 General

 How to Play: Basics

 How to Play: Displacement

 How to Play: Concentrations

 How to Play: Toeholds

 How to Play: Advanced Interface Tips

 Challenges: Solving

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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.


and move the camera around by clicking on the game background and dragging. If you click and drag in the middle section of a domain . This is useful for binding domains (see below).  Concentration: See the "concentrations" section for more information. World levels are accessed on the sidebar to the right of the game.  Locked/unlocked: Domains can be either locked (gray ends) or unlocked (white ends). but may distort the layout of the molecule in undesired ways. you will immediately lose. the basic unit of displacement reactions. If they meet all those criteria. if a hazard is ever not hydrogen bonded after hitting the Play button. Conversely. This is useful for moving around large molecules without disrupting their organization.buttons in the lower left of the game screen. Moving Domains All domains can be moved around.that and any connected domains will follow the cursor fluidly.the colored part . Completing Levels 2 . Camera controls After the first couple of worlds you will be able to control the camera. Domains must have the same color or colors to hydrogen bond with each other. covered in the Challenges sections. You can zoom in or out by clicking the + and . and unlock when you have played a related preceding level.the white or gray part .  Shape: Domains have either bumps or divets. Mouse scroll wheels generally work to control zooming. To hydrogen bond unlocked domains.  Target: Most domains are not targets. If you click and drag the front or back of a domain . Covalently bonded domains form a "strand".that and any connected domains will be moved but their orientation will not change. The ones that are either have stars (goals) or cracks (hazards). You will see a glow indicating that they can hydrogen bond. but some browsers prevent them from functioning. short domains are always a single color. They can be moved one of two ways. and world levels. they must be the same length.  Color: Long domains can have either one or two colors in their midsection. Bonding Domains Any unlocked domains can be covalently bonded together by dragging the front of one domain to the tail of another. Two domains that can hydrogen bond are called "complements". Level Types There are two types of levels: challenge levels. simply drag the domains so they are side-by-side. when not hydrogen bonded they will glow yellow. nor can you delete them. All levels in a world must be completed to unlock the next world. You cannot manually change the bonds or concentrations of locked domains. All goal domains must not be hydrogen bonded to win a level. or vice versa. and domains must have the opposite shape to hydrogen bond with each other. and have opposite shapes. Most world levels start locked. have the same colors.

at least one of the pairs of complementary domains must not have hydrogen bonds. and those complements are in reverse order on the strands.Once you are satisfied with your solution to a level. No win or loss conditions are enforced in Sandbox mode. you are given the option to Rewind or Reload. Reload will completely reset the level to its initial state. Sandbox mode Sandbox mode. Once a displacement reaction starts it travels in both directions down the strands. the level will fail because of indeterminacy. Back to top How to Play: Displacement Displacement Displacement reactions occur between complementary strands. Strands are complementary when two or more of their domains are complements. Remember that releasing a goal once is not enough: it must remain released when the reactions complete!  Success. you will immediately lose. accessed in the lower right. After the reactions complete. Double displacement 3 . the level will end in success or failure based on several conditions:  Failure from a hazard being released. you can click the Save/Share button in the lower right at any time to save the level you are working on. If you fail a level. lets you build any structures you want with the domains of your choice. and not enough quantity of those molecules to complete all those reactions. Saving If you are logged in. If there are no more reactions possible and all goal tokens haven't been released from their hydrogen bonds. If a hazard (cracked) domain is ever not hydrogen bonded after pressing play. If at any point there are multiple equally likely reactions possible for the same molecules. until either strand ends or it gets to a pair of domains that are not complementary. the level will fail. For a displacement reaction to begin. Make sure you don't accidentally displace a hazard as part of your reactions!  Failure from an indeterminate reaction. Rewind will take you back to the level state right before you hit the play button. you always need to click the Play button in the lower right to initiate reactions. It will appear in "MY SAVES" in the sidebar.  Failure from one or more goals not being released. See the "indeterminacy" section of displacement for more information. see the "oscillation" section of toeholds) and all of the goals are not hydrogen bonded. 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. You win a level when the reactions complete (or it enters a repeating state. displacing (removing) any existing hydrogen bonds.

A concentration of two is identical to two copies of the piece. Use this to ensure that desired reactions will happen instead of undesired ones! Propensity is also affected by concentrations. If a reacting strand runs out of complementary domains to displace. Reactions between two complex molecules. Unbroken hydrogen bonded complementary strands are rigid. either! Spatial considerations Two strands that are part of the same molecule can react with each other. 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 4 .Initially. there will be a failure due to indeterminacy. the reaction will "jump" to the third strand. and can hold possible reactants far enough apart that they cannot react. you will be presented with displacement reactions involving one complex molecule and one simple strand. all domains and molecules have a concentration of one. so they aren't acceptable here. but is complementary to a third strand attached to the one it was reacting to. This means that the reaction cannot complete in a consistent way. Double displacement can be deceptively complicated! Propensity The likelihood of a displacement reaction occurring is called its "propensity". in which both reacting strands see their hydrogen bonds displaced. and reactions with higher propensity will always occur first. are called double displacement. Inconsistent reactions aren't scientifically useful. Indeterminacy If two reactions have identical propensity. with the advantage of taking up less space and possibly necessitating fewer reactions. Branch migration Displacement reactions are not restricted to two strands. Each open domain in two complementary strands increases the propensity of the reaction. Viewing concentration Pieces with concentrations greater than one appear as "stacks". This is called branch migration. Back to top How to Play: Concentrations Concentration is the quantity of a domain or molecule within the game. but only if they are close enough to reach. and there are not sufficient quantity of the involved molecules to complete both reactions. as detailed in that section. and it will cause junctions of three or more strands. Previous to World 3.

and there will be a quantity of the higher concentration reactant left over equal to the difference in their concentrations. Changing concentration You can only change the concentrations of unlocked domains (those with white ends). Strands connected by nothing more than a toehold will split apart. each of which has a concentration of 2. Concentrations and reactions If two pieces of the same concentration react. To change the concentration of an unlocked domain. If pieces of differing concentration react. hold Tab or press Shift-Tab to get concentrations showing. the propensity is no different than if both had a concentration of 1. but only up to the quantity that both reacting strands possess. For example. and the former will always occur first. Toehold propensity Reactions initiated by the bonding of long domains are more likely than those initiated by the bonding of toeholds. and details as to why the game works this way are available in the first post of the Science Discussion forum. then click the piece and drag left (to decrease concentration) or right (to increase concentration). they will output a molecule with the concentration of the lower concentration reactant. they will react fully and produce an output of that same concentration. You can lock concentration displays on by pressing Shift-Tab. But if one has a concentration of 1.they will be stabilized and the bond will not break. a single toehold reaction between two strands. Back to top How to Play: Toeholds Toeholds are shorter domains. Toeholds and oscillation 5 . If the bonded toeholds are in a double strand with any other bonded pair of domains . Concentrations and propensity Concentrations act as a multiplier on propensity. Pressing Tab again will unlock concentration display.including another pair of toeholds . This deviates somewhat from the science behind the game. hold the Tab key down.  Concentration 101-1000: three stacks To see the exact concentration number for every piece. Toehold instability Hydrogen bonds between toeholds are not strong enough by themselves to keep the domains together. and the other has a concentration of 2. would have double the propensity of the same reaction in which both strands had a concentration of 1. While they mostly act just like their longer counterparts. there are a few important differences.

Hotkeys  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  o key: increase zoom  o key: decrease zoom 6 .  Double-clicking a domain or molecule flips it around.Because of their weak bonds. all complementary unlocked domains will glow. This doesn't affect the structure of the molecule in any way. If the game detects an endless oscillation. but some will oscillate endlessly.  Covalently bonding two hydrogen-bonded pairs will covalently bond both strands together. 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.  Bonding domains or molecules of differing concentrations always results in a new molecule of the higher concentration. it will stop the simulation and assign a win or loss for the level. it is just a convenience. toeholds tend to be used to intentionally create unstable bonds. Interface  When dragging an unlocked domain. Back to top How to Play: Advanced Interface Tips Here are some features that experienced players may use to speed up gameplay.

