Hello and welcome back to the molpigs newsletter! All the past podcasts and tutorial can be found here. Enjoy! Feel free to hang out at the molpigs Forum!

  1. Thomas Ouldridge: Molecular Programming and the Physics of Computation
  2. More events coming!
  3. Job Advertisement - Parabon NanoLabs: Seeking a DNA Nanotechnology Research Scientist for Therapeutics!
  4. Interested in helping out, sharing something interesting, or have an idea for something we could do?

1. Thomas Ouldridge: Molecular Programming and the Physics of Computation

We had a great conversation with Dr. Thomas Ouldridge about a story entangling thermodynamics, information and biomolecules. Check it out here!

Abstract: Maxwell’s demon and Szilard’s engine—thought experiments from the 19th and early 20th centuries about the interplay of thermodynamics and information-processing—have long captured the imagination of theoretical physicists. Many still disagree about the interpretation of these ideas, the implications for the second law of thermodynamics, and the consequences for thermodynamics of computation. We have designed a theoretical Szilard engine from biomolecules; by explicitly rendering each step of the engine as a biochemical process, we are able to demystify the whole story. Doing so is helpful not only in resolving old thought experiments, but because the crucial idea—that the generation of correlation between non-interacting degrees of freedom is thermodynamically costly—is of fundamental significance to natural and synthetic molecular information-processing systems.

Tom Ouldridge is a Royal Society University Research Fellow in the Bioengineering Department at Imperial College London, where he leads the “Principles of Biomolecular Systems” group. His group probes the fundamental principles underlying complex biochemical systems through theoretical modelling, simulation and experiment. In particular, they focus on the interplay between the detailed biochemistry and the overall output of a process such as sensing, replication or self-assembly. They are inspired by natural systems, and aim to explore the possibilities of engineering artificial analogs.


2. More events coming!

We will soon talk with Dr. Josie Kishi and Dr. Yuan-Jyue Chen! Please send us your questions by Wednesday and the 25th respectively so we can get their thoughts!

Josie Kishi‘s interest in molecular programming was sparked when she took an elective course in biomolecular computing during college. She went on to work with Peng Yin and others at the Wyss Institute, where her primary focus was to develop the Primer Exchange Reaction (PER) synthesis method. She showed how PER cascades can be used to perform logical operations and record temporal molecular events (Nature Chemistry 2017) and for generating long single-stranded concatemers for amplifying multiplexed fluorescence imaging signal (Nature Methods 2019). Josie holds a B.S. in Computer Science from Caltech and a Ph.D. in Systems Biology from Harvard.

Yuan-Jyue Chen is a senior researcher at Microsoft Research. He is also an affiliate professor in the Paul G. Allen School of Computer Science & Engineering at the University of Washington. His research focuses on DNA Storage and DNA computing. He collaborate closely with Molecular Information System Lab (MISL) from University of Washington to make DNA storage a reality. Prior to Microsoft, he received his PhD in Electrical Engineering from University of Washington in 2015, advised by Georg Seelig. His PhD project was a collaboration between the biological computation research group at MSR Cambridge and Caltech. He came to Microsoft Research as a postdoc in 2015 and became a researcher in the DNA storage group in 2017.


3. Job Advertisement - Parabon NanoLabs: Seeking a DNA Nanotechnology Research Scientist for Therapeutics!

Parabon NanoLabs is recruiting a DNA Nanotechnology Research Scientist for its therapeutics division. If you have hands-on experience designing, synthesizing, and characterizing advanced DNA-based nanostructures, check out the position description to learn about the full time employment opportunity and obtain instructions for how to apply.


4. Interested in helping out, sharing something interesting, or have an idea for something we could do?

If so, please get in touch with us! Shoot us an email at contributions AT <this domain>, there are loads of ways you can get involved, and many we haven’t even thought of, but here’s a few ideas of what you could do:

We’re looking forward to getting to hear from you, and getting to know you better!