Microscale devices can easily detect the collision of individual air particles and by measuring the recoil determine their density;

https://www.youtube.com/watch?v=ygiCHALySmM

Soot is 0.1 micron in diameter, whilst nanoscale machinery that self replicates, are on the order of 2 microns in diameter. Molecules include;

CH4 - 16 amu
H2O - 18 amu
N2 - 28 amu
O2 - 32 amu
CO2 - 44 amu

Which cause small cantilevers to recoil when hit, and thus are easily detected in the gas. A surface that is made preferentially reactive based on detection of individual molecules, absorbs the selected species, rotates the cantilever and releases the molecule that is captured into a controlled atmosphere of that molecule.

This is a very low energy way to extract any species from a gas.

At 10,100 Pascals, there are 2.69x10^25 molecules per cubic meter. 8.97x10^16 molecules per square meter 3.41x10^19 molecules striking each square meter per second. With only 0.04% of these CO2 that means 1.364x10^16 CO2 molecules strike each square meter of absorber per second. That's 1 microgram per second of CO2 absorption per square meter. A square kilometer of absorber area absorbs 1 gram per second of CO2. Anyone who understands the structure of clays like montmorillonite which is made up of 2 um diameter particles, understands that a few grams of the material possess a square kilometer of surface area.

A large number of microscopic machine cells 2 um in diameter and 0.1 um thick, have a surface area of 6.912x10^(-12) square meters and occupy a volume of 628.32x10^(-21) cubic meters. Made of silicene (graphenes silicon based cousin) cells that have 0.5x the void volume as cell volume, it masses 776 kg/m3 and contains cells totalling 28,936 square kilometers -thus 28.936 kg/sec can be absorbed by 776 kg/m3 of this smart material. 37.29 grams per second CO2 per kg of the material.

The change in partial pressures of the CO2 in the atmosphere at 0.04% and the CO2 in the bottle, at 100% - is 451,440 joules per kg of CO2. So, to operate the system requires 16.83 kW per kg of active material. 6.78 grams per second of H2 derived from 61.02 cc of water per second requires an additional 961.41 kW per kg of active material to reduce the CO2 to 13.56 grams per second of CH4. 978.24 kW total. 21.7 grams of the nanoscale material is required to operate per 5.2 m diameter collector.