Constantine Evans

I research the physics of complex self-assembly processes, examining how small, relatively simple particles can assemble themselves by basic processes into complex structures.

Recent Publications

• C. G. Evans, J. O'Brien, E. Winfree, A. Murugan. "Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly." Preprint on arXiv, 2022.
• C. G. Evans and E. Winfree. "Optimizing tile set size while preserving proofreading with a DNA self-assembly compiler." DNA24, 2018.
• C. G. Evans and E. Winfree. "Physical principles of DNA tile self-assembly." Chem. Soc. Rev., 2017.
• C. G. Evans, "Experimental Implementation of Tile Assembly," in Encyclopedia of Algorithms, M.-Y. Kao, Ed. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015.
• C. G. Evans, "Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly" (PhD Thesis). California Institute of Technology, 2014.
• C. G. Evans and E. Winfree. "DNA sticky end design and assignment for robust algorithmic self-assembly." DNA19, LNCS 8141, pp. 61–75. Springer, 2013.
• C. G. Evans, R. F. Hariadi, and E. Winfree. "Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level." J. Am. Chem. Soc. 134, pp. 10485–10492. 2012.

Alternatively, see my ORCID page (0000-0002-7053-1670) or my research CV.

Recent Talks

• C.G. Evans, D. Doty, D. Woods, Growth dynamics: Precisely controlled self-assembly order of DNA tile nanostructures. at DNA 28.
• C.G. Evans, J. O'Brien, E. Winfree, A. Murugan, Pattern recognition in the nucleation kinetics of molecular self-assembly at FNANO 2020. (In-person conference cancelled; online talk available on YouTube.)
• C.G. Evans, J. O'Brien, E. Winfree, A. Murugan, Kinetic control of spontaneous nucleation in uniquely-addressed multifarious self-assembly at DNA25, Aug 2019.

Software Packages

• Alhambra: a design system for DNA tile systems as a whole.
• qslib: a library for controlling qPCR machines for non-qPCR experiments.
• rgrow: a modular kinetic Tile Assembly Model simulator for fast, short simulations (prerelease).
• StickyDesign (at the Winfree Lab): design software for sticky end sequences. This package is described in our 2013 DNA19 paper. It tries to create sets of sequences that are highly isoenergetic while being reasonably orthogonal (read the paper to see why these two constraints are important). Intended for the sticky ends of DX tiles, the output has also been used for toehold domains in strand displacement systems and sticky end regions of single-stranded tiles; we hope in the future to better support these.
• Xgrow (at the Winfree Lab): the venerable aTAM and kTAM tile assembly simulator, first written by Erik Winfree. I work on maintaining, improving, and extending it, especially in areas that connect with more physical models, like support for sequence energetics, complementary ends, double tiles and fission.
• scikits-bootstrap: a Python/Scipy package for bootstrap statistics and confidence interval estimation.
• caltech_thesis: having stubbornly employed LaTeX for writing since I was ten or so (much to the dismay of my teachers), it would not have done for me to use just any document class for my thesis! Based off the memoir documentclass, this package is intended as a modern documentclass for Caltech theses that uses modern LaTeX packages like fontspec, biblatex/biber, and microtype to produce aesthetically superior output—or, at least, to impress other LaTeX devotees.

Recent posters / other presentations

• C.G. Evans, Qslib: Python control of qPCR machines for molecular programming experiments at DNA28 (2022)
• C.G. Evans, D. Doty, D. Woods, Simple software to design recipes for complicated sample mixes at DNA28 (2022)