Can a test tube compute? And if so, can it compute with the same efficiency over a wide range of inputs? Recent advances in synthetic biology have made it possible to deploy chemical reactions that implement computation inside a cell. Chemical reactions function as analog computers โ they are ideally suited for solving differential equations and interface naturally with real-world analog...
The implementation of abstract dynamical systems with molecular systems has gained scientific interest. Automated theoretical schemes can compile formal reaction networks into DNA oligonucleotide sequences; thereby providing a potential molecular implementation of the dynamics of the formal reaction network. In this context, we propose a novel algorithm for learning parameters of Hidden Markov...
Transcriptional networks represent one of the most extensively studied types of reaction networks in synthetic biology. While transcriptional networks typically rely on cooperativity and highly non-linear behavior of transcription factors to regulate production of proteins, they are often modeled with simple linear degradation terms. In contrast, general analog computation requires both...
DNA strand displacement systems have enabled the construction of molecular circuits capable of performing complex computations, typically relying on irreversible reactions and non-equilibrium dynamics for signal amplification and restoration. An alternative paradigm is equilibrium computation, where outputs are determined by the steady-state concentrations of molecular species.
In this...
A fundamental question in the field of molecular computation is what computational tasks biochemical systems are capable of carrying out. In this talk, we will see that chemical reaction networks can do maximum likelihood estimation of log-affine models in the following sense: Given a basis for the kernel of the design matrix of a given model, we construct a detailed-balanced network such that...
A common goal in the theory of Chemical Reaction Networks (CRNs) is to design systems that reproduce or approximate a desired dynamics. This theory supports ongoing efforts in synthetic biology and molecular nanotechnology to emulate the functional molecular networks seen in nature. Here, we propose a molecular version of a recurrent artificial neural network, the RNCRN, which we prove is able...
Biomolecules can be repurposed to build programmable chemical computers, either in vitro or in living cells. A particularly promising technology is DNA strand displacement, which has been shown capable of implementing arbitrary systems of chemical reactions. Since chemical reactions can perform computation, this raises fundamental mathematical questions: What types of computation can...
