The course will roughly be divided into the following sections:

• Computing with molecules (CRNs)

• Computing with crystals (Self-Assembly)

• Computing with thermodynamics (TBNs)

• Computing with mechanical systems (if time permits)

• Computing with subatomic particles (if time permits)

Books, papers, etc...

• Molecular Computing Slides. Luchsinger, A. 2025.

• Models of Computation. Erickson, J., 2015.

• Computation: Finite and Infinite Machines. Minsky, M., 1967.

• Petri Net Theory and the Modeling of Systems. Peterson, J. 1981.

• Optimal Information Encoding in CRNs. Luchsinger, Doty, Soloveichik. 2023.
  [slides]

• Composable Computation in CRNs. [discrete] [continuous]

• Deterministic Function Computation in CRNs. Chen, Doty, Soloveichik. 2014.

• Tile Self-Assembly Survey. Matthew Patitz. 2013.

• aTAM Arithmetic: Addition and Multiplication. Yuriy Brun. 2006.

• aTAM Arithmetic: Subtraction and Division. Xang et al. 2008.

• Fast Arithmetic in Tile Self-Assembly. Keenan et al. 2016.

• Concentration Independent Coin Flipping. Chalk et al. 2015.

• Program Complexity of Shapes. Adleman et al. 2001.

• Self-assembly of Patterns. Drake, Patitz, Summers, Tracy. 2024.

• Tile Complexity of Linear Assemblies. Chandran, Gopalkrishnan, Reif. 2012.

• Thermodynamic Binding Networks. Doty et al. 2017.

• Computing Properties of Stable TBN Configs. [original] [IP approach]

• Programmable Kinetic Barriers in TBNs. Breik et al. 2021.

• Barrier-1 Reachability in TBNs. Luchsinger. 2022.

• TBN Experiments. Wang, Chalk, Doty, Soloveichik. 2025.

Problem Set #1

Class Exercise #1

Problem Set #2

Class Exercise #2

Final Project