3 papers
cs.ET2020
Computing properties of thermodynamic binding networks: An integer programming approach
David Haley, David Doty
The thermodynamic binding networks (TBN) model is a tool for studying engineered molecular systems. The TBN model allows one to reason about their behavior through a simplified abs…
cs.DC2019
Composable computation in discrete chemical reaction networks
Eric E. Severson, David Haley, David Doty
We study the composability of discrete chemical reaction networks (CRNs) that stably compute (i.e., with probability 0 of error) integer-valued functions $f:\mathbb{N}^d\to\mathbb{…
cs.ET2018
Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks
Keenan Breik, Cameron Chalk, David Doty +2
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the…