Aleks Reinhardt

Free energy landscapes for homogeneous nucleation of ice for a monatomic water model

We simulate the homogeneous nucleation of ice from supercooled liquid water at 220 K in the isobaric-isothermal ensemble using the MW monatomic water potential. Monte Carlo simulations using umbrella sampling are performed in order to determine the nucleation free energy barrier. We find the Gibbs energy profile to be relatively consistent with that predicted by classical nucleation theory; the free energy barrier to nucleation was determined to be ~18 k(B)T and the critical nucleus comprised ~85 ice particles. Growth from the supercooled liquid gives clusters that are predominantly cubic, whilst starting with a pre-formed subcritical nucleus of cubic or hexagonal ice results in the growth of predominantly that phase of ice only.

Numerical Evidence for Nucleated Self-Assembly of DNA Brick Structures

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, predesigned DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever achieved the same degree of complexity. That failure seemed easy to rationalize: the larger the number of distinct building blocks, the higher the expected error rate for self-assembly. The experiments of Ke et al. have disproved this argument. Here, we report Monte Carlo simulations of the self-assembly of a DNA brick cube, comprising approximately 1000 types of DNA strand, using a simple model. We model the DNA strands as lattice tetrahedra with attractive patches, the interaction strengths of which are computed using a standard thermodynamic model. We find that, within a narrow temperature window, the target structure assembles with high probability. Our simulations suggest that misassembly is disfavored because of a slow nucleation step. As our model incorporates no aspect of DNA other than its binding properties, these simulations suggest that, with proper design of the building blocks, other systems, such as colloids, may also assemble into truly complex structures.

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

Rational design of self-assembly pathways for complex multicomponent structures

Significance Recent experiments have demonstrated that complex, three-dimensional nanostructures can be self-assembled out of thousands of short strands of preprogrammed DNA. However, the mechanism by which robust self-assembly occurs is poorly understood, and the same feat has not yet been achieved using any other molecular building block. Using a new theory of “addressable” self-assembly, we explain how the design of the target structure and the choice of interparticle interactions determine the self-assembly pathway, and, to our knowledge, for the first time predict that a time-dependent protocol, rather than merely a carefully tuned set of conditions, may be necessary to optimize the yield. With an understanding of these design principles, it should be possible to engineer addressable nanostructures using a much wider array of materials. The field of complex self-assembly is moving toward the design of multiparticle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such “addressable complexity,” we need to understand the factors that optimize the yield and the kinetics of self-assembly. Here we use a simple theoretical method to explain the key features responsible for the unexpected success of DNA-brick experiments, which are currently the only demonstration of reliable self-assembly with such a large number of components. Simulations confirm that our theory accurately predicts the narrow temperature window in which error-free assembly can occur. Even more strikingly, our theory predicts that correct assembly of the complete structure may require a time-dependent experimental protocol. Furthermore, we predict that low coordination numbers result in nonclassical nucleation behavior, which we find to be essential for achieving optimal nucleation kinetics under mild growth conditions. We also show that, rather surprisingly, the use of heterogeneous bond energies improves the nucleation kinetics and in fact appears to be necessary for assembling certain intricate 3D structures. This observation makes it possible to sculpt nucleation pathways by tuning the distribution of interaction strengths. These insights not only suggest how to improve the design of structures based on DNA bricks, but also point the way toward the creation of a much wider class of chemical or colloidal structures with addressable complexity.

Effects of surface interactions on heterogeneous ice nucleation for a monatomic water model

Despite its importance in atmospheric science, much remains unknown about the microscopic mechanism of heterogeneous ice nucleation. In this work, we perform hybrid Monte Carlo simulations of the heterogeneous nucleation of ice on a range of generic surfaces, both flat and structured, in order to probe the underlying factors affecting the nucleation process. The structured surfaces we study comprise one basal plane bilayer of ice with varying lattice parameters and interaction strengths. We show that what determines the propensity for nucleation is not just the surface attraction, but also the orientational ordering imposed on liquid water near a surface. In particular, varying the ratio of the surfaces attraction and orientational ordering can change the mechanism by which nucleation occurs: ice can nucleate on the structured surface even when the orientational ordering imposed by the surface is weak, as the water molecules that interact strongly with the surface are themselves a good template for further growth. We also show that lattice matching is important for heterogeneous nucleation on the structured surface we study. We rationalise these brute-force simulation results by explicitly calculating the interfacial free energies of ice and liquid water in contact with the nucleating surface and their variation with surface interaction parameters.

Note: Homogeneous TIP4P/2005 ice nucleation at low supercooling.

We present a partial free energy profile for the homogeneous nucleation of ice using an all-atom model of water at low supercooling, at which ice growth dynamics are reasonably accessible to simulation. We demonstrate that the free energy profile is well described by classical nucleation theory, and that the nucleation barrier is entropic in origin. We also estimate to first order the temperature dependence of the interfacial free energy.

Re-entrant phase behavior for systems with competition between phase separation and self-assembly.

In patchy particle systems where there is a competition between the self-assembly of finite clusters and liquid-vapor phase separation, re-entrant phase behavior can be observed, with the system passing from a monomeric vapor phase to a region of liquid-vapor phase coexistence and then to a vapor phase of clusters as the temperature is decreased at constant density. Here, we present a classical statistical mechanical approach to the determination of the complete phase diagram of such a system. We model the system as a van der Waals fluid, but one where the monomers can assemble into monodisperse clusters that have no attractive interactions with any of the other species. The resulting phase diagrams show a clear region of re-entrance. However, for the most physically reasonable parameter values of the model, this behavior is restricted to a certain range of density, with phase separation still persisting at high densities.

Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.

Computing Phase Diagrams for a Quasicrystal-Forming Patchy-Particle System

We introduce an approach to computing the free energy of quasicrystals, which we use to calculate phase diagrams for systems of two-dimensional patchy particles with five regularly arranged patches that have previously been shown to form dodecagonal quasicrystals. We find that the quasicrystal is a thermodynamically stable phase for a wide range of conditions and remains a robust feature of the system as the potentials parameters are varied. We also demonstrate that the quasicrystal is entropically stabilized over its crystalline approximants.

Effects of co-ordination number on the nucleation behaviour in many-component self-assembly

We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behaviour, in the form of free-energy barriers to nucleation, changes significantly as the co-ordination number of the building blocks is changed from 4 to 8 to 12. Unlike tetrahedral structures - which roughly correspond to DNA bricks that have been studied in experiments - the shapes of the free-energy barriers of higher co-ordination structures depend strongly on the supersaturation, and such structures require a very significant driving force for structure growth before nucleation becomes thermally accessible. Although growth at high supersaturation results in more defects during self-assembly, we show that high co-ordination number structures can still be assembled successfully in computer simulations and that they exhibit self-assembly behaviour analogous to DNA bricks. In particular, the self-assembly remains modular, enabling in principle a wide variety of nanostructures to be assembled, with a greater spatial resolution than is possible in low co-ordination structures.