2013 MPP Workshop Retreat

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Welcome to the web page for the 2013 Molecular Programming Project Workshop, to be held on 13-15 December 2013 at the Embassy Suites Mandalay Beach Hotel in Oxnard, CA. The workshop, held yearly, brings together researchers (a) studying the principles of programming with chemistry and biochemistry; and (b) building novel molecular systems that implement useful computations. The workshop is sponsored by the National Science Foundation, through the Molecular Programming Project, an Expeditions grant funded by NSF 2008-2013, and through the Molecular Programming Architectures, Abstractions, Algorithms, and Applications grant, an Expedition funded by NSF 2013-2018.

The organizers of the workshop are Erik Winfree and Lucinda Acosta. If you have any questions or concerns, let us know at lucinda@caltech.edu.


Friday, 13 December

Saturday, 14 December

Sunday, 15 December

  • 8:30 am: Registration opens
  • 8:50 am: Welcome (Erik Winfree)

Session 1 (Erik Winfree)

  • 9:00 am: Rhiju Das (Stanford)
    "Towards massively parallel RNA engineering"
  • 9:30 am: Georg Seelig (U Washington)
    "Strand displacement reactions in living mammalian cells"
  • 10:00 am: Nils Napp (Harvard, Nagpal group)
    "Message passing inference with chemical reaction networks"
  • 10:30 am: Break

Session 2 (Richard Murray)

  • 11:00 am: Reshma Shetty (Ginkgo Bioworks)
    "Developing a fab for engineering microorganisms"
  • 11:30 am: Dan Siegal-Gaskins (Caltech, Murray group)
    "Resource limits in transcription/translation circuits"
  • 12:00 pm: Lunch

Session 3 (Lulu Qian)

  • 3:00 pm: Anne Condon (U British Columbia)
    "Ideas for supporting reversible and volume-efficient DNA computations"
  • 3:30 pm: Brian Wolfe (Caltech, Pierce group)
    "Constrained design of nucleic acid reaction pathways"
  • 4:00 pm: David Doty (Caltech, Winfree group)
    "Rate-independent computation by mass-action chemistry"
  • 4:30 pm: Break

Session 4 (Shuki Bruck)

  • 5:00 pm: Ann Erpino (Artist, Napa, CA)
    "Life, evolution, and algorithms in art"
  • 5:30 pm: Lightning Poster Blitz Session
  • 6:00 pm: Poster session
  • 7:30 pm: Group dinner

Session 5 (Eric Klavins)

  • 9:00 am: Frances Arnold (Caltech)
    "New enzymes by evolution: expanding the protein universe"
  • 9:30 am: Alex Green (Harvard, Yin group)
    "Conditional gene expression with toehold switches"
  • 10:00 am: Kevin Oishi (U Washington, Klavins group)
    "A framework for implementing finite state machines in gene regulatory networks"
  • 10:30 am: Break

Session 6 (Paul Rothemund)

  • 11:00 am: Tanja Kortemme (UCSF)
    "Design of modular sensor/actuators and light-controlled protein machines"
  • 11:30 am: Ashwin Gopinath (Caltech, Rothemund group)
    "Covalently coupled origami on planar substrates"
  • 12:00 pm: Lunch

  • 3:00 pm: tutorials, discussions, and other activities
    • discussion on building artificial cells (Murray/Noireaux)
    • discussion on visualizing ideas (Erpino)
    • discussion on DNA origami and lithography (Gopinath)
    • Q & A : philosophy and ethics (Lunshof)

  • 6:00 pm: Poster session
  • 7:30 pm: Group dinner

Session 7 (Niles Pierce)

  • 9:00 am: Przemyslaw Prusinkiewicz (U Calgary)
    "Molecular-level self-organization of plant development"
  • 9:30 am: Lisa Hochrein (Caltech, Pierce group)
    "Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs"
  • 10:00 am: Jeantine Lunshof (Harvard and VU Amsterdam)
    "Joining the molecular expedition - a philosopher's notes"
  • 10:30 am: Break

Session 8 (Shawn Douglas)

  • 11:00 am: William Shih (Harvard)
    "O-Bricks as 3D pegboards"
  • 11:30 am: Wei Sun (Harvard, Yin group)
    "Programming inorganic nanomaterials with DNA nanostructures"
  • 12:00 pm: Lunch

  • 1:00 pm: workshop ends


The hotel for the work shop is the Embassy Suites Mandalay Beach in Oxnard, CA:

Embassy Suites Mandalay Beach - Hotel & Resort
2101 Mandalay Beach Road
Oxnard, California, 93035
TEL: 1-805-984-2500

Lodging will be arranged for you, expecting arrival Thursday afternoon and departure Sunday afternoon.

Driving Directions

Oxnard is ~65 miles from Pasadena (California 134 West to US-101N). From LAX it's also ~65 (Interstate 405 North to US-101 North).

  • We can provide a link for coordinating carpooling for those interested

Shuttle services from LAX providing transportation to and from Oxnard/LAX are:

  • The Coast Shuttle, 1 800 449 8267 info@coastshuttle.co
  • RoadRunner Shuttle 1 800 247 7919

Please contact Lucinda Acosta if you require assistance with booking your travel/transportation arrangements.

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