Browsing by Subject "transition paths"

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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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    Calculating transition rates from durations of transition paths
    (AIP, 2017-03) Zhu, Fangqiang; Physics, School of Science
    Calculating the kinetic rates for rare transitions is an important objective for molecular simulations. Here I prove equalities that relate the transition rates to the equilibrium free energy and the statistics of the transition paths. In particular, the durations of the transition paths within given intervals of the reaction coordinate provide the kinetic pre-factor in the rate formula. Based on the available free energy, the transition rates can further be rigorously calculated by initiating forward and backward simulations and evaluating the duration of each transition path. Validation on a model system confirms that the approach correctly predicts the transition rates from the simulations and demonstrates that whereas the relations here are general and valid for any chosen reaction coordinate, a good reaction coordinate will enable a more efficient sampling of the transition paths and thus a more reliable rate calculation.