Related papers: DNA-based chemical compiler
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
This paper is concerned with programming adaptive linear neural networks (ALNNs) using chemical reaction networks (CRNs) equipped with mass-action kinetics. Through individually programming the forward propagation and the backpropagation of…
Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all…
Chemical reaction networks (CRNs) model the behavior of molecules in a well-mixed system. The emerging field of molecular programming uses CRNs not only as a descriptive tool, but as a programming language for chemical computation.…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
We propose novel chemical reaction networks to translate levels of concentration into unique DNA strand species, which we call concentration translators. Our design of the concentration translators is based on combination of two chemical…
A quantum compiler is a software program for decomposing ("compiling") an arbitrary unitary matrix into a sequence of elementary operations (SEO). Coppersmith showed that the $\nb$-bit Discrete Fourier Transform matrix $U_{FT}$ can be…
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…
DNA-mediated computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA and has tremendous computational ability to compete with the current silicon-mediated computing, due to massive parallelism…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
This paper answers an open question of Chen, Doty, and Soloveichik [1], who showed that a function f:N^k --> N^l is deterministically computable by a stochastic chemical reaction network (CRN) if and only if the graph of f is a semilinear…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
Chemical databases store information in text representations, and the SMILES format is a universal standard used in many cheminformatics software. Encoded in each SMILES string is structural information that can be used to predict complex…
DNA computing is an unconventional approach to computing that harnesses the parallelism and information storage capabilities of DNA molecules. It has emerged as a promising field with potential applications in solving a variety of…
This paper introduces ChemGen, a software package that uses code generation to integrate multispecies thermodynamics and chemical kinetics into C+-based computational physics codes. ChemGen aims to make chemical kinetics more accessible in…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media.…
Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical reaction network (CRN) model…
Assembly code search is vital for reducing the burden on reverse engineers, allowing them to quickly identify specific functions using natural language within vast binary programs. Despite its significance, this critical task is impeded by…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…