Tiny pores in a cell’s entryway act like miniature bouncers, letting in some electrically charged atoms—ions—but blocking others. Operating as exquisitely sensitive filters, the “ion channels” play a serious role in biological functions like muscle contractions and the firing of brain cells.

In order to rapidly transport the right ions through the cell membrane, the tiny channels rely on a complex interplay between the ions and surrounding molecule that has an affinity for the charged atoms. But these molecular processes have traditionally been difficult to model and understand using computers or artificial structures.

In this simulation, a biological membrane (gray) with an ion channel (center) is immersed in a solution of water and ions. This cross section of a simulation "box" shows the electric potential, the externally supplied "force" that drives ions through the channel. A dazzling pattern emerges in this potential due to the presence of the channel -- the colors show the lines of equal potential. The slowly decaying nature of this pattern in space makes simulations difficult. The golden aspect ratio -- the chosen ratio of height to width of this box -- allows for small simulations to effectively capture the effect of the large spatial dimensions of the experiment. (NIST)

Researchers at the National Institute of Standards and Technology (NIST) and their colleagues have demonstrated that nanometer-scale pores etched into layers of graphene can provide a simple model for the complex operation of ion channels.

The model allows scientists to measure a host of properties related to ion transport. In addition, graphene nanopores may ultimately provide scientists with efficient mechanical filters that are suitable for such processes as removing salt from ocean water and identifying defective DNA in genetic material.

NIST scientists Michael Zwolak and Subin Sahu have discovered a way to simulate aspects of ion channel behavior while accounting for such computationally intensive details as molecular-scale variations in the size or shape of the channel.

To squeeze through a cell’s ion channel, which is an assemblage of proteins with a pore that measures at only a few atoms wide, ions must lose some or all of the water molecules that are bound to them. But the amount of energy required to do this is often prohibitive, so ions need some extra help. They get that assistance from the ion channel itself, which is lined with molecules that have opposite charges to certain ions so it is attracted to them. Moreover, the arrangement of the charged molecules provides a better fit for some ions versus others, creating a highly selective filter. For example, certain ion channels are lined with negatively charged molecules that are distributed in a way that they can easily accommodate potassium ions but not sodium ions.

The selectivity of ion channels is what the scientists want to understand better in order to learn how biological systems functions and because the operation of these channels may suggest a promising way to engineer non-biological filters for a lot of new industrial uses.

By turning to a simpler system of graphene nanopores, Zwolas, Sahu and Massimilano Di Ventra of the University of California, San Diego simulated conditions that resemble the activity of actual ion channels.

The team’s simulations demonstrated that nanopores could be made to permit only some ions to travel through them by changing the diameter of the nanopores etched in a single sheet of graphene or adding additional sheets. Unlike biological ion channels, this selectivity comes from the removal of water molecules, also known as dehydration.

Graphene nanopores will allow this dehydration-only selectivity to be measured under a variety of conditions, a new feat.

A paper on this research was published in both Nano Letters and Nanoscale.