Molecular Simulations Of Several Typical Physical Processes

Aggregation, adsorption and deposition are physical phenomenon that widely present in nature. Dipeptide molecules aggregate into cross-linked gel structures in solution that can be used in drug delivery or water procession; Proteins secreted by marine organisms attach to surface of ships can accelerate corrosion and slow down the speed; template induced area selective growth of deposited organic molecule in vacuum can be used to synthesize functional materials. The above physical processes were widely used in our everyday life and production. So understanding the mechanism or driving forces behind them will help us to improve our production or life.In this thesis, we adopted molecular simulation method to research the mechanisms of several typical physical processes in order to make some guidance to production. As some of processes usually occur in large time scales, we used coarse grained model and mesoscopic Monte Carol method. The specific research contents are listed as below.1. A series of coarse grained molecular dynamics simulation were conducted to investigate the aggregation in solution. After200ns simulation, the Fmoc-dipeptide entangled to mutual cross-linked network which served as the three-dimensional hydrogel structure. In the architecture, obvious π-π stacking of neighbor Fmoc rings were found, convincing the π interaction as a driving force during the assembly. The process of the aggregation was:the Fmoc-dipeptides aggregate into small aggregations at the driving of π interaction and hydrophobic forces between Fmoc rings. Then the small aggregations grow and merged into larger one, and finally entangled with each other that served as the structure of gel. The dynamics of surrounding waters of hydrogel were largely slowed down by increasing the concentration of Fmoc-dipeptide. 2. A series of molecular dynamics simulations were conducted to investigate the non-fouling mechanisms of two typical materials PDMS and SBMA. At the end of simulations, both the proteins were adsorbed on membranes. We concluded that PDMS has a better combination with Lysozyme than SBMA by analyzing the types of residues near adsorption sites, contact areas, hydrogen bonds, VDW contacts between protein and membranes. This closely adsorption makes the protein not easy to leave from membranes. The interaction between protein and membrane, interaction between surface hydration layer and membrane also confirmed this. Then we concluded:1) PDMS has a larger attractive force on protein than SBMA at the whole distance range. Both the interactions between protein and membranes were energetically favorable, but Lysozyme interacted much more strongly with PDMS than SBMA.2) SBMA has plenty of hydrogen bonds, electrostatic interactions, and cage effects with surface waters that lead to a stable surface hydration layer. The hydration layers were believed to form a physical and energetic barrier to prevent protein adsorption on the surface. At last we proposed a possible mechanism of protein adsorption or anti-fouling:the first obligatory step of protein adsorption was the dehydration of both protein and the membrane. After that, protein induced a series of conformation changes to change its surface hydrophobic/hydrophilic properties, charge distributions etc. Then it came to the final stable adsorption state by forming hydrogen bonds, VDW contacts and electrostatic interactions between protein and substrates.3. A series of kinetic lattice Monte Carlo simulations were conducted to investigate the growth process, nucleation control efficiency and structure formation of particles deposited on gold patterned SiO2substrates. The growth process can clearly be divided into three stages:step-edge induced area selective growth stage, layer-by-layer growth stage and central nucleation growth stage. In the first stage, deposited particles diffuse over the surface and nucleate at the edge of the gold stripes. In the second stage, the particles follow a layer-by-layer growth regime to fill the topographically low particle layers for large mutual interaction energies. In the third stage, deposited particles tend to nucleate in the central areas owing to slow diffusivity there. Then the relationship of template size and nucleation control efficiency is investigated. It turns out that increasing both gold stripe’s width and SiO2distance can reduce the nucleation control efficiency. Because of limited diffusion length of molecules over surface, large template size leads to insufficient transport of the deposited molecules to the predefined positions, resulting additional island formation outside predefined positions. Finally, the morphology evolution dependence of εpp is examined through average height of particles between two gold stripes and numbers of particles on the gold strips. By tuning εpp while keeping εpg and εps fixed, three typical growth regimes are found. For the large εpp, particles cluster in the central areas between two nearest gold stripes. The simulation results are in good agreements with experiments that no significant lateral growth happens even after the thickness of the organic layer exceeds the height of Au stripes. Decreasing εpp will lead to lateral growth of particles onto Au area, indicating a very strong molecule-molecule interaction is required for a completely selective growth.