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Found 7 papers, 3 papers with code
Fibration symmetry uncovers minimal regulatory networks for logical computation in bacteria
Symmetry principles have proven important in physics, deep learning and geometry, allowing for the reduction of complicated systems to simpler, more comprehensible models that preserve the system's features of interest.
BioSimulators: a central registry of simulation engines and services for recommending specific tools
To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators. org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool.
Flux cost functions and optimal metabolic states
Here I propose two methods for flux modelling: Flux Cost Minimisation, a nonlinear variant of FBA with flux minimisation, and Flux Benefit Optimisation, a nonlinear variant of FBA with molecular crowding.
Optimal enzyme rhythms in cells
Starting from an enzyme-optimised steady state, I score the effects of possible enzyme rhythms on a metabolic objective and optimise their amplitudes and phase shifts.
Enzyme economy and metabolic control
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost.
Metabolic fluxes and value production
Local value production implies that the cost of an enzyme must be balanced by a benefit, given by the economic potential difference the catalysed reaction multiplied by the flux.
Structural thermokinetic modelling
Thermodynamics can be used to obtain more precise predictions of flux control, enzyme synergies, correlated flux and metabolite variations, and of the emergence and propagation of metabolic noise.
