Session C58: Self-Assembly III

Droplets that decay, droplets that fährt: Restriction enzymes induce degradation, bubbling and propulsion in a DNA liquid phase

Multi-armed DNA particles (‘nanostars’) can be engineered to have weak inter-particle attractions, causing them to phase separate into liquid droplets. We are motivated to study this system both on the general grounds that bio-macromolecular liquids are interesting, and with the specific idea of using it to create a chromatin-inspired active matter system. To that end, we studied the interactions of proteins with DNA nanostar droplets, particularly measuring droplet degradation by DNA-cleaving restriction enzymes. Despite the droplet’s small DNA volume fraction, enzyme degradation occurred primarily on surface of droplets, likely because enzyme transport was arrested by binding of the protein to the DNA. The degradation rate was surprisingly insensitive to variations in the number of restriction sites, but did vary with the strength of bonds between DNA particles. With certain tricks it was possible to force the enzyme inside the droplet, which caused the enzyme to carve out vacuoles that rose to the droplet surface and popped, driving droplet motion. I will discuss potential mechanisms behind this enzyme-induced motility.   

Single-particle thick microstructure printing via synergetic action of electric-field assembly, capillary and electrostatic interactions

Assembly of single-particle thick one-dimensional microstructures on substrates is desired for performing different fundamental studies, and holds promise for a variety of practical applications. There are many approaches for fabrication of such structures, but they are expensive, time-consuming, or inefficient, requiring access to advanced tools and laboratories. Moreover, they are not suitable for fabricating microstructures with programmable shapes, arbitrary lengths, and positioning. Here we report a method that overcomes these limitations and facilitates the continuous production of particle paths outside bulk liquid on various substrate materials and morphologies, using a variety of particle materials with wide size range. We also demonstrate that the method enables printing particle microstructures using two or more particle types to form binary superstructures. The method is simple yet robust and easy to implement, and is straightforwardly scalable, involving a synergetic action of electric-field assembly, capillary and electrostatic interactions. Various aspects of our method, including the role of particle size and the voltages needed, are studied in detail.   

Multi-scale simulations of polymeric nanoparticle fabrication through rapid solvent exchange

Tailored nanoparticles are increasingly sought after for many scientific and technological applications, such as optoelectronic devices and selective catalysts. However, both research and commercialization of these materials has been impeded by the lack of suitable fabrication techniques. One promising approach for overcoming this hurdle is flash nanoprecipitation, where (soft) nanoparticles are assembled through rapid micromixing of polymers in solution with a miscible poor solvent. This continuous process allows for high yields as well as precise control over particle size and morphology. We employed multiscale simulations of this process to understand its underlying mechanisms and to efficiently explore parameter space. We first performed explicit solvent molecular dynamics (MD) simulations of a bead-spring polymer model to study the microscopic properties of the fabrication process. Then, we fed the MD data into a kinetic Monte Carlo algorithm to reach macroscopic length- and timescales. We discovered that the nanoparticle size can be reliably tuned through the initial polymer concentration and the mixing rate. Further, we were able to fabricate a wide variety of structured colloids, such as Janus and core-shell particles, when polymer blends were used in the feed stream.   

Evaporation-induced Cluster Formation in High-Concentration and Low-Tg Colloidal Suspensions

Cluster formation in colloidal suspensions is often observed during drying, and understanding the origins and physical properties of the clusters is important to optimizing coating formulation. This talk reports a study of cluster formation induced by drying latex with initial volume fraction of 50% in a microfluidic channel, in a manner that allows the dynamic structure evolution to be observed by light microscopy as a function of evaporation rates, salt concentrations and particle concentrations. For our experiments, we synthesized latex particles with average diameter of 200 nm, and a glass transition temperature (Tg) that could be robustly tuned from 0 °C to 80 °C. We find that fluid flow induced by evaporation drives an initially equilibrated, well-mixed sample into a phase-separated state, raising questions of how flow forces can overcome electrostatic repulsion. Since particles deform and adhere when heated above Tg, we varied the ambient temperature to investigate whether adhesion also played a role in cluster formation. Comparing with experimental data, we are developing theoretical models to study the competition between flow force which induces clusters and electrostatic repulsion which stabilizes the suspensions.   

