| Aggregation is a general phenomenon in nature.The study of aggregation process contributes to understand and reveal the internal mechanism of aggregation.Hence,this thesis focuses on the aggregation process of diphenylalanine and active particles at multi-scale level via molecular dynamics simulations.Among them for diphenylalanine,we concentrate on the influence of p H on molecular aggregation state of diphenylalanine.The first chapter presents the research background.The second chapter mainly introduces the basic principle,integral algorithm and molecular force field of the molecular dynamics simulation methods.In chapter 3,the effects of p H on the aggregation process and morphology of diphenylalanine in aqueous solution is investigated by coarse-grained molecular dynamics simulations.It is found that neutral environment is favorable for the aggregation of diphenylalanine,while diphenylalanine molecules are less prone to aggregate in alkaline solution.According to the energy analysis,van der Waals interaction exhibits rather great effects on the aggregation process of dipeptide molecules,but the electrostatic interaction is dominant factor that results in the occurrence of various aggregation morphologies of diphenylalanine molecules.The different aggregation morphologies of diphenylalanine are found in various p H conditions,indicating that aggregation morphology of diphenylalanine can be regulated by p H.In chapter 4,the influences of p H on the aggregation behavior of diphenylalanine is investigated by all-atom molecular dynamics simulations,and intramolecular hydrogen bonding interaction is discussed in detail.The simulation results show that the aggregation tendency of diphenylalanine is the most obvious in neutral solution,which indicates that dipeptide molecules are more likely to aggregate in neutral environment.According to the hydrogen bond analysis,the intermolecular hydrogen bond can affect the aggregation behavior of diphenylalanine in aqueous solution,and hydrogen bond has better driving ability for the aggregation of diphenylalanine in neutral aqueous solution.In chapter 5,the aggregation morphology of diphenylalanine in aqueous solution regulatied via a periodical change of p H is studied by coarse-grained molecular dynamics simulations.By ananlyzing typical morphologies of diphenylalanine,it can be found that the aggregation morphology of diphenylalanine changes regularly with p H.At the initial stage of simulation,diphenylalanine molecules form a random structure.With the change of solution from acid to neutral,diphenylalanine molecules show an aggregation and form a cylinder-like structure.With the change of solution environment from neutral to acid,the cylinder-like structure is decomposed into irregular configuration.According to the morphological changes of diphenylalanine during the change of p H,it can be considered that the change process of solution environment from acidic to neutral is aggregation process,while the change process of solution environment from neutral to acidic is dispersion process.Also,this can illustrate that diphenylalanine molecules are easier to aggregate in neutral solution.In chapter 6,two kinds of binary-mixtures are simulated in two dimensions.one is the mixture of passive and self-propelled spheres,and the other is the mixture of rod-like particles and self-propelled spheres.The research shows that a very small number of active particles strongly influence the distribution and the dynamics of the dense mixtures.At a small active force,the high-density and low-density regions appear in both systems,indicating an emergence of phase separation.The rod-like particles accumulate loosely due to the shape anisotropy,compared with the spherical particles at the high-density region.Then it vanishes at higher active forces due to the velocity improvement induced by frequent collision.We also find that there is a positive correlation between between Voronoi area and velocity of particles in both systems.Moreover,the passive particles occurs a super-diffusive behavior when lower proportion of active particles in both systems start self-propelled force.In chapter 7,the conclusion of this thesis is summarized and the future research of diphenylalanine and active particles is prospected. |
