Friday afternoon impromptu parallel sessions

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Would you like to give an impromptu session on a topic of your choice? Sign up here!

The rules:

  • The topic can be anything that might be of interest to this scientific community. Your research. A birds-of-a-feather discussion on a topic of your choice. A software demonstration. A tutorial. A brainstorming session. You choice.
  • Sessions must be open to the public. No closed or exclusive events.
  • To propose a session, first create an account for yourself (upper left button), then click 'edit' on the room and time you would prefer. Enter a description of the event, and be sure to include your name as the session organizer.
  • No individual may organize more than one impromptu session.
  • To express enthusiasm about a session, you must also 'edit' the entry, and add your initials.

Note that we are still in the process of figuring out which rooms are equipped with what. (Feel free to help us out by finding out that information and entering it here.)

Also note that impromptu sessions may be moved around, either by the organizer of the session, or by the conference organizers. So check back here before the impromptu sessions start!

(Note from Constantine regarding Wikis: please be careful when editing this page; if someone else is editing it while you are, you can easily end up removing all of their edits, which can end up inadvertently removing their entire impromptu session.)

Room Beckman Institute 115

Capacity: 35, classroom style. projector. blackboard.




Current Advances in DNA Automata Ron Piran, Sivan Shoshani, Tamar Ratner, Natasha Jonoska, and Ehud Keinan. We will review our techniques to use DNA and DNA enzymes for the construction of finite automata, presenting new applications such as their introduction to living cells and organisms. We will give special attention to unpublished data on the application of such automata to decipher encrypted information and on the newly developed push down automaton, which represent a major advance in the computation power of such devices.


Multiscale Information Processing and Cellular Machinery (Misha Pesenson, CMS Dept., Caltech)

It is well-known that the human brain networks perform multiscale information processing: time-frequency analysis of auditory and multiresolution analysis of visual information. Are molecular networks capable of such analysis? The goal of this session is to explore this question by looking into possible connections between these two seemingly different types of networks (for the first network of artificial neurons made from DNA see Qian, L., Winfree, E. & Bruck, J. Nature 475, 368–372 (2011)). There is a potential synergistic opportunity here and we look forward to sharing ideas from various perspectives and stimulating discussions.


DSD Tutorial - Andrew Phillips

DSD is a programming language for modelling, simulating and analysing DNA strand displacement systems.

In this tutorial I'll first give a very brief overview of DSD, using a few simple examples.

I'll also highlight what features are coming up in the next release of DSD, including hairpins and localised circuits, and take requests for new features.

The rest of the tutorial will be dedicated to helping you program your favourite strand displacement system and use DSD to its full potential.

DSD is available from and works on Windows and OS X. It requires Silverlight 4 to be installed, which is available from for both platforms.

Click on the [?] button in the top right corner of the tool for instructions on how to install DSD, and also to take the introductory tutorial

Additional background information is at

Bring your laptops to try out the online tutorial

Room Beckman Institute 121

Capacity: 35, classroom style. projector. blackboard.


Practical Considerations and Results of Real-Time Super-Resolution Imaging/Tracking of Single Deoxyribozyme Based Molecular Robots

Tony Manzo (Nils G. Walter Group, University of Michigan, Ann Arbor)

We will present experimental methods and results of probing and characterizing the behavior of individual nucleic acid based molecular robots using total internal reflection fluorescence microscopy (TIRFM). Nucleic acid based molecular assemblies, called “spiders”, implemented as robots with multiple deoxyribozyme sensor-actuator legs traverse and cleave two-dimensional landscapes of surface bound chimeric oligonucleotide substrates. We analyze the movement of spiders to determine the characteristics of their random and directional walks on various substrates. We observe heterogeneities in behavior and demonstrate effects of varying spider leg multivalency and leg-substrate recognition sequences. The experimental approach demonstrated here should allow for control over the cybernetic properties of spiders, resulting in the integration and synthesis of complex robotic behaviors at the nanoscale based on RNA and DNA nanotechnology.

Note: Criticism and questions will be good. This is mostly about experiments with molecular robots and not too much theory.


Experimental Algorithmic Self-Assembly: Where is it? Where can we take it? And how can theory help? --- Constantine Evans, Winfree group, Caltech

To copy a controversial strategy, I'd like to start a discussion stemming from two claims:

  • DNA tile self-assembly systems will never be able to do anything much beyond what has already been done, and is a waste of time.
  • Most theoretical work on self-assembly will never apply to experimental systems, and is completely useless.

In particular, I'd like to have a short conversation about the following topics:

  • Where experimental self-assembling systems are now, and where we hope they can go in the near future.
  • Software tools for the design of tile systems: what we need to consider in building compilers and design tools for things like tile logic in a realistic model and sticky end sequence design, how simulations can be improved, and how we can use simulations to influence design and experiments.
  • The limits of the experimental tile systems we have now, like DX tiles, and possibilities for better systems.
  • Interesting directions that recent theoretical work might suggest for future experimental research.
  • The theoretical directions that might be useful for what we currently want to do with experimental systems.


A few tough problems in the tile assembly model -- Dave Doty, Caltech

We will tackle a few open problems in self-assembly that have annoyed a few of us for a while. The first is the power of the temperature-1 model, in which we hope to prove that temperature-1 tile systems are not capable of universal computation. The second is the problem of verification for hierarchical systems. Specifically, is there an efficient algorithm that, given a shape S and a hierarchical tile set T, determines whether T assembles precisely one unique assembly, and that assembly has shape S?

Lastly, there are some interesting directions in which to take the staged self-assembly model; specifically, relaxing the constraint that all incomplete assemblies are washed away at each step, which would be easier to implement experimentally. What tasks are possible in such a model that are not possible in one-pot reactions?


NUPACK design tutorial

Brian Wolfe

  • External sequence constraints
  • Automatic dimensioning
  • Multi-state design syntax
  • How to get faster design times and other tricks
  • How to use concentration-based design

Room Beckman Institute 228

Capacity: 10, conference style. projector. blackboard.




Discussion: unusual arithmetic and stickers

Mark Arnold

My talk showed unusual arithmetic systems could improve DNA sticker computation. Maybe unusual representations could help other DNA paradigms, like strand displacement. Maybe further development of actual sticker-DNA hardware is possible. Maybe I am just daydreaming. My talk probably went by fast. Please stop by if you would like to chat.


Discussions about Molecular Robot Contest@BIOMOD 2011
Shogo Hamada and Ebbe S. Andersen

  • status quo
  • future plans

related with Molecular Robot Contest ("Pilot" Category of BIOMOD 2011) will be discussed. Please see this page for more details.