Related papers: Collective Variables for the Study of Crystallizat…
The persistent problem posed by the glass transition is to develop a general atomic level description of a solidification process that is not associated with any change in the symmetry of the atomic structure. The answer proposed in this…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Identifying optimal collective variables to model transformations, using atomic-scale simulations, is a long-standing challenge. We propose a new method for the generation, optimization, and comparison of collective variables, which can be…
We extend the phase field crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of…
We describe experimentally observed collective dynamics in colloidal suspensions of model hard-sphere particles using a modified mode coupling theory (MCT). This rescaled MCT is capable to describe quantitatively the wave-vector and…
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…
Graphs are used to model interactions in a variety of contexts, and there is a growing need to quickly assess the structure of such graphs. Some of the most useful graph metrics are based on triangles, such as those measuring social…
Performance-based engineering for natural hazards facilitates the design and appraisal of structures with rigorous evaluation of their uncertain structural behavior under potentially extreme stochastic loads expressed in terms of failure…
Simulation within the grand canonical ensemble is the method of choice for accurate studies of first order vapour-liquid phase transitions in model fluids. Such simulations typically employ sampling that is biased with respect to the…
We make the case for studying the complexity of approximately simulating (sampling) quantum systems for reasons beyond that of quantum computational supremacy, such as diagnosing phase transitions. We consider the sampling complexity as a…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
Molecular simulations produce very high-dimensional data-sets with millions of data points. As analysis methods are often unable to cope with so many dimensions, it is common to use dimensionality reduction and clustering methods to reach a…
Microcanonical Monte Carlo simulations of a polydisperse soft-spheres model for liquids and colloids have been performed for very large polydispersity, in the region where a phase-separation is known to occur when the system (or part of it)…
Crystallisation is an important phenomenon which facilitates the purification as well as structural and bulk phase material characterisation using crystallographic methods. However, different conditions can lead to a vast set of different…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
Identifying local structural motifs and packing patterns of molecular solids is a challenging task for both simulation and experiment. We demonstrate two novel approaches to characterize local environments in different polymorphs of…
The most efficient MC weights for the calculation of physical, canonical expectation values are not necessarily those of the canonical ensemble. The use of suitably generalized ensembles can lead to a much faster convergence of the…
Atomistic simulations of the molecular dynamics/statics kind are regularly used to study small scale plasticity. Contemporary simulations are performed with tens to hundreds of millions of atoms, with snapshots of these configurations…
We investigate the variation of the driving force for crystallization of a supercooled liquid along isomorphs, curves along which structure and dynamics are invariant. The variation is weak, and can be predicted accurately for the…