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simulation-based-characterization.pdf (5.93 MB)

Simulation-based characterization of electrolyte and small molecule diffusion in oriented mesoporous silica thin films

submitted on 24.10.2017, 15:52 and posted on 25.10.2017, 16:58 by Bin Sun, Ryan Blood, Selcuk Atalay, Dylan Colli, Stephen E. Rankin, Barbara L. Knutson, Peter M. Kekenes-Huskey
We developed a new workflow for simulating ion reaction-adsorption-diffusion in nanoporous silica-based materials that are resolved through electron microscopy. Firstly, we propose a matched filtering procedure to identify and segment unique porous regions of the material that will be subject to PDE simulation. Secondly, we perform reaction-adsorption-diffusion PDE simulations on representative material regions that are then applied to characterize the entire microscopy-resolved film surface. Using this model, we examine the capacity of a recently synthesized mesoporous film to tune small molecule permeation through modulating the material permeability, surface chemistry
including buffering and adsorption, as well as electrolyte composition. Specifically, we find that our proposed matched filtering approach reliably discriminates hexagonal close packed (HCP) porous regions (bulk) from characterized defect regions in transmission electron microscopy (EM) data for nanoporous silica films. Further, based on our implementation of a pH-/surface-chemistry dependent Poisson-Nernst-Planck (PNP) model that is consistent with existing experimental measurements of KCl and CaCl2 conductance, we characterize ion and 5(6)-Carboxyfluorescein (CF) dye permeability in silica-based nanoporous materials over a broad range of ionic strengths, pHs, and surface chemistries. Using this protocol, we probe conditions for selectively tuning small molecule permeability based on mesoporous film pore size, surface charge, ionic strength and surface reactions in the rapid-equilibrium limit.


Maximizing Investigators’ Research Award (MIRA) (R35) with grant number R35GM124977



  • Computational chemistry and modeling

Email Address of Submitting Author


University of Kentucky, Chemistry Department


United States

ORCID For Submitting Author


Declaration of Conflict of Interest

no competing financial interest.