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Engineering and Computational Insights into Photosynthesis

Teaser

Biology and Time

Biological processes are typically described in the time domain because, unlike in physics, biological systems are always dissipative and irreversible in time. Life is maintained far from the thermodynamic equilibrium by the exchange of energy and matter with the environment. Biological systems are therefore thermodynamically open, dissipative, and far from equilibrium. Oscillations often occur in such systems, and the frequency-domain characterization of biological systems hence represents a productive alternative to the time domain. More on this was presented in the workshop in Český Krumlov in one of the introductory lectures. 

Tens and hundreds of years of highly productive frequency-domain applications in engineering and physics leave no doubt about its utility, and the required mathematical tools are cornerstones of early education in these fields.

 

This is not the case in biology. The question of whether the benefits of frequency-domain approaches justify the effort required to master tools such as the Fourier and Laplace transforms for studying essentially irreversible dissipative systems must be answered.        

The successful frequency-domain applications in physics and engineering motivate the use of the shared methods in photosynthesis. Intuitive metaphors and parallels in music can strengthen motivation and illustrate that the underlying shared concepts are not difficult to understand.

 

David Colliaux of SONY CSL exploited the metaphor in his “The sound of photosynthesis”. The animations show Nyquist plots, i.e. represent the dynamics of the chlorophyll fluorescence emission,  and redox changes of plastocyanine, P700, and ferredoxin in A.thaliana using polar coordinates for different periods of oscillating light.  

 

Ladislav Nedbal used the musical metaphor, on the light side, in the comic cartoon: