 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.


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

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

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

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

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

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

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

However.yet human creativity and insight to build systems can lead to focused discoveries in this space. humans exceedingly outperform computers with their creativity. 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 . 9 . By designing new inventions and then simulating them in the game.something that would be tedious and inefficient for humans to perform. computers can quickly simulate. 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 .Why is this game important? The key to Nanocrafter is to allow humans to do what they are good at. verify. In this case.

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