Proton transport simulation

Marrink, S.J., Jahnig, F., Berendsen, H.J.C. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophys. J. 71 (1996) 632-647. 

Methods similar to those discussed in this chapter have been applied to determine free energies of activation in enzyme kinetics and quantum effects on proton transport. They hold promise to be coupled with QM/MM and ab initio simulations to compute accurate estimates of nulcear quantum effects on rate constants in TST and proton transport rates through membranes. 

Zahn, D. Brickmann, J., Quantum-classical simulation of proton transport via a phospholipid bilayer, Phys. Chem. Chem. Phys. 2001, 3, 848-852... 

If only electrostatics are considered, significant attractive interaction between the excess protons in the aqueous phase and the immobile anionic mirror charge is expected.27 Recent MD simulations of proton transport in slab pores with sulfonate groups... 

A second important application of CMD has been to study the dynamics of the hydrated proton. This study involved extensive CMD simulations to determine the proton transport rate in on our Multi-State Empirical Valence Bond (MS-EVB) model for the hydrated proton. = Shown in Fig. 4 are results for the population correlation function, (n(t)n(O)), for the Eigen cation, HsO, in liquid water. Also shown is the correlation function for D3O+ in heavy water. It should be noted that the population correlation function is expected to decay exponentially at long times, the rate of which reflects the excess proton transport rate. The straight line fits (dotted lines) to the semi-log plots of the correlation functions give this rate. For the normal water case, the CMD simulation using the MS-EVB model yields excellent agreement with the experimental proton hopping... 

In this work, we have approaehed the understanding of proton transport with two tasks. In the first task, deseribed above, we have sought to identify the moleeular-level stmeture of PFSA membranes and their relevant interfaees as a funetion of water content and polymer architecture. In the second task, described in this Section, we explain our efforts to model and quantify proton transport in these membranes and interfaces and their dependence on water content and polymer architecture. As in the task I, the tool employed is molecular dynamics (MD) simulation. A non-reactive algorithm is sufficient to generate the morphology of the membrane and its interfaces. It is also capable of providing some information about transport in the system such as diffusivities of water and the vehicular component of the proton diffusivity. Moreover, analysis of the hydration of hydronium ion provides indirect information about the structural component of proton diffusion, but a direct measure of the total proton diffusivity is beyond the capabilities of a non-reactive MD simulation. Therefore, in the task II, we develop and implement a reactive molecular dynamics algorithm that will lead to direct measurement of the total proton diffusivity. As the work is an active field, we report the work to date. 

To date, our reactive molecular dynamics simulations of proton transport have been limited to bulk water. However, the extension of Ae RMD algorithm to proton transport in PFSA membranes is analogous to what has been done in bulk water and simi-... 

Substantial efforts are being invested world-wide into the design and development of such a dream membrane . Understanding the mechanisms and bottlenecks of proton transport in existing materials is one necessary prerequisite for the design of improved materials. Computer simulation and theory contribute significantly to this endeavor. 

In the following sections, the key properties of PEM materials used in fuel cells are briefly reviewed and theoretical and simulation results on proton transport are discussed. 

Theory and computer simulation of proton transport in membranes... 

Our group has combined the EVB model with a complete atomistic description of the Nafion subphase [76]. The pore structure obtained (see Fig. 4) supports the disordered Nafion model by Yeager and Steck [49] more than the symmetrical one by Gierke [48]. Activation energies obtained for proton transport at A = 5 and A = 10 are similar to the ones discussed above for the simpler pore model. This is not unexpected since the total simulation time... 

Smondyrev, A.M. and Voth, G.A. (2002). Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. Biophys. J. 82, 1460-1468... 

Braun-Sand, S., Strajbl, M. and Warshel, A. (2004). Studies of proton translocations in biological systems simulating proton transport in carbonic anhydrase by EVB based models. Biophys. J. 87, 2221-2239... 

In its present form the theory and simulations of proton transport in single... 

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