Computational design of nucleic acid feedback control circuits

B Yordanov, J Kim, RL Petersen, A Shudy… - ACS synthetic …, 2014 - ACS Publications
The design of synthetic circuits for controlling molecular-scale processes is an important
goal of synthetic biology, with potential applications in future in vitro and in vivo …

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

AJ Thubagere, C Thachuk, J Berleant… - Nature …, 2017 - nature.com
Biochemical circuits made of rationally designed DNA molecules are proofs of concept for
embedding control within complex molecular environments. They hold promise for …

Leakless DNA strand displacement systems

C Thachuk, E Winfree, D Soloveichik - … Cambridge, MA, USA, August 17-21 …, 2015 - Springer
While current experimental demonstrations have been limited to small computational tasks,
DNA strand displacement systems (DSD systems)[25] hold promise for sophisticated …

Parallel and scalable computation and spatial dynamics with DNA-based chemical reaction networks on a surface

L Qian, E Winfree - International Workshop on DNA-Based Computers, 2014 - Springer
We propose a theoretical framework that uses a novel DNA strand displacement mechanism
to implement abstract chemical reaction networks (CRNs) on the surface of a DNA …

A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

S Badelt, C Grun, KV Sarma… - Journal of the …, 2020 - royalsocietypublishing.org
Information technologies enable programmers and engineers to design and synthesize
systems of startling complexity that nonetheless behave as intended. This mastery of …

Comparing chemical reaction networks: A categorical and algorithmic perspective

L Cardelli, M Tribastone, M Tschaikowski… - Proceedings of the 31st …, 2016 - dl.acm.org
We study chemical reaction networks (CRNs) as a kernel language for concurrency models
with semantics based on ordinary differential equations. We investigate the problem of …

Enzyme-Free scalable DNA digital design Techniques: A review

AK George, H Singh - IEEE transactions on nanobioscience, 2016 - ieeexplore.ieee.org
With the recent developments in DNA nanotechnology, DNA has been used as the basic
building block for the design of nanostructures, autonomous molecular motors, various …

Verifying chemical reaction network implementations: A pathway decomposition approach

SW Shin, C Thachuk, E Winfree - Theoretical Computer Science, 2019 - Elsevier
The emerging fields of genetic engineering, synthetic biology, DNA computing, DNA
nanotechnology, and molecular programming herald the birth of a new information …

Modular verification of chemical reaction network encodings via serializability analysis

MR Lakin, D Stefanovic, A Phillips - Theoretical computer science, 2016 - Elsevier
Chemical reaction networks are a powerful means of specifying the intended behavior of
synthetic biochemical systems. A high-level formal specification, expressed as a chemical …

Design of a biochemical circuit motif for learning linear functions

MR Lakin, A Minnich, T Lane… - Journal of the Royal …, 2014 - royalsocietypublishing.org
Learning and adaptive behaviour are fundamental biological processes. A key goal in the
field of bioengineering is to develop biochemical circuit architectures with the ability to adapt …