University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Spring 2010 Computational Study of DNA-Directed Self-Assembly of Colloids Raynaldo Theodore Scarlett University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Atomic, Molecular and Optical Physics Commons, Chemical Engineering Commons, and the Materials Science and Engineering Commons Recommended Citation Scarlett, Raynaldo Theodore, "Computational Study of DNA-Directed Self-Assembly of Colloids" (2010). Publicly Accessible Penn Dissertations. 420. https://repository.upenn.edu/edissertations/420 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/420 For more information, please contact [email protected]. Computational Study of DNA-Directed Self-Assembly of Colloids Abstract Immense insight into fundamental processes necessity for the fabrication of nanostructures is gathered from studying the self-assembly of colloidal suspensions. These fundamental processes include crystal nucleation and particle aggregation. In this thesis, we developed an efficient computational ameworkfr to study the self-assembly of same-sized, spherical colloids with intermolecular interactions, such as the programmable DNA-mediated interaction. In the first part of this thesis, we studied the interfacial dynamics during colloidal crystallization. The interfacial dynamics of binary crystals was probed by weak impurity segregated growth. This segregated growth was interpreted as the number of surface bonds required to crystallize a fluid particle. For short- ranged DNA-mediated interactions, an integer number of surface bonds are needed for a particle to crystallize, which was verified yb experiments. This demonstrates the utility of our computational framework to replicate growth kinetics of DNA-directed particle self-assembly. In the second part of this thesis, we studied the kinetic control of crystal structure in DNA-directed self- assembly. For a dilute colloidal suspension, with weak intermolecular interaction between similar particles, binary crystals can assemble into close-packed (cp) or body-centered-cubic (bcc) structures based on thermodynamic or kinetic factors. Under fast kinetic conditions bcc crystals assemble from the suspension. For the same intermolecular interactions and slow kinetic conditions, cp crystals are observed within the suspension. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Chemical and Biomolecular Engineering First Advisor Dr. Talid Sinno Keywords DNA-directed self-assembly, superlattice, colloidal crystallization, segregated growth, DNA-mediated interactions, and thermodynamics Subject Categories Atomic, Molecular and Optical Physics | Chemical Engineering | Materials Science and Engineering This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/420 COMPUTATIONAL STUDY OF DNA-DIRECTED SELF-ASSEMBLY OF COLLOIDS Raynaldo Theodore Scarlett A DISSERTATION in CHEMICAL AND BIOMOLECULAR ENGINEERING Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2010 Dr. Talid Sinno, Supervisor of Dissertation Dr. Matthew J. Lazzara, Graduate Group Chair Dissertation Committee: Dr. Talid Sinno Dr. John Crocker Dr. Ravi Rahakrishnan Dr. Arjun Yodh Computational Study of DNA-Directed Self-Assembly of Colloids COPYRIGHT 2010 Raynaldo Theodore Scarlett ABSTRACT COMPUTATIONAL STUDY OF DNA-DIRECTED SELF-ASSEMBLY OF COLLOIDS Raynaldo Theodore Scarlett Dr. Talid Sinno Immense insight into fundamental processes necessity for the fabrication of nanostructures is gathered from studying the self-assembly of colloidal suspensions. These fundamental processes include crystal nucleation and particle aggregation. In this thesis, we developed an efficient computational framework to study the self-assembly of same-sized, spherical colloids with intermolecular interactions, such as the programmable DNA-mediated interaction. In the first part of this thesis, we studied the interfacial dynamics during colloidal crystallization. The interfacial dynamics of binary crystals was probed by weak impurity segregated growth. This segregated growth was interpreted as the number of surface bonds required to crystallize a fluid particle. For short-ranged DNA-mediated interactions, an integer number of surface bonds are needed for a particle to crystallize, which was verified by experiments. This demonstrates the utility of our computational framework to replicate growth kinetics of DNA-directed particle self-assembly. iii In the second part of this thesis, we studied the kinetic control of crystal structure in DNA-directed self-assembly. For a dilute colloidal suspension, with weak intermolecular interaction between similar particles, binary crystals can assemble into close-packed (cp) or body-centered-cubic (bcc) structures based on thermodynamic or kinetic factors. Under fast kinetic conditions bcc crystals assemble from the suspension. For the same intermolecular interactions and slow kinetic conditions, cp crystals are observed within the suspension. iv Contents Abstract iii Contents v List of Figures viii 1 Introduction 1 1.1 Design of Colloidal Self-Assembly ............................................................... 2 1.1.1 Engineered Colloidal Building Blocks .......................................................... 3 1.1.2 Colloidal Interactions ..................................................................................... 5 1.2 Classic Intermolecular Colloidal Interactions ................................................ 6 1.2.1 Depletion Interaction ..................................................................................... 6 1.2.2 Electrostatic Interaction ................................................................................. 8 1.3 DNA-Mediated Interaction ............................................................................ 9 1.3.1 Specificity and Tunability of DNA-Assembly .............................................. 9 1.3.2 Directed Self-Assembly of DNA-Functionalized Colloids ......................... 11 1.4 Crystal Nucleation and Growth ................................................................... 14 1.4.1 Classical Nucleation Theory ........................................................................ 15 1.4.2 Crystal Growth ............................................................................................. 17 1.5 Thesis Objective and Outline ....................................................................... 19 2 Computational Analysis of Interfacial Dynamics during Colloidal Crystallization with DNA-Mediated Interactions 21 2.1 Introduction .................................................................................................. 21 2.2 Experimental System for Binary Solid-Solution Crystallization ................. 25 2.2.1 Pair-Potential Model for DNA-Mediated Interactions ................................ 26 2.2.2 Summary of Experimental Results for Binary Segregation in Solid-Solution Crystallization.................................................................. 32 v 2.3 Simulation Protocol ..................................................................................... 35 2.3.1 Monte Carlo and Brownian Dynamics Simulation Details.......................... 39 2.3.2 Identifying Solid and Fluid particles............................................................ 40 2.4 Results and Discussion ................................................................................ 43 2.4.1 Simulating Crystal Growth “Dynamics” with Monte Carlo ........................ 43 2.4.2 MMC Simulation of Binary Solid-Solution Colloidal Crystals ................... 46 2.4.3 Connections to Segregation in Atomic Systems .......................................... 53 2.5 Analysis of MMC Simulation of Brownian Dynamics................................ 57 2.6 Conclusion ................................................................................................... 69 3 Kinetic Control of Crystal Structure in DNA-Directed Self-Assembly 71 3.1 Introduction .................................................................................................. 71 3.2 Binary Superlattice Optimization ................................................................ 75 3.3 Thermodynamic Anaylsis of Ideal 1:1 Binary Superlattice Crystals........... 79 3.4 An Equilibrium Phase Diagram for Superlattice Formation........................ 83 3.5 Kinetic Limitations in Superlattice Formation ............................................ 89 3.5.1 A Thermodynamic-Kinetic Model for Compositional Ordering During Superlattice Growth ......................................................... 91 3.5.2 Pseudo-Phase Diagrams for Superlattice Stability in Binary DNA-Mediated Systems .............................................................. 96 3.5.3 A Hypothesis to Explain Some Recent Experimental Findings ................ 103 3.6 Conclusion ................................................................................................. 105 4 Summary and Future Work 106 4.1 Summary .................................................................................................... 106 4.1.1 Segregated Growth of Binary Crystals from Solid-Solutions.................... 107 4.1.2 Kinetic Control of Structure in Self-Assembled Binary Crystals