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《中国化学会-生物物理化学专业委员会第四届全国生物物理化学会议论文集》2016年
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Anomalous diffusion and dynamic disorder in biomolecular systems based on mesoscopic statistical modeling

赵南蓉  
【摘要】:In this talk, I will present three relevant topics concerning anomalous diffusion of nanoparticles proteins in polymer solutions, dynamic disorder effect in single molecule pulling experiments as well as non-exponential kinetics of DNA transport through bimolecular nanopores. Firstly, I will talk about diffusion of nanoparticles in semidilute polymer solutions based on mode-coupling theory study. We proposed a theoretical formalism to study the long-time diffusion behavior of nanoparticles in polymer solutions by using mode-coupling theory(MCT). The non-hydrodynamic part of the total diffusion coefficient D is calculated in the MCT framework where the polymer dynamic scattering function in the solution plays an important role. We compute D straightforwardly and investigate explicitly how D depends on the volume fraction of the polymer solution, the nanoparticle size, the degree of polymerization, as well as the entanglement effects. For illustration, we adopt our theoretical approach to analyze the diffusion of gold nanoparticles in semidilute poly(ethylene glycol)(PEG)-water solutions which has been studied in detail experimentally. We found that our theoretical results show very good quantitative agreements with the experimental data in many aspects, such as the strong dependence on volume fraction, the large deviation from Stokes-Einstein relation particularly for small particles, as well as the effects of the PEG molecular weight. Such good agreements clearly demonstrate the validity of our MCT framework, which may serve as a good starting point to study many more complex dynamical behaviors associated with polymer solutions. Secondly, I will talk about the kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments. Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. We present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers' rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments. Finally, I will talk about the non-exponential kinetics study for DNA escape from α-hemolysin nanopores. We proposed a fluctuation bottleneck(FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels.
【作者单位】:四川大学化学学院
【分类号】:Q50

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