Atoms-to-microns model for small solute transport through sticky nanochannels

Abstract

Modeling the transport of solutes through fluidic systems that have adsorbing surfaces is challenging due to the range of length and time scales involved. The components of such systems typically have dimensions from hundreds of nanometers to microns, whereas adsorption of solutes is sensitive to the atomic-scale structure of the solutes and surfaces. Here, we describe an atomic-resolution Brownian dynamics method for modeling the transport of solutes through sticky nanofluidic channels. Our method can fully recreate the results of all-atom molecular dynamics simulations at a fraction of the computational cost of the latter, which makes simulations of micron-size channels at a millisecond time scale possible without losing information about the atomic-scale features of the system. We demonstrate the capability of our method by simulating the rise and fall of solute concentration in sub-micron-long sticky nanochannels, showing that the atomic-scale features of the channels’ surfaces have a dramatic effect on the kinetics of solute transport in and out of the channel. We expect our method to find applications in design and optimization of micro and nanofluidic systems for solute-specific transport and to complement existing approaches to modeling lab-on-a-chip devices by providing atomic scale information at a low computational cost.

Experimental and Theoretical Methods of Study of Ionic Channels

“…Однако, если говорить о пространственно-временном разрешении, то на данный момент QM/MM-методы только начинают привлекаться к задачам моделирования макроскопических биосистем [87,88] и проблемам ионного транспорта [89]. С другой стороны, ведутся работы по объединению методов BD и PNP [90,91].…”

Computer Simulations of Soft Matter: Linking the Scales

“…For many types of solutes the solute-solute PMF has been used as an interaction potential in implicit solvent models [126,127]. One prominent example is the use of the solute-solute pair PMF for implicit solvent models of aqueous electrolyte solutions, i.e., implicit solvent ion models [37,79,85,128,129].…”

Ion fluxes through nanopores and transmembrane channels

“…Nevertheless, BD simulations still require solution of Poisson partial-differential equation at each new time step of the simulation, making them quite difficult to implement. Recently new atomic-resolution BD simulations have been proposed [28]. Using PMFs derived from allatom MD simulations, this method was able to access large simulation times at reasonably low computational cost [28].…”

“…Recently new atomic-resolution BD simulations have been proposed [28]. Using PMFs derived from allatom MD simulations, this method was able to access large simulation times at reasonably low computational cost [28].…”