![]() Hakami Zanjani, Ali Asghar ![]() in Biophysical Journal (2020), 118 Several atomic structures have now been found for micrometer-scale amyloid fibrils or elongated microcrystals using a range of methods, including NMR, electron microscopy, and X-ray crystallography, with ... [more ▼] Several atomic structures have now been found for micrometer-scale amyloid fibrils or elongated microcrystals using a range of methods, including NMR, electron microscopy, and X-ray crystallography, with parallel beta-sheet appearing as the most common secondary structure. The etiology of amyloid disease, however, indicates nanometer-scale assemblies of only tens of peptides as significant agents of cytotoxicity and contagion. By combining solution X-ray with molecular dynamics, weshow that antiparallel structure dominates at the first stages of aggregation for a specific set of peptides, being replaced by parallel at large length scales only. This divergence in structure between small and large amyloid aggregates should inform future design of molecular therapeutics against nucleation or intercellular transmission of amyloid. Calculations and an overview from the literature argue that antiparallel order should be the first appearance of structure in many or most amyloid aggregation processes, regardless of the endpoint. Exceptions to this finding should exist, depending inevitably on the sequence and on solution conditions. [less ▲] Detailed reference viewed: 112 (11 UL)![]() Hakami Zanjani, Ali Asghar ![]() 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 ▲] Detailed reference viewed: 147 (16 UL)![]() Heymans, Sven ![]() ![]() in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2017), 96(022708), We present a Monte Carlo simulation study of suspensions of hard ellipsoids of revolution. Based on the spatial fluctuations of the orientational order, we have computed the Frank elastic constants for ... [more ▼] We present a Monte Carlo simulation study of suspensions of hard ellipsoids of revolution. Based on the spatial fluctuations of the orientational order, we have computed the Frank elastic constants for prolate and oblate ellipsoids and compared them to the affine transformation model. The affine transformation model predicts the right order of magnitude of the twist and bend constant but not of the splay constant. In addition, we report the observation of a stable nematic phase at an aspect ratio as low as 2.5. [less ▲] Detailed reference viewed: 131 (7 UL)![]() ; Schilling, Tanja ![]() 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 ▲] Detailed reference viewed: 140 (5 UL)![]() Kuhnhold, Anja ![]() ![]() in Journal of Chemical Physics (2016), 145(194904), We present a Monte Carlo simulation study of helical Yukawa rods as a model for chiral liquid crystal mesogens.To simulate the cholesteric phase, we introduce a newsimulation method that uses softwalls ... [more ▼] We present a Monte Carlo simulation study of helical Yukawa rods as a model for chiral liquid crystal mesogens.To simulate the cholesteric phase, we introduce a newsimulation method that uses softwalls and self-determined boundary conditions. We observe that the isotropic-nematic phase transition is shifted to lower volume fractions with decreasing salt concentration as well as with increasing internal pitch of the rods. For particular sets of interaction parameters, the sense of the cholesteric pitch inverts, i.e., depending on concentration, mesogens of a given handedness can produce cholesteric phases of both chiral senses. [less ▲] Detailed reference viewed: 142 (3 UL)![]() ; Kuhnhold, Anja ![]() ![]() 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 ▲] Detailed reference viewed: 239 (14 UL)![]() ; ; Dixit, Mohit ![]() in Journal of Chemical Physics (2016), 145 The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off-lattice model ... [more ▼] The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off-lattice model featuring spherocylinders with continuous positional and orientational degrees of freedom. Both models are treated using density functional theory and Monte Carlo simulations. Upon increasing the density of rods in the monolayer, there is a continuous ordering of the rods along the monolayer normal (“standing up” transition). The continuous transition also persists in the case of an external potential which favors flat-lying rods in the monolayer. This behavior is found in both the lattice and the continuum models. For the lattice model, we find very good agreement between the results from the specific DFT used (lattice fundamental measure theory) and simulations. The properties of lattice fundamental measure theory are further illustrated by the phase diagrams of bulk hard rods in two and three dimensions. [less ▲] Detailed reference viewed: 231 (22 UL)![]() Mravlak, Marko ![]() 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 ▲] Detailed reference viewed: 157 (6 UL)![]() Honorato Rios, Camila ![]() ![]() in Frontiers in Materials (2016), 3 The cholesteric liquid crystal self-assembly of water-suspended cellulose nanocrystal (CNC) into a helical arrangement was observed already