Here are solutions to some common issues with the game and site:

  • Created account, but unable to log in: check the email you registered your account with. You should have received an activation link. Click the activation link to activate your account and log in.
  • The game or sidebar don't load at all: make sure you have Flash version 11.5 or later, and that you don't already have the game open in another tab or window.
  • The game loses my place when I go to another part of the site or close and reopen the page: make sure you have local storage enabled for Flash.
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How to Play: Basics


Domains are the basic unit of construction in Nanocrafter. Each domain has a number of relevant attributes:

  • Length: Domains can be long or short. Short domains are covered in greater detail in the "toeholds" section. Domains must be of the same length to hydrogen bond with each other.
  • Color: Long domains can have either one or two colors in their midsection, short domains are always a single color. Domains must have the same color or colors to hydrogen bond with each other.
  • Shape: Domains have either bumps or divets, and domains must have the opposite shape to hydrogen bond with each other.
  • Locked/unlocked: Domains can be either locked (gray ends) or unlocked (white ends). You cannot manually change the bonds or concentrations of locked domains, nor can you delete them.
  • Target: Most domains are not targets. The ones that are either have stars (goals) or cracks (hazards). All goal domains must not be hydrogen bonded to win a level, when not hydrogen bonded they will glow yellow. Conversely, if a hazard is ever not hydrogen bonded after hitting the Play button, you will immediately lose.
  • Concentration: See the "concentrations" section for more information.

Moving Domains

All domains can be moved around. They can be moved one of two ways. If you click and drag in the middle section of a domain - the colored part - that and any connected domains will be moved but their orientation will not change. This is useful for moving around large molecules without disrupting their organization. If you click and drag the front or back of a domain - the white or gray part - that and any connected domains will follow the cursor fluidly. This is useful for binding domains (see below), but may distort the layout of the molecule in undesired ways.

Bonding Domains

Any unlocked domains can be covalently bonded together by dragging the front of one domain to the tail of another, or vice versa. Covalently bonded domains form a "strand", the basic unit of displacement reactions. To hydrogen bond unlocked domains, they must be the same length, have the same colors, and have opposite shapes. If they meet all those criteria, simply drag the domains so they are side-by-side. You will see a glow indicating that they can hydrogen bond. Two domains that can hydrogen bond are called "complements".

Camera controls

After the first couple of worlds you will be able to control the camera. You can zoom in or out by clicking the + and - buttons in the lower left of the game screen, and move the camera around by clicking on the game background and dragging. Mouse scroll wheels generally work to control zooming, but some browsers prevent them from functioning.

Level Types

There are two types of levels: challenge levels, covered in the Challenges sections, and world levels. World levels are accessed on the sidebar to the right of the game. Most world levels start locked, and unlock when you have played a related preceding level. All levels in a world must be completed to unlock the next world.

Completing Levels

Once you are satisfied with your solution to a level, you always need to click the Play button in the lower right to initiate reactions. After the reactions complete, the level will end in success or failure based on several conditions:

  • Failure from a hazard being released. If a hazard (cracked) domain is ever not hydrogen bonded after pressing play, you will immediately lose. Make sure you don't accidentally displace a hazard as part of your reactions!
  • Failure from an indeterminate reaction. If at any point there are multiple equally likely reactions possible for the same molecules, and not enough quantity of those molecules to complete all those reactions, the level will fail because of indeterminacy. See the "indeterminacy" section of displacement for more information.
  • Failure from one or more goals not being released. If there are no more reactions possible and all goal tokens haven't been released from their hydrogen bonds, the level will fail. Remember that releasing a goal once is not enough: it must remain released when the reactions complete!
  • Success. You win a level when the reactions complete (or it enters a repeating state, see the "oscillation" section of toeholds) and all of the goals are not hydrogen bonded.

If you fail a level, you are given the option to Rewind or Reload. Rewind will take you back to the level state right before you hit the play button. Reload will completely reset the level to its initial state.

Sandbox mode

Sandbox mode, accessed in the lower right, lets you build any structures you want with the domains of your choice. No win or loss conditions are enforced in Sandbox mode.


If you are logged in, you can click the Save/Share button in the lower right at any time to save the level you are working on. It will appear in "MY SAVES" in the sidebar. You will also be given a direct link to the level that you can use to show off the level to friends! This works for world levels as well as sandbox levels.

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How to Play: Displacement


Displacement reactions occur between complementary strands. Strands are complementary when two or more of their domains are complements, and those complements are in reverse order on the strands. For a displacement reaction to begin, at least one of the pairs of complementary domains must not have hydrogen bonds. Once a displacement reaction starts it travels in both directions down the strands, displacing (removing) any existing hydrogen bonds, until either strand ends or it gets to a pair of domains that are not complementary.

Double displacement

Initially, you will be presented with displacement reactions involving one complex molecule and one simple strand. Reactions between two complex molecules, in which both reacting strands see their hydrogen bonds displaced, are called double displacement. Double displacement can be deceptively complicated!


The likelihood of a displacement reaction occurring is called its "propensity". Each open domain in two complementary strands increases the propensity of the reaction, and reactions with higher propensity will always occur first. Use this to ensure that desired reactions will happen instead of undesired ones! Propensity is also affected by concentrations, as detailed in that section.


If two reactions have identical propensity, and there are not sufficient quantity of the involved molecules to complete both reactions, there will be a failure due to indeterminacy. This means that the reaction cannot complete in a consistent way. Inconsistent reactions aren't scientifically useful, so they aren't acceptable here, either!

Spatial considerations

Two strands that are part of the same molecule can react with each other, but only if they are close enough to reach. Unbroken hydrogen bonded complementary strands are rigid, and can hold possible reactants far enough apart that they cannot react.

Branch migration

Displacement reactions are not restricted to two strands. If a reacting strand runs out of complementary domains to displace, but is complementary to a third strand attached to the one it was reacting to, the reaction will "jump" to the third strand. This is called branch migration, and it will cause junctions of three or more strands.

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How to Play: Concentrations

Concentration is the quantity of a domain or molecule within the game. A concentration of two is identical to two copies of the piece, with the advantage of taking up less space and possibly necessitating fewer reactions. Previous to World 3, all domains and molecules have a concentration of one.

Viewing concentration

Pieces with concentrations greater than one appear as "stacks". The number of stacks gives you a ballpark figure of the piece's concentration:

  • Concentration 1: no stacks
  • Concentration 2-10: one stack
  • Concentration 11-100: two stacks
  • Concentration 101-1000: three stacks

To see the exact concentration number for every piece, hold the Tab key down. You can lock concentration displays on by pressing Shift-Tab. Pressing Tab again will unlock concentration display.

Changing concentration

You can only change the concentrations of unlocked domains (those with white ends). To change the concentration of an unlocked domain, hold Tab or press Shift-Tab to get concentrations showing, then click the piece and drag left (to decrease concentration) or right (to increase concentration).

Concentrations and reactions

If two pieces of the same concentration react, they will react fully and produce an output of that same concentration. If pieces of differing concentration react, they will output a molecule with the concentration of the lower concentration reactant, and there will be a quantity of the higher concentration reactant left over equal to the difference in their concentrations.

Concentrations and propensity

Concentrations act as a multiplier on propensity, but only up to the quantity that both reacting strands possess. For example, a single toehold reaction between two strands, each of which has a concentration of 2, would have double the propensity of the same reaction in which both strands had a concentration of 1. But if one has a concentration of 1, and the other has a concentration of 2, the propensity is no different than if both had a concentration of 1.

This deviates somewhat from the science behind the game, and details as to why the game works this way are available in the first post of the Science Discussion forum.

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How to Play: Toeholds

Toeholds are shorter domains. While they mostly act just like their longer counterparts, there are a few important differences.

Toehold instability

Hydrogen bonds between toeholds are not strong enough by themselves to keep the domains together. Strands connected by nothing more than a toehold will split apart. If the bonded toeholds are in a double strand with any other bonded pair of domains - including another pair of toeholds - they will be stabilized and the bond will not break.

Toehold propensity

Reactions initiated by the bonding of long domains are more likely than those initiated by the bonding of toeholds, and the former will always occur first.

Toeholds and oscillation

Because of their weak bonds, toeholds tend to be used to intentionally create unstable bonds. These may lead to cycles of two or more unstable states, called "oscillation". Most reactions involving oscillation are designed to eventually settle into a stable state, but some will oscillate endlessly. If the game detects an endless oscillation, it will stop the simulation and assign a win or loss for the level.

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How to Play: Advanced Interface Tips

Here are some features that experienced players may use to speed up gameplay.


  • When dragging an unlocked domain, all complementary unlocked domains will glow.
  • Double-clicking a domain or molecule flips it around. This doesn't affect the structure of the molecule in any way, it is just a convenience.
  • Covalently bonding two hydrogen-bonded pairs will covalently bond both strands together.
  • Bonding domains or molecules of differing concentrations always results in a new molecule of the higher concentration.


  • Space bar: play
  • Backspace: reload level
  • F1 key: show rules overlay
  • F5 key: save/share level
  • Tab: show concentrations
  • Shift-Tab: lock concentrations on
  • Arrow keys: pan camera
    • key: increase zoom
    • key: decrease zoom
  • ] key: increase animation speed
  • [ key: decrease animation speed
  • key: hide UI elements
  • s key: toggle sound on/off
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Challenges: Solving

Challenges are special levels that are periodically posted by Nanocrafter's developers. There are typically two types of challenges: regular and expert.

  • Regular challenges start with empty or mostly-empty sandboxes, and present very basic objectives. The emphasis of these challenges is not just to satisfy the objective, but to do so in interesting ways.
  • Expert challenges are either more difficult versions of regular challenges, taking considerably more thought and understanding of the game's mechanics to solve, or tied to the science behind the game, presenting a solved or unsolved scientific problem and leaving it to the player to create an invention that satisfies the problem's parameters.

Accessing challenges

Challenges are located in the sidebar to the right of the game under the CHALLENGES heading. If you move your mouse over the title of the challenge you will see a description of its objective. Click the PLAY button to create an invention for the challenge. One or more featured challenges are displayed at the top of the site, and clicking the featured challenge link will take you directly to that challenge.

Challenge prerequisites

Most challenges have a prerequisite level associated with them. This is the level we recommend you complete to ensure you understand all concepts required to submit a valid invention to the challenge. Prerequisites are not enforced, and you are free to submit solutions without having attempted the prerequisite for that challenge.

Submitting solutions

When you are satisfied with your invention, you can click the "Submit" button in the lower left of the game screen. You must be logged in to submit inventions. You are welcome to submit as many inventions as you want to each challenge.

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