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On a model of online analog computation in the cell with absolute functional robustness: algebraic characterization, function compiler and error control
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.
A Skin Microbiome Model with AMP interactions and Analysis of Quasi-Stability vs Stability in Population Dynamics
On the time scale of 2 days of the experiments, the model predicts that certain changes of the environment, like the elevation of skin surface pH, create favorable conditions for the emergence and colonization of the skin by the opportunistic pathogen population, while the production of human AMPs has non-linear effect on the balance between pathogens and commensals.
On Estimating Derivatives of Input Signals in Biochemistry
The online estimation of the derivative of an input signal is widespread in control theory and engineering.
Neural-based classification rule learning for sequential data
Discovering interpretable patterns for classification of sequential data is of key importance for a variety of fields, ranging from genomics to fraud detection or more generally interpretable decision-making.
Reactmine: a statistical search algorithm for inferring chemical reactions from time series data
We present a CRN inference algorithmwhich enforces sparsity by inferring reactions in a sequential fashion within a search tree of boundeddepth, ranking the inferred reaction candidates according to the variance of their kinetics on theirsupporting transitions, and re-optimizing the kinetic parameters of the CRN candidates on the wholetrace in a final pass.
Stability versus Meta-stability in a Skin Microbiome Model
Imbalance in the cutaneous microbiome, also called dysbiosis, has been correlated with several skin conditions, including acne and atopic dermatitis.
Algebraic Biochemistry: a Framework for Analog Online Computation in Cells
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.
Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs
The Turing completeness result for continuous chemical reaction networks (CRN) shows that any computable function over the real numbers can be computed by a CRN over a finite set of formal molecular species using at most bimolecular reactions with mass action law kinetics.
On the Complexity of Quadratization for Polynomial Differential Equations
We show that both problems of minimizing either the number of variables (i. e., molecular species) or the number of monomials (i. e. elementary reactions) in a quadratic transformation of a PIVP are NP-hard.
Graphical Conditions for Rate Independence in Chemical Reaction Networks
The Turing-completeness of that notion of chemical analog computation has been established by proving that any computable real function can be computed by a CRN over a finite set of molecular species.
