Graduate level course on DNA-coated colloids. This course will cover models of DNA-coated colloids, including the thermodynamics of DNA hybridization and the physics of polymer brushes and their interactions.

Background in thermodynamics or statistical mechanics

Problem sets will be assigned for each class meeting.

Because research on DNA-coated colloids has developed so recently, the sources for the course will primarily be research articles from the current literature augmented by lecture notes from the instructor. PDFs of all the relevant papers will be provided by the instructor.

1. Programming Self-Assembled Materials With DNA-Coated Colloids, Frontiers in Physics 9
1–17 (2021) by T. Zhang, D. Lyu, W. Xu, Y. Mu & Y. Wang
2. Comprehensive view of microscopic interactions between DNA-coated colloids (Main article
& Supplementary Information), Nat. Commun. (2022) [in press] by F. Cui, S. Marbach, J.
A. Zheng, M. Holmes-Cerfon & D. J. Pine
3. Using DNA to program the self-assembly of colloidal nanoparticles and microparticles, Nat. Rev. Mater. 1, 16008 (2016) by W. B. Rogers, W. M. Shih & V. N. Manoharan
4. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermody- namics, Proc. Nat. Acad. Sci. 95, 1460–1465 (1998) by J. SantaLucia
5. The thermodynamics of DNA structural motifs, Annu. Rev. Biophys. Biomol. Struct. 33
415–440 (2004) by J. SantaLucia Jr. & D. Hicks
6. A general theory of DNA-mediated and other valence-limited interactions, J. Chem. Phys.
137 094108 (2012) by P. Varilly, S. Angioletti-Uberti, B. M. Mognetti & D. Frenkel
7. Communication: A simple analytical formula for the free energy of ligand–receptor-mediated interactions, J. Chem. Phys. 138 021102 (2013) by S. Angioletti-Uberti, P. Varilly, B. M. Mognetti, A. V. Tkachenko & D. Frenkel
8. Linker-Mediated Phase Behavior of DNA-Coated Colloids, Phy. Rev. X 9 041054 (2019) by
J. Lowensohn, B. Oyarzu´n, G. N. Paliza, B. M. Mognetti & W. B. Rogers
9. Self-assembly of photonic crystals by controlling the nucleation and growth of DNA-coated colloids, Proc. Nat. Acad. Sci. 119 e2114050118 (2022) by A. Hensleya, W. M. Jacobs & W.
B. Rogers
10. Using DNA strand displacement to control interactions in DNA-grafted colloids, Soft Matter
14 969-984 (2018) by E. W. Gehrels, W. B. Rogers & V. N. Manoharan
11. Reconfigurable Transitions between One- and Two-Dimensional Structures with Bifunctional DNA-Coated Janus Colloids, ACS Nano 14 15786-15792 (2020) by J. S. Oh, G.-R. Yi & D. J. Pine

6/27 (Mon) 2:00PM-3:15PM, 3:30PM~4:45PM
6/29 (Wed) 2:00PM-3:15PM, 3:30PM~4:45PM
7/4 (Mon) 2:00PM-3:15PM, 3:30PM~4:45PM
7/6 (Wed) 2:00PM-3:15PM, 3:30PM~4:45PM
7/11 (Mon) 2:00PM-3:15PM, 3:30PM~4:45PM

Detailed Course Schedule
1. High altitude overview of DNA-coated colloids (DNACCs)
• History of DNA nanotechnology and DNACCs starting from 1982
• DNA cubes, walkers, and nano smiley faces
• Overview of DNA hybridization and multivalent interactions
• Overview of colloidal interactions and phase behavior
2. Colloidal dynamics
• Brownian motion
• Free Diffusion: Langevin equation
• Diffusion in a harmonic potential; in a confined space.
3. Phase behavior
• Gas-liquid-solid phase diagram
• Lattice-gas model
• Hard-sphere crystallization & role of entropy
4. Colloidal interactions I
• van der Waals, Derjaguin approximation
• screened Coulomb (Poisson-Boltzmann and Debye-Hu¨ckel theory)
5. Colloidal interactions II
• polymer brush (Dolan-Edwards & Milner-Witten-Cates models)
• Depletion interaction
6. DNA structure and hybridization
• DNA-structure, bases & base pairing
• thermodynamics of hybridization: nearest-neighbor model
• Multivalency of DNA-coated colloids: Frenkel model
7. Interactions between DNA-coated colloids II
• Formulation of DNACC suspensions: colloids, buffer, surfactants
• Integrated model of DNACC interactions: DNA, brushes, ….
8. DNACC colloidal crystals
• DNACCs colloidal crystals and superstructures
• Nucleation and growth of crystals from DNACCs
9. DNACC patchy particles
• Synthesis of patchy particles
• 2D and 3D structures formed with patchy particles
10. Strand displacement interactions
• Re-entrant phase transitions
• Dynamic reconfigurability