Molecular Machines
Engineering at the limits of complexity with molecular-scale parts.
The Molecular Machines group is focused on pioneering the field of Avogadro scale engineering, which seeks to understand and approach the fundamental limit of engineered complexity deliverable per unit cost. The group has a particular focus on applications within synthetic biology, novel computing machines, and nanostructured devices for energy production.

Research Projects

  • Context-Aware Biology

    Joseph M. Jacobson and Charles Fracchia

    Current biological research workflows make use of disparate, poorly integrated systems that impose a large mental burden on the scientist, leading to mistakes, often on long, complex, and costly experimental procedures. The lack of open tools to assist in the collection of distributed experimental conditions and data is largely responsible for making protocols difficult to debug, and laboratory practice hard to learn. In this work, we describe an open Protocol Descriptor Language (PDL) and system to enable a context-rich, quantitative approach to biological research. We detail the development of a closed-loop pipetting technology and a wireless sample-temperature sensor that integrate with our Protocol Description platform, enabling novel, real-time experimental feedback to the researcher, thereby reducing mistakes and increasing overall scientific reproducibility.

  • Context-Aware Pipette

    Charles Fracchia, Jason Fischman, Matt Carney, and Joseph M. Jacobson

    Pipettes are the equivalent in biology of the keyboard for computer science: a key tool that enables interface with the subject matter. In the case of the pipette, it enables the scientist to move precise amounts of liquids. Pipette design hasn't changed in over 30 years. We've designed a new type of pipette that allows wireless, context-aware operation.

  • GeneFab

    Bram Sterling, Kelly Chang, Joseph M. Jacobson, Peter Carr, Brian Chow, David Sun Kong, Michael Oh and Sam Hwang
    What would you like to "build with biology"? The goal of the GeneFab project is to develop technology for the rapid fabrication of large DNA molecules, with composition specified directly by the user. Our intent is to facilitate the field of synthetic biology as it moves from a focus on single genes to designing complete biochemical pathways, genetic networks, and more complex systems. Sub-projects include: DNA error correction, microfluidics for high throughput gene synthesis, and genome-scale engineering (rE. coli).

  • NanoFab

    Kimin Jun, Jaebum Joo, and Joseph M. Jacobson
    We are developing techniques to use a focused ion beam to program the fabrication of nanowires-based nanostructures and logic devices.

  • Scaling Up DNA Logic and Structures

    Joseph M. Jacobson and Noah Jakimo

    Our goals include novel gene logic and data logging systems, as well as DNA scaffolds that can be produced on commercial scales. State of the art in the former is limited by finding analogous and orthogonal proteins for those used in current single-layer gates and two-layered circuits. State of the art in the latter is constrained in size and efficiency by kinetic limits on self-assembly. We have designed and plan to demonstrate cascaded logic on chromosomes and DNA scaffolds that exhibit exponential growth.

  • Synthetic Photosynthesis

    Kimin Jun

    We are using nanowires to build structures for synthetic photosynthesis for the solar generation of liquid fuels.