Current research interests
- molecular-scale information storage and processing devices
- in-vivo DNA manipulation
- self-assembly of nano-robotic systems
- enabling technologies for functional connectomics
Nanoscale containers
Students: Nick Perkons, Sherrie Wang and Evan Wu
Other mentors: Wei Sun, Tom Schaus, Steve Perrault, Ralf Jungmann, Dave Zhang, William Shih and Peng Yin
I mentored a team of students on a project to design and construct molecular containers.
Results: Team Wiki
Public lecture: Video
GASP: Gene Assembly by Subpool PCR
with Sri Kosuri, Nikolai Eroshenko and Nick Conway
GASP consists of a web server and open-source standalone scripts for the design of oligonucleotides that can be used to synthesize genes from high-complexity DNA pools (e.g., libraries cleaved from DNA microchips). Sri Kosuri led the project.
Software: GASP
Tutorial: Gene Assembly from Chip-Synthesized Oligonucleotides (PDF)
Platform: Synthetic Biology Shared Implementation Service (SynBioSIS)
Exponential quantum enhancement for distributed addition with local nonlinearity
with Michel Devoret
Publication: PDF
Using quantum entanglement, it is theoretically possible to perform so-called "pseudo-telepathy": groups of separated, non-communicating individuals can perform collective tasks which would, in a non-quantum universe, absolutely require them to communicate. To do so, they must establish quantum entanglement beforehand: the prior entanglement serves as a kind of substitute for later communication. Intrigued by limited examples of such quantum pseudo-telepathy schemes, I wondered whether quantum mechanics could allow complex computations (involving chains of non-linear logic operations) to be performed using less communication than would be required classically. Michel Devoret and I showed that this was true: the non-linear logic involved in performing a distributed binary addition operation can be done using exponentially less communication than would normally be necessary, provided the parties involved share prior entanglement.
Rapid prototyping of 3D DNA-origami shapes with caDNAno
with Shawn Douglas and William Shih
Software: www.cadnano.org
Publication: PDF
I helped to write the first version of the open-source software CADnano for design of three-dimensional scaffolded DNA origami nanostructures. Shawn Douglas led the project, and has since led the development of improved versions.
I helped to design a new type of amplifier for microwave-frequency electronic signals. The device operates in a regime where macroscopic electrical quantities like voltage and current exhibit "spooky" quantum behavior. The above image shows output from a frequency-domain simulation of the amplifier.