| Summary: | Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2008. === Cataloged from PDF version of thesis. === Includes bibliographical references (p. 140-142). === 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. === (cont.) We have found that experiment and simulation agree well in terms of the crossover temperature TL at hydration level 0.3: TL (experiment) is 226 K and T, (simulation) is 221 K, and those are in the crossover temperature range of 220 + 10 K. The crossover temperature obtained from the average translational relaxation time increases as the hydration level becomes lower. The crossover phenomenon is also observed in the number of hydration bonds between water and water. It only appears in hydrogen bonds between water and water (not in bonds between water and Lysozyme case), so we can say that water can trigger the biomolecules' functionality. The main observations of this thesis is that the crossover temperature depends on the hydration level even though the crossover phenomenon occurs at any hydration level and water possibly triggers the biomolecules' functionality. === by Chansoo Kim. === S.M.
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