There are typically two types of challenges: regular and expert. Click the PLAY button to create an invention for the challenge. Prerequisites are not enforced. You are welcome to submit as many inventions as you want to each challenge. Submitting solutions When you are satisfied with your invention. 7 . and present very basic objectives. Challenge prerequisites Most challenges have a prerequisite level associated with them. but to do so in interesting ways. and clicking the featured challenge link will take you directly to that challenge. This is the level we recommend you complete to ensure you understand all concepts required to submit a valid invention to the challenge. and you are free to submit solutions without having attempted the prerequisite for that challenge. The emphasis of these challenges is not just to satisfy the objective. presenting a solved or unsolved scientific problem and leaving it to the player to create an invention that satisfies the problem's parameters. You must be logged in to submit inventions. If you move your mouse over the title of the challenge you will see a description of its objective. One or more featured challenges are displayed at the top of the site. taking considerably more thought and understanding of the game's mechanics to solve.  ] key: increase animation speed  [ key: decrease animation speed  key: hide UI elements  s key: toggle sound on/off Back to top Challenges: Solving Challenges are special levels that are periodically posted by Nanocrafter's developers.  Expert challenges are either more difficult versions of regular challenges.  Regular challenges start with empty or mostly-empty sandboxes. or tied to the science behind the game. you can click the "Submit" button in the lower left of the game screen. Accessing challenges Challenges are located in the sidebar to the right of the game under the CHALLENGES heading.

dependable reaction to harness. Strand displacement is the process through which two strands with partial or full complementarity hybridize to each other. Why build things with DNA? Nucleic acids . the genes encoded in DNA are turned into the proteins that organisms are built from and kept alive by. DNA can act as a building block. DNA has been used as a material for the self-assembly of complex two. the Seelig Lab at the University of Washington discovered a new way of constructing these DNA circuits. and produce new ones in custom patterns. Many of these devices rely on a phenomenon know as strand displacement. This has lead to the use of DNA for something besides their natural purpose: when removed from their normal place within cellular machinery. In Nanocrafter. as a substrate for molecular computation and for the rational design of molecular devices and motors with moving parts. So the Center for Game Science and the Seelig Lab teamed up to build Nanocrafter: a game that lets you build DNA circuits to solve problems. they can be easily programmed by logically designing their base sequences. and part of what makes it such a good molecule for synthetic biology: not only is it inexpensive to produce. More recently and perhaps more impressively. and eventually invent new structures that may be of scientific value.and three- dimensional structures. using only a few simple rules that we think even non-scientists can learn.and to go beyond that to start building our own systems. strand displacement gives DNA a predictable. you use DNA as a building block rather than for its normal genetic function.are the ideal molecules for creating many types of biomolecular systems. Nucleic acids are a uniquely promising substrate for a molecular programming approach because the base sequence and the rules of Watson Crick base pairing predictably determine how single-stranded nucleic acids interact with one another. DNA consists of hundreds of thousands to billions of chemicals called nucleotides attached in a long chain. This is a key mechanism for the dynamic DNA systems that you can design in Nanocrafter. and chemically well-understood. called DNA circuits. In 2006. relatively hearty.DNA and RNA . Scientists racing to catalog the genetic material of the organisms living on Earth developed new technologies: technologies that allow them to identify molecules of DNA easily and cheaply. can be used to solve logic problems in much the way computers can. What is synthetic biology? The past few decades have seen incredible advances in biology that have allowed us to look deeper into the systems of life and understand them better . Specific sequences of these nucleotides describe genes. share them with your friends. RNA has been engineered to play functional roles within the cell and in biotech applications. 8 . displacing one or more pre-hybridized strands in the process. scientists discovered that certain specially-designed DNA molecules. In the 1990s. the instructions for how and when to create specific proteins. For decades.NANOCRAFTER> THE SCIENCE What is DNA? DNA is a molecule that acts as a library of genetic information. Via another molecule. RNA.

However. humans exceedingly outperform computers with their creativity.something that would be tedious and inefficient for humans to perform. and computers to do what they are good at. The space of all possible bio- molecular systems is vastly larger than what a computer can search . In this case. we hope that players will come up with new ideas that can be applied to ongoing research in the field. and potentially perform local optimizations on player designs . verify.Why is this game important? The key to Nanocrafter is to allow humans to do what they are good at. 9 .yet human creativity and insight to build systems can lead to focused discoveries in this space. computers can quickly simulate. By designing new inventions and then simulating them in the game.