Session L48: Polymers and DNA Coated Colloid Particles

Structure and Assembly of Polymeric Dots Formed by Conjugated Polymers

Rigid conjugated polymers assume extended conformation in dilute solution and often behave as colloidal suspensions. When forced into a collapsed configuration, they form highly fluorescing particles, or poly-dots, which have demonstrated potential as intracellular imaging markers, as well as building blocks for light harvesting devices. The current work investigates the structure and stability of poly-dots of \textit{di-alkyl} \textit{para polyphenyleneethynylene} (PPE) conjugated polymers in solution and follows their assembly at interfaces. Small angle neutron scattering measurements of the poly-dots in water have shown that at low concentrations, stable unimolecular spherical poly-dots are formed with a polydispersity that corresponds to that of the polymer itself. With increasing concentration, yet, below the critical micelle concentration of these rod-like polymers in good solvents, the size and density of the NPs increases, however the spherical symmetry is retained. The nature and length of the substituents affect the internal density and the degree of swelling of the poly dots. Atomic Force Microscopy results show that these PPE poly-dots assemble into arrays with different symmetries, depending on molecular parameters and assembly conditions.   

Molecular dynamics study of polymer-silica nanoparticle hybrids: Building blocks for directed assembly

Molecular dynamic simulations have been used to study the conformation and interactions of a polymer nanoparticle hybrid that consists of \textit{para} dialkyl phenyleneethynylenes (PPEs) grafted to a silica nanoparticle, with the goal of deriving the factors that control their assembly. PPEs are electro-optically active polymers whose conformation determines their degree of conjugation and their assembly mode which in turn affects the electro-optical properties of the nanoparticle-polymer complexes. When confined to a nanoparticle surface, the PPE chains are fully extended in good solvents but cluster as the quality of the solvents is decreased. Tuning the degree of clustering by tuning the solvent-polymer interaction is expected to direct the assembly of the particles. Results for the conformation of grafted PPE molecules on a single nanoparticle and the forces between two nanoparticles as a function of solvent quality will be presented.   

Structural and Dynamical Characteristics of Polyelectrolyte Dendrimer Solutions Revealed by Neutron Scattering and Atomistic Simulation

Solutions of polyelectrolyte dendrimers were investigated using small angle neutron scattering (SANS) and dynamical measurements including quasi-elastic neutron scattering, neutron spin-echo and high resolution NMR. The goal of the experiments was to understand the structural and dynamical responsiveness polymer toward the variation of molecular charge. Experimental spatial correlation functions and temporal correlation functions such as intermediate scattering functions and the dynamic structure factor were evaluated quantitatively. Complementary atomistic simulations were developed for providing the microscopic interpretation of the scattering measurements and for investigating the material characteristics that are not accessible experimentally. Based on this synergistic approach, we attempt to provide a detailed understanding of the microscopic mechanisms underlying the observed electrostatic responsive properties in these very important classes of materials.   

A theoretical study of the phase behavior of spherical colloids decorated with adhesive domains

We propose a nonlinear self-consistent phonon theory for the self-assembly of spherical particles with patterned adhesive surfaces, such as Janus colloids. The approach is first tested against the known crystallization behavior of hard spheres, and also homogeneous particles that interact via short range attractions. Janus colloid pair interactions are described by an anisotropic extension of the Baxter adhesive sphere potential where particles attract only if their hydrophobic domains are in contact. Given various crystalline symmetries, the effective harmonic potential experienced by a colloid confined to its Wigner-Seitz cell is self-consistently computed. The characteristic vibrational displacements or localization lengths are determined by the lattice symmetry as well as the strength and surface pattern of adhesive interactions. The crystal free energy is then computed, and thermodynamic stability evaluated, including pressure-driven solid-solid transitions, and the fluid-solid coexistence boundary based on the Baxter solution of the Percus-Yevick integral equation for adhesive hard sphere liquids. A primary goal is to evaluate the influence of patch size, attraction strength, and geometric patterning on the formation of heterogeneous crystalline phases.   

In situ electrochemical small-angle neutron scattering (eSANS) for quantitative structure and redox properties of polymer-coated nanoparticles

Rapid growth in nanomaterial applications (energy, cosmetics and healthcare products) highlights limitations of available physicochemical characterization methods. An in situ electrochemical small-angle neutron scattering (eSANS) methodology was devised that enables direct measurements of nano and colloid material dispersion structure while undergoing reduction-oxidation (redox) reactions. By combining the electrochemical signal with contrast variant SANS, the structure of the polymer-nanoparticle complexes can be examined under electrochemical conditions. Specially-synthesized poly(ethyleneglycol)-stabilized zinc oxide nanoparticles were examined by eSANS showing an irreversible change in nanoparticle-complex structure during the potential cycle. We will report on the kinetics of the nanoparticle transformation as measured at BL-6 EQSANS, Spallation Neutron Source, Oak Ridge National Laboratory.   

