field correction. These new single-point models are more efficient than the more common multi-point models and better capture the dynamic properties of water. SSD/RF can be used with damped SF through the multipolar extension described in the previous chapter. The final chapter deals with a unique polymorph of ice that was discovered while performing simulations with the SSD models. This form of ice, called imaginary ice (Ice-i), has a low-density structure which is different from any previously known ice polymorph. The free energy analysis discussed here shows that it is the thermodynamically preferred form of ice for both the single-point and commonly used multi-point water models. Including electrostatic corrections is necessary to obtain more realistic results; however, the free energies of the studied polymorphs are typically so similar that system properties, like the volume in NVT simulations, can directly influence the ice polymorph expressed. Advisors/Committee Members: Professor Dennis C. Jacobs, Committee Member, Professor S. Alex Kandel, Committee Member, Professor Gregory V. Hartland, Committee Member, Professor J. Daniel Gezelter, Committee Member.

Subjects/Keywords: molecular dynamics; computer simulations; water; ice polymorphs; electrostatic corrections

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Fennell, C. J. (2006). Development of Molecular Dynamics Techniques for the Study of Water and Biochemical Systems</h1>. (Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/fx719k4450v

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Fennell, Christopher Joseph. “Development of Molecular Dynamics Techniques for the Study of Water and Biochemical Systems</h1>.” 2006. Thesis, University of Notre Dame. Accessed July 02, 2020. https://curate.nd.edu/show/fx719k4450v.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Fennell, Christopher Joseph. “Development of Molecular Dynamics Techniques for the Study of Water and Biochemical Systems</h1>.” 2006. Web. 02 Jul 2020.

Vancouver:

Fennell CJ. Development of Molecular Dynamics Techniques for the Study of Water and Biochemical Systems</h1>. [Internet] [Thesis]. University of Notre Dame; 2006. [cited 2020 Jul 02]. Available from: https://curate.nd.edu/show/fx719k4450v.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fennell CJ. Development of Molecular Dynamics Techniques for the Study of Water and Biochemical Systems</h1>. [Thesis]. University of Notre Dame; 2006. Available from: https://curate.nd.edu/show/fx719k4450v

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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