 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.


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

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

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

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

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

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

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

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

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