Session B58: Self-Assembly II

Self-assembly of Designed Nanoarchitectures via Shape and DNA-programmability

Creating complex nanoscale structures from simple building blocks is a well-recognized challenge. In this work, we show that a simple hollow square-bucket DNA frame can be used as a basic building block to prescribe self-assembly of one-dimensional(1D), two-dimensional (2D) and three-dimensional (3D) scaffolds, whose symmetry is only determined by DNA frame geometry. Due to the empty space of hollow square frame, these 1D, 2D and 3D scaffolds can be further utilized to host guest nano-objects such as nanoparticles via sequence-specified binding. We demonstrate a variety of linear architectures, such as the homo-chain-like, alternating-chain-like nanoparticles structures, and chiral organizations. We apply the developed method for generating 2D and 3D lattices with prescribed particle organizations.   

Self-assembly of Nematic Liquid Crystals in Drying Drops of Lysozyme Protein Solution

In the recent years, an active area of research involves liquid crystals (LCs), e.g. 5CB (4-Cyano-4'-pentylbiphenyl) for sensing biological and chemical analytes. Another active area studies drying protein drops resulting in emergent patterns at the final dried state. In this presentation, these two areas are bridged by adding 5CB, with initial protein solution of lysozyme and de-ionized water. The investigation is done using bright-field and cross-polarizing microscopy, analyzed using ImageJ and Fiji and quantified using statistical tests. It is observed that the crack patterns in the final dried state of the protein is influenced by the presence of small amounts of 5CB. Since the protein lysozyme is not birefringent, cross-polarizing microscopy closely monitors the distribution of the LC, while the bright-field microscopy probes the crack patterns that emerge. The time evolution of the drying dynamics of the drops with and without 5CB are monitored. It is concluded that partial phase separation of LC makes some LC remains mixed and some dispersed into the domains formed by protein cracks. This work demonstrates the utility of using a bulk thermotropic LC as a probe material in a protein solution, revealing new information on the protein self-assembly during the drying process.   

Towards a Bayesian Interpretation of DNA Self-assembly in Hydrogels

While widely known as the molecule of life, DNA is also an amazing building block at the nanoscale, since it allows the design and programming of the structure and dynamics of functional nanomaterials. A class of such materials are DNA hydrogels, which exploit elastic or viscous behaviour that is finely regulated by temperature. These functional materials are promising candidates for medical applications, and specifically controlled drug delivery, tissue engineering and biosensing.
In my research I am using computational tools to study the self-assembly of branched-shaped DNA building blocks that form a hydrogel. By using molecular dynamics I am simulating the assembling process, and calculate the equilibrium elastic and viscous moduli of DNA hydrogels. Moreover, I am working towards the design of a model that will employ Bayesian inference in order to associate the hydrogel properties with the different configurations of the DNA building blocks. In my talk I will outline the significance of a model that will describe DNA hydrogels, and how it can lead to the design of novel DNA-based materials.   

Self-Assembly of DNA origami capsids

DNA origami is an fruitful method to create a wide range of simple and complex objects on the nanometer scale. By folding DNA into truncated tetrahedra ("triangles") with protrusions and recessions on their outer edges, one can add attractive interaction between these triangles.
With the right design these triangles self-assemble into icosahedra similarly to virus coat proteins but on larger length- and timescales, with potential applications in functional materials.

To guide the design of these building blocks we perform molecular dynamics and kinetic Monte Carlo simulations of coarse-grained, rigid triangles with reactive patches. Specifically, we aim to identify regimes at which the triangles optimally self-assemble into icosahedra of 20 and 60 subunits. Finally, we qualitatively compare the predicted self-assembly kinetics and structures to experiments.   

The self-assembly of icosahedral shells depends on kinetics and thermodynamics

We study the out-of-equilibrium self-assembly of subunits whose equilibrium ground state corresponds to an icosahedral shell, in the absence of template. We adapt a method introduced by Rostkoff and Geissler [1], which allows computationally efficient simulation of self-assembly via microscopically reversible dynamics. This allows sampling the non-equilibrium distribution of shell morphologies that arises at long, but finite times, over a wide range of shell sizes. We find that the size and morphology distribution is determined by a competition between kinetic and thermodynamic factors, and can vary significantly from the ground state equilibrium distribution as also seen in dynamical simulations [2]. Our results are general and should be applicable to diverse systems, including the self-assembly of viral capsids, bacterial microcompartments, nano tubules, or DNA origami subunits.


