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Nature Chemistry

  • Nikitin, M.P., 2023. Non-complementary strand commutation as a fundamental alternative for information processing by DNA and gene regulation. Nature Chemistry, pp.1-13. [ www ] ( EC | Continuous Optimization )
    • "An evolutionary algorithm is developed here that finds the set of ssDNAs that generates the best fit to the algebraic equations."
  • Schissel, C.K., Mohapatra, S., Wolfe, J.M., Fadzen, C.M., Bellovoda, K., Wu, C.L., Wood, J.A., Malmberg, A.B., Loas, A., Gómez-Bombarelli, R. and Pentelute, B.L., 2021. Deep learning to design nuclear-targeting abiotic miniproteins. Nature Chemistry, 13(10), pp.992-1000. [ www ] ( GA | Discrete Optimization )
    • "The optimization was done using a genetic algorithm, in which single residue mutations involved insertion, deletion and swapping, and multiresidue mutation was done using hybridization."
  • Walker, D.R., Hulgan, S.A., Peterson, C.M., Li, I.C., Gonzalez, K.J. and Hartgerink, J.D., 2021. Predicting the stability of homotrimeric and heterotrimeric collagen helices. Nature Chemistry, 13(3), pp.260-269. [ www ] ( GA | Function | Continuous Optimization )
    • "The parameters of SCEPTTr were then optimized by a genetic algorithm. Due to the high number of potential variables in SCEPTTr and the comparatively low population of each cycle and the number of cycles, the genetic algorithm cannot quite find the most optimal function; for this reason, we found it useful to run the genetic algorithm many times and use the results of the best iteration."
  • Dong, X., Oganov, A.R., Goncharov, A.F., Stavrou, E., Lobanov, S., Saleh, G., Qian, G.R., Zhu, Q., Gatti, C., Deringer, V.L. and Dronskowski, R., 2017. A stable compound of helium and sodium at high pressure. Nature Chemistry, 9(5), pp.440-445. [ www ] ( EC | Continuous Optimization )
  • Genot, A.J., Baccouche, A., Sieskind, R., Aubert-Kato, N., Bredèche, N., Bartolo, J.F., Taly, V., Fujii, T. and Rondelez, Y., 2016. High-resolution mapping of bifurcations in nonlinear biochemical circuits. Nature Chemistry, 8(8), pp.760-767. [ www ] ( CMA-ES | Continuous Optimization )
    • "The optimization algorithm CMA-ES was used to optimize the parameters so as to minimize the fitting error."
  • Zhu, L., Liu, H., Pickard, C.J., Zou, G. and Ma, Y., 2014. Reactions of xenon with iron and nickel are predicted in the Earth's inner core. Nature Chemistry, 6(7), pp.644-648. [ www ] ( PSO | Continuous Optimization )
  • Miao, M.S., 2013. Caesium in high oxidation states and as ap-block element. Nature Chemistry, 5(10), pp.846-852. [ www ] ( PSO | Continuous Optimization )