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Documents authored by Evans, Constantine G.

Document
DOI: 10.4230/LIPIcs.DNA.31.7
Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics

Authors: Constantine G. Evans, Angel Cervera Roldan, Trent Rogers, and Damien Woods

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
A fundamental problem in crystallisation, and in molecular tile-based self-assembly in particular, is how to simultaneously control its two main constituent processes: seeded growth and spontaneous nucleation. Often, we desire out-of-equilibrium growth without spontaneous nucleation, which can be achieved through careful calibration of temperature, concentration and experimental time-scale a laborious and overly-sensitive approach. Another technique is to find alternative nucleation-resistant tile designs [Minev et al, 2001]. Rogers, Evans and Woods [In prep] propose blockers: short DNA strands designed to dynamically block DNA tile sides, altering self-assembly dynamics. Experiments showed independent and tunable control on nucleation and growth rates. Here, we provide a theoretical explanation for these surprising results. We formally define the kBlock model where blockers bind to tiles at thermodynamic equilibrium in solution and stochastic kinetics allow self-assembly of a tiled structure. In an intentionally simplified mathematical setting we show that blockers permit reasonable seeded growth rates, akin to a non-blocked tile system at lower tile concentration, crucially giving nucleation rates that are exponentially suppressed. We then implement the kBlock model in a stochastic simulator, with results showing remarkable alignment with oversimplified theory. We provide evidence of blocker-induced tile buffering, where a large reservoir of blocked tiles slowly feeds a small unblocked tile subpopulation which acts like a regular, non-blocked, low tile concentration system, yet is capable of long-term buffered assembly. Finally, and perhaps most satisfyingly, theory and simulations align remarkably well with DNA self-assembly experiments over a wide range of concentrations and temperatures, matching the size of growth temperature windows to within 12%. Blockers are a straightforward solution to the challenging problem of simultaneously and independently controlling growth and nucleation, using a motif compatible with many DNA tile systems.
Cite as

Constantine G. Evans, Angel Cervera Roldan, Trent Rogers, and Damien Woods. Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{evans_et_al:LIPIcs.DNA.31.7,
  author =	{Evans, Constantine G. and Cervera Roldan, Angel and Rogers, Trent and Woods, Damien},
  title =	{{Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{7:1--7:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.7},
  URN =		{urn:nbn:de:0030-drops-238564},
  doi =		{10.4230/LIPIcs.DNA.31.7},
  annote =	{Keywords: Self-assembly, kinetic model, kinetic simulation, thermodynamic prediction}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.DNA.29
LIPIcs, Volume 276, DNA 29, Complete Volume

Authors: Ho-Lin Chen and Constantine G. Evans

Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)

Abstract
LIPIcs, Volume 276, DNA 29, Complete Volume
Cite as

29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 1-230, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Proceedings{chen_et_al:LIPIcs.DNA.29,
  title =	{{LIPIcs, Volume 276, DNA 29, Complete Volume}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{1--230},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29},
  URN =		{urn:nbn:de:0030-drops-187827},
  doi =		{10.4230/LIPIcs.DNA.29},
  annote =	{Keywords: LIPIcs, Volume 276, DNA 29, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.DNA.29.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Ho-Lin Chen and Constantine G. Evans

Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as

29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{chen_et_al:LIPIcs.DNA.29.0,
  author =	{Chen, Ho-Lin and Evans, Constantine G.},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{0:i--0:xiv},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.0},
  URN =		{urn:nbn:de:0030-drops-187839},
  doi =		{10.4230/LIPIcs.DNA.29.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
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