ACM SYMPOSIUM ON
COMPUTATIONAL FABRICATION

Computational tools for designing, simulating, and thinking about biomolecules

Abstract: Biopolymers such as DNA, RNA, and polypeptides are extremely powerful and versatile building materials found in all living organisms. If we can master the art of design and nanofabrication with biopolymers, we will overcome many longstanding technical challenges in materials science, computing, and medicine. To that end, our group is developing software, simulation models, and experimental methods to design, fabricate, and optimize tools and devices built from biopolymers. We are also creating nontraditional simulation tools to lower barriers to characterize, understand, and communicate about these nanoscale materials.

Bio: Shawn Douglas is interested in inventing new methods to construct and manipulate biological molecules at the nanometer scale. To learn more, visit the Douglas Lab at UCSF in the department of Cellular and Molecular Pharmacology.

You might also check out BIOMOD and cadnano.

Genomes as software: An operating system for a minimal bacterial cell

Abstract: Living cells, like computers, can be seen as material implementations of Turing machines… Consider two of the signature accomplishments of the new field of synthetic biology. In building what has been called a synthetic bacterial cell and in designing and building a synthetic bacterial cell that encodes only a minimal set of genes necessary for cellular life, we have come to view living cells through the metaphor of a computer. The hardware is the membrane envelope, the protein synthesizing ribosomes, the proteins, metabolites, and the cytoplasm. The software, i.e. the operating system of the cell, is the DNA genome. The cell is capable of replicating itself. From this formalism of the Turing machine metaphor for a living cell, the question of “what are the tasks that a living cell must perform?” will be discussed to provide a somewhat utilitarian answer to the question of “what is life”?

Bio: Dr. John Glass is a Professor and leader of the JCVI Synthetic Biology and Bioenergy Group. His expertise is in molecular biology, microbial pathogenesis, RNA virology, and microbial genomics. Glass is part of the Venter Institute team that created a synthetic bacterial cell. In reaching this milestone the Venter Institute scientists developed the fundamental techniques of the new field of synthetic genomics including genome transplantation and genome assembly. Glass was also leader of the JCVI project that rapidly made synthetic influenza virus vaccine strains in collaboration with Novartis Vaccines and Diagnostics, Inc. and Synthetic Genomics, Inc. At the JCVI he has also led the bacterial outer membrane vesicle based vaccine, genome transplantation, and Mycoplasma genitalium minimal genome projects, and projects studying other mycoplasma and ureaplasma species. Glass and his Venter Institute colleagues are now using synthetic biology and synthetic genomics approaches developed at the JCVI to create cells and organelles with redesigned genomes to make microbes that can produce biofuels, pharmaceuticals, and industrially valuable molecules. Glass is an adjunct faculty member of the University of Maryland at College Park Cellular and Molecular Biology Program, and member of the Global Viral Network Scientific Leadership Board.

Prior to joining the JCVI, Glass spent five years in the Infectious Diseases Research Division of the pharmaceutical company Eli Lilly. There he directed a hepatitis C virology group and a microbial genomics group (1998-2003).

Glass earned his undergraduate (Biology) and graduate degrees (Genetics) from the University of North Carolina at Chapel Hill. His Ph.D. work was on RNA virus genetics in the laboratory of Gail Wertz. He was on the faculty and did postdoctoral fellowships in the Microbiology Department of the University of Alabama at Birmingham in polio virology with Casey Morrow and mycoplasma pathogenesis with Gail Cassell (1990-1998). On sabbatical leave in Ellson Chen’s lab at Applied Biosystems, Inc.(1995-1997) he sequenced the genome of Ureaplasma parvum and began his study of mycoplasma genomics.

Bio: Chuck Hoberman, internationally known for his transformable structures, seamlessly fuses the disciplines of art, architecture and engineering, Through his products, patents, and structures, Hoberman demonstrates how objects can be foldable, retractable, or shape-shifting.

Caitlin Mueller is a researcher, designer, and educator working at the interface of architecture and structural engineering. She is currently an Assistant Professor in the Building Technology Program, where she leads the Digital Structures research group.

As a researcher, Mueller focuses on developing new computational methods and tools for synthesizing architectural and structural intentions in early-stage design. She also works in the field of digital fabrication, with a focus on linking high structural performance with new methods of architectural making. In addition to her digital work, she conducts research on the nature of collaboration between architects and engineers from a historical perspective. Mueller also aims for interdisciplinary learning and integration in her teaching efforts, which include subjects in structural design and computational methods.

Nadya Peek develops unconventional digital fabrication tools, small scale automation, networked controls, and advanced manufacturing systems. Spanning electronics, firmware, software, and mechanics, her research focuses on harnessing the precision of machines for the creativity of individuals.

Nadya is an assistant professor at the University of Washington in the Human-Centered Design and Engineering department where she directs the Machine Agency. She is VP of the Open Source Hardware Association, half of the design studio James and the Giant Peek, and plays drum machines and synths in the band Construction. She completed her PhD on "Making Machines that Make" at MIT in 2016, advised by Neil Gershenfeld. Machines and systems Nadya has built like the "Modular Machines that Make" are shared widely including at SIGGRAPH, CHI, Guggenheim Berlin, and the White House Maker Faire, and she has given keynotes at Chaos Computer Congress, SolidCon, and H.O.P.E. Nadya is an active member of the global fab lab community, making digital fabrication more accessible with better CAD/CAM tools and developing open source hardware machines and control systems.

Nadya is equally comfortable eating street food in China or gathering mushrooms in a Siberian forest, but thinks McMaster-Carr is a great reason to take up residence in the US.

Making Legs and Practicing Neurosurgery with Maker Software

Abstract: Computational Tools for Digital Fabrication have vastly expanded the spaces of what can be made and who can make it. While Fabrication Research tends to focus on creative and/or amateur Making, there is increasing use of "Maker Tools" by professionals for serious applications. Autodesk Meshmixer is a Maker design tool that has been downloaded over a million times by a userbase that includes aerospace engineers, dental surgeons, and fourth graders. I will describe how this software has been used to address real-world problems in digital prosthetics and neurosurgery. This usage is being driven by the growing acceptance of Additive Manufacturing (3D Printing) in many industries. I will discuss some of the current challenges in the adoption of Additive techniques, and suggest some ways in which Fabrication Research could have a significant impact in advanced manufacturing.

Bio: Ryan Schmidt is the founder of Gradientspace, a 3D software studio developing Advanced Manufacturing and VR-based design tools in Toronto, Canada. He previously led the Design & Fabrication Group at Autodesk Research, after a PhD at the University of Toronto. His 3D design/print tool Meshmixer, acquired by Autodesk in 2011, has been downloaded over 1 million times. He also works with Nia Technologies to bring 3D-printed prosthetics to the developing world.