Theory and simulation in systems chemistry

Network design and kinetic analyses of network behavior (lead scientist Dr. Nathaniel Wagner). A mixture of molecules can be regarded as a 'network' if all the molecular components interact with other molecules - either via physical or functional interactions. In several review papers we have described and analyzed how one can use bottom-up approaches to design artificial networks of different size and complexity. It has been postulated that even networks made up of small numbers of molecules possess a wealth of molecular information sufficient to perform rather complex behavior. To probe this assumption, we study different arrays consisting of replicating molecules through theory and simulation. We have shown that using realistic parameters from peptides or DNA replication experiments, it is possible to construct Boolean logic gates, and even more complex arithmetic units, and network motifs. Recently, we have further analyzed the construction of increasingly complex networks, demonstrating bistability, and oscillatory behavior mimicking the natural circadian clocks. With the goal of further developing understanding of evolutionary dynamics in higher order autocatalytic networks, we have also developed (together with the late Prof. Emmanuel Tannenbaum) RNA quasispecies models that can be used for analyzing mutation-selection balance and the formation of higher 'animate' features within these networks. As was shown in various numerical studies of replication networks, our systems also display patterns of behavior that are difficult to predict without simulation. Furthermore, the simulations reveal fundamental trends and characteristics potentially useful for design of future experiments.

References:

1. N. Wagner et al. ChemSystemsChem (2019).
2. Wagner, N., Mukherjee, R., Maity, I., Peacock-Lopez, E. & Ashkenasy, G. Bistability and bifurcation in minimal self-replication and nonenzymatic catalytic networks. ChemPhysChem. 2017, 18, 1842-1850.
3. Wagner, N., Alasibi, S., Peacock-Lopez, E. & Ashkenasy, G. Coupled Oscillations and Circadian Rhythms in Molecular Replication Networks. J. Phys. Chem. Lett. 2015, 6, 60-65.
4. Gurevich, L., Cohen-Luria, R., Wagner, N. & Ashkenasy, G. Robustness of synthetic circadian clocks to multiple environmental changes. Chem. Commun. 2015, 51, 5672-5675.
5. Wagner, N., Tannenbaum, E. & Ashkenasy, G. Second order catalytic quasispecies yields discontinuous mean fitness at error threshold. Phys. Rev. Lett. 2010, 104, 188101/188101-188101/188104.
6. Wagner, N. & Ashkenasy, G. Systems chemistry: logic gates, arithmetic units, and network motifs in small networks. Chem. Eur. J. 2009, ​15, 1765-1775.​