Nanopore Studio
| Nanopore Studio | |
|---|---|
 The simulator's canvas: a membrane with a pore, drifting ions and the current trace | |
| Developer(s) | Molecular Reality Corporation |
| Initial release | April 16, 2026 (to members) |
| Written in | JavaScript (HTML canvas) |
| Operating system | Web browser |
| Type | Physics simulation, tutorial |
Nanopore Studio is a two-dimensional simulator of a solid-state nanopore made by Molecular Reality Corporation and played inside EQBio-OS, the company's member software, where it opens within a message. The player chooses the pore, the membrane, the salt, the voltage and the molecule, clicks to release molecules, and watches them cross the pore while an oscilloscope traces the current. A built-in tutorial of ten chapters and 43 lessons ends with a badge, and its lowest grade is bronze.[1]
The simulator is the second of the company's nanopore simulators, after Nanopore Physics Studio. An internal tool that reads a scientific paper and writes out the simulator settings that would reproduce its experiment describes a version with different controls.
Interface
The canvas shows a horizontal membrane with a gap for the pore, potassium and chloride ions drifting and jittering around it, and the line "click anywhere to inject analyte". Along the top run the buttons Tutorial, Pause, Clear Trace and Reset, a frame-rate counter and a badge that names the pore's regime: SUB below 2 nm, NANO up to 100 nm and MICRO above. Below the canvas an oscilloscope labeled "I(t)" draws the current, with its own controls for the current and time scales.[1]
Most controls run on logarithmic sliders over wide ranges. The pore can be from 0.3 nm to 10 µm across and the membrane from 0.34 nm thick, the thickness of one sheet of graphene, to 10 µm. The membrane can be silicon nitride, graphene, molybdenum disulfide, glass or the silicone rubber PDMS, each with its own dielectric constant and surface charge; graphene and PDMS, and to a small degree molybdenum disulfide, also let water slip along their walls. Voltage runs from −1,000 to +1,000 mV, salt from 1 mM to 3 M, pressure to a megapascal either way, and temperature from 273 to 373 K. Simulated time can run from a picosecond to a full second per second of real time. The six analytes are a single ion, a 30-nucleotide strand of single-stranded DNA, a 1,000-base-pair double strand, a protein of about 20 kilodaltons, a virus about 30 nm across and a red blood cell of about 8 µm, described as a "Deformable biconcave disk", which the simulator lets through any pore wider than 800 nm.[1]
By default the pore is 10 nm wide in 5 nm of silicon nitride, at 100 mV in 150 mM potassium chloride, with single-stranded DNA loaded.
Physics
Two things set the current: the conductivity of the salt and the geometry of the pore. For the conductivity the program multiplies the concentration by the sum of the potassium and chloride mobilities, which gives about 15 S/m for 1 M potassium chloride, against about 11 S/m measured at 25 °C, because the mobilities used are those of infinitely dilute solution. The resistance is that of the channel plus an access resistance for its two mouths, 1/(σd) for a pore of diameter d in a solution of conductivity σ, the combination published by Kowalczyk and colleagues in 2011.[2] For pores below 100 nm a term for conduction along the charged walls is added, weighted by the Debye length. It is the reason the conductance does not fall to zero as the salt does, the subject of one of the tutorial's questions.
Molecules diffuse by Brownian motion. Electrophoresis moves charged ones along the field, and electroosmotic flow, computed from the surface charge, and pressure-driven flow carry neutral ones too. A molecule inside the pore lowers the current by the ratio of its cross-section to the pore's, at most 95 percent, and the event counter advances when a molecule that has entered the pore leaves it on the far side, a translocation.[1] A change of voltage produces a capacitive transient that decays with the time constant of the pore's resistance and the system's capacitance.
