Simulation studies of slow dynamics of hydration water in lysozyme : hydration level dependence and comparison with experiment using new time domain analysis

A series 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 applied to investigate mainly behaviors of water molecules than those of biopolymers, which has been originally the simulation target of GROMACS package. The protein (Lysozme) - water system is simulated using TIP4P water potential to model the slow dynamics of the hydration water at low temperatures well. Besides the simulation works, a new time domain Relaxing-Cage Model (RCM) fitting methodology is introduced in the experiment part. We use the Gaussian functions to convert the Intermediate Scattering Functions (ISF) from Quasi-Elastic Neutron Scattering (QENS) experiments from frequency domain to time domain. Then, the Relaxing-Cage Model (RCM) fitting is performed on the converted ISF in time domain. The average translational relaxation time of the MD simulation is compared with the QENS experiment. Three different hydration levels are designed and used in the MD simulations. Other quantities, which can be used to observe the crossover phenomena of the hydration water, such as the number of hydrogen bonds, Mean Squared Displacement (MSD), the structure factors S(Q) and the radial distribution functions g(r) are compared at the different hydration levels.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Nuclear Science and Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2008

Author dc:creator

• Kim, Chansoo, S.M. Massachusetts Institute of Technology

Advisor dc:contributor.advisor

• Sow-Hsin Chen.

• Nuclear Science and Engineering.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/53283

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/53283