Browsing by Author "Zhou, Xiaoyan"

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    Calculating Single-Channel Permeability and Conductance from Transition Paths
    (ACM, 2019-02) Zhou, Xiaoyan; Zhu, Fangqiang; Physics, School of Science
    Permeability and conductance are the major transport properties of membrane channels, quantifying the rate of channel crossing by the solute. It is highly desirable to calculate these quantities in all-atom molecular dynamics simulations. When the solute crossing rate is low, however, direct methods would require prohibitively long simulations, and one thus typically adopts alternative strategies based on the free energy of single solute along the channel. Here we present a new method to calculate the crossing rate by initiating unbiased trajectories in which the solute is released at the free energy barrier. In this method, the total time the solute spends in the barrier region during a channel crossing (transition path) is used to determine the kinetic rate. Our method achieves a significantly higher statistical accuracy than the classical reactive flux method, especially for diffusive barrier crossing. Our test on ion permeation through a carbon nanotube verifies that the method correctly predicts the crossing rate and reproduces the spontaneous crossing events as in long equilibrium simulations. The rigorous and efficient method here will be valuable for quantitatively connecting simulations to experimental measurement of membrane channels.
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    Kinetic mechanism for water in vibrating carbon nanotubes
    (APS, 2018-09) Zhou, Xiaoyan; Zhu, Fangqiang; Physics, School of Science
    Recent simulations revealed that, when an atom in a single-wall carbon nanotube was artificially driven to oscillate radially with the two ends of the nanotube fixed, water transport became highly unusual at some oscillation frequencies. Here we systematically investigate the underlying mechanism for such effects through a series of simulations and detailed analysis. We find that the pattern and magnitude for the vibration of the nanotube are sensitive to the driving frequency but largely independent of the presence of water. At certain resonance frequencies, some carbon atoms of the nanotube oscillate at much larger amplitudes than does the driving atom. Furthermore, a strongly vibrating nanotube tends to have a much-reduced water occupancy, which is mainly due to the heating effect rather than the induced deformation. Indeed, the water molecules inside the nanotube can be significantly heated and gain large kinetic energies due to the collisions with the vibrating carbon atoms. Consequently, the kinetic rate of water exchange through the nanotube could be enhanced even when the water occupancy is low. Our findings here may help understanding the physical mechanisms of similar nanodevices.