Molecular Dynamics Study On Bio-macromolecule Suspension Flows At The Nanoscale

In recent years, burgeoning development of micro-fabrication technology and nanoengineering triggers a large number of amazing inventions of various micro/nano-fluidic systems with compact structure and diverse functions. Such a great stride in technology revolutionizes many scientific fields such as microelectronics, micro-mechanics, chemistry, pharmaceutics, life science and environmental testing, etc. Micro/nano-fluidic systems usually involve usage of fluids. Therefore, fluid transport in these miniature devices plays an important role in their design and operation. It has been found fluid confined in a narrow space behaves quite differently from that at the macroscale. In particularly, in micro/nano fluidic systems in bioengineering, the internal fluid dynamics presents multiscale complexity due to existence of suspended biomacromolecules. Nowadays, the development of new-generation efficient and compact micro/nano fluidic systems calls for a deep understanding of multiscale interaction of fluid transport with biological macromolecule dynamics. To respond this increasing technology demand, in this thesis, a molecular dynamics study on nano-scale fluid transport is performed. By introducing deformable polymer macromolecules in solution, our simulations systematically reveal the complex interaction of fluid transport with macro molecular dynamics at very small confined space. Specifically, this thesis is organized as followsWe first studied pure nano-scale fluid transport without biological macromolecules. Both static and dynamic characteristics of fluids were fully discussed by simulations using equilibrium molecular dynamics method and non-equilibrium molecular dynamics method, respectively. We then extended our molecular dynamics simulations to the case when biological macromolecules suspends in solutions. , we carried out a series numerical simulations to study deformable polymer in static/flowing fluids in both open and confined space to gain an insight of mutual interactions of suspended macromolecules with the ambient fluid transport under various conditions. The salient conclusions in this thesis are summarized as follows:①The wall potential leads to an uneven layered distribution of fluid molecules in nanochannel. The detailed structure of these layers is determined by the wall potential strength, channel width and average molecule density of fluid in a nanochannel.②The strength of attraction between wall particles and fluid molecules is a primary contribution to microscopic velocity slip and temperature jump at the channel walls. It is also found that external force exerts a negligible effect on the average layered density distribution while plays an significant role in the temperature/velocity distribution in the nanochannel.③In open space the polymer suspended in fluid presents a good extension with the increased chain length. It is also noted that the surrounding solvent particles can enhance the agglomeration of polymer chain.④The strength of wall potential determines the motion range of a single polymerchain in a nanochannel. A strong wall attraction can make the polymer be firmly adsorbed on the wall. It is found that the wall potential also influences the radius of gyration of polymer chains when the chain length is given.Morever, both the radius of gyration and end-to-end distance are determined by the chain length. Simulations show that the former increases exponentially while the latter linearly when the chain length increases.⑤The external force makes the polymer be inclined to the extended state. As to channel width, it is shown that when it is smaller than the radius of gyration, the polymer will extend along the surface of wall in z direction. Moreover, a further decrease in channel width will enhance such a confined extention. On the other hand, when channel width becomes big enough, polymer chain will agglomerate itself to form a three-dimensional spherical structure in the channel. .