CRN++: Molecular Programming Language

Vasić, Marko; Soloveichik, David; Khurshid, Sarfraz

doi:10.1007/978-3-030-00030-1_1

Cited by 17 publications

(25 citation statements)

References 13 publications

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“…Les résultats théoriques précédents fournissent une méthode de conception automatisée de RRC pour toute fonction réelle calculable, présentée comme solution d'un système d'équations différentielles polynomial avec des valeurs initiales également polynomiales en fonction des entrées. Ce compilateur est implémenté suivant ces principes dans le logiciel BIOCHAM-4 1 de modélisation, analyse et synthèse de RRC, ainsi qu'avec certaines variantes dans le système CRN++ (Vasic et al 2018).…”

Section: Compilateur Chimique De Fonctions Calculablesunclassified

La cellule, un calculateur analogique chimique

Fages¹,

Molina²

2022

Approches Symboliques De La Modélisation Et De L’analyse Des Systèmes Biologiques

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La thèse de Church-Turing énonce qu’il n’y a qu’une seule notion universelle de calcul mécaniste, qui donc, d’une façon ou d’une autre, doit permettre de réconcilier le traitement de l’information en informatique et en biologie cellulaire. La preuve récente de Turing-complétude des réseaux de réactions chimiques continus sur un nombre fini d’espèces moléculaires, fournit les bases d’une telle réconciliation, sans construction artificielle, avec des capacités à la fois d’analyse des programmes chimiques naturels dans les cellules vivantes, et de synthèse de programmes chimiques artificiels dans des vésicules non vivantes. Ces résultats ouvrent un vaste champ de recherche fondamentale sur l’informatique analogique chimique de la cellule et des applications nouvelles en santé et environnement.

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Section: Compilateur Chimique De Fonctions Calculablesunclassified

La cellule, un calculateur analogique chimique

Fages¹,

Molina²

2022

Approches Symboliques De La Modélisation Et De L’analyse Des Systèmes Biologiques

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“…The above issues can be resolved by a three-phase (input sampling, input reset, and output valuation) approach in an iteration of computation. The three phases are triggered by a multi-phase oscillator [7].…”

Section: Threshold Function Constructionmentioning

confidence: 99%

Biochemical Threshold Function Implementation with Zero-Order Ultrasensitivity

Huang¹,

Jiang²,

Fages³

et al. 2019

2019 IEEE Biomedical Circuits and Systems Conference (BioCAS)

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Engineering biochemical reactions is a key task in synthetic biology to enable biomedical and other applications. The biochemical threshold function is a crucial component in the biosensor circuits to be deployed in living cells or synthetic vesicles for disease diagnosis. In this work, based on the zero-order ultrasensitivity, we propose an economic biochemical implementation of threshold functions with reconfigurable threshold values. We show that the so-constructed threshold function module well approximates the unit step function and allows robust composition with other function modules for complex computation tasks.

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“…This compiler, implemented in our CRN modeling, analysis and synthesis software Biocham [2] as the one presented here 1 , generates a CRN over a finite set of abstract molecular species, through several symbolic computation steps, mainly composed of polynomialization [17], quadratization [16] and lazy dual-rail encoding of negative variables. A similar approach is undertaken in the CRN++ system [22], also related to [3]. Now, it is worth remarking that in the definition above, and in our implementation in Biocham, the input is defined by the initial concentration of the input species which may be consumed by the synthesized CRN to compute the result.…”

Section: Introductionmentioning

confidence: 99%

Algebraic Biochemistry: a Framework for Analog Online Computation in Cells

Hemery,

Fages

2022

Preprint

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The Turing completeness of continuous chemical reaction networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e. with at most two reactants and mass action law kinetics. In this paper, we introduce a notion of online analog computation for the CRNs that stabilize the concentration of their output species to the result of some function of the concentration values of their input species, whatever changes are operated on the inputs during the computation. We prove that the set of real functions stabilized by a CRN with mass action law kinetics is precisely the set of real algebraic functions.

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CRN++: Molecular Programming Language

Cited by 17 publications

References 13 publications

La cellule, un calculateur analogique chimique

La cellule, un calculateur analogique chimique

Biochemical Threshold Function Implementation with Zero-Order Ultrasensitivity

Algebraic Biochemistry: a Framework for Analog Online Computation in Cells

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