Simulating Hepatitis B Virus antiviral agents

The infectivity of a virus depends on the complete assembly of a protein shell (capsid) around the viral nucleic acid. Molecules which block or alter assembly pathways have the potential to be used as antiviral agents. Recent in vitro experiments have identified a class of small molecules (assembly effectors) that accelerate assembly of Hepatitis B virus (HBV) capsids. In vivo experiments have shown that this acceleration of assembly in vitro correlates to antiviral activity in cells. However, the mechanism by which these molecules alter assembly pathways is unclear. In this talk I will describe a computational model which allows extremely efficient simulation of assembly dynamics of large protein shells. I will then show how application of this model to HBV assembly can elucidate the mechanism of action of assembly effectors. In particular, I will describe how the assembly effectors result in malformed capsid shapes, as seen in experiments.   

Disorder Foreshadows Order in Colloidal Cubes

Prior molecular simulations have revealed that dense suspensions of hard nano-cubes are remarkable in that they form a mesophase near the ordering transition which is highly unusual when compared to typical crystals, plastic crystals, or liquid crystals. Monte Carlo simulations are used to study the disorder-to-order phase transition for a bulk system of colloidal hard cubes. It is observed that the ordered phase does not form via nucleation from the disordered phase, despite the prevalence in the latter of small locally ordered domains occurring transiently and sparsely. Instead, as the isotropic phase is brought to a marginally metastable concentration, such ordered domains increase in size and number, eventually reaching a critical point where they percolate the entire system and consolidate to form the mesophase. This process, quite different from nucleation observed for other particle shapes, arises presumably from a small interfacial tension. Simulations reveal that cubes infallibly form single-grain ‘crystals’ in the mesophase. This is traced to the abundant delocalized and transient vacancies and the high particle mobility in the mesophase which lead to formation of an active ‘recrystallization zone’ next to any grain boundary.   

Structure and dynamics of kinked line-slip defects in confined colloidal crystals

Line-slip defects are found in crystals confined to the surface of a finite sized cylinder. These defects are identified by a line of particle pairs, each of which has one fewer contact than in bulk. They are known to appear in ground state of a cylindrical crystal when the cylinder cannot accommodate a perfect crystal. We study the structure and dynamics of these defects using an experimental system where submicron-sized colloidal spheres self-assemble into hexagonal lattices on a silica fiber with a diameter of a few micrometers. We find that most line-slip defects have kinks in them. A kink can be recognized from a discontinuity in the line-slip structure. The simplest kink in a line slip has four fewer bonds compared to a straight line-slip without any kink. We observe that the number of kinks in a line-slip defect does not change significantly over long time, but instead shows small fluctuations. We show that the average kink density is related to the average roughness of a 2D crystal grain. We find that by tuning the strength of interaction, we can tune the size of the crystal and the total length of the line-slip defects, allowing us to control the number of kinks in a line-slip defect and hence its shape.   

Defect mediated coarsening of colloidal crystals on a cylinder

We perform Brownian dynamics simulations to investigate how geometrically stabilized defects in colloidal crytals on a cylindrical surface facilitate the approach to equilibrium. At intermediate times, a patchwork emerges of grains that generically exhibit vacancy-roughened helical line-slip defects, resulting in an ensemble of crystallites distinct from what is observed in the growth of crystals on planar surfaces. Interfaces between adjacent crystal grains typically exhibit a characteristic notch at the point of intersection with the line slip defect; this acts as a source for excitations of the line slip defect, coupling interfacial relaxation on opposite ends of each crystallite.   

Directing Colloidal Assembly via Selective Depletion

The ability to synthesize and assemble matter on the colloidal scale has recently been at the forefront of research in materials science and nanotechnology. In particular, the ability to direct the assembly of colloids in a directional manner presents a challenge, as many methods of assembly are inherently nonselective. In this work, colloids are synthesized via an emulsion-based method and depletants are made to selectively adsorb onto colloidal surfaces to direct assembly, thus allowing for depletion to only occur under certain conditions. We are able to achieve selective assembly by introducing polymers, changing the pH, and tuning the nature of the depletant. We demonstrate selective assembly by selectively forming single or mixed crystals from a bidispersed suspension of particles by modifying the environment that the colloids are suspended in. We further demonstrate degree of selectivity of the depletion interaction in our colloidal systems by directing the patch-to-patch assembly of Janus colloids into complex structures. Selective depletion offers a new tool to direct assembly in colloidal systems and has the potential to be used to direct the hierarchical assembly of building blocks such as patchy particles and Janus colloids towards desired complex structures.   

Stability and Free Energy of Nanocrystal Chains and Superlattices

I present simulations of hydrocarbon-capped monodisperse nanocrystal superlattices. I compute the free energy for both bcc and fcc, including several ligand lengths, as well as the entropy and Gibbs free energy. We find that bcc superlattices with oriented or random nanocrystal cores have slightly different free energy and lattice constant. Consistent with experimental findings, we observe that nanocrystals capped with relatively long ligands form bundles. We also compared our calculated lattice constants to experimental values and predictions for the OTM (Orbifold Topological Model).   

