We investigated the effect of hydrodynamic interaction(HI) on flow-induced polymer translocation through a nanotube by Brownian dynamics simulations. Whether there is HI in the simulation system is separately controlled by using different diffusion tensors. It is found that HI has no effect on critical velocity flux for long polymer chains due to the competition between more drag force and the hindrance of chain stretching from HI, however, HI broadens the transition interval. In addition, for flow-induced polymer translocation with HI, the critical velocity flux firstly slowly decreases with the increase of chain length and then becomes identical to that of it without HI, that is, the critical velocity flux is independent of chain length. At the same time, HI also accelerates the translocation process and makes the relative variation amplitude of single bead translocation time smaller. In fact, HI can enhance the intrachain cooperativity to make the whole chain obtain more drag force from fluid field and hinder chain stretching, both of which play an important role in translocation process. 相似文献
A new Brownian dynamics code was developed that is capable of computing trajectories of several spherical particles in the presence of a charged planar surface. The code takes into account electrostatic, van der Waals, and hydrodynamic interactions. In this work we describe the methods used in the program and show results from calculations for cytochrome cmolecules interacting with a negatively charged lipid bilayer. This system is of particular biological interest since these molecules play a major role as electron carriers, e.g., in photosynthesis. The shape and charge distribution of cytochrome cmolecules can be well approximated as spherical particles with an embedded monopole and dipole and can therefore easily be handled by the program. That level of approximation makes it possible to study large systems with many (up to 100) particles over time scales up to milliseconds, which would be computationally too expensive using detailed atomistic models. 相似文献
Summary: We have shown that the components of Cartesian rotation vectors can be used successfully as generalized coordinates describing angular orientation in Brownian dynamics simulations of non‐spherical nanoparticles. For this particular choice of generalized coordinates, we rigorously derived the conformation‐space diffusion equations from kinetic theory for both free nanoparticles and nanoparticles interconnected by springs or holonomic constraints into polymer chains. The equivalent stochastic differential equations were used as a foundation for the Brownian dynamics algorithms. These new algorithms contain singularities only for points in the conformation‐space where both the probability density and its first coordinate derivative equal zero (weak singularities). In addition, the coordinate values after a single Brownian dynamics time step are throughout the conformation‐space equal to the old coordinate values plus the respective increments. For some parts of the conformation‐space these features represent a major improvement compared to the situation when Eulerian angles describe rotational dynamics. The presented simulation results of the equilibrium probability density for free nanoparticles are in perfect agreement with the results from kinetic theory.
Simulation of p(eq)(Φ) for free nanoparticles. 相似文献
We have recently developed a new singularity‐free algorithm for Brownian dynamics simulation of free rotational diffusion. The algorithm is rigorously derived from kinetic theory and makes use of the Cartesian components of the rotation vector as the generalized coordinates describing angular orientation. Here, we report on the application of this new algorithm in Brownian dynamics simulations of transient electro‐optical properties. This work serves two main purposes. Firstly, it demonstrates the integrity of the new algorithm for BD‐simulations of the most common transient electro‐optic experiments. Secondly, it provides new insight into the performance of the new algorithm compared to algorithms that make use of the Euler angles. We study the transient electrically induced birefringence in dilute solutions of rigid particles with anisotropic polarization tensor in response to external electric field pulses. The use of both one single electric pulse and two electric pulses with opposite polarity are being analyzed. We document that the new singularity‐free algorithm performs flawlessly. We find that, for these types of systems, the new singularity‐free algorithm, in general, outperforms similar algorithms based on the Euler angles. In a wider perspective, the most important aspect of this work is that it serves as an important reference for future development of efficient BD‐algorithms for studies of more complex systems. These systems include polymers consisting of rigid segments with single‐segment translational–rotational coupling, segment–segment fluid‐dynamic interactions and holonomic constraints.
