Nanopore Physics Studio

Nanopore Physics Studio is a browser simulator of a nanopore made by Molecular Reality Corporation, published at the address /nps/ on the company's websites under the title "Nanopore Physics Studio v2.0". It draws ions jostling around a pore in a membrane, lets the user inject one of four molecules, and shows the ionic current falling as a molecule passes through.^[1] Its files are dated February 8, 2026, two months before the company's second simulator, Nanopore Studio, which models several effects this one leaves out.

The page is a black canvas with a crosshair cursor and a control panel in its upper left corner, built with the dat.GUI library and divided into four folders.^[1]

• Parameters: the salt (potassium, sodium or lithium chloride), its molarity from 0.1 to 10, the voltage from −5 to +5 V, the speed of the simulation and a "Vis Ratio" that sets how many real ions each drawn ion stands for.
• Geometry: the pore's diameter and the membrane's thickness, each with a choice of units, ångströms, nanometers or micrometers. The pore can be up to 50 nm across and the membrane up to 100 nm thick.
• Inject: single-stranded DNA ("Poly-T"), double-stranded DNA ("Helix"), ubiquitin or albumin, with buttons marked INJECT and CLEAR.
• View: a zoom from 0.1 to 10.

In the lower right corner the current is printed in nanoamperes, over a small green trace of the last 500 samples. The figure is cyan while the pore is open, pink while a molecule is in it, and red whenever the voltage is set beyond 4 V in either direction. By default the program simulates a 20 nm pore in a 20 nm membrane in 1 M potassium chloride at 0.2 V, and reads about 31.6 nA.^[1]

The simulation works in ångströms, in a square 1,500 Å on a side. Ions are drawn as discs of their hydrated radius: 3.3 Å for potassium and chloride, 3.6 Å for sodium and 3.8 Å for lithium.^[1] These are the values tabulated by Nightingale in 1959, and they run backward from the bare ions: lithium, the smallest bare ion, holds its water most tightly and is the largest in solution.^[2] Cations are yellow and anions cyan. They jitter at random, are pushed in opposite directions by the electric field, which is uniform inside the pore and fans out from its mouths, and shove each other apart on contact.

The current does not come from the drawn ions. It is computed from a formula: the applied voltage divided by the resistance of a cylinder of salt water the size of the pore, plus an access resistance for the region outside it. The conductivity is a fixed figure for each salt at 1 M, 14 S/m for potassium chloride, 12 for sodium chloride and 10 for lithium chloride, multiplied by the molarity.^[1] A molecule inside the pore removes a share of the current equal to the ratio of its cross-section to the pore's. A small white noise, 2 percent of the current plus 0.05 nA, is added to each sample.

Molecules are injected 600 Å from the pore, on the side from which the field will pull them, and are drawn toward it only once they come within four pore diameters of the mouth. A molecule wider than the pore stops at the entrance. Single-stranded DNA is drawn as a stroke 80 Å long, and the other three as discs; the double helix has no drawing of its own. None of them rotates.

The membrane has no surface charge, so the program has no electric double layer, no conduction along the pore's walls and no electroosmotic flow; a molecule moves only if the field pulls on its own charge. There is no temperature, no capacitance and no amplifier, so the noise has no spectrum and the trace no filtering. The conductivity rises in proportion to concentration without limit, where real salt solutions conduct less than proportionally as they grow stronger: measured 1 M potassium chloride conducts about 11 S/m at 25 °C, against the program's 14. The molarity slider goes to 10 M. Above the solubility limit it assigns to the chosen salt, 4.8 M for potassium chloride, the program stops adding ions to the picture but keeps raising the current.^[1]

The access resistance is that of one entrance. For a pore of diameter d in a solution of conductivity σ, the program uses 1/(2σd), the value J. E. Hall derived in 1975 for one side of a circular pore; a pore through a membrane has two sides, and the usual total is 1/(σd).^[3][a] With the default settings the second mouth would lower the current by about a fifth.

The voltage reaches 5 V, at which the default membrane carries a field of 0.25 V/nm. Experimenters seldom go much above 1 V, since fields of a few tenths of a volt per nanometer can break a thin membrane down; the effect is used on purpose to make pores, in controlled dielectric breakdown.

The company's later simulator, Nanopore Studio, posted to members in April 2026, keeps the same basic arrangement of a pore, drifting ions and a current trace, and adds most of what is missing here: both access resistances, conduction along charged walls, the Debye length, electroosmotic and pressure-driven flow, temperature, a capacitance and five sources of noise. It also adds a tutorial of 43 lessons. Nanopore Physics Studio has none; its only text is the labels on its controls.^[4]

• Pore conductance
• Current blockade
• Translocation (nanopore)