טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentRina Oldek
SubjectMolecular Simulations and Cluster Formation in Solutions of
Globular Proteins
DepartmentDepartment of Chemical Engineering
Supervisor Full Professor Brandon Simon
Full Thesis textFull thesis text - English Version


Abstract

Investigation of phase equilibrium and dynamics of protein solutions is important for understanding fundamental phenomena associated with solution growth, pharmaceutical processes, and mechanisms underlying the development of a variety of diseases. In protein solutions, a variety of interaction forces can arise between the protein molecules and are often modeled using a short-ranged attractive potential. The resultant model phase diagram exhibits a region of metastable coexistence, a dilute fluid phase with its dense counterpart. Moreover, in these solutions, solvent structuring observed around the protein surface is sometimes modeled by introducing a long-ranged repulsive part to the potential.

Brownian dynamics were used to study phase behavior of a model protein solution, using a short-ranged attractive potential without (alpha-LJ) and with (h-LJ) an additional term that can account for longer range repulsion forces (h-LJ). Deposition of protein molecules on an FCC (110) surface is also investigated using the short-ranged potential.

We show that, at moderate densities, a two-step nucleation mechanism occurs for both model systems, as was suggested by experiments and simulations. However, the nucleation rate exhibits a dependency according to the classical nucleation theory for the alpha-LJ potential, while for the h-LJ potential a maximum in nucleation rate is observed slightly above the L-L coexistence line. At low densities the same qualitative results are achieved regarding the nucleation rate, although under these conditions many drops are formed, exhibiting non-trivial dynamics of growth, dissolution, aggregation and crystallization.

The size of the first cluster that nucleates is shown to be correlated to the nucleation rate. We show that for both model systems, as the size of the first nucleated cluster increases, the nucleation rate either decreases (at constant density) or increases (at constant temperature).  A possibly unstable region is observed for intermediate density values under the L-L coexistence line, where the density is found to have no effect on the nucleation rate for both systems.

Clusters that are formed using the alpha-LJ potential tend to obtain a compact structure while in the h-LJ system arched-like clusters are formed. Furthermore, a new cluster-growth mechanism is observed in the h-LJ system, where a drop, which is close enough to a large crystalline cluster, interacts with the cluster by wetting its surface. 

 In systems which include a crystalline planar surface (substrate), liquid clusters are also formed below the L-L coexistence line. Nucleation of these clusters begins only as they approach close enough to interact with the surface.