arXiv subjects

John Russo

Publications and source records attributed to John Russo.

At least 37 records · Page 2Linked to original sources

arXiv2023

Colloidal Hard Spheres: Triumphs, Challenges and Mysteries

The simplicity of hard spheres as a model system is deceptive. Although the particles interact solely through volume exclusion, that nevertheless suffices for a wealth of static and dynamical phenomena to emerge, making the model an important target for achieving a comprehensive understanding of matter. In addition, while real colloidal suspensions are typically governed by complex interactions, Pusey and Van Megen [Nature 320 340--342 (1986)] demonstrated that suitably tuned suspensions result in hard-sphere like behavior, thus bringing a valuable experimental complement to the celebrated theoretical model. Colloidal hard spheres are thus both a material in their own right and a platform upon which phenomena exhibited by simple materials can be explored in great detail. These various purposes enable a particular synergy between experiment, theory and computer simulation. Here we review the extensive body of work on hard spheres, ranging from their equilibrium properties such as phase behavior, interfaces and confinement to some of the non--equilibrium phenomena they exhibit such as sedimentation, glass formation and nucleation.

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arXiv2023

Structural signatures of ultrastability in a deposited glassformer

Glasses obtained from vapor deposition on a cold substrate have superior thermodynamic and kinetic stability with respect to ordinary glasses. Here we perform molecular dynamics simulations of vapor deposition of a model glass-former and investigate the origin of its high stability compared to that of ordinary glasses. We find that the vapor deposited glass is characterized by locally favoured structures (LFS) whose occurrence correlates with its stability, reaching a maximum at the optimal deposition temperature. The formation of LFS is enhanced near the free surface, hence supporting the idea that the stability of vapor deposited glasses is connected to the relaxation dynamics at the surface.

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arXiv2023

Design strategies for the self-assembly of polyhedral shells

The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of amorphous aggregates. Here we investigate in detail the problem of the self-assembly of the three Archimedean shells with five contact points per vertex, i.e. the icosahedron, the snub cube, and the snub dodecahedron. We use patchy particles with five interaction sites (or patches) as model for the building blocks, and recast the assembly problem as a Boolean satisfiability problem (SAT) for the patch-patch interactions. This allows us to find effective designs for all targets, and to selectively suppress unwanted structures. By tuning the geometrical arrangement and the specific interactions of the patches, we demonstrate that lowering the symmetry of the building blocks reduces the number of competing structures, which in turn can considerably increase the yield of the target structure. These results cement SAT-assembly as an invaluable tool to solve inverse design problems.

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arXiv2023

Two-step nucleation in a binary mixture of Patchy Particles

Nucleation in systems with a metastable liquid-gas critical point is the prototypical example of a two-step nucleation process, in which the appearance of the critical nucleus is preceded by the formation of a liquid-like density fluctuation. So far, the majority of studies on colloidal and protein crystallization have focused on one-component systems, and we are lacking a clear description of two-step nucleation processes in multicomponent systems, where critical fluctuations involve coupled density and concentrations inhomogeneities. Here, we examine the nucleation process of a binary mixture of patchy particles designed to nucleate into a diamond lattice. By combining Gibbs-ensemble simulations and direct nucleation simulations over a wide range of thermodynamic conditions, we are able to pin down the role of the liquid-gas metastable phase diagram on the nucleation process. In particular, we show that the strongest enhancement of crystallization occurs at an azeotropic point with the same stoichiometric composition of the crystal.

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arXiv2023

A neural network potential with self-trained atomic fingerprints: a test with the mW water potential

We present a neural network (NN) potential based on a new set of atomic fingerprints built upon two- and three-body contributions that probe distances and local orientational order respectively. Compared to existing NN potentials, the atomic fingerprints depend on a small set of tuneable parameters which are trained together with the neural network weights. To tackle the simultaneous training of the atomic fingerprint parameters and neural network weights we adopt an annealing protocol that progressively cycles the learning rate, significantly improving the accuracy of the NN potential. We test the performance of the network potential against the mW model of water, which is a classical three-body potential that well captures the anomalies of the liquid phase. Trained on just three state points, the NN potential is able to reproduce the mW model in a very wide range of densities and temperatures, from negative pressures to several GPa, capturing the transition from an open random tetrahedral network to a dense interpenetrated network. The NN potential also reproduces very well properties for which it was not explicitly trained, such as dynamical properties and the structure of the stable crystalline phases of mW.