[1]: GM Rostkoff, PL Geissler, PNAS 115 (25), 6341-6346 (2018)
[2]: F Mohajerani, MF Hagan, PLoS computational biology, 14(7), e1006351 (2018)   

Solvent Effects in Nanocrystal Self-Assembly

Materials which are composed of long-range, ordered nanocrystals exhibit many potentially revolutionary properties as compared with traditional materials. There is much to be learned about the dynamics associated with the assembly of these materials. We have previously characterized the equilibrium configuration of arrangements of highly symmetric nanocrystal clusters, and we seek now to determine solvent effects during the process of assembly via computer simulation. We have simulated the process of solvent evaporation using HOOMD and HOODLT and have found that the preferred orientation of the nanocrystals is on the boundary of the liquid solvent. As solvent is evaporated, the nanocrystals are forced to move closer together until the solvent is evaporated out completely, leaving behind nanocrystals in ordered structures.   

Folding dynamics of colloidal clusters

We follow the evolution of colloidal clusters from a well-defined initial configuration towards various stable structures in order to understand how a system traverses a free-energy landscape. We use optical tweezers to assemble individual colloidal particles into an initial extended structure held together by a short-range attraction between particles. Particles diffuse across their neighbours' surfaces, lowering the cluster's free energy when particles come into contact. We precisely track the coordinates of all particles in the rearranging cluster throughout this assembly process with a three-dimensional imaging technique, digital holographic microscopy, and we quantify the various pathways from the initial state to the ground states.   

Band Gap Optimization of Colloidal MgCu2 Photonic Crystals

It was recently shown that a colloidal MgCu₂ lattice can be self-assembled using a combination of DNA coated spheres and compressed tetrahedral clusters of spheres. The spheres and compressed clusters form two interpenetrating sublattices, diamond and pyrochlore, respectively. Both sublattices have a photonic band gap. We calculate the photonic band structures of the compressed cluster crystals, which differ from those of the standard pyrochlore lattice that has been considered previously. We find that the compression of the clusters can make the band gap significantly wider than for the typical pyrochlore lattices. We can precisely tune the compression of our synthesized tetrahedral clusters, giving us the opportunity to explore the full range of MgCu₂ assembly and optimize their photonic properties.   

Assembly of Silica Particles at Free Standing Smectic-A Films

The ability of liquid crystals (LCs) to organize particles into regular structures provides novel routes to control ordering transitions, with the possibility of building complex artificial structures for diverse applications. Since LCs are readily reconfigurable, they offer opportunities to make responsive devices including smart energy-efficient windows, responsive optical components, and sensors. Furthermore, colloidal particles at complex fluid interfaces and within films assemble to form ordered structures via interactions that include capillarity, elasticity, and other fields. Here we study microparticle interactions within free-standing smectic-A films, in which the elasticity arising from the director field distortion and capillary interactions arising from interface deformation compete to direct the assembly of particles. New colloidal assemblies and patterns, ranging from 1D chains to 2D aggregates, sensitive to the initial wetting conditions of particles at the smectic film, are reported. This work paves the way to exploiting LC interfaces as a means to direct spontaneously formed, reconfigurable, and optically active materials.   

Polymeric Janus Nanoparticles at Water/Oil Interfaces

We present a study on the assembly of polymeric Janus nanoparticles (pJNPs) at the toluene/water interface. The soft spherical polymeric Janus nanoparticles pJNPs, made by cross-linking polystyrene-block-polybutadiene-block-poly(methyl methacrylate) (PS-PB-PMMA), show a high interfacial activity, even though neither component is soluble in water. The preferential affinity of the PMMA to the aqueous phase causes a spreading of the PMMA block at the interface. Unlike hard NPs where, after the interfacial tension has decreased and stabilized, only a small volume reduction of the pendant droplet is required to induce wrinkling, for soft pJNPs, there must be a significant reduction in the pendant drop volume to induce wrinkling. A series of pJNPs where the molecular weight at constant weight fraction or where the weight fraction at constant molecular weight of the brushes and cores were varied to probe the influence of molecular weight, brush lengths and volume fractions of the component arms on the areal density of the assemblies and the response of the assemblies to a compression. We also investigated the influence of metal ions in the aqueous phase that can complex with the PMMA on the assembly, packing, stability and responsiveness of pJNP assemblies.
  

