Jonas Hannestad: Nature as Technology: Strategies for Nano-Scale, DNA-Based Communication #STU05

This presentation was given on wednesday, 7th of December 2011, 8 pm GMT, by Jonas Hannestad, @jhannestad, PhD student at Chemical and Biological Engineering at Chalmers University of Technology, Gothenburg. Jonas works with bio-inspired nanotechnology, with a particular focus on nano-scale photonic devices.

Links to further reading below.

Tweeter

Jonas Hannestad

Room

#stu05

This is @ozonist tweeting to welcome you to yet another lecture on The Swedish Twitter University!  
In just a few minutes Jonas Hannestad will take over the account and make a 25 tweet presentation of his intriguing field of research.  
Before he starts let me remind you to add the #stu05 tag to any questions or comments you want to throw in. That way everybody can see them!  
I would also like to say that the hashtag flow and Jonas’ tweets will be archived on the http://t.co/CFaoXxMh blog.  
Now let’s enjoy this event titled “Nature as Technology: Strategies for Nano-Scale, DNA-Based Communication”. Take it away, Jonas!  
Thanks @ozonist and good evening. My name is Jonas Hannestad an I’m a PhD student at Chalmers University of Technology, Gothenburg, Sweden.  
I’m approaching the subject of bionanotechnology as a physical chemist, trying to develop photonic applications inspired by natural systems  
In Tonight’s talk I will describe my research in brief and try to put it in a context of a novel view on technology as a whole. let’s begin  
1. The ability to create technological devices on an ever-smaller scale forces us to question what we mean by technology  
2. Nanotechnology deals with objects on the size scale of 1-100 nm, comparable to biological macromolecules such as proteins and DNA.  
  @Cotesia1
Tweets by Hannestad on bionanotechnology just started at @SVTwuni #STU05. Join us!
3. Biotech. has defined biological organisms as objects of technology, utilized, for example, as production facilities or as disease models.  
  @cerreyes
Nanosocieties. It’s a small world | @jhannestad about to start at @SvTwuni http://t.co/eW7yTuVh #stu05
4. Bioinspired nanotechnology does the same thing, but on a molecular level. Biomoluecules are used as building material for technology.  
5. Utilizing self-assembly, nanometer-scale structures are built from the bottom-up to perform functions similar to natural ones.  
6. The use of self-assembly and bottom-up design is an important difference to conventional technology which relies on top-down techniques.  
7. Our research has two primary foci: assembly of nanometer-scale geometries from DNA and creation of photonic devices mimicking biology.  
8. DNA is code. In nature, the genetic code is executed inside cells, which (eventually) leads to the production of proteins.  
9. However, DNA can also be used to code other things, for instance structures in two and three dimensions.  
10. DNA is a linear polymer with four constituents (A, T, G, C) which forms a double helix with a complementary counterpart (A-T, G-C).  
11. By designing the complementarity pattern of multiple strands, they can be forced to fold into a specific shape http://t.co/8c2Mbfhm  
12. Assemblies can also be designed to perform functions such as mechanical work or computation, building systems resembling neural networks  
13. We want to modify DNA-based structures to perform nanoscale optical communication and to coordinate light driven chemical reactions.  
14. This work is inspired by the way photosynthetic bacteria gather energy by directed energy migration through molecular assemblies  
  @cerreyes
RT @SvTwuni 8. DNA is code. In nature, the genetic code is executed inside cells [...] #stu05 #datathanatology
15. Light-harvesting complexes are energetic funnels where energy absorbed in the outer parts flows towards the center. http://t.co/sHIzESTZ  
16. This flow of energy can be mimicked by attachment of fluorescent dyes to DNA structures, controlling energy and positioning of the dyes.  
17. Linear arrangement of dyes results in photonic wires where energy is transferred between the dyes, from end to end http://t.co/TJwkRqim  
18. The input and output of the wire is a photon of high and low energy, respectively. Energy transfer occurs by dipole-dipole interaction.  
19. The energy transfer mechanism is called FRET. FRET proceeds without emission of photons and has a distance dependence on the nm scale  
  @Cotesia1
@svtwuni: Is there a good reference (review) link for interesting points 14 & 15? Thanks! #STU05
20. The flow of energy in the systems can directed to separate outputs in controlled ways or regulated between on/off http://t.co/vpji0vxT  
21. Inclusion of other modifications to DNA can introduce anchoring to bio-membranes or coupling of transferred energy to chem. reaction.  
22. This coupling of energy transfer to electron transfer reactions is similar to the key mechanism in photosynthesis. http://t.co/wlCzZOvl  
23. These examples show how self-assembled structures built from DNA can be used to coordinate a multitude of functionalities.  
  @ozonist
@SvTwuni I lost tweet no 20… Just me? #stu05
24. A somewhat speculative application could be to use similar devices as a seamless interface between cells and conventional technology  
  @fredrikedin
@ozonist I got it #stu05 @SvTwuni
@Cotesia1 I added a link to a PNAS paper (where the images are from) in the description. I recommend the work by Klaus Schulten in general  
25. The use of biomolecules and biological functions and design principles challenges our perceived boundaries between nature and technology  
@ozonist I see it too, I can repost it if you like  
That was the last tweet. I am now happy to answer any questions. Remember to use the #stu05 hashtag  
  @ozonist