Multiscale Modeling of Precursor Molecule Alignment for Improving Pitch-Based Carbon Fiber Production

Carbon fiber (CF) is a versatile material widely applied in many fields, and one main method to produce CF is from pitch, a viscoelastic material composed of aromatic hydrocarbons. Though it is well known that the early stage alignment of precursor molecules has significant effects on the pitch-based fibers, a deeper understanding of its underlying microscopic mechanisms is lacking. Here we perform fully atomistic (FA) and coarse-grained (CG) simulations to study the alignment of pitch molecules. While the FA simulations generates accurate atomistic descriptions, the CG simulations provide a means to efficiently explore larger time and length scales. The ellipsoid algorithm is adopted to extract geometric features of these molecules from the FA trajectories, enabling a quantitative analysis of the intermolecular alignment as well as the construction of anisotropic CG particles. Our multiscale simulations identify the dependences of alignment on the molecule size, temperature and loading conditions. Further, the model suggests specific additives and operation conditions that can improve the molecule alignment. These calculations provide guidelines for optimizing the synthesis pathways for low cost and high-quality CF.   

Controlled Self-Assembly of Peptide Nanotubes via Sequence Modification and Kinetic Control

Synthetic peptides with the high sequence- and shape-specificity can serve as the assembly building blocks for the construction of controllable and complex nanoarchitectures. Computational design was employed to design peptides that can form antiparallel, alpha-helical tetrameric coiled-coil bundles in solution that then further assemble into higher order structures with targeted organization. The bundles self-assemble into homogenous nanotubes at pH 4.5. As analyzed by cryo-TEM, SAXS and STEM, a mono-layer tilted-bundle model is proposed to explain the nanotube structure. The charged state and distribution of the peptide bundles associated with the acidic solution condition are believed to be the reason triggering the formation of nanotubes. Rational sequence modifications were applied to control the dimensions of the nanotubes or to disrupt the tube nanostructure or to add metal-binding functionality. Moreover, kinetic control was applied in the assembly process to produce a branched nanotube morphology. Further crosslinking treatment can be applied to the branched nanotube system for the development of stable hyper-branched materials with potential applications.   

Hierarchical Self-assembly, Spongy Architecture and Phase States of Laponite in low polar solvents

We propose an alternative method to tune the electrostatic interactions to obtain a transition from a repulsive to an attractive system of nanoplatelets by increasing the alcohol concentration, i.e. increasing the Bjerrum length. A phase diagram of Laponite^® in alcohol solutions has been proposed, which clearly demarcates regions of stable sol, unstable sol, transparent gel, turbid gel, glass, and flocculation. A new class of soft materials, called nanoclay-organogels, was deeply explored using confocal and scanning electron microscopy that depicted spongy architecture and presence of nano and micron size pores inside the gel matrix indicating the hierarchical self-assembly of the nanoplatelets in the binary solvent. Universal power-law scaling of storage modulus and yield stress with alcohol concentration was observed. We have extensively examined the dispersion stability, aggregation and gelation behaviour of Laponite nanoplatelets in different alcohol -water binary solvents, thereby proposing a universal description of nanoclay dispersion in alcoholic solutions, which is poorly probed and marginally understood in the literature.   

Investigating magnetic switching behavior of Permalloy nanocap layers deposited on the spin-coated nanospheres

A monolayer of close-packed nanospheres can be used as a template or a mask to produce interesting magnetic nanostructures. Multi-step spin coating process was used to create the densely packed monolayer of nanospheres. Various parameters, such as, spin speed, spin acceleration, spin duration, nanosphere concentration, volume of the solution deposited on the substrate, the duration of each step, and the interval in between the steps, were adjusted to maximize uniform area of monolayer. After a systematic study, we found that the excess solution between the nanospheres should be removed quickly during the spin-coating process so the spheres move closer each other and form the close-packed monolayer. The spin coated nanospheres were examined using an optical microscope and a scanning electron microscope. Magnetic materials, such as Permalloy or cobalt, were sputter coated on top of monolayer nanospheres. Magnetic switching behavior of these curved magnetic thin films were investigated using an alternating gradient magnetometer, a vibrating sample magnetometer, and through the magneto-optical Kerr effect measurement. Nanocap layer showed a wider magnetic switching and distinctive magnetic anisotropy compared to the flat thin film samples.