arXiv subjects

Robert L. Jack

Publications and source records attributed to Robert L. Jack.

At least 109 records · Page 6Linked to original sources

arXiv2014

Self-assembly of colloidal polymers via depletion-mediated lock and key binding

We study the depletion-induced self-assembly of indented colloids. Using state-of-the-art Monte Carlo simulation techniques that treat the depletant particles explicitly, we demonstrate that colloids assemble by a lock-and-key mechanism, leading to colloidal polymerization. The morphology of the chains that are formed depends sensitively on the size of the colloidal indentation, with smaller values additionally permitting chain branching. In contrast to the case of spheres with attractive patches, Wertheim's thermodynamic perturbation theory fails to provide a fully quantitative description of the polymerization transition. We trace this failure to a neglect of packing effects and we introduce a modified theory that accounts better for the shape of the colloids, yielding improved agreement with simulation.

cond-mat.soft↗

arXiv2013

Large deviations of the dynamical activity in the East model: analysing structure in biased trajectories

We consider large deviations of the dynamical activity in the East model. We bias this system to larger than average activity and investigate the structure that emerges. To best characterise this structure, we exploit the fact that there are effective interactions that would reproduce the same behaviour in an equilibrium system. We combine numerical results with linear response theory and variational estimates of these effective interactions, giving the first insights into such interactions in a many-body system, across a wide range of biases. The system exhibits a hierarchy of responses to the bias, remaining quasi-equilibrated on short length scales, but deviating far from equilibrium on large length scales. We discuss the connection between this hierarchy and the hierarchical aging behaviour of the system.

cond-mat.stat-mech↗

arXiv2013

Investigating amorphous order in stable glasses by random pinning

We use a random pinning procedure to investigate stable glassy states associated with large deviations of the activity in a model glass-former. We pin particles both from active (equilibrium) configurations and from stable (inactive) glassy states. By comparing the distribution of the overlap between states that share pinned particles, we infer that the inactive states are characterised by a structural length scale that is comparable with the system size. This is a manifestation of amorphous order in these glassy states, which helps to explain their stability.

cond-mat.stat-mech↗

arXiv2013

The effect of boundary adaptivity on hexagonal ordering and bistability in circularly confined quasi hard discs

The behaviour of materials under spatial confinement is sensitively dependent on the nature of the confining boundaries. In two dimensions, confinement within a hard circular boundary inhibits the hexagonal ordering observed in bulk systems at high density. Using colloidal experiments and Monte Carlo simulations, we investigate two model systems of quasi hard discs under circularly symmetric confinement. The first system employs an adaptive circular boundary, defined experimentally using holographic optical tweezers. We show that deformation of this boundary allows, and indeed is required for, hexagonal ordering in the confined system. The second system employs a circularly symmetric optical potential to confine particles without a physical boundary. We show that, in the absence of a curved wall, near perfect hexagonal ordering is possible. We propose that the degree to which hexagonal ordering is suppressed by a curved boundary is determined by the `strictness' of that wall.

cond-mat.soft↗

arXiv2013

Counting metastable states in a kinetically constrained model using a patch repetition analysis

We analyse metastable states in the East model, using a recently-proposed patch-repetition analysis based on time-averaged density profiles. The results reveal a hierarchy of states of varying lifetimes, consistent with previous studies in which the metastable states were identified and used to explain the glassy dynamics of the model. We establish a mapping between these states and configurations of systems of hard rods, which allows us to analyse both typical and atypical metastable states. We discuss connections between the complexity of metastable states and large-deviation functions of dynamical quantities, both in the context of the East model and more generally in glassy systems.

cond-mat.stat-mech↗

arXiv2013

Dynamical correlations in a glass-former with randomly pinned particles

The effects of randomly pinning particles in a model glass-forming fluid are studied, with a focus on the dynamically heterogeneous relaxation in the presence of pinning. We show how four-point dynamical correlations can be analysed in real space, allowing direct extraction of a length scale that characterises dynamical heterogeneity. In the presence of pinning, the relaxation time of the glassy system increases by up to two decades, but there is almost no increase in either the four-point correlation length or the strength of the four-point correlations. We discuss the implications of these results for theories of the glass transition.

cond-mat.stat-mech↗

arXiv2013

Dynamical phase transitions in supercooled liquids: interpreting measurements of dynamical activity

We study dynamical phase transitions in a model supercooled liquid. These transitions occur in ensembles of trajectories that are biased towards low (or high) dynamical activity. We compare two different measures of activity that were introduced in recent papers and we find that they are anti-correlated with each other. To interpret this result, we show that the two measures couple to motion on different length and time scales. We find that inactive states with very slow structural relaxation nevertheless have increased molecular motion on short scales. We discuss these results in terms of the potential energy landscape of the system and in terms of the liquid structure in active/inactive states.

cond-mat.stat-mech↗

arXiv2013

Controlling crystal self-assembly using a real-time feedback scheme

We simulate crystallisation of hard spheres with short-ranged attractive potentials, as a model self-assembling system. We show how measurements of correlation and response functions during assembly can be used to tune the interaction parameters as assembly proceeds, in order to obtain high-quality crystals. The method we use is independent of details of the interaction potential and of the structure of the final crystal - we propose that it could be applied to a wide range of self-assembling systems.

cond-mat.soft↗

arXiv2012

Space-time phase transitions in the East model with a softened kinetic constraint

