Biomolecule Detection And Simulation Research Based On Solid Nanopores Of Master Thesis

In recent years,nanopore detection technology has been widely used in the detection of proteins,viruses,nucleotide chains and other biomolecules and nanoparticle characterization due to its significant advantages such as no label,low cost,short time-consuming,and high sensing performance.Considered to be the most promising next-generation sequencing technology.A full understanding of the principles of nanopore detection technology and the physical processes in nanopores is essential for improving the sensing performance of nanopores.Numerical simulation technology can simulate the physical field distribution in nanopores and can help understand the physical processes occurring in nanopores.A powerful tool for optimizing nanopore sensing performance.At present,numerical simulation methods include finite element simulation and molecular dynamics simulation.Finite element can accurately simulate the physical field distribution of nanopores under steady state,and the amount of calculation is small;although molecular dynamics simulation can simulate the occurrence of nanopores under transient conditions However,the large amount of calculation,time-consuming,and huge cost of molecular translocation events are not conducive to the wide application of numerical simulation technology.Therefore,this thesis combines the mature nanopore finite element simulation model and molecular dynamics simulation ideas,and uses the arbitrary Lagrangian-Euler method(ALE)to construct the transient state of biomolecular translocation based on the steady-state simulation of the nanopore Simulate the model and use double-stranded DNA as the sample to be tested to complete the nanopore-to-DNA translocation detection experiment.Through the combination of experiment and simulation data,the model is tested and verified.The specific research content is as follows:1.Build a steady-state simulation model for solid-state nanoporesThe model uses the Poisson-Nernst-Bronck(PNP-NS)equation to model the geometric model of the nanopore,which can solve the physical field distribution such as the electric field strength,fluid velocity,and concentration distribution in the nanopore.The steady-state model is the basis for constructing the transient simulation model.Therefore,in order to improve the accuracy of the transient simulation model,this article first determines the appropriate simulation parameters and explores the degree of IV curve matching under the simulation and experimental conditions to build an accurate steady-state simulation model.2.Build a transient simulation model of biomolecular translocation to complete the simulation of DNA translocation under different experimental conditionsBased on the steady-state simulation model,this paper further analyzes the force of the analyte in the nanopore,mainly considering the electrophoretic force driving the analyte through the hole and the hydrodynamic force that hinders the movement of the analyte.The double-stranded DNA molecule is abstracted into a rigid column,a Newtonian force equation controlled by the physical field is constructed,and the trajectory of the analyte is solved through mathematical operations.Use any Lagrangian-Euler method(ALE)to control DNA passing through the nanopore and simulate the blocking current generated by DNA molecular translocation.In addition,this paper completed the simulation of DNA translocation under different voltages and different salt concentration gradients applied on both sides of the nanopore,and obtained the blocking current amplitude and time under the corresponding simulation conditions.3.Complete the DNA translocation detection experiment under the experimental conditions corresponding to the simulationThis part is the experimental research part of this article,including the nanopore preparation experiment by dielectric breakdown method,the DNA molecular translocation detection experiment and the statistical analysis of experimental data.Through the statistics and analysis of the experimental data,the amplitude and time of the blocking current under the corresponding experimental conditions are obtained.It is found through experiments that the salt concentration gradient can not only effectively increase the blocking current amplitude and the capture efficiency of DNA molecules generated during the translocation of DNA molecules,but also reduce the background noise of the nanopores.4.Complete the verification of simulation results and experimental resultsThis paper verifies the ?-? curve obtained by simulation with the ?-? curve obtained by experiment.It is found that the simulation and experimental ?-? curve results are very similar.Under the experimental conditions above 130 m V,the hole current has a partial deviation,but the deviation result is less than 10%.In addition,this paper further compares the simulated blocking current with the experimental blocking current to verify the accuracy of the transient simulation model of biomolecular translocation.It is found by comparison that under the same simulation and experimental conditions,the blocking current amplitudes of the two are like each other and their changing trends are consistent.However,the translocation time of the two is quite different,but the change trend is the same.The main reason for this phenomenon is that the transient simulation model does not consider the interaction between the DNA molecule and the wall of the nanopore when the DNA molecule passes through the nanopore.This phenomenon is inevitable in actual experiments,which leads to a longer translocation time.Big difference.After comparison,the application range of the transient simulation model of biomolecular translocation is verified.The model can more accurately predict the blocking current amplitude and change trend of biomolecular translocation,and can effectively verify the change trend of biomolecular translocation time.The comparison results verify the accuracy of the simulation model.In addition,the transient simulation model of biomolecular translocation can be used as the basis to further improve and optimize the simulation to guide the experiment by changing the geometric size of the nanopore or selecting biomolecules of different sizes.