Tutorial #1 – 2D Computation
Presenters: Rebecca Schulman and Ilya Finkelstein
Nucleic acid computation can differ fundamentally from electronic computation, in part because the circuitry involved relies upon the diffusion of matter rather than the speed of light transfer of electrons. While this can sometimes prove limiting for computational power, it nonetheless greatly expands the possible for integrating computation with materials. This tutorial aims to introduce you to the possibilities inherent in carrying out 2D computations on surfaces based on diffusive and proximity effects, and to provide you with some insights into how such computations may be scaled using modern molecular biology and genomics techniques and devices.
Rebecca Schulman, PhD
Assistant Professor of Chemical and Biomolecular Engineering and Computer Science
John Hopkins University
Dr. Schulman arrived at Johns Hopkins after working as a Miller Research Fellow in Physics at the University of California Berkeley. She received her Doctoral Degree from the California Institute of Technology in Computation and Neural Systems, where she studied with Erik Winfree, and undergraduate degrees in Computer Science and Mathematics from the Massachusetts Institute of Technology.
The Schulman Lab interested in building integrated machines and materials where chemical information processing mechanisms inspired by biology enable new form and function. Using ideas from structural and dynamic DNA nanotechnology, the lab is working to engineer similarly complex, functional nanoscale devices. The Schulman lab also self-assembles synthetic DNA into reconfigurable structures, soft materials and patterns. These structures serve as soft robots, templates for wires, and architectures for controlled delivery and sensing.
Ilya Finkelstein, PhD
Assistant Professor of Molecular Biosciences,
The University of Texas, Austin
The Finkelstein Lab focuses on understanding how cells are able to stave off genomic instability and avoid premature aging. The highly interdisciplinary research program combines aspects of single-molecule biophysics, traditional biochemistry and micro-/nano-scale engineering to directly observe the key biochemical steps of DNA maintenance. Dr. Finkelstein address fundamental questions regarding how cells coordinate multi-protein assemblies on DNA, how these biochemical reactions occur on a highly condensed DNA-protein substrate, and how defects in these pathways lead to genomic instability. To increase understanding of this essential problem, the Finkelstein Lab develop new techniques that allows those to directly observe, in real time, the key biochemical reactions as they occur on DNA.
Tutorial #2 – Electron Microscopy
Presenters: David Taylor and Nicoli Francesca
The structural characterization of DNA nanostructures and materials is of greatest import for rational design and self-assembly. Beyond widely-used AFM methods, electron microscopy is an excellent tool for identifying atomic-level features of DNA assemblies. However, electron microscopy, especially combining SEM or TEM with other optical microscopy methods, can be daunting for a lab entering the field. This tutorial will address how to best begin to utilize electron microscopy for DNA nanotechnology, and will offer up exciting new approaches for exquisitely high resolution structural characterizations via the burgeoning field of cryo-EM.
David Taylor, PhD
Assistant Professor of Molecular Biosciences
The University of Texas, Austin
David Taylor, a structural biologist, enhances UT Austin’s base of expertise in a recently revitalized imaging technology known as cryo-electron microscopy (cryo-EM). Dr. Taylor also focuses on how macromolecular machines assemble and function including understanding the structural basis for CRISPR RNA-guided adaptive immunity in prokaryotes and genome maintenance and double-strand DNA break repair in eukaryotes. To accomplish these goals, we directly visualizes the structures of these protein-nucleic acid complexes using cryo-electron microscopy. Before coming to UT Austin, Taylor worked as a postdoctoral researcher at the University of California, Berkeley in the labs of Eva Nogales and Jennifer Doudna, pioneers in the study of CRISPR-Cas9. Dr. Taylor is also scholar of the Cancer Prevention and Research Institute of Texas (CPRIT).
Francesca Nicoli, MSc
Ludwig Maximilians Universität München, Germany
I received my bachelor in physics from the University of Milan, Italy, and then perused my master degree in nanotechnology at the Royal Institute of Technology (KTH) in Stockholm, Sweden. Within my master program, I spent a year at Delft Technical University (TU Delft), Netherlands, in Cees Dekker lab to work on DNA detection and sequencing with plasmonic nanopores. I am currently perusing my PhD degree at Ludwig Maximilians University in Munich, Germany, in Tim Liedl lab, where I work on DNA origami based photonic structures.
Tutorial #3 – Strand displacement and tile assembly
Presenters: David Soloveichik and David Doty
This tutorial reviews two foundational molecular programming models, each with strong theoretical and experimental presence at this conference: strand displacement and tile assembly. In the first part, we overview how DNA strand displacement can be systematically composed into coupled cascades implementing complex dynamics from first principles. The second part of the talk reviews the algorithmic tile assembly model, which abstracts aggregation of square tiles based on DNA hybridization rules. Properly designing the DNA sequences of sticky ends allows the spontaneous self-assembly of complex structures. Combining the design principles of chemical dynamics as well as chemical assembly could lead to compelling new molecular devices. In our tutorial, we will briefly introduce some of the exciting work that will appear in this conference.
David Soloveichik, PhD
Assistant Professor of Electrical and Computer Engineering,
University of Texas, Austin
Prior to joining Texas ECE, Dr. Soloveichik was a Fellow at the Center for Systems and Synthetic Biology at the University of California, San Francisco. He received his undergraduate and Masters degree from Harvard University in Computer Science. He completed his PhD degree in Computation and Neural Systems at the California Institute of Technology, where his dissertation was awarded the Milton and Francis Clauser Doctoral Prize for the best doctoral thesis. His scientific area of interest is Molecular Programming and he is also studying underlying theoretical connections between distributed computing and molecular information processing. Dr. Soloveichik was the recipient of the Feynman Prize in Nanotechnology (Theory) from the Foresight Institute in 2012, and the Tulip Award from the International Society for Nanoscale Science, Computation and Engineering in 2014.
David Doty, PhD
Assistant Professor of Computer Science,
University of California, Davis
David Doty is broadly interested in problems at the intersection of computer science, physics, chemistry, and biology, but not the traditional “computation in service of natural science” (e.g., bioinformatics, computational chemistry, or molecular dynamics simulation). Rather, certain molecular systems—such as a test tube of reacting chemicals, a genetic regulatory network, or a growing crystal—can be interpreted as doing computation themselves. He wants to understand the fundamental logical and physical limits to computation by such means. He has worked on the theory of computation by chemical reaction networks, self-assembling tiles, and agent-based models of distributed computing.