Molecular Simulation Of Colloidal Particles Self-assembly Systems And Theoretical Insights Into The Interactions Between Colloidal Particles And Membranes

Self-assembly of colloidal particles is an effective method to prepare advanced materials,and has important applications in materials,medicine,photoelectric and other fields.The phase structure and behavior of the system are the core scientific issues in colloidal particle self-assembly,and provide important guidance for the preparation of high-quality self-assembled materials and the realization of their functions.In this paper,molecular simulation studies were conducted on the self-assembly processes,nucleation pathways and phase structures of DNA-functionalized gold nanoparticles and rounded cube particles respectively,and theoretical insights into the interactions between star-shaped antimicrobial peptides nanoparticles and membranes.The following results were obtained:Firstly,how to evade metastable states in self-assembly is the key to obtain high quality nanoparticle assembly.The conventional thermal annealing,known as the entropy-mediated strategy,is commonly used in directing the self-assembly of DNAfunctionalized gold nanoparticles(DNA-AuNPs)which is known as "programmable atom equivalent"(PAE).The enthalpy-mediated strategy is another tractable approach,which can circumvent metastability by controlling the dynamic pathways at a condition with temperature remaining constant.However,the missing of direct measurements and observations of the assembly processes limit our understanding of the mechanism how the systems avoid kinetic trapping and realize the phase transition successfully.In Chapter Three,we introduce a toy model for the self-assembly of DNA-AuNPs,which suggests that using the enthalpy-mediated strategy can effectively avoid undesired defects during the self-assembly.The effectiveness of this strategy in directing the self-assembly is proved through coarse-grained molecular dynamics simulations of DNA-AuNPs,which achieve the crystallization through orderly structural transformations.Based on that,we study the assembly processes which are controlled by enthalpymediated and entropy-mediated strategies.The DNA-AuNPs in the self-assembly control led by the entropy-mediated strategy organize themselves during the thermal annealing process,and are slowly annealing to achieve the crystallization.In contrast,we find that DNA-AuNPs in the primary stage of self-assembly which is controlled by enthalpymediated strategy experience an organization-breakdown-reorganization process before forming stable crystallites,highlighting the importance of bond reversibility in the structural transitions and in avoiding the kinetic traps.The conventional approach of thermal annealing may indiscriminately destroy all noncovalent bonds,causing disassembly of the self-assembled structure.Although the recently developed enthalpy-mediated strategy can solve this dilemma at room temperature,it required a complex catalytic-assembly DNA strand-displacement circuitry to mediate components interaction.In Chapter Four,we present a simple but effective catalytic assembly method that allows the DNA-functionalized colloidal nanoparticle system to escape metastable state and obtain a high quality assembly.A removable molecule named "Catassembler" that acts as a catalyst was employed to rectify imperfect linkages and prevent metastability without affecting the assembled framework.Leveraging this tractable catalytic-assembly approach,different ordered architectures were easily produced by directly mixing all reactants,as in chemical reactions.By switching bonding identities,solid-solid phase transformations between different colloidal crystals were achieved.This work can be potentially used for the self-assembled system mediated by non-covalent interactions to prevent metastability.Firstly,we propose an ideal experiment to verify our conjecture about the formation of percolation network through automatic bond breaking strategy.Then,by adding catassemblers,the transition from disordered solid phase to ordered solid phase can be realized by switching bonds.In addition,by calculating the phase diagrams,we give the optimal amount of catassembler and the interaction strength between catassemblers and sticky ends.At the same time,we clarified the assembly mechanism by using the catassembly strategy.The simulation results are in agreement with the experimental results,which shows that the accelerated assembly strategy is practical and effective for the system to escape metastable state.Rounded cubes can form Deformed C1 and plastic FCC crystal structures,but the nucleation pathways of corresponding crystals are not very clear.In Chapter Five,the nucleation barrier profile for plastic FCC was calculated using the Seeding Approach based on the classical nucleation theory.We find that nucleation free energy barrier for FCC formed by spherical particles was higher than that for plastic FCC formed by rounded cubes.This can be explained by classical nucleation theory,because the only difference in this case is the surface tension.So one may perhaps conclude that the surface tension is lower for the rounded cubes,which lowers the nucleation barrier.In Chapter Six,we introduce a structurally nanoengineered star-shaped antimicrobial polypeptide nanoparticle consisting of lysine and valine residues,which is a new class of antimicrobial agent with superior antibacterial activity against multidrugresistant bacteria and low toxicity toward mammalian cells.Utilizing coarse-grained models,we studied the interactions of microbial cytoplasmic membranes with polypeptides of either(K2V1)5(star-KV)or CM15(star-CM15).Our computational results verify the low toxicity of polypeptides of(K2V1)5 toward the dipalmitoyl phosphatidylcholine bilayer(mammalian cell membrane).This low toxicity is demonstrated to originate from weakened hydrophobicity combined with its random coil conformation for(K2V1)5 because of the highly abundant valine,compared with the typical antimicrobial peptides,such as CM15.In the interactions with palmitoyloleoyl-phosphatidylethanolamine/palmitoyl-oleoyl-phosphatidylglycerol bilayer(bacterial membrane),star-KV has greater ability in phase separation and generation of phase boundary defects not only in lipid redistribution but also in lateral dynamics movements,although both star-KV and star-CM15 can extract the phosphatidylglycerol(POPG)lipids and purify the phosphatidylethanolamine(POPE)lipids into continuum domains.We suggest that the polypeptide of(K2V1)5 can nondisruptively kill bacteria by hampering bacterial metabolism through reorganizing lipid domain distribution and simultaneously "freezing" lipid movement.