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Cameron Chalk

PhD Candidate in the Soloveichik Lab at UT Austin

E-mail: ctchalk2 ατ gmail.com / ctchalk ατ utexas.edu

Research Interests

I work mostly in theory and partially in experiments involving molecular programming, DNA nanotechnology, and algorithmic self-assembly.

Cells provide proof of principle that complex information processing happens in chemistry. We view chemistry through the lens of computer science to understand how. This understanding allows the engineering of molecular systems that compute. Currently, we use this approach to build computers out of DNA molecules (Watson-Crick pairing makes them programmable) as proofs of principle (and with some near-term applications). In the future we will find the best substrates for rationally designed molecular computers for applications like smart drugs, control of molecular factories, diagnostics, and more--wetware for places that electronic microcontrollers cannot go.

Publications

[abc] indicates alphabetical author ordering as theoretical computer science convention

[*] indicates equal contribution

Programming and Training Rate-Independent Chemical Reaction Networks

Marko Vasic*, Cameron Chalk*, Austin Luchsinger, Sarfraz Khurshid, David Soloveichik

Proceedings of the National Academy of Sciences, 119 (24) e2111552119, 2022.

Deep Molecular Programming: A Natural Implementation of Binary-Weight ReLU Neural Networks

Marko Vasic, Cameron Chalk, Sarfraz Khurshid, David Soloveichik

Proceedings of the 37th International Conference on Machine Learning (ICML 2020), 2020

SIMD||DNA: Single Instruction, Multiple Data Computation with DNA Strand Displacement Cascades

Boya Wang*, Cameron Chalk*, David Soloveichik

(Best Student Paper Award) Proceedings of the 25th International Conference on DNA Computing and Molecular Programming (DNA25), 2019

Self Assembly of Any Shape with Constant Tile Types using High Temperature

[abc] Cameron Chalk, Austin Luchsinger, Robert Schweller, Tim Wylie

Proceedings of the 26th Annual European Symposium on Algorithms (ESA 2018), 2018

Freezing Simulates Non-freezing Tile Automata

[abc] Cameron Chalk, Austin Luchsinger, Eric Martinez, Robert Schweller, Andrew Winslow, Tim Wylie

Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA24), 2018

Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks

[abc] Keenan Breik, Cameron Chalk, David Doty, David Haley, David Soloveichik

IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 18, no. 1, pp. 283-295, 1 Jan.-Feb. 2021
Proceedings of the 16th International Conference on Computational Methods in Systems Biology (CMSB 2018), 2018

Composable Rate-Independent Computation in Continuous Chemical Reaction Networks

[abc] Cameron Chalk, Niels Kornerup, Wyatt Reeves, David Soloveichik

IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 18, no. 1, pp. 250-260, 1 Jan.-Feb. 2021
(Best Paper Award) Proceedings of the 16th International Conference on Computational Methods in Systems Biology (CMSB 2018), 2018

Thermodynamically Favorable Computation via Tile Self-Assembly

[abc] Cameron Chalk, Jacob Hendricks, Matthew J. Patitz, Michael Sharp

Proceedings of the 17th International Conference on Unconventional Computation and Natural Computation (UCNC 2018), 2018

Optimal Staged Self-Assembly of Linear Assemblies

[abc] Cameron Chalk, Eric Martinez, Robert Schweller, Luis Vega, Andrew Winslow, Tim Wylie

Natural Computing 18, 527–548 (2019).
Proceedings of the 17th International Conference on Unconventional Computation and Natural Computation (UCNC 2018) Fontainebleau, 2018

Universal Shape Replicators via Self-Assembly with Attractive and Repulsive Forces

[abc] Cameron Chalk, Erik D. Demaine, Martin L. Demaine, Eric Martinez, Robert Schweller, Luis Vega, Tim Wylie

Proceedings of the 28th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2017) Barcelona, Spain, January 16-19, 2017

Optimal Staged Self-Assembly of General Shapes

[abc] Cameron Chalk, Eric Martinez, Robert Schweller, Luis Vega, Andrew Winslow, Tim Wylie

Algorithmica, Volume 80, Issue 4, 2018, pp 1383-1409
Proceedings of the 24th Annual European Symposium on Algorithms (ESA 2016) Aarhus University, Aarhus, Denmark, August 22-26, 2016
Slides of talk given at ESA 2016

Concentration Independent Random Number Generation in Tile Self-Assembly

[abc] Cameron Chalk, Bin Fu, Eric Martinez, Robert T. Schweller, Tim Wylie

Theoretical Computer Science, Volume 667, March 8, 2017, pp 1-15

Flipping Tiles: Concentration Independent Coin Flips in Tile Self-Assembly

[abc] Cameron Chalk, Bin Fu, Alejandro Huerta, Mario A. Maldonado, Eric Martinez, Robert T. Schweller, Tim Wylie

Proceedings of the 21st International Conference on DNA Computing and Molecular Programming (DNA21), 2015
Slides of talk given at DNA21

Strict Self-Assembly of Fractals using Multiple Hands

[abc] Cameron Chalk, Dominic A. Fernandez, Alejandro Huerta, Mario A. Maldonado, Robert T. Schweller, Leslie Sweet

Algorithmica, Volume 76, Issue 1, September 2016, pp 195-224

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