Jonathan K. Whitmer

Supracolloidal Reaction Kinetics of Janus Spheres

Colloidal particles that are charged on one side and hydrophobic on the other can form chiral helices in salt solutions. Clusters in the form of aggregates of a small number of elemental units display structural, thermodynamic, and dynamic properties different from those of bulk materials. We studied the kinetic pathways of self-assembly of “Janus spheres” with hemispherical hydrophobic attraction and found key differences from those characteristic of molecular amphiphiles. Experimental visualization combined with theory and molecular dynamics simulation shows that small, kinetically favored isomers fuse, before they equilibrate, into fibrillar triple helices with at most six nearest neighbors per particle. The time scales of colloidal rearrangement combined with the directional interactions resulting from Janus geometry make this a prototypical system to elucidate, on a mechanistic level and with single-particle kinetic resolution, how chemical anisotropy and reaction kinetics coordinate to generate highly ordered structures.

Triblock colloids for directed self-assembly.

Methods for functionalizing micrometer-sized colloidal spheres with three or more zones of chemical functionality (ABA or ABC) are described. To produce ABA triblock colloids, we functionalized the north pole, south pole, and equator to produce what we call X, Y, and K functionality according to the number of allowed nearest neighbors and their spatial arrangements. These synthesis methods allowed targeting of various lattice structures whose bonding between neighboring particles in liquid suspension was visualized in situ by optical microscopy.

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering.

Chirality-selected phase behaviour in ionic polypeptide complexes

Polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with a β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.

Fluid-solid boundary conditions for multiparticle collision dynamics.

The simulation of colloidal particles suspended in solvent requires an accurate representation of the interactions between the colloids and the solvent molecules. Using the multiparticle collision dynamics method, we examine several proposals for stick boundary conditions, studying their properties in both plane Poiseuille flow (where fluid interacts with the boundary of a stationary macroscopic solid) and particle-based colloid simulations (where the boundaries are thermally affected and in motion). In addition, our simulations compare various collision rules designed to remove spurious slip near solid surfaces, and the effects of these rules on the thermal motion of colloidal particles. Furthermore, we demonstrate that stochastic reflection of the fluid at solid boundaries fails to faithfully represent stick boundary conditions, and conclude that bounce-back conditions should be applied at both mobile and stationary surfaces. Finally, we generalize these ideas to create partial slip boundary conditions at both stationary and mobile surfaces.

Orientationally glassy crystals of Janus spheres

Colloidal Janus spheres in water (one hemisphere attractive and the other repulsive) assemble into twodimensional hexagonal crystals with orientational order controlled by anisotropic interactions. We exploit the decoupled translational and rotational order to quantify the orientational dynamics. Via imaging experiments and Monte Carlo simulations we demonstrate that the correlations in the orientation of individual Janus spheres exhibit glasslike dynamics that can be controlled via the ionic strength. Thus, these colloidal building blocks provide a particularly suitable model glass system for elucidating nontrivial dynamics arising from directional interactions, not captured by the consideration of just translational order.

Influence of hydrodynamics on cluster formation in colloid-polymer mixtures.

We investigate the role of hydrodynamic interactions in the formation of clusters of attractive colloids by means of computer simulations. In simulations employing the multiparticle collision dynamics scheme to represent hydrodynamics, larger and, to a lesser extent, more elongated transient clusters are formed than in simulations merely employing Langevin dynamics. As these clusters constitute the precursors to a colloidal gel, their shape affects the structure of the gel as well as the threshold concentration and colloidal attraction strength at which gelation occurs. Our findings support recent observations regarding the effect of hydrodynamics on colloidal gel formation.

Coarse-grained modeling of DNA curvature

The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and minor groove widths, and local curvature. The model represents an extension of the recently proposed 3SPN.2 description of DNA [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)], into which sequence-dependent shape and mechanical properties are incorporated. The proposed model is validated against experimental data including melting temperatures, local flexibilities, dsDNA persistence lengths, and minor groove width profiles.

Sedimentation of aggregating colloids

We investigate the combined effects of gravity, attractive interactions, and brownian motion in suspensions of colloidal particles and nonadsorbing polymer. Depending on the effective strength of gravitational forces, resulting from a density mismatch between the colloids and the solvent, and the magnitude and range of the depletion interactions induced by the polymer, sedimentation in these suspensions can result in an equilibrium structure or a kinetically arrested state. We employ large-scale molecular dynamics simulations to systematically classify the different regimes that arise as a function of attraction strength and gravitational stress. Whereas strong attractions lead to cluster aggregation and low-density arrested states, moderate attractions can enhance crystallization of the colloidal particles in the sediment. We make direct comparisons to experimental results to infer general conclusions about the mechanisms leading to mechanically stable sediments.

Sculpting bespoke mountains: Determining free energies with basis expansions

The intriguing behavior of a wide variety of physical systems, ranging from amorphous solids or glasses to proteins, is a direct manifestation of underlying free energy landscapes riddled with local minima separated by large barriers. Exploring such landscapes has arguably become one of statistical physicss great challenges. A new method is proposed here for uniform sampling of rugged free energy surfaces. The method, which relies on special Greens functions to approximate the Dirac delta function, improves significantly on existing simulation techniques by providing a boundary-agnostic approach that is capable of mapping complex features in multidimensional free energy surfaces. The usefulness of the proposed approach is established in the context of a simple model glass former and model proteins, demonstrating improved convergence and accuracy over existing methods.