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We introduce applied shear as a method to control viscous fingering by smoothing the interface between miscible fluids. In the viscous fingering instability, a less viscous fluid displaces a more viscous one through the formation of fingers. The instability, which requires a confined geometry, is often studied in the thin gap of a quasi–two-dimensional Hele-Shaw cell. When the two fluids are miscible, the structures that form in the dimension traversing the gap are important for determining the instability onset. We demonstrate with experiments and simulations that oscillatory translational shear of the confining plates changes the gap-averaged viscosity profile so that it becomes less abrupt at the fingertips. Increasing the amplitude or velocity of the shear delays the instability onset and decreases the finger growth rate. Shear can thus be used to stabilize a pair of miscible fluids against fingering. The results show a direct correlation between a smoother viscosity profile and delayed instability. 

Self-closing assembly is prone to polymorphism due to thermally excited bending fluctuations, which permit the formation of off-target assemblies at the point of self-closure. One way to overcome this source of polymorphism is to use templated growth, a process in which assembly initiates from a precisely defined seed rather than by spontaneous nucleation. We explore this approach to quelling polymorphism in the self-closing assembly of cylindrical tubules assembled from DNA-origami subunits with user-specified inter-subunit binding angles and specific interactions. We develop two strategies to create seeds with precisely defined diameters and helicity: (1) using multicomponent assembly and (2) purifying a specific seed-type from a polymorphic mixture using gel electrophoresis and gel extraction. By tuning the seed and monomer concentrations and adjusting the assembly temperature, we determine the conditions under which tubules grow from the seed while avoiding spontaneous nucleation. We observe that templated tubules tend to follow the guidance of the seed, thereby increasing the selectivity of the target geometry. In addition, we find that by tuning the diameter of the seed, one can template the growth of monodisperse tubules over a range of target diameters, even while using a single monomer type with a single preferred local curvature. Our results demonstrate that employing precisely defined seeds to guide assembly can significantly decrease polymorphism in self-closing assembly in a controllable and economical way. 

Organic mixed ionic-electronic conductors are promising materials for next generation bioelectronic devices. While they readily interface with biological systems, the volumetric doping mechanism renders them susceptible to biofouling and operational instability. Thus, there is a materials science challenge requiring strategic focus on rational, molecular-level design materials to control the complex bio-abiotic interface. Here, biofouling and operational instability are explored, and strategies developed to address these interconnected problems are traced. 

In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global minima in free energy landscapes; they are often ordered and periodic on length scales comparable to the building block size. Coupling the assembly process to an exergonic reaction drives the system out of equilibrium so that an assembly pathway can be engineered to target a specific kinetically stabilized state, which in principle opens up a vast design space with access to diverse complex structures with features on multiple length scales. However, the question of how such features might be specifically targeted remains unanswered. Here, we explore this design space using a DNA-encoded recipe consisting of multiple biomolecular reactions that dictate the time-dependent binding strength and specificity of each type of subunit in the sample independently, which makes it possible to program an assembly pathway that leads to a kinetically trapped final state. With this kinetic control, we show that the same set of building blocks can form clusters with different final structures. These structures, with tunable core-shell compositions, have feature sizes much larger than the building block size and are governed by the DNA-encoded assembly kinetics. Tuning the timing of individual biomolecular reactions using DNA-encoded recipes offers the opportunity to independently regulate how the many interactions of a large set of coassembling components evolve over time, opening up the potential of creating morphogenesis-like assembly processes involving engineered species. 

Abstract Modern experimental methods in programmable self-assembly make it possible to precisely design particle concentrations, shapes and interactions. However, more physical insight is needed before we can take full advantage of this vast design space to assemble nanostructures with complex form and function. Here we show how a substantial part of this design space can be quickly and comprehensively understood by identifying a class of thermodynamic constraints that act on it. These thermodynamic constraints form a high-dimensional convex polyhedron that determines which nanostructures can be assembled at high equilibrium yield and reveals limitations that govern the coexistence of structures. We validate our predictions through detailed, quantitative assembly experiments of nanoscale particles synthesized using DNA origami. Our results uncover physical relationships underpinning many-component programmable self-assembly in equilibrium and form the basis for robust inverse design, applicable to various systems from biological protein complexes to synthetic nanomachines.