Next Article in Journal
Dynamics Analysis of a Wireless Rechargeable Sensor Network for Virus Mutation Spreading
Next Article in Special Issue
Introduction to the Physics of Ionic Conduction in Narrow Biological and Artificial Channels
Previous Article in Journal
Visual Secure Image Encryption Scheme Based on Compressed Sensing and Regional Energy
Previous Article in Special Issue
Application of a Statistical and Linear Response Theory to Multi-Ion Na+ Conduction in NaChBac
Article

Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations

1
Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA
2
SETI Institute, 189 Bernardo Ave, Suite 200, Mountain View, CA 94043, USA
3
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Peter V. E. McClintock
Entropy 2021, 23(5), 571; https://doi.org/10.3390/e23050571
Received: 1 December 2020 / Revised: 24 April 2021 / Accepted: 28 April 2021 / Published: 6 May 2021
We use stochastic simulations to investigate the performance of two recently developed methods for calculating the free energy profiles of ion channels and their electrophysiological properties, such as current–voltage dependence and reversal potential, from molecular dynamics simulations at a single applied voltage. These methods require neither knowledge of the diffusivity nor simulations at multiple voltages, which greatly reduces the computational effort required to probe the electrophysiological properties of ion channels. They can be used to determine the free energy profiles from either forward or backward one-sided properties of ions in the channel, such as ion fluxes, density profiles, committor probabilities, or from their two-sided combination. By generating large sets of stochastic trajectories, which are individually designed to mimic the molecular dynamics crossing statistics of models of channels of trichotoxin, p7 from hepatitis C and a bacterial homolog of the pentameric ligand-gated ion channel, GLIC, we find that the free energy profiles obtained from stochastic simulations corresponding to molecular dynamics simulations of even a modest length are burdened with statistical errors of only 0.3 kcal/mol. Even with many crossing events, applying two-sided formulas substantially reduces statistical errors compared to one-sided formulas. With a properly chosen reference voltage, the current–voltage curves can be reproduced with good accuracy from simulations at a single voltage in a range extending for over 200 mV. If possible, the reference voltages should be chosen not simply to drive a large current in one direction, but to observe crossing events in both directions. View Full-Text
Keywords: computational electrophysiology; electrodiffusion model; stochastic simulations; current–voltage dependence; reversal potential; committor probabilities computational electrophysiology; electrodiffusion model; stochastic simulations; current–voltage dependence; reversal potential; committor probabilities
Show Figures

Figure 1

MDPI and ACS Style

Wilson, M.A.; Pohorille, A. Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations. Entropy 2021, 23, 571. https://doi.org/10.3390/e23050571

AMA Style

Wilson MA, Pohorille A. Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations. Entropy. 2021; 23(5):571. https://doi.org/10.3390/e23050571

Chicago/Turabian Style

Wilson, Michael A., and Andrew Pohorille. 2021. "Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations" Entropy 23, no. 5: 571. https://doi.org/10.3390/e23050571

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop