Dissipative Particle Dynamics Simulation Of DNA In Micro-channel

BioMEMS is an important research direction in MEMS. Now it has became a new crossed science included machinery, electronics, biology, material, physics, chemistry, computer science and so on.BioMEMS has many important application, such as finding a new gene, DNA sequencing, disease diagnosis, drug filter.MEMS technology has made it possible to manufacture microdevices to processing,analyzing and delivering biochemical material in a wide range of biomedical application.One interesting application is the microneedle,used for drug and DNA delivery into cells,local tissue.The microchannel is needed to control the flow of the polymer(Such is DNA).We must first know how these polymer flows in the micro-channel.Because DNA has a lot of heredity information,and the biology chip which used for deliverying DNA has many application in medicine.The most important part of these chips is microchannel.So before we designing the microchannel, it is important to understand the effects of DNA conformation and flow behavior on microchannel.Because the restriction of DNA separate technique, one DNA chain used in experiment is very expensive.And every experiment needs several to hundreds of DNA chain.So the simulation of DNA flow in microchannel can give a reasonable experiment scheme.It also can improve successful probability of experiment and reduce outlay.The characteristic size of a microchannel is usually in the same order of magnitude as the length of a typical DNA molecule. For example, the size of a typical microchannel is about 9-40μm, and the stretched length ofλ? DNA is about 22μm to 32.8μm.The ratio of the macromolecular length to the characteristic length of flow field can be taken as a Knudsen number(Kn) in the flow. When Kn <<1, the suspension can be treated as a continuum and the standard viscoelastic constitutive modeling.When Kn≈1, the suspension may not be treated as a continuum.In the latter case, DNA conformations may have a strong influence on the flow and even Brownian motion of DNA segments may not be neglected.It may be misleading to use the rheological constitutive models, which have been developed for continuum description, to describe this kind of flow. Although Brownian dynamics simulation made tremendous success in simulating polymer, but could not simulate complex flow.The simulative length scale of traditional molecular dynamics is about a few nano-meter. And each simulation time step is about 0.5 to 1 femtosecond. According to the current computer speed and memory capacity, the reasonable number of simulation steps is between 1 million and 10 million. Therefore, the simulation time is about several nanoseconds. The time of the conformation of DNA changing in solution is far larger than this time.Although molecular dynamics can provide the detailed information ,it can not simulate the whole process. The dissipative particle dynamics is a mesoscale fluid simulation method. DPD facilitates the simulations of static and dynamics complex fluid systems on physically interesting length and time scales.DPD has been applied to various complex systems, such as polymer suspensions, colloids, and multiphase fluids.So we use DPD to simulate the flow DNA in this paper.Now several methods are used to research in DNA dynamics.Molecule dynamics and Monte Carlo have been used for a long time.Some countries have exploited the commerce software.They have sold this software in China.But the price of these software is very high.In this paper,we exploited a DPD programme to simulate fluid and DNA flow behavior as a good base to exploit a DPD commerce software.In the first chapter,we introduced some development of DNA flow behavior and development of DPD.In the second chapter, we introduced the basic DPD theory. In the third chapter,we used DPD to simulate the Poiseuille flow and Coutte flow. When simulating the poiseuille flow, we focus on how boundary conditions effect simulation result.The simulation results show that,when the wall is built by freezing the DPD particles, both the method of increase the wall's density and the method of increase the wall's conservative force coefficient can prevent the fluid particle from penetrating the walls.But these methods can make large density fluctuation and lead to a large velocity slip. When we employ the bounce-back boundary condition on the surface of the walls,we found that this method also can not satisfy our request.At last,we found that only Igor V. Pivkin's method can reduce the density fluctuation and impose no-slip boundary conditions.When simulating the coutte flow, we found that the maximal velocity of the flow can not follow the above wall's move. According to Groot's theory,we chose the DPD fluid's density value 3 to simulate the real water. So there is no actual meaning for simulating DNA flow, if we use the method of increasing the the DPD fluid's density to solve this problem. In order to solve this problem, we take shear flow as a example.we focus on how to use low DPD density fluid to simulate the shear flow.The simulation results show that,the viscosity of DPD fluid and conservative force can effect the simulation results.If you want the shear flow's maximal velocity follow the above wall's move, you must increase the DPD fluid viscosity firstly.Then you must use Igor V. Pivkin's boundary condition and choose small conservative force coefficient of fluid particle. And we found this method's density curve fluctuation is very small.In this paper, DNA molecules is modeled by WLC chain. Beacuse WLC chain has made great success in simulating DNA.In the four chapter, we simulated the flow of DNA in Poiseuille flow.We research the effect of the flow strength,the lengh of DNA chain,the distance between the wall on the probalility distribution of center-of-mass.The results show that,there is a depletion layer near the wall due to steric hindrance from the wall.As the increase of the flow strength,the larger probalility distribution of DNA is close to the wall.As the increase of the lengh of DNA chain,both the probalility distribution of DNA near the wall and center of the flow is larger.As the reduce the the distance between the wall,the probalility distribution of DNA in the center of flow is decrease.And the probalility distribution of DNA near the wall is increase.Why DNA migrates like these? The reason is both the depletion layer and flow effect on DNA migrate.The depletion layer effect will give the repulsive force to drive the DNA (very close to the wall) away from the wall,but the Poiseuille flow will migrate DNA out of regions of lower shear rate to regions of higher shear rate.The result is the competition between these two effect.In the five chapter, we simulated the stretch process of DNA chain in no pressure driven flow. In order to stretch the DNA chain, the force acted on the two ends of DNA chain.The research result shows that: Each force stretched DNA chain to a steady stretch rate. When the simulation time is enough large, DNA chain will reach this steady stretch rate .As we increased the force, the steady stretch rate also became large.After steady stretch rate approach 0.9, the increased extent of steady stretch rate become unconspicuous, even we used a larger force. Before the DNA chain reach steady stretch rate, there is a fluctuation. As we increased the force or reduced the length of DNA chain, this fluctuation become larger. As the DNA chain has the same rigidity, but different length, the same force stretched DNA chain to the same steady stretch rate.Then, we increased the viscosity of DPD fluid.We simulated the stretch process of DNA chain over again. The simulation results show that,when we increased the viscosity of DPD fluid, we need a larger force to stretch DNA chain.But the fluctuation before DNA chain reach the steady stretch rate decreased. These show that viscosity of DPD fluid influence the stretch characteristic of DNA chain.On the one hand, the viscosity of DPD fluid prevent the force stretching DNA chain.So, we need a larger force to stretch DNA chain.On the other hand, the viscosity of DPD fluid also prevent DNA chain twisting. So the fluctuation before DNA chain reach the steady stretch rate decreased.As the DNA chain has the same rigidity, but different length, the same force stretched DNA chain at different steady stretch rate. This shows the longer DNA chain get a larger viscosity effect.