Theoretical Insights Into The Folding Thermodynamics And Kinetics Of Single Homopolymer Chain Under Confinement

How does confinement regulate the static and dynamic properties of polymer chains is not only an important scientific question in polymer physics,but also one of the focuses in the field of life sciences,for example,how do protein molecules fold efficiently in vivo?Although several works have investigated the folding behavior of macromolecules under the confinement,however,for polymer chains with different properties,it is still not very clear how geometric properties and repulsive volume effects of confined space affect the stability,structure,as well as scaling behavior of single macromolecules.To elucidate the folding behavior of flexible and semiflexible polymer chains in confined space,this paper mainly carried out the following two research works:(1)The study on folding thermodynamics and dynamics of flexible polymer chain under confinement.The difference of folding behavior for flexible homopolymer confined within a spherical cavity(radius L)or cylindrical boxes(height H=2L or H=4L)have been systematically investigated by computer simulations.In thermodynamics,with decreasing confined cavity size L,the stability of the polymer chain is enhanced,while the change in stability is differing under the same volume fraction η and different shapes of confinement.Moreover,there are two scaling laws between the change in stability and the confined cavity size L,described as(Tf-Tfbulk)/Tfbulk～L-v.where the Tfbulk is the bulk folding temperature:within the larger cavity,the values of v are in general agreement with those derived from the theoretical analysis,while within the smaller cavity,the creation of a new scaling regime arises from the strong repulsion interaction between the confined cavity and the polymer chains.Additionally,it is found that different confined cavity shapes and size could affect the phase behavior and structure,described by the phase diagrams in terms of temperature T and L.Kinetically,the folding rate increases firstly and then decreases with the decrease of the L,and the decrease in folding rate originates from the appearance of metastable state.Furthermore,only a single scaling relation exists between the folding rate and the confined cavity size in spherical and cylindrical confinement with H=2L,while two scaling relations are observed for cylindrical confinement with H=4L due to the change of collapsing structures.(2)The study of folding thermodynamics and kinetic behavior of semiflexible polymeric chains in confined environments.The folding behavior of semiflexible polymer chains under the spherical confinement was studied by using Langevin dynamics.Thermodynamically,the coil globule transition temperature increases as the confined cavity size decreases.Structure phase diagrams are constructed with the confined cavity size L and bending strength kθ as a function of temperature T,the results indicate that the conformation of semiflexible polymer chains changed significantly with the decrease of confined cavity size as well as the increase of bending strength.Moreover,the smaller the confined cavity size L is,the higher the number of turns of the ring structure in the ground state is,and the more collapsed polymer chains are.In Kinetics,we find that the confinement accelerated the folding of the polymer chains,and the stronger the rigidity of the chains is,the greater the folding rates increase.Although there are four folding pathways for the folding process of semiflexible polymer chains,as the size of confined cavity decreases,the folding pathway tends to choose a random coil to the small ring structure directly(C→Ts).In addition,we find that there are two main ways to form hairpin structure:one is that the semiflexible polymer chains form first from one end and then slip slowly to form hairpin structure,while the second one was formed first from the middle and subsequently the polymer strand pulled on both sides to give the hairpin structure.Under confined environment,the formation of hairpin structure by the semiflexible polymer chain is more inclined to adopt the second way.