@SvTwuni Thank you, but I can see it in my phone… Weird. :) #stu05
  @Cotesia1
Interesting world. Attended a tweet lecture originating in Sweden – was then referred to work by person at UIUC. I think that’s gr8 #stu05
  @ozonist
@SvTwuni What does one need to hack these kind of technologies? #stu05
@Cotesia1 small world. The light harvesting complexes are really fascinating examples of nanoscale architecture in biology  
@ozonist it depends on what one wants to do. Just creating DNA structures is fairly straightforward, albeit still a bit expensive #stu05  
  @dromograf
RT @Cotesia1: Interesting world. Attended a tweet lecture originating in Sweden – was then referred to work by person at UIUC. I think that’s gr8 #stu05
@ozonist the material is readily available and the designed can be done by hand (or using simple software). #stu05  
@ozonist since the structures self-assemble, all you have to do is to mix them in water. characterization can be another thing though #stu05  
@ozonist and if you want to add some functionalities things become more complex. most straightforward is the DNA origami I think  
@ozonist and if you want to add some functionalities things become more complex. most straightforward is the DNA origami I think #stu05  
  @cerreyes
@SvTwuni Any possible application for architecture? e.g. surfaces harvesting light to feed energy inside buildings #stu05
  @ozonist
Thank you! Interesting. And very much a part of a maker paradigm rather than a tweaker paradigm… #STU05
@cerreyes I think, for that type of large-scale applications, these designs would not be very suitable. #stu05  
@cerreyes instead, I think it might be very interesting for researchers in the solar cell community to think more about architecture #stu05  
  @ozonist
Could you tell us a bit more about the “specualtive” seamless interface between cells and conventional technology application? #stu05
@cerreyes one possible application is in high density optical data storage. #stu05  
@cerreyes light would be gathered over a large are and transferred to a target molecule the interacts with an underlying surface #stu05  
  @doktorsbloggen
@SvTwuni @cerreyes as someone who could call herself a solar cell researcher, I agree with your achitecture point. #stu05
@ozonist since we use biomolecules, interaction with e.g. cells is possible, at the same time, we are using light as input and output #stu05  
@ozonist light signals is something that can be processed by conventional technology. #stu05  
@ozonist eventually it would be interesting to link this to the chemistry inside the cells, to probe and control the cell using light #stu05  
@ozonist and, finally, to effectively interact with whole organs. but then we’re really, really far out #stu05  
  @ozonist
@SvTwuni Yes! Btw, saw that Clinton warned earlier today about new bioweapons coming from things like this: http://bit.ly/uC688Y #stu05
@ozonist reminds me of this: http://t.co/yDDLoW9p (from @monki a while ago)  
@doktorsbloggen @cerreyes what possibilities are there to incorporate solar cells in e.g. the windows of large glass buildings?  
  @doktorsbloggen
@SvTwuni @cerreyes depends on if we are willing to accept slightly colored windows (since need to absorb visible light) or… #stu05
  @doktorsbloggen
@SvTwuni @cerreyes …or if we can learn to use 2 IR photons and upconvert them. So, it’s not supereasy, but probably doable #stu05
  @doktorsbloggen
@SvTwuni @cerreyes but the easiest way out is of course the walls of buildings, or roofs. Which is already happening #stu05
I will also take the opportunity to recommend anyone who is interested in a broader discussion on nanotech, society and culture to >> #stu05  
<< visit the blogg nanosocieties (http://t.co/LPM7hKXN), run by me (@jhannestad) and @karlpalmas  
  @cerreyes
Thanks @doktorsbloggen @SvTwuni > Yes it’s happening… as glass facades w. solar cells http://t.co/EtsibHo0 #stu05
  @ozonist
@SvTwuni Okay! I think it’s time to say thank you for this very interesting hour and a half. I’ll surely tune in on nanosocieties! #stu05
  @ozonist
@SvTwuni I hop you can hear the clapping hands, Jonas… :) #stu05
  @cerreyes
@doktorsbloggen @SvTwuni >By the way I was thinking in a responsive surface like DUNE but harvesting light bit.ly/uLzHLI Thxs again #stu05
and thank you @ozonist for inviting me. if there are any remaining question you can send the directly to me @jhannestad #stu05  
  @cerreyes
Thanks @jhannestad + @SvTwuni + @ozonist for another compelling tweet conference #stu05
  @ozonist
@SvTwuni #stu05 Yes, and you’re all welcome to continue the discussion on the http://t.co/nv0Ag3tF blog as well. Tonight’s tweets will be
  @ozonist
@SvTwuni #stu05 put up there shortly! Thank you again, @jhannestad!

Further reading

Light harvesting complex:
Architecture and mechanism of the light-harvesting apparatus of purple bacteria, Xiche Hu, Ana Damjanovic´, Thorsten Ritz, and Klaus Schulten
http://dx.doi.org/10.1073/pnas.95.11.5935

DNA nanotechnology:
DNA Nanotechnology and the Double Helix, Nadrian C. Seeman
http://dx.doi.org/10.1038%2Fscientificamerican0604-64 (pdf)

Challenges and opportunities for structural DNA nanotechnology, Andre V. Pinheiro, Dongran Han, William M. Shih and Hao Yan
http://dx.doi.org/10.1038/nnano.2011.187

Paul Rothemund details DNA folding
http://www.ted.com/talks/paul_rothemund_details_dna_folding.html

DNA-based photonic devices (requires journal access):
Self-Assembled DNA Photonic Wire for Long-Range Energy Transfer, Jonas K. Hannestad, Peter Sandin and Bo Albinsson
http://dx.doi.org/10.1021/ja803407t

Self-Assembled DNA-Based Fluorescence Waveguide with Selectable Output, Jonas K. Hannestad, Simon R. Gerrard, Tom Brown, Bo Albinsson
http://dx.doi.org/10.1002/smll.201101144

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