University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 Nucleation, Growth And Transformations In Dna Linked Colloidal Assemblies Ian Collins Jenkins University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Chemical Engineering Commons Recommended Citation Jenkins, Ian Collins, "Nucleation, Growth And Transformations In Dna Linked Colloidal Assemblies" (2016). Publicly Accessible Penn Dissertations. 2361. https://repository.upenn.edu/edissertations/2361 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2361 For more information, please contact [email protected]. Nucleation, Growth And Transformations In Dna Linked Colloidal Assemblies Abstract The use of short, synthetic DNA strands to mediate self-assembly of a collection of colloidal particles into ordered structures is now quite well established experimentally. However, it is increasingly apparent that DNA-linked colloidal assemblies (DLCA) are subject to many of the processing challenges relevant to atomic materials, including kinetic barriers related to nucleation and growth, defect formation, and even diffusionless transformations between different crystal symmetries. Understanding, and ultimately controlling, these phenomena will be required to truly utilize this technology to make new materials. Here, I describe a series of computational studies—based on a complementary suite of tools that includes Brownian dynamics, free energy calculations, vibrational mode theory, and hydrodynamic drag analysis—that address several issues related to the nucleation, growth, and stability of DNA-linked colloidal assemblies. The primary focus is on understanding the nature of the apparently enormous number of diffusionless solid-solid phase transformations that occur in crystallites assembled from DNA- functionalized colloidal particles. We find that the ubiquitous nature of these transformations is largely due to the short-ranged nature of DNA mediated interactions, which produces a panoply of zero-energy barrier pathways (or zero frequency vibrational modes) in a number of crystalline configurations. Furthermore, it is shown that hydrodynamic drag forces play a key role in biasing the transformations towards specific pathways, leading to unexpected order in the final arrangements. Additional studies also highlight how heterogeneity in the surface density of DNA strands grafted onto the particles may be used to improve nucleation and growth behavior, which is generally difficult in systems near thesticky-spher ‘ e’ limit in which the interaction range is short relative to the particle size. In the final chapter of the thesis, a general and powerful technique is presented for extracting particle-particle interactions directly from particle trajectory data. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Chemical and Biomolecular Engineering First Advisor Talid Sinno Keywords Colloids, DNA, Self-assembly Subject Categories Chemical Engineering This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/2361 NUCLEATION, GROWTH AND TRANSFORMATIONS IN DNA LINKED COLLOIDAL ASSEMBLIES Ian C. Jenkins 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 2017 Supervisor of Dissertation ________________________ Talid Sinno, Professor of Chemical and Biomolecular Engineering Graduate Group Chairperson ________________________ Dr. John C. Crocker, Professor of Chemical and Biomolecular Engineering Dissertation Committee Dr. Daeyeon Lee, Professor of Chemical and Biomolecular Engineering Dr. John C. Crocker, Professor of Chemical and Biomolecular Engineering Dr. Kathleen J. Stebe, Professor of Chemical and Biomolecular Engineering Dr. Paulo E. Arratia, Professor of Mechanical Engineering & Applied Mechanics ABSTRACT NUCLEATION, GROWTH AND TRANSFORMATIONS IN DNA LINKED COLLOIDAL ASSEMBLIES Ian C. Jenkins Talid Sinno The use of short, synthetic DNA strands to mediate self-assembly of a collection of colloidal particles into ordered structures is now quite well established experimentally. However, it is increasingly apparent that DNA-linked colloidal assemblies (DLCA) are subject to many of the processing challenges relevant to atomic materials, including kinetic barriers related to nucleation and growth, defect formation, and even diffusionless transformations between different crystal symmetries. Understanding, and ultimately controlling, these phenomena will be required to truly utilize this technology to make new materials. Here, I describe a series of computational studies—based on a complementary suite of tools that includes Brownian dynamics, free energy calculations, vibrational mode theory, and hydrodynamic drag analysis—that address several issues related to the nucleation, growth, and stability of DNA-linked colloidal assemblies. The primary focus is on understanding the nature of the apparently enormous number of diffusionless solid-solid phase transformations that occur in crystallites assembled from DNA- functionalized colloidal particles. We find that the ubiquitous nature of these transformations is largely due to the short-ranged nature of DNA mediated interactions, which produces a panoply of zero-energy barrier pathways (or zero frequency vibrational modes) in a number of crystalline configurations. Furthermore, it is shown that ii hydrodynamic drag forces play a key role in biasing the transformations towards specific pathways, leading to unexpected order in the final arrangements. Additional studies also highlight how heterogeneity in the surface density of DNA strands grafted onto the particles may be used to improve nucleation and growth behavior, which is generally difficult in systems near the ‘sticky-sphere’ limit in which the interaction range is short relative to the particle size. In the final chapter of the thesis, a general and powerful technique is presented for extracting particle-particle interactions directly from particle trajectory data. iii TABLE OF CONTENTS ABSTRACT ................................................................................................................................... II LIST OF ILLUSTRATIONS ..................................................................................................... VII 1. INTRODUCTION .................................................................................................................... 1 1.1 DNA Mediated Self-Assembly ................................................................................................. 1 1.2 Numerical Simulations of DNA Functionalized Particles................................................... 11 1.3 Thesis Outline ........................................................................................................................ 22 2. A CASE STUDY: PHASE TRANSFORMATIONS IN CSCL SUPERLATTICES .......... 24 2.1 Introduction ............................................................................................................................ 24 2.2 Langevin Dynamics Simulations .......................................................................................... 29 2.3 Vibrational Mode Analysis .................................................................................................... 41 2.4 Hydrodynamic Correlation and Anisotropic Diffusion ....................................................... 57 2.5 Conclusions ............................................................................................................................ 66 3. EXPLORING ZERO‐ENERGY PHASE TRANSFORMATIONS IN ASYMMETRIC BINARY SYSTEMS ................................................................................................................... 69 iv 3.1 Introduction ............................................................................................................................ 69 3.2 Asymmetric Interaction Matrices ......................................................................................... 71 3.3 Asymmetry in Size and Interaction ...................................................................................... 81 3.4 Phase Transformations Beyond the CsCl Superlattice Family ......................................... 90 3.5 Conclusions ............................................................................................................................ 94 4. THE SUPRISING ROLE OF INTERACTION HETEROGENEITY IN COLLOIDAL CRYSTALLIZATION ................................................................................................................. 96 4.1 Introduction ............................................................................................................................ 96 4.2 Method .................................................................................................................................... 97 4.3 Results .................................................................................................................................. 102 4.4 Conclusions .......................................................................................................................... 111 5. EXTRACTING POTENTIALS FROM PARTICLE TRAJECTORIES ......................... 113 5.1 Introduction .........................................................................................................................