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Modeling biochemical systems with differential equations, stochastic processes, and constraint-based optimizations
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Abstract
With the demand from modeling systems level cellular biochemistry as a reaction network, different applied mathematical approaches are now being pursued. I will discuss three approaches based on (1) systems of ODE with nonlinearity, (1) stochastic processes with irreversibility, and (3) constraint-based optimization suggesting an oriented matroid. A unifying theme of these approaches is the nonequilibrium thermodynamics of living (open) systems
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