Off-campus UMass Amherst users: To download campus access theses, please use the following link to log into our proxy server with your UMass Amherst user name and password.

Non-UMass Amherst users: Please talk to your librarian about requesting this thesis through interlibrary loan.

Theses that have an embargo placed on them will not be available to anyone until the embargo expires.

Access Type

Open Access

Document Type

thesis

Degree Program

Mechanical Engineering

Degree Type

Master of Science (M.S.)

Year Degree Awarded

2009

Month Degree Awarded

May

Keywords

Elastic Network Model, Normal Mode Analysis, Spectroscopy

Abstract

A novel method of analysis of macromolecules has been worked upon through this research. In an effort to understand the dynamics of macromolecules and to further our knowledge, pertaining specifically to the low frequency domain and also to elucidate certain important biological functions associated with it, a theoretical technique of chemical information based Normal Mode Analysis has been developed. These simulations render users with the ability to generate animations of modeshapes as well as key insight on the associated vibration frequencies. Harmonic analysis using atomistic details is performed taking into account appropriate values of masses of constituent atoms of a given macromolecule. In order to substantiate the applicability of such a technique, simple linear molecules were first worked upon. Subsequently, this technique has been applied to relatively more complex structures like amino acids, namely Cysteine. Consequently, this approach was extended to large macromolecules like Lactoferrin. Animations of modeshapes from simulations suggest a one to one correspondence with other computational techniques reported by other researchers. Computed β-factors are also in close agreement with the experimentally observed values of the same. Hence, as opposed to a simple Cα coarse grained model, our method with right masses and reasonable force fields yields not only the correct modeshapes but also provides us with useful information on wavenumbers that can be used to extract useful information about the frequency domain. Moreover, as opposed to conventional Molecular Dynamics’ simulations and Laser spectroscopy, the proposed methodology is significantly faster, cheaper and efficient.

DOI

https://doi.org/10.7275/752396

First Advisor

Moon Ki Kim

Second Advisor

Byung H. Kim

COinS