Publications by authors named "Nikolaus Carl Awtrey"
Article Synopsis
- - Kinetic diagrams help visualize biochemical systems for studying energy transfer and ion selectivity, but manual calculations for complex systems become impractical due to the exponential growth of intermediate diagrams needed.
- - A new Python library called KDA automates the generation of these diagrams and outputs precise algebraic expressions for key system properties, making complex analysis easier and more efficient.
- - The KDA library was tested on models relevant to biophysics, showing its utility in quantifying transport efficiency in examples like antiporters and the small multidrug resistance transporter EmrE, and it is available as open source software.
Kinetic diagrams are commonly used to represent biochemical systems in order to study phenomena such as free energy transduction and ion selectivity. While numerical methods are commonly used to analyze such kinetic networks, the diagram method by King, Altman and Hill makes it possible to construct exact algebraic expressions for steady-state observables in terms of the rate constants of the kinetic diagram. However, manually obtaining these expressions becomes infeasible for models of even modest complexity as the number of the required intermediate diagrams grows with the factorial of the number of states in the diagram.
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