Related papers: Collective Variables for the Study of Crystallizat…

We demonstrate a simple method by which time-dependent interactions can be exploited to improve self-assembly in colloidal systems. We apply this method to two systems: a model colloid with short-ranged attractive potentials that undergoes…

The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…

I present a strategy for unsupervised manifold learning on local atomic environments in molecular simulations based on simple rotation- and permutation-invariant three-body features. These features are highly descriptive, generalize to…

A routine crystallography technique, crystal structure analysis, is rarely performed in computational condensed matter research. The lack of methods to identify and characterize crystal structures reliably in particle simulation data…

The concept of randomized measurements on individual particles has proven to be useful for analyzing quantum systems and is central for methods like shadow tomography of quantum states. We introduce $\textit{collective}$ randomized…

Complex crystal structures are composed of multiple local environments, and how this type of order emerges spontaneously during crystal growth has yet to be fully understood. We study crystal growth across various structures and along…

Crystallization of the amorphous phases into metastable crystals plays a fundamental role in the formation of new matter, from geological to biological processes in nature to synthesis and development of new materials in the laboratory.…

Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…

Micrometre sized colloidal particles can be viewed as large atoms with tailorable size, shape and interactions. These building blocks can assemble into extremely rich structures and phases, in which the thermal motions of particles can be…

In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…

The simplest prescription for building a patterned structure from its constituents is to add particles, one at a time, to an appropriate template. However, self-organizing molecular and colloidal systems in nature can evolve in much more…

We describe a Monte Carlo procedure which allows sampling of the disjoint configuration spaces associated with crystalline and fluid phases, within a single simulation. The method utilises biased sampling techniques to enhance the…

Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…

Discovering the underlying dynamics of complex systems from data is an important practical topic. Constrained optimization algorithms are widely utilized and lead to many successes. Yet, such purely data-driven methods may bring about…

Standard approaches to tackle high-dimensional supervised classification problem often include variable selection and dimension reduction procedures. The novel methodology proposed in this paper combines clustering of variables and feature…

Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…

This paper deals with the problem of simulating dense dispersed systems composed by large numbers of particles undergoing ballistic aggregation. The most classical approaches for dealing with such problems are represented by the so-called…

Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…

Atomistic simulations provide valuable insights into the physical processes governing material behavior. However, their applicability is fundamentally constrained by the limited time scales accessible to brute-force simulations. This…

Enhanced sampling methods are indispensable in computational physics and chemistry, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of…