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arXiv2022

A simple solution to the problem of self-assembling cubic diamond crystals

The self-assembly of colloidal diamond (CD) crystals is considered as one of the most coveted goals of nanotechnology, both from the technological and fundamental points of view. For applications, colloidal diamond is a photonic crystal which can open new possibilities of manipulating light for information processing. From a fundamental point of view, its unique symmetry exacerbates a series of problems that are commonly faced during the self-assembly of target structures, such as the presence of kinetic traps and the formation of crystalline defects and alternative structures (polymorphs). Here we demonstrate that all these problems can be systematically addressed via SAT-assembly, a design framework that converts self-assembly into a satisfiability problem. Contrary to previous solutions (requiring four or more components), we prove that the assembly of the CD crystal only requires a binary mixture. Moreover, we use molecular dynamics simulations of a system composed by nearly a million nucleotides to test a DNA nanotechnology design that constitutes a promising candidate for experimental realization.

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arXiv2022

SAT-assembly: A new approach for designing self-assembling systems

We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as building blocks, where the different units bind at specific interaction sites (the patches), and we exploit the possibility of having mixtures with several components. The interaction rules between the patches is determined by transforming the combinatorial problem into a Boolean satisfiability problem (SAT) which searches for solutions where all bonds are formed in the target structure. Additional conditions, such as the non-satisfiability of competing structures (e.g. metastable states) can be imposed, allowing to effectively design the assembly path in order to avoid kinetic traps. We demonstrate this approach by designing and numerically simulating a cubic diamond structure from four particle species that assembles without competition from other polymorphs, including the hexagonal structure.

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arXiv2021

The physics of Empty Liquids: from Patchy particles to Water

Empty liquids represent a wide class of materials whose constituents arrange in a random network through reversible bonds. Many key insights on the physical properties of empty liquids have originated almost independently from the study of colloidal patchy particles on one side, and a large body of theoretical and experimental research on water on the other side. Patchy particles represent a family of coarse-grained potentials that allows for a precise control of both the geometric and the energetic aspects of bonding, while water has arguably the most complex phase diagram of any pure substance, and a puzzling amorphous phase behavior. It was only recently that the exchange of ideas from both fields has made it possible to solve long-standing problems and shed new light on the behavior of empty liquids. Here we highlight the connections between patchy particles and water, focusing on the modelling principles that make an empty liquid behave like water, including the factors that control the appearance of thermodynamic and dynamic anomalies, the possibility of liquid-liquid phase transitions, and the crystallization of open crystalline structures.

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arXiv2021

Towards glasses with permanent stability

Unlike crystals, glasses age or devitrify over time, reflecting their non-equilibrium nature. This lack of stability is a serious issue in many industrial applications. Here, we show by numerical simulations that the devitrification of quasi-hard-sphere glasses is prevented by suppressing volume fraction inhomogeneities. A monodisperse glass known to devitrify with `avalanche'-like intermittent dynamics is subjected to small iterative adjustments to particle sizes to make the local volume fractions spatially uniform. We find that this entirely prevents structural relaxation and devitrification over aging time scales, even in the presence of crystallites. There is a dramatic homogenization in the number of load-bearing nearest neighbors each particle has, indicating that ultra-stable glasses may be formed via `mechanical homogenization'. Our finding provides a physical principle for glass stabilization and opens a novel route to the formation of mechanically stabilized glasses.

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arXiv2021

Crystallisation and Polymorph Selection in Active Brownian Particles

We explore crystallisation and polymorph selection in active Brownian particles with numerical simulation. In agreement with previous work [Wysocki $\textit{et al.}$ $\textit{Europhys. Lett.}$, $\textbf{105}$ 48004 (2014)], we find that crystallisation is suppressed by activity and occurs at higher densities with increasing $Péclet$ number ($Pe$). While the nucleation rate decreases with increasing activity, the crystal growth rate increases due to the accelerated dynamics in the melt. As a result of this competition we observe the transition from a nucleation and growth regime at high $Pe$ to "spinodal nucleation" at low $Pe$. Unlike the case of passive hard spheres, where preference for FCC over HCP polymorphs is weak, activity causes the annealing of HCP stacking faults, thus strongly favouring the FCC symmetry at high $Pe$. When freezing occurs more slowly, in the nucleation and growth regime, this tendency is much reduced and we see a trend towards the passive case of little preference for either polymorph.

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arXiv2021

Non-classical nucleation pathways in stacking-disordered crystals

The nucleation of crystals from the liquid melt is often characterized by a competition between different crystalline structures or polymorphs, and can result in nuclei with heterogeneous compositions. These mixed-phase nuclei can display nontrivial spatial arrangements, such as layered and onion-like structures, whose composition varies according to the radial distance, and which so far have been explained on the basis of bulk and surface free-energy differences between the competing phases. Here we extend the generality of these non-classical nucleation processes, showing that layered and onion-like structures can emerge solely based on structural fluctuations even in absence of free-energy differences. We consider two examples of competing crystalline structures, hcp and fcc forming in hard spheres, relevant for repulsive colloids and dense liquids, and the cubic and hexagonal diamond forming in water, relevant also for other group 14 elements such as carbon and silicon. We introduce a novel structural order parameter that combined with a neural network classification scheme allows us to study the properties of the growing nucleus from the early stages of nucleation. We find that small nuclei have distinct size fluctuations and compositions from the nuclei that emerge from the growth stage. The transition between these two regimes is characterized by the formation of onion-like structures, in which the composition changes with the distance from the center of the nucleus, similarly to what seen in two-step nucleation process.

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arXiv2021

Structural and topological changes across the liquid-liquid transition in water

It has recently been shown that the TIP4P/Ice model of water can be studied numerically in metastable equilibrium at and below its liquid-liquid critical temperature. We report here simulations along a subcritical isotherm, for which two liquid states with the same pressure and temperature, but different density, can be equilibrated. This allows for a clear visualisation of the structural changes taking place across the transition. We specifically focus on how the topological properties of the H-bond network change across the liquid-liquid transition. Our results demonstrate that the structure of the high-density liquid, characterised by the existence of interstitial molecules and commonly explained in terms of the collapse of the second neighbour shell, actually originates from the folding back of long rings, bringing pairs of molecules separated by several hydrogen-bonds close by in space.

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arXiv2020

Designing patchy interactions to self-assemble arbitrary structures

One of the fundamental goals of nanotechnology is to exploit selective and directional interactions between molecules to design particles that self-assemble into desired structures, from capsids, to nano-clusters, to fully formed crystals with target properties (e.g. optical, mechanical, etc.). Here we provide a general framework which transforms the inverse problem of self-assembly of colloidal crystals into a Boolean satisfiability problem for which solutions can be found numerically. Given a reference structure and the desired number of components, our approach produces designs for which the target structure is an energy minimum, and also allows to exclude solutions that correspond to competing structures. We demonstrate the effectiveness of our approach by designing model particles that spontaneously nucleate milestone structures such as the cubic diamond, the pyrochlore and the clathrate lattices.

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arXiv2019

Decorated Protein Networks: Functional Nanomaterials with Tunable Domain Size

The implementation of natural and artificial proteins with designer properties and functionalities offers unparalleled opportunity for functional nanoarchitectures formed through self-assembly. However, to exploit the opportunities offered we require the ability to control protein assembly into the desired architecture while avoiding denaturation and therefore retaining protein functionality. Here we address this challenge with a model system of fluorescent proteins. Using techniques of self-assembly manipulation inspired by soft matter where interactions between components are controlled to yield the desired structure, we show that it is possible to assemble networks of proteins of one species which we can decorate with another, whose coverage we can tune. Consequently, the interfaces between domains of each component can also be tuned, with applications for example in energy transfer. Our model system of fluorescent proteins eGFP and mCherry retain their fluorescence throughout the assembly process, thus demonstrating that functionality is preserved.

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arXiv2019

Crystalline clusters in mW water: stability, growth, and grain boundaries

With numerical simulations of the mW model of water, we investigate the energetic stability of crystalline clusters for both Ice I (cubic and hexagonal ice) and for the metastable Ice 0 phase as a function of the cluster size. Under a large variety of forming conditions, we find that the most stable cluster changes as a function of size: at small sizes the Ice 0 phase produces the most stable clusters, while at large sizes there is a crossover to Ice I clusters. We further investigate the growth of crystalline clusters with the seeding technique and study the growth patterns of different crystalline clusters. While energetically stable at small sizes, the growth of metastable phases (cubic and Ice 0) is hindered by the formation of coherent grain boundaries. A five-fold symmetric twin boundary for cubic ice, and a newly discovered coherent grain boundary in Ice 0, that promotes cross nucleation of cubic ice. Our work reveals that different local structures can compete with the stable phase in mW water, and that the low energy cost of particular grain boundaries might play an important role in polymorph selection.

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arXiv2018

Coupling of sedimentation and liquid structure: influence on hard sphere nucleation

The discrepancy in nucleation rate densities between simulated and experimental hard spheres remains staggering and unexplained. Suggestively, more strongly sedimenting colloidal suspensions of hard spheres nucleate much faster than weakly sedimenting systems. In this work we consider firstly the effect of sedimentation on the structure of colloidal hard spheres, by tuning the density mismatch between solvent and colloidal particles. In particular we investigate the effect on the degree of five fold symmetry present. Secondly we study the size of density fluctuations in these experimental systems in comparison to simulations. The density fluctuations are measured by assigning each particle a local density, which is related to the number of particles within a distance of 3.25 particle diameters. The standard deviation of these local densities gives an indication of the fluctuations present in the system. Five fold symmetry is suppressed by a factor of two when sedimentation is induced in our system. Density fluctuations are also increased by a factor of two in experiments compared to simulations. The change in five fold symmetry makes a difference to the expected nucleation rates, but we demonstrate that it is ultimately too small to resolve the discrepancy between experiment and simulation, while the fluctuations are shown to be an artefact of 3d particle tracking.

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arXiv2018

The race to the bottom: approaching the ideal glass?

Key to resolving the scientific challenge of the glass transition is to understand the origin of the massive increase in viscosity of liquids cooled below their melting temperature (avoiding crystallisation). A number of competing and often mutually exclusive theoretical approaches have been advanced to describe this phenomenon. Some posit a bona fide thermodynamic phase to an "ideal glass", an amorphous state with exceptionally low entropy. Other approaches are built around the concept of the glass transition as a primarily dynamic phenomenon. These fundamentally different interpretations give equally good descriptions of the data available, so it is hard to determine which -- if any -- is correct. Recently however this situation has begun to change. A consensus has emerged that one powerful means to resolve this longstanding question is to approach the putative thermodynamic transition sufficiently closely, and a number of techniques have emerged to meet this challenge. Here we review the results of some of these new techniques and discuss the implications for the existence -- or otherwise -- of the thermodynamic transition to an ideal glass.

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arXiv2018

Water-like anomalies as a function of tetrahedrality

Tetrahedral interactions describe the behaviour of the most abundant and technologically important materials on Earth, such as water, silicon, carbon, germanium, and countless others. Despite their differences, these materials share unique common physical behaviours, such as liquid anomalies, open crystalline structures, and extremely poor glass-forming ability at ambient pressure. To reveal the physical origin of these anomalies and their link to the shape of the phase diagram, we systematically study the properties of the Stillinger-Weber potential as a function of the strength of the tetrahedral interaction $λ$. We uncover a new transition to a re-entrant spinodal line at low values of $λ$, accompanied with a change in the dynamical behaviour, from Non-Arrhenius to Arrhenius. We then show that a two-state model can provide a comprehensive understanding on how the thermodynamic and dynamic anomalies of this important class of materials depend on the strength of the tetrahedral interaction. Our work establishes a deep link between the shape of phase diagram and the thermodynamic and dynamic properties through local structural ordering in liquids, and hints at why water is so special among all substances.

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