Predicting properties of proteins and polymers by coarse grained methods and using nanoprobes

The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the different methodologies used for constructing residue networks from knowledge of the experimental coordinates. In the first part of the thesis, we present a systematical study of network construction strategies, and we study their effect on the predicted properties using Anisotropic Network Model (ANM). The analysis is based on the radial distribution function and the spectral dimensions of a large set of proteins as well as a newly defined quantity, the angular distribution function. In the second part of the study, we apply ANM to the well-relaxed atomistic coordinates of a 32- chain C128 cis-1,4-polybutadiene system to test the extent of applicability of the method. 15- 60 ns long molecular dynamics (MD) simulations are carried out for a wide variety of temperatures and pressures. The mean-square fluctuations of the central carbon atoms obtained by applying ANM on a few snapshots are shown to be in good agreement with values from full MD simulations. This leads to predict average flexibility values of the system under different conditions. We extend the methodology to approximate the virial of the system. In the third part, to understand the nanoclusters' behavior and influence on the polymer's viscoelastic and thermodynamic properties, different nanoclusters having 10 to 150 atoms are embedded in the cis-1,4-polybutadiene matrix. First, the diffusion coefficient and zero shear viscosity are calculated from the simulations and compared with the experimental results obtained with rotational viscosimeter. In addition, correlation times of C-H bond vectors of simulation at four different temperatures were compared with the C-NMR experiments of cis-1,4-polybutadiene with high-cis-content polybutadiene (%93 cis, %3 trans and %4 vinyl). The agreement between simulation results and experiments confirm that the united atom force field used in the simulations well-describes the dynamics of the real system. It is also possible to manipulate mechanical properties by tuning the interaction strength of the nanoclusters with the chains. From a practical point of view, we can assume that bulk modulus is not much affected by the size of the nanocluster, whereas it linearly increases as the interaction strength changes from normal to strong. Another thermodynamical quantity, glass transition temperature (Tg) increases from ~176 K to ~184 K as the nanoclusters are introduced to the polymer melt. Tg decreases to ~178 K as their interaction strength is made much stronger than the standard value