▸ Research

 

Interactive Programming and Biophysics of Multi-Cellular Patterns

 

We are fascinated by the self-organization of multi-cellular morphologies and patterns at microscopic scales, such as in early development, protist swarms, or bacterial biofilms. We study the biophysical principles underlying these phenomena, and we develop devices that enable a tangible interactive experience with such systems.
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These collective spatiotemporal dynamics constitute a generalized form of spatial / distributed / amorphous computing, where the individual units, i.e., the cells, are powerful “machines” that differentiate, move, divide, communicate, die, morph, synthesize, and more.

 

If we take the notion of “multi-cellular computation” seriously (and take some inspiration from electronics), the following questions spring to mind:

  • What are the biophysical algorithms?
  • What are the properties of the biophysical hardware?
  • What is the equivalent of the personal computer?
  • How would humans interact with such computers?
  • How could these computing devices be used to solve human challenges?

A potential manifestation of such a computer contains multiple living cells that interact with each other, and where a human can stimulate these cells in a closed feedback loop to change their spatiotemporal collective dynamics. As for conventional computers, such interactions enable free exploration, programming, research, play, and much more.

 

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Interactions with electronic devices have become ubiquitous over the past 50 years. How will interactive biotic devices (‘biotic computers’) revolutionize the next 50 years?

 

Specifically:


(1) We study the biophysics and algorithms of natural multi-cellular systems in early zebrafish development and biofilm formation.

 

Embryonic development is one of the true master examples of how multi-cellular assemblies “compute” 3D structures, providing inspirations of algorithms for amorphous computing devices. We study zebrafish development and synthetic biofilm formation to gain conceptually deeper insights into the utility of entrained genetic oscillators and the properties of mechanical signals.


(2) We engineer practical devices that enable versatile human-biology interactions such as cloud experimentation labs and biotic games.

 

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We develop cloud labs that enable researches and students to execute open-ended biology experiments online, for example to interrogate the chemotaxic behavior of slimemolds or phototactice behavior of euglena. Users can then analyze their data and develop and test biophysical models; and we analyze the user data to understand this HCI (or better HBI).


(3) We employ these devices to help solving significant social and scientific challenges such as enabling cloud experimentation for other researchers, online education with true lab components, learning analytics, and informal education via games.

 

Playing games is deeply rooted in human culture. Biotechnology had virtually no impact on gaming yet. We developed ‘biotic games’, i.e., games that require biological process to run (Riedel-Kruse et al. Lab Chip). We believe that biotic games have significant educational potential by enabling non-scientist to engage and interact with modern biotechnology. We now perform the corresponding user studies.

 

We combine a range of approaches such as molecular and cell biology, synthetic biology, imaging, instrumentation, theory and modeling, computer science and mobile interfaces and more. We work with different of organisms, i.e., zebrafish, physarum, e. coli, and euglena.

 

Stanford Bioengineering provides a stimulating environment for our interdisciplinary research program: We share an open lab space with the Prakash and Quake labs, and we closely collaborate with the labs of Rhiju Das (Biochemistry), Alex Dunn (Chemical Engineering), Paulo Blikstein (Education) and Daniel Schwartz (Education).

 

It is our long-term vision that every scientist and layperson has convenient access to interact with, explore, and utilize micro-biological systems. The rapid advancements of biotechnology promises the enabling power. We see it is our mission to help conceptualize and pioneer this field.