A brief review on DNA storage, compression, and digitalization

Y Cevallos, T Nakano, L Tello-Oquendo… - Nano Communication …, 2022‏ - Elsevier
Deoxyribonucleic acid (DNA) comprises four nucleotides and twenty amino acids (a
combination of nucleotides) that generate living organisms' structures. These discrete …

BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts

W Poole, A Pandey, A Shur, ZA Tuza… - PLOS Computational …, 2022‏ - journals.plos.org
Biochemical interactions in systems and synthetic biology are often modeled with chemical
reaction networks (CRNs). CRNs provide a principled modeling environment capable of …

Design and simulation of a multilayer chemical neural network that learns via backpropagation

MR Lakin - Artificial Life, 2023‏ - direct.mit.edu
The design and implementation of adaptive chemical reaction networks, capable of
adjusting their behavior over time in response to experience, is a key goal for the fields of …

Reservoir computing using DNA oscillators

X Liu, KK Parhi - ACS Synthetic Biology, 2022‏ - ACS Publications
This paper presents novel implementations for reservoir computing (RC) using DNA
oscillators. An RC system consists of two parts: reservoir and readout layer. The reservoir …

Supervised learning in a multilayer, nonlinear chemical neural network

D Arredondo, MR Lakin - IEEE Transactions on Neural …, 2022‏ - ieeexplore.ieee.org
The development of programmable or trainable molecular circuits is an important goal in the
field of molecular programming. Multilayer, nonlinear, artificial neural networks are a …

Domain-specific programming languages for computational nucleic acid systems

MR Lakin, A Phillips - ACS Synthetic Biology, 2020‏ - ACS Publications
The construction of models of system behavior is of great importance throughout science
and engineering. In bioengineering and bionanotechnology, these often take the form of …

NeuralCRNs: A Natural Implementation of Learning in Chemical Reaction Networks

RT Nagipogu, JH Reif - arxiv preprint arxiv:2409.00034, 2024‏ - arxiv.org
The remarkable ability of single-celled organisms to sense and react to the dynamic
changes in their environment is a testament to the adaptive capabilities of their internal …

A cooperative DNA catalyst

DN Taylor, SR Davidson, L Qian - Journal of the American …, 2021‏ - ACS Publications
DNA catalysts are fundamental building blocks for diverse molecular information-processing
circuits. Allosteric control of DNA catalysts has been developed to activate desired catalytic …

Deep molecular programming: a natural implementation of binary-weight ReLU neural networks

M Vasic, C Chalk, S Khurshid… - … on Machine Learning, 2020‏ - proceedings.mlr.press
Embedding computation in molecular contexts incompatible with traditional electronics is
expected to have wide ranging impact in synthetic biology, medicine, nanofabrication and …

Traceback: A fault localization technique for molecular programs

MC Gerten, JI Lathrop, MB Cohen - Proceedings of the 33rd ACM …, 2024‏ - dl.acm.org
Fault localization is essential to software maintenance tasks such as testing and automated
program repair. Many fault localization techniques have been developed, the most common …