Rational Design of Anisotropic Colloids to Self-assemble Open Lattices with Omnidirectional Band Gaps

Patchy colloids possessing anisotropic interactions are versatile building blocks for the self-assembly of complex functional materials. The main challenge in assembling these materials is the rational and efficient discovery of colloidal architectures and chemistries that make the desired aggregate both thermodynamically stable and kinetically accessible. We have previously devised an inverse design strategy termed “landscape engineering” wherein we combine molecular simulations, nonlinear dimensionality reduction, and genetic algorithms to recover and sculpt the low-dimensional free energy landscape governing assembly by rational modulation of building block design. We apply this data-driven design strategy to perform de novo design of patchy colloids that spontaneously assemble into an open pyrochlore lattice with an omnidirectional photonic bandgap. Our particle design assembles the crystal in a two-stage hierarchy where tetrahedral clusters representing the fundamental motif of the crystal are formed at high temperature with >90% yield, and then a gentle ramp to low temperature induces the aggregation of the tetrahedra into the pyrochlore lattice. Our design approach can be extended to other finite-sized and periodic assemblies including Platonic solids and diamond lattices.   

Interactions and Energy Scales in Self Assembly and Directed Assembly of Nanocrystal Superlattices

Long range ordered structures of nanocrystals or nanoparticles are known as superlattices. We, and others, have shown that the cohesive energy of nanocrystals in superlattices is very large, of the order of hundrends of $k_BT$. In this talk we will show theoretical and computational results on nanocrystals capped with hydrocarbons showing how these systems overcome these scales and successfully self-assemble into orderes structures with long range order. Irrespectively of the interactions, these systems show a tendency towards local icosahedral order. Time permitting, issues related to polydipersity will be discussed.   

Three-dimensional particle-based simulations of fluctuation-stabilized copolymer mesophases

Binary blends of A-b-(B-b-A’)_n miktoarm star block copolymers and A homopolymers have been experimentally shown to self-assemble into an aperiodic “bricks-and-mortar” mesophase, which combines a continuous “mortar” phase of the B-type polymer with a discrete “bricks” phase of the A-type polymer. Such materials have been proposed for use as thermoplastic elastomers, combining high mechanical strength and high elastic recovery. It has been demonstrated theoretically that the mesophase is not predicted to exist in the absence of thermal fluctuations, suggesting it is a unique fluctuation-stabilized morphology. A critical feature of this mesophase is that the A-type domains possess a wide range of sizes, from tens to hundreds of nanometers, representing a challenge to simulation-based approaches. Consequently, prior theoretical work has been limited to simulation in two-dimensions. In this work, we use three-dimensional particle-based simulations, which include fluctuations, to extend understanding of the phase diagram of these blends. Our simulations verify that the bricks-and-mortar mesophase emerges in the presence of three-dimensional thermal fluctuations and more accurately capture experimental systems’ phase behavior.   

Characterization of Martensitic Phase Transformations in Blue Phase Liquid Crystals Using Resonant Soft X-ray Scattering

In this work, we introduce resonant soft X-ray scattering (RSoXS)[1] to study the martensitic transformation of blue phase (BP) liquid crystals (LCs).[2] The combination of RSoXS and single crystal BP LCs—directed and stabilized by the chemically-nanopatterned surfaces—enable to provide a clear picture of how the BP lattice symmetry and molecular orientations change during this transformation. In particular, twin lamellae formation is observed during martensitic transformation to release the residual strain caused by the rapid martensitic transformation. We anticipate that these experiments will provide one of the most comprehensive studies yet of BP and, therefore, soft matter martensitic phase transformations.

[1] B. A. Collins et al., Nat. Mater. 11, 536 (2012).
[2] X. Li, et al., P.N.A.S. 114, 10011 (2017).
  

The Effects of Ligand Concentration on the Mechanical Properties of Nanoparticle Films

When dodecanethiol-ligated gold nanopartlices are deposited on an air-water interface, they self-assemble into Langmuir films. Experiments in which the films are compressed uniaxially have demonstrated that as the ligand concentration decreases, the ligand-ligand and ligand-core interactions change and the 2-dimensional compressive and shear moduli of the films increases. However, these experiments were largely done upon films while on an air-water interface – this study focuses on films which are dried and removed from the air-water interface. This is important, since many potential applications of these films are in electronic devices, which require the films to operate in a dry environment. This study examines how variations in the concentrations of ligands in a gold nanoparticle solution and by extension the fractional surface coverage, impact a dried film’s mechanical properties. Specifically, the Young’s Moduli of the films are measured through contact-mode Atomic Force Microscopy (AFM), which demonstrates that low thiol concentrations are conducive to higher young’s moduli.