Kinetic Control of Parallel versus Antiparallel Amyloid Aggregation via Shape of the Growing Aggregate

in Nature Scientific Reports (2019)

By combining atomistic and higher-level modelling with solution X-ray diffraction we analyse self-assembly pathways for the IFQINS hexapeptide, a bio-relevant amyloid former derived from human lysozyme ... [more ▼]

By combining atomistic and higher-level modelling with solution X-ray diffraction we analyse self-assembly pathways for the IFQINS hexapeptide, a bio-relevant amyloid former derived from human lysozyme. We verify that (at least) two metastable polymorphic structures exist for this system which are substantially different at the atomistic scale, and compare the conditions under which they are kinetically accessible. We further examine the higher-level polymorphism for these systems at the nanometre to micrometre scales, which is manifested in kinetic differences and in shape differences between structures instead of or as well as differences in the small-scale contact topology. Any future design of structure based inhibitors of the IFQINS steric zipper, or of close homologues such as TFQINS which are likely to have similar structures, should take account of this polymorphic assembly. [less ▲]

Sequencing chess

in Europhysics Letters (2016), 116(10009),

We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess ... [more ▼]

We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess pieces into another, we conclude that the state space consists of several pockets between which transitions are rare. Skilled players explore an even smaller subset of positions that populate some of these pockets only very sparsely. These results suggest that the usual measures to estimate both the size of the state space and the size of the tree of legal moves are not unique indicators of the complexity of the game, but that considerations regarding the connectedness of states are equally important. [less ▲]

Enhancing Self-Assembly in Cellulose Nanocrystal Suspensions Using High-Permittivity Solvents

in Langmuir (2016)

Helical liquid crystal self-assembly in suspensions of cellulose nanocrystals (CNCs), bioderived nanorods exhibiting excellent mechanical and optical properties, opens attractive routes to sustainable ... [more ▼]

Helical liquid crystal self-assembly in suspensions of cellulose nanocrystals (CNCs), bioderived nanorods exhibiting excellent mechanical and optical properties, opens attractive routes to sustainable production of advanced functional materials. For convenience, in most studies until now, the CNCs were suspended in water, leaving a knowledge gap concerning the influence of the solvent. Using a novel approach for aggregation-free solvent exchange in CNC suspensions, here we show that protic solvents with a high dielectric permittivity εr significantly speed up self-assembly (from days to hours) at high CNC mass fraction and reduce the concentration dependence of the helix period (variation reducing from more than 30 μm to less than 1 μm). Moreover, our computer simulations indicate that the degree of order at constant CNC content increases with increasing εr, leading to a shorter pitch and a reduced threshold for liquid crystallinity. In low-εr solvents, the onset of long-range orientational order is coupled to kinetic arrest, preventing the formation of a helical superstructure. Our results show that the choice of solvent is a powerful parameter for tuning the behavior of CNC suspensions, enhancing our ability to control the self-assembly and thereby harvesting valuable novel cellulose-based materials. [less ▲]

Structure diagram of binary Lennard-Jones clusters

in Journal of Chemical Physics (2016), 145(024302),

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and ... [more ▼]

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory. lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures. [less ▲]

Dissipation by a crystallization process

in Europhysics Letters (2016), 113(10004),

We discuss crystallization as a non-equilibrium process. In a system of hard spheres under compression at a constant rate, we quantify the amount of heat that is dissipated during the crystallization ... [more ▼]

We discuss crystallization as a non-equilibrium process. In a system of hard spheres under compression at a constant rate, we quantify the amount of heat that is dissipated during the crystallization process. We interpret the dissipation as arising from the resistance of the system against phase transformation. An intrinsic compression rate is identified that separates a quasistatic regime from one of rapidly driven crystallization. In the latter regime the system crystallizes more easily, because new relaxation channels are opened, at the cost of forming a higher fraction of non-equilibrium crystal structures. We rationalize the change in the crystallization mechanism by analogy with shear thinning, in terms of a kinetic competition between near-equilibrium relaxation and external driving. [less ▲]

Percolation in colloidal model systems

Presentation (2016, January)

The early crystal nucleation process in hard spheres shows synchronised ordering and densification

in Journal of Chemical Physics (2016), 145

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the ... [more ▼]

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the overcompressed liquid, beginning approximately one diffusion time before the appearance of the first “solid-like” particle of the nucleating cluster, and that a collective influx of particles towards the nucleation site occurs simultaneously to the ordering process: the density increases leading to nucleation are generated by the same individual particle displacements as the increases in order. We rule out the presence of qualitative differences in the early nucleation process between medium and low overcompressions and also provide evidence against any separation of translational and orientational order on the relevant lengthscales. [less ▲]

Pressure-controlled formation of crystalline, Janus, and core–shell supraparticles

in Nanoscale (2016), (27),

Binary mixtures of nanoparticles self-assemble in the confinement of evaporating oil droplets and form regular supraparticles. We demonstrate that moderate pressure differences on the order of 100 kPa ... [more ▼]

Binary mixtures of nanoparticles self-assemble in the confinement of evaporating oil droplets and form regular supraparticles. We demonstrate that moderate pressure differences on the order of 100 kPa change the particles’ self-assembly behavior. Crystalline superlattices, Janus particles, and core–shell particle arrangements form in the same dispersions when changing the working pressure or the surfactant that sets the Laplace pressure inside the droplets. Molecular dynamics simulations confirm that pressure-dependent interparticle potentials affect the self-assembly route of the confined particles. Optical spectrometry, small-angle X-ray scattering and electron microscopy are used to compare experiments and simulations and confirm that the onset of self-assembly depends on particle size and pressure. The overall formation mechanism reminds of the demixing of binary alloys with different phase diagrams. [less ▲]

Graphene liquid crystal retarded percolation for new high-k materials

in Nature Communications (2015)

Graphene flakes with giant shape anisotropy are extensively used to establish connectedness electrical percolation in various heterogeneous systems. However, the percolation behaviour of graphene flakes ... [more ▼]

Graphene flakes with giant shape anisotropy are extensively used to establish connectedness electrical percolation in various heterogeneous systems. However, the percolation behaviour of graphene flakes has been recently predicted to be far more complicated than generally anticipated on the basis of excluded volume arguments. Here we confirm experimentally that graphene flakes self-assemble into nematic liquid crystals below the onset of percolation. The competition of percolation and liquid crystal transition provides a new route towards high-k materials. Indeed, near-percolated liquid-crystalline graphene-based composites display unprecedented dielectric properties with a dielectric constant improved by 260-fold increase as compared with the polymer matrix, while maintaining the loss tangent as low as 0.4. This performance is shown to depend on the structure of monodomains of graphene liquid-crystalline phases. Insights into how the liquid crystal phase transition interferes with percolation transition and thus alters the dielectric constant are discussed. [less ▲]

Percolation in suspensions of hard nanoparticules: From Spheres to needles

in Europhysics Letters (2015), 111

We investigate geometric percolation and scaling relations in suspensions of nanorods, covering the entire range of aspect ratios from spheres to extremely slender needles. A new version of connectedness ... [more ▼]

We investigate geometric percolation and scaling relations in suspensions of nanorods, covering the entire range of aspect ratios from spheres to extremely slender needles. A new version of connectedness percolation theory is introduced and tested against specialised Monte Carlo simulations. The theory accurately predicts percolation threshold for aspect ratios of length to width as low as 10. The percolation threshold for rod-like particules of aspect ratios below 1000 deviates significantly from the inverse aspect ratio scaling prediction, thought to be valid in the limit of infinitely slender rods and often used as a rule of thumb for nanofibres in composites materials. Hence, most fibres that are currently used as fillers in composite materials cannot be regarded as pratically infinitely slender for the purposes of percolation theory. Comparing percolation thresholds of hard rods and new benchmark results for ideal rods, we find that i) for large aspect ratios, they differ by a factor that is inversely proportional to the connectivity distance between the hard cores, and ii) they approach the slender rod limit differently. [less ▲]