 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.


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

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

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

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

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

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

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

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

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