The noise is the sum of five terms: thermal noise, shot noise, 1/f noise, dielectric loss, and the amplifier's voltage noise across the capacitance, integrated over 10 kHz. The capacitance of the membrane is computed from the area of the pore itself, which gives about one attofarad for the default pore. A fixed baseline of 50 pF is added, about fifty million times larger, and for any pore of nanometer size it sets the high-frequency noise.[a]
Tutorial
"Nanopore Studio Tutorial: A guided tour of solid-state nanopore sensing" sets the controls for each lesson, sometimes moves them itself while the reader watches, and asks questions at the end of each chapter.[1]
| No. | Title | Subtitle |
|---|---|---|
| 0 | Orientation | Meet every control |
| 1 | What is a Nanopore? | From Coulter to today |
| 2 | Ionic Conductance | Where the current comes from |
| 3 | The Debye Length | Electrical screening |
| 4 | Membrane Materials | The physical substrate matters |
| 5 | Electrokinetic Transport | Getting analytes to the pore |
| 6 | The Translocation Event | Reading the signal |
| 7 | Noise & Sensing Limits | What sets your detection floor |
| 8 | Transients & Artifacts | Avoiding false positives |
| 9 | Design Challenges | Apply what you've learned |
The first chapter traces resistive-pulse sensing to Wallace Coulter's patent of 1953 for counting cells, the Coulter counter, and cites the 1996 detection of single strands of DNA in a protein pore and the 2001 solid-state pore made by ion-beam sculpting.[3] The questions are practical: "A 10 nm nanopore in 1 M KCl at 100 mV gives a current of order 10 nA. Why?"; "Dominant noise of a 100 GΩ pore at 10 Hz?"; "A 5 µs current spike right after a voltage polarity flip is most likely:".
There are 37 scored items worth 112 points, and progress is kept in the browser. A score of 95 percent or more earns a platinum badge, 90 gold, 75 silver; anything lower, zero included, earns bronze.[1]
The last chapter sets three challenges, each checked by the program. "Design a DNA sensor" asks for a blockade of more than 20 percent and a pore resistance between 50 and 500 MΩ, with a reference answer of a 3 nm pore in 10 nm of silicon nitride, 1 M salt and +200 mV, giving about 130 MΩ and a 54 percent blockade. The check accepts single-stranded DNA as well as double, and it does not read the voltage, so a sensor with no voltage across it passes. "Move a neutral protein" requires three translocations of a protein with no charge, which only electroosmosis or pressure can drive. "Minimize noise" asks for less than 5 pA of noise; its reference answer recommends a 3 nm pore for a "small C_pore", and notes that the total capacitance is "dominated by baseline 50 pF" and "can't reduce below that in our model".[1]
Configurator
An internal tool sends the text of a paper to an open-weights language model of 70 billion parameters, released by Meta, with instructions to turn it into the settings that "faithfully reproduce the experimental conditions described", ending: "Return ONLY the JSON object. No markdown fences, no explanation, no commentary."[4] The instructions describe a simulator with eight settings: a pore of 2 to 50 nm, a membrane of 2 to 20 nm, ±200 mV, a temperature, 0 to 50 pA of noise, a "coating" of solid silicon nitride, lipid, protein or graphene, an amplifier gain and a low-pass filter. Its current is given as "voltage × π × (poreDiameter/2)² / membraneThickness", with no term for the salt. Nanopore Studio as members see it has no coating, gain or filter control, and the tool displays its settings as text without loading them.[4]
Development
A quest on the company's member software, worth 2,500 experience points and later switched off, asked for a "nanopore simulation teaching game": "Make a simulator that teaches people how nanopores work and lets more advanced players test out ideas."[4] The founder posted the simulator to members on April 16, 2026, in a message titled "Nanopore Studio" and labeled "simulator", with the note "Very much a work-in-progress!"[1] The whole program, tutorial included, is one file of 155 kilobytes, dated May 3, 2026. In the software's code it is filed under the heading "MoleculArcade", the name the company later gave to its arcade page.
EQBio-OS lists the simulator's messages under a Nanopore Studio filter, with a red lab-bench icon, in the left rail. The software's guided tour introduces it as "A fun, easy place to play with nanopore ideas", and adds: "No pressure to be productive. Mess around. See what shapes signal makes."[5]
See also
Notes
- ^ For the default pore, 7.5 × ε0 × π × (5 nm)2 / 5 nm ≈ 1.0 × 10−18 F. A real membrane's capacitance comes from its whole area, typically tens of micrometers across, and is of the order of picofarads or more.
References
- ^ a b c d e f g h Kemmishtree (April 16, 2026). "Nanopore Studio". EQBio-OS.
- ^ Kowalczyk, S. W. (2011). "Modeling the conductance and DNA blockade of solid-state nanopores". Nanotechnology 22 (31): 315101. doi:10.1088/0957-4484/22/31/315101.
- ^ "Characterization of individual polynucleotide molecules using a membrane channel". Proceedings of the National Academy of Sciences 93 (24): 13770-13773. 1996. doi:10.1073/pnas.93.24.13770.
- ^ a b c "Company records". Molecular Reality Corporation. May 2026.
- ^ "EQBio-OS tour". Molecular Reality Corporation. 2026.