Related papers: A powerful computational crystallography method to…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…
Topological properties of crystalline ice structures are studied by considering ring statistics, coordination sequences, and topological density of different ice phases. The coordination sequences (number of sites at topological distance k…
The ability to reliably predict the structures and stabilities of a molecular crystal and its polymorphs without any prior experimental information would be an invaluable tool for a number of fields, with specific and immediate applications…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
Water exhibits rich polymorphism, where more than 20 crystalline phases have been experimentally reported. Five of them are metastable and form at low temperatures by either heating amorphous ice or degassing clathrate hydrates. However,…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
Calculating sublimation enthalpies of molecular crystal polymorphs is relevant to a wide range of technological applications. However, predicting these quantities at first-principles accuracy -- even with the aid of machine learning…
Predictive modeling of the phonon/thermal transport properties of materials is vital to rational design for a diverse spectrum of engineering applications. Classical Molecular Dynamics (MD) simulations serve as a tool to simulate the time…
Using molecular dynamics simulations, we investigate the crystallization pathways of two exemplary systems that form the same complex crystal structure but differ fundamentally in the nature of their particle interactions. One system is…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective…
Polynomial machine learning potentials (MLPs) based on polynomial rotational invariants have been systematically developed for various systems and applied to efficiently predict crystal structures. In this study, we propose a robust…
This monograph reviews our current understanding of the physical dynamics of ice crystal growth, focusing on the spontaneous formation of complex structures from water vapor (called snow crystals) as a function of temperature,…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
Unsupervised machine learning methods are used to identify structural changes using the melting point transition in classical molecular dynamics simulations as an example application of the approach. Dimensionality reduction and clustering…
Solubility and interfacial energy are two fundamental parameters underlying the competitive nucleation of polymorphs. However, solubility measurement of metastable phases comes with a risk of solventmediated transformations which can render…
The Dynamic Monte Carlo (DMC) method is an established molecular simulation technique for the analysis of the dynamics in colloidal suspensions. An excellent alternative to Brownian Dynamics or Molecular Dynamics simulation, DMC is…
Polymorphs in molecular crystals are often very close in energy, yet they may possess markedly different physical and chemical properties. The understanding and prediction of polymorphism is of paramount importance for a variety of…
We have carried out molecular dynamics simulations of the crystallization of hard spheres modelling colloidal systems that are studied in conventional and space-based experiments. We use microscopic probes to investigate the effects of…