Topological Interaction by Entanglement of DNA

We find and study a new type of interaction between colloids, Topological Interaction by Entanglement of DNA (TIED), due to concatenation of loops formed by palindromic DNA. Consider a particle coated with palindromic DNA of sequence ``P1.'' Below the DNA hybridization temperature ($T_m$), loops of the self-complementary DNA form on the particle surface. Direct hybridization with similar particle covered with a different sequence P2 do not occur. However when particles are held together at $T > T_m$, then cooled to $T < T_m$, some of the loops entangle and link, similar to a Olympic Gel. We quantitatively observe and measure this topological interaction between colloids in a $\sim 5^{\circ} C$ temperature window, $\sim 6^{\circ} C$ lower than direct binding of complementary DNA with similar strength and introduce the concept of entanglement binding free energy. To prove our interaction to be topological, we unknot the purely entangled binding sites between colloids by adding Topoisomerase I which unconcatenates our loops. This research suggests novel history dependent ways of binding particles and serves as a new design tool in colloidal self-assembly.   

Measuring in situ primary and competitive hybridization events on microspheres

Understanding hybridization events at surfaces is crucial for optimizing nucleic acid detection platforms as well as DNA-mediated colloidal assembly. We used flow cytometry to measure time-dependent primary and competitive hybridization events of perfectly matched and mismatched targets on microsphere surfaces. In addition to more conventional sample preparation involving multiple wash and resuspension steps prior to measurement, we sampled the reaction volume directly for in situ measurements to minimize potential dissociation events between weaker partner strands during wash steps. Similar to prior reports for oligonucletide solutions, the nearly identical rates for primary hybridization events on microsphere surfaces were independent of target sequence and reached an equilibrium value within 30 min. The extent of in situ primary hybridization events for immobilized probes, however, deviated from solution model predictions. In situ competitive hybridization events were at least 100-fold slower than primary hybridization events and did not appear to reach equilibrium. The kinetics of competitive hybridization events on microspheres are consistent with predicted effects stemming from toehold effects or base length differences between primary and secondary targets.   

You can always get what you want

Colloidal particles coated with DNA strands can self assemble into complex structures. Which structures are formed and with what yield depends on the specifics of the design rules. We numerically study the directed self assembly of DNA coated colloidal particles. By testing different design rules for self-assembly with short-range interactions and studying the stability of equilibrium structures, we uncover the principles for always getting a desired assembled structure.   

Rigid and Soft Minima of DNA-colloid Clusters

What are the limits of self-assembly via short-ranged, isotropic potentials? We investigate how carefully tuning the interaction matrix--breaking the permutation symmetry--of a small number of particles leads to unique ground states and novel energy landscape features, including soft local and global minima. We coat microspheres with highly specific and thermodynamically optimized DNA-sequences, and observe a few of these at a time organize in wells and droplets. DIC and other imaging techniques reveal 3D cluster structure, and fluorescence reveals the identity of each bead in the cluster. Although our experiments equilibrate timely over only a small temperature window, they elucidate how discrete sphere packing geometry governs both the statistical equilibrium and theoretical ``zero T'' cluster probabilities. Finally, I'll describe how relaxing some constraints can shift equilibria and flatten maxima on the energy landscapes of these specific spheres.   

Uniform colloidal clusters from random aggregation of bidisperse spheres

Using a combination of experiment and simulation, we investigate the structures that form when colloidal spheres cluster around smaller spheres. We use either oppositely charged particles or particles coated with complementary DNA sequences to form the clusters, and we observe them under optical microscopy. We find that random sphere parking serves as a useful model for cluster self-assembly in these systems and that the sphere diameter ratio controls the distribution of cluster sizes. In particular, near a critical diameter ratio, random parking produces tetrahedral clusters in theoretically unlimited yield. Experimentally we observed 90\% tetramer yield near this geometrical singularity. We investigate how this method can be used to assemble tetrahedral plasmonic resonators from metallo-dielectric nanospheres in order to create a bulk, isotropic, optical metamaterial.   

The Internal Structure of Nanoparticle Dimers Linked by DNA

The self-assembly of inorganic units controlled by the interactions of biological molecules, like DNA, has received attention for the possibility to specify higher-order structure, with potential biological, optical and electronic applications. In biology, self-assembly of complex materials (eg. bone, spider silk) frequently occurs in a stepwise, hierarchical fashion. Here, we consider a first step towards a hierarchical approach for synthetic nanostructures of nanoparticles (NPs) linked by DNA. The most basic unit in this multiscale approach is a dimer of NPs linked by DNA. We use a coarse-grained molecular model to explain experimental measurements of the separation of two DNA-coated NPs connected by linking single-stranded DNA (ssDNA). We show that the dimer separation is primarily controlled by the number of DNA links between NPs. If these links are not constrained to lie along the axis between NPs, the separation is limited by off-axis connections that force the NPs to be closer. We also determine how the number of connections alters the effective persistence length of the ssDNA that connects the dimer. We discuss how these dimers might be used for subsequent assembly at larger scales.   

Specific interactions in complex mixtures: effects on the thermodynamic stability of multicomponent protein solutions

Multicomponent protein solutions, such as the cytosol, comprise complex networks of specific interactions in a crowded environment of molecules with nonspecific interactions, with dissociation constants spanning many orders of magnitude. We investigate the phase behavior of a multicomponent lattice model with both specific and non-specific interactions. We use bit strings to encode the binding strength between interacting patches on particles at neighboring lattice sites. The boundary of the well-mixed dilute phase is calculated for a statistical ensemble of mixtures using semi-grand Monte Carlo simulations and multicanonical histogram reweighting techniques. We examine the sensitivity of this phase boundary to the distribution of component interactions and demonstrate that the phase behavior is extremely sensitive to the high-end tail of the distribution of interaction strengths.