Related papers: An introduction to stochastic self-assembly: theor…
We discuss different approaches for studying the influence of disorder in the three-dimensional Ising model. From the theoretical point of view, renormalisation group calculations provide quite accurate results. Experiments carried out on…
Triboelectric charging of insulating particles through contact is critical in diverse physical and engineering processes, from dust storms and volcanic eruptions to industrial powder handling. However, many experiments over the years have…
Existing variance reduction techniques used in stochastic simulations for rare event analysis still require a substantial number of model evaluations to estimate small failure probabilities. In the context of complex, nonlinear finite…
We describe a novel approach to statistical learning from particles tracked while moving in a random environment. The problem consists in inferring properties of the environment from recorded snapshots. We consider here the case of a fluid…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
Patterns generated by a colloidal suspension of nanospheres drying on a frictional substrate are studied by experiments and computer simulations. The obtained two-dimensional self-assembled structures are commonly used for nanosphere…
We propose a one-dimensional nonlocal stochastic model of adsorption and desorption depending on one parameter, the adsorption rate. At a special value of this parameter, the model has some interesting features. For example, the spectrum is…
We present simulations of stochastic fluid dynamics in the vicinity of a critical endpoint belonging to the universality class of the Ising model. This study is motivated by the challenge of modeling the dynamics of critical fluctuations…
Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from…
An optimal control strategy is developed to construct nanostructures of desired geometry along line segments by means of directed self-assembly of charged particles. Such a control strategy determines the electric potentials of a set of…
We apply a recently proposed novel thermostating mechanism to an interacting many-particle system where the bulk particles are moving according to Hamiltonian dynamics. At the boundaries the system is thermalized by deterministic and…
Recent studies have shown that synaptic unreliability is a robust and sufficient mechanism for inducing the stochasticity observed in cortex. Here, we introduce Synaptic Sampling Machines, a class of neural network models that uses synaptic…
Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with…
This discussion serves as an introduction to the use of Monte Carlo simulations as a useful way to evaluate the observables of a ferromagnet. Key background is given about the relevance and effectiveness of this stochastic approach and in…
The entropic sampling dynamics based on the reversible information transfer to and from the environment is applied to the globally coupled Ising model in the presence of an oscillating magnetic field. When the driving frequency is low…
The 1D Ising model is the simplest Hamiltonian-based model in statistical mechanics. The sim- plest interacting particle process is the Symmetric Exclusion Process (SEP), a 1D lattice gas of particles that hop symmetrically and cannot…
Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks, to hierarchical sequences of intermediates, all the way to the fully…
The quantum theory of coherent Ising machines, based on degenerate optical parametric oscillators and measurement-feedback circuits, is developed using the positive $P({\alpha},{\beta})$ representation of the density operator and the master…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly…