CRN++: Molecular programming language

M Vasić, D Soloveichik, S Khurshid - Natural Computing, 2020 - Springer
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in
biology, nanofabrication, and medicine. A key technical challenge lies in embedding …

[HTML][HTML] Efficient synthesis of robust models for stochastic systems

R Calinescu, M Češka, S Gerasimou… - Journal of Systems and …, 2018 - Elsevier
We describe a tool-supported method for the efficient synthesis of parametric continuous-
time Markov chains (pCTMC) that correspond to robust designs of a system under …

PID control of biochemical reaction networks

M Whitby, L Cardelli, M Kwiatkowska… - … on Automatic Control, 2021 - ieeexplore.ieee.org
Principles of feedback control have been shown to naturally arise in biological systems and
have been applied with success to build synthetic circuits. Here, we present an …

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 …

Counterexample-driven synthesis for probabilistic program sketches

M Češka, C Hensel, S Junges, JP Katoen - International symposium on …, 2019 - Springer
Probabilistic programs are key to deal with uncertainty in, eg, controller synthesis. They are
typically small but intricate. Their development is complex and error prone requiring …

Counterexample-guided inductive synthesis for probabilistic systems

M Češka, C Hensel, S Junges, JP Katoen - Formal Aspects of Computing, 2021 - Springer
This paper presents counterexample-guided inductive synthesis (CEGIS) to automatically
synthesise probabilistic models. The starting point is a family of finite-stateMarkov chains …

Optimal Program Synthesis via Abstract Interpretation

S Mell, S Zdancewic, O Bastani - Proceedings of the ACM on …, 2024 - dl.acm.org
We consider the problem of synthesizing programs with numerical constants that optimize a
quantitative objective, such as accuracy, over a set of input-output examples. We propose a …

Peregrine: A Tool for the Analysis of Population Protocols

M Blondin, J Esparza, S Jaax - International Conference on Computer …, 2018 - Springer
We introduce P eregrine, the first tool for the analysis and parameterized verification of
population protocols. Population protocols are a model of computation very much studied by …

Towards programmable chemistries

D Flumini, MS Weyland, JJ Schneider… - Artificial Life and …, 2020 - Springer
We provide a practical construction to map (slightly modified) GOTO-programs to chemical
reaction systems. While the embedding reveals that a certain small fragment of the …

Synthesizing and tuning stochastic chemical reaction networks with specified behaviours

N Murphy, R Petersen, A Phillips… - Journal of The …, 2018 - royalsocietypublishing.org
Methods from stochastic dynamical systems theory have been instrumental in understanding
the behaviours of chemical reaction networks (CRNs) arising in natural systems. However …