Related papers: Evolutionary approach for finding the atomic struc…
Accurate structural analysis is essential to gain physical knowledge and understanding of atomic-scale processes in materials from atomistic simulations. However, traditional analysis methods often reach their limits when applied to…
Recently, Smajic et al. published an article on numerical structural opti- mizations of two-dimensional photonic crystals using two different classes of optimization algorithms i.e, deterministic for