The East model has a dynamical phase transition between an active (fluid) and inactive (glass) state. We show that this phase transition generalizes to "softened" systems where constraint violations are allowed with small but finite probabilities. Moreover, we show that the first order coexistence line separating the active and inactive phases terminates in a finite-temperature space-time critical point. Implications of these results for equilibrium dynamics are discussed.

cond-mat.stat-mech↗

arXiv2012

Quantifying reversibility in a phase-separating lattice gas: an analogy with self-assembly

We present dynamic measurements of a lattice gas during phase separation, which we use as an analogy for self-assembly of equilibrium ordered structures. We use two approaches to quantify the degree of 'reversibility' of this process: firstly, we count events in which bonds are made and broken; secondly, we use correlation-response measurements and fluctuation-dissipation ratios to probe reversibility during different time intervals. We show how correlation and response functions can be related directly to microscopic (ir)reversibility and we discuss time-dependence and observable- dependence of these measurements, including the role of fast and slow degrees of freedom during assembly.

cond-mat.soft↗

arXiv2011

Preparation and relaxation of very stable glassy states of a simulated liquid

We prepare metastable glassy states in a model glass-former made of Lennard-Jones particles by sampling biased ensembles of trajectories with low dynamical activity. These trajectories form an inactive dynamical phase whose `fast' vibrational degrees of freedom are maintained at thermal equilibrium by contact with a heat bath, while the `slow' structural degrees of freedom are located in deep valleys of the energy landscape. We examine the relaxation to equilibrium and the vibrational properties of these metastable states. The glassy states we prepare by our trajectory sampling method are very stable to thermal fluctuations and also more mechanically rigid than low-temperature equilibrated configurations.

cond-mat.stat-mech↗

arXiv2011

Analyzing mechanisms and microscopic reversibility of self-assembly

We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements of dynamical activity and assembly progress to compare their propensities for kinetic trapping. We use the analytic solution of a simple minimal model to illustrate the key features associated with such trapping, paying particular attention to the number of ways that particles can misbind. We discuss the relevance of our results for the design and control of self-assembly in general.

cond-mat.soft↗

arXiv2011

Random pinning in glassy spin models with plaquette interactions

We use a random pinning procedure to study amorphous order in two glassy spin models. On increasing the concentration of pinned spins at constant temperature, we find a sharp crossover (but no thermodynamic phase transition) from bulk relaxation to localisation in a single state. At low temperatures, both models exhibit scaling behaviour. We discuss the growing length and time scales associated with amorphous order, and the fraction of pinned spins required to localize the system in a single state. These results, obtained for finite dimensional interacting models, provide a theoretical scenario for the effect of random pinning that differs qualitatively from previous approaches based either on mean-field, mode-coupling, or renormalization group reatments.

cond-mat.stat-mech↗

arXiv2011

Mechanisms of kinetic trapping in self-assembly and phase transformation

In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions.

q-bio.BM↗

arXiv2011

Predicting the self-assembly of a model colloidal crystal

We investigate the self-assembly (crystallisation) of particles with hard cores and isotropic, square-well interactions, using a Monte Carlo scheme to simulate overdamped Langevin dynamics. We measure correlation and response functions during the early stages of assembly, and we analyse the results using fluctuation-dissipation theorems, aiming to predict which systems will self-assemble successfully and which will get stuck in disordered states. The early-time correlation and response measurements are made before significant crystallisation has taken place, indicating that dynamical measurements are valuable in measuring a system's propensity for kinetic trapping.

cond-mat.soft↗

arXiv2010

Finite-temperature critical point of a glass transition

We generalize the simplest kinetically constrained model of a glass-forming liquid by softening kinetic constraints, allowing them to be violated with a small finite rate. We demonstrate that this model supports a first-order dynamical (space-time) phase transition, similar to those observed with hard constraints. In addition, we find that the first-order phase boundary in this softened model ends in a finite-temperature dynamical critical point, which we expect to be present in natural systems. We discuss links between this critical point and quantum phase transitions, showing that dynamical phase transitions in $d$ dimensions map to quantum transitions in the same dimension, and hence to classical thermodynamic phase transitions in $d+1$ dimensions. We make these links explicit through exact mappings between master operators, transfer matrices, and Hamiltonians for quantum spin chains.

cond-mat.stat-mech↗

arXiv2009

Duality symmetries and effective dynamics in disordered hopping models

We identify a duality transformation in one-dimensional hopping models that relates propagators in general disordered potentials linked by an up-down inversion of the energy landscape. This significantly generalises previous results for a duality between trap and barrier models. We use the resulting insights into the symmetries of these models to develop a real-space renormalisation scheme that can be implemented computationally and allows rather accurate prediction of propagation in these models. We also discuss the relation of this renormalisation scheme to earlier analytical treatments.

cond-mat.stat-mech↗

arXiv2009

Metastable states and space-time phase transitions in a spin-glass model

We study large deviations of the dynamical activity in the random orthogonal model (ROM). This is a fully connected spin-glass model with one-step replica symmetry breaking behaviour, consistent with the random first-order transition scenario for structural glasses. We show that this model displays dynamical (space-time) phase-transitions between active and inactive phases, as demonstrated by singularities in large deviation functions. We argue that such transitions are generic in systems with long-lived metastable states.

cond-mat.stat-mech↗