| Algorithms in Nature (original) (raw)

Below are papers on “algorithms in nature” that I have read and enjoyed. I tried to restrict the papers to only those that study a detailed biological mechanism. I am more forgiving in the other direction; i.e., I included papers that did not propose an algorithm but that make a biological observation that seems to me ripe for algorithmic translation.

Molecular biology

• • Optimal regulatory circuit topologies for fold-change detection. Adler et al., Cell. Syst., 2017
• • Parallel computation with molecular-motor-propelled agents in nanofabricated networks. Nicolau et al. Proc. Natl. Acad. Sci. U.S.A., 2016.
• • Robustness and compensation of information transmission of signaling pathways.Uda et al. Science, 2013.
• • Evidence of non-random mutation rates suggests an evolutionary risk management strategy.Martincorena et al. Nature, 2012.
• • The cell cycle switch computes approximate majority.L. Cardelli and A. Csikasz-Nagy. Sci. Rep., 2012.
• • A biological solution to a fundamental distributed computing problem.Y. Afek et al. Science, 2011.
• • Evolution of a modular software network.M. Fortuna et al. Proc. Natl. Acad. Sci. U.S.A., 2011.
• • Information transduction capacity of noisy biochemical signaling networks.R. Cheong et al. Science, 2011.
• • Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.K-K. Yan et al. Proc. Natl. Acad. Sci. U.S.A., 2010.
• • Defining network topologies that can achieve biochemical adaptation.Ma et al. Cell, 2009.
• • Spontaneous evolution of modularity and network motifs.N. Kashtan and U. Alon. Proc. Natl. Acad. Sci. U.S.A., 2005.
• • Intracellular signaling as a parallel distributed process.D. Bray. J. Theor. Biol., 1990.

Insects & other organisms (e.g., fish, bats)

• • A distributed algorithm to maintain and repair the trail networks of arboreal ants.A. Chandrasekhar et al. Nature Sci. Rep., 2018.
• • How regulation based on a common stomach leads to economic optimization of honeybee foraging.Schmickl and Karsai. J. Theor. Biol., 2015.
• • Designing collective behavior in a termite-inspired robot construction team.Werfel et al. Science, 2014.
• • Space partitioning without territoriality in gannets.E. D. Wakefield et al. Science, 2013.
• • A universal strategy for visually guided landing.Baird et al. Proc. Natl. Acad. Sci. U.S.A., 2013.
• • The regulation of ant colony foraging activity without spatial information.Prabhakar et al. PLoS Comput. Biol., 2012.
• • Predatory fish select for coordinated collective motion in virtual prey.Ioannou et al. Science, 2012.
• • Fast and accurate decisions through collective vigilance in fish shoals.Ward et al. Proc. Natl. Acad. Sci. U.S.A., 2011.
• • Optimal localization by pointing off axis.Yovel et al. Science, 2010.
• • On optimal decision-making in brains and social insect colonies.J.A. Marshall et al. J. Roy. Soc. Interface, 2009.
• • Infotaxis as a strategy for searching without gradients.Vergassola et al. Nature, 2007.