more than 20 years ago, and the phenomenon was used to produce ... [more ▼] The cholesteric liquid crystal self-assembly of water-suspended cellulose nanocrystal (CNC) into a helical arrangement was observed already more than 20 years ago, and the phenomenon was used to produce iridescent solid films by evaporating the solvent or via sol–gel processing. Yet, it remains challenging to produce optically uniform films and to control the pitch reproducibly, reflecting the complexity of the three-stage drying process that is followed in preparing the films. An equilibrium liquid crystal phase formation stage is followed by a non-equilibrium kinetic arrest, which in turn is followed by structural collapse as the remaining solvent is evaporated. Here, we focus on the first of these stages, combining a set of systematic rheology and polarizing optics experiments with computer simulations to establish a detailed phase diagram of aqueous CNC suspensions with two different values of the surface charge, up to the concentration where kinetic arrest sets in. We also study the effect of varying ionic strength of the solvent. Within the cholesteric phase regime, we measure the equilibrium helical pitch as a function of the same parameters. We report a hitherto unnoticed change in character of the isotropic–cholesteric transition at increasing ionic strength, with a continuous weakening of the first-order character up to the point where phase coexistence is difficult to detect macroscopically due to substantial critical fluctuations. [less ▲] Detailed reference viewed: 242 (14 UL)![]() Dorosz, Sven ![]() ![]() 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 ▲] Detailed reference viewed: 139 (3 UL)![]() Dixit, Mohit ![]() ![]() ![]() in Physical Review. E ,Statistical, Nonlinear, and Soft Matter Physics (2016), (93), 012116 We have studied the connectivity percolation transition in suspensions of attractive square-well spherocylinders by means ofMonte Carlo simulation and connectedness percolation theory. In the 1980s the ... [more ▼] We have studied the connectivity percolation transition in suspensions of attractive square-well spherocylinders by means ofMonte Carlo simulation and connectedness percolation theory. In the 1980s the percolation threshold of slender fibers has been predicted to scale as the fibers’ inverse aspect ratio [Phys. Rev. B 30, 3933 (1984)]. The main finding of our study is that the attractive spherocylinder system reaches this inverse scaling regime at much lower aspect ratios than found in suspensions of hard spherocylinders. We explain this difference by showing that third virial corrections of the pair connectedness functions, which are responsible for the deviation from the scaling regime, are less important for attractive potentials than for hard particles. [less ▲] Detailed reference viewed: 237 (38 UL)![]() Schilling, Tanja ![]() Presentation (2016, January) Detailed reference viewed: 60 (2 UL)![]() Schilling, Tanja ![]() Presentation (2016, January) Detailed reference viewed: 66 (6 UL)![]() Berryman, Josh ![]() ![]() ![]() 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 ▲] Detailed reference viewed: 136 (3 UL)![]() ; ; et al in Physical Review Letters (2016), 116(9), A thermodynamically equilibrated fluid of hard spheroids is a simple model of liquid matter. In this model, the coupling between the rotational degrees of freedom of the constituent particles and their ... [more ▼] A thermodynamically equilibrated fluid of hard spheroids is a simple model of liquid matter. In this model, the coupling between the rotational degrees of freedom of the constituent particles and their translations may be switched off by a continuous deformation of a spheroid of aspect ratio t into a sphere (t=1). We demonstrate, by experiments, theory, and computer simulations, that dramatic nonanalytic changes in structure and thermodynamics of the fluids take place, as the coupling between rotations and translations is made to vanish. This nonanalyticity, reminiscent of a second-order liquid-liquid phase transition, is not a trivial consequence of the shape of an individual particle. Rather, free volume considerations relate the observed transition to a similar nonanalyticity at t=1 in structural properties of jammed granular ellipsoids. This observation suggests a deep connection to exist between the physics of jamming and the thermodynamics of simple fluids. © 2016 American Physical Society. [less ▲] Detailed reference viewed: 166 (10 UL)![]() ; Mravlak, Marko ![]() ![]() 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 ▲] Detailed reference viewed: 182 (4 UL)![]() ![]() Schilling, Tanja ![]() Scientific Conference (2015, December) Detailed reference viewed: 61 (2 UL)![]() ; ; et al 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 ▲] Detailed reference viewed: 157 (7 UL)![]() ![]() Schilling, Tanja ![]() Scientific Conference (2015, October) Detailed reference viewed: 50 (0 UL)![]() Schilling, Tanja ![]() 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 ▲] Detailed reference viewed: 99 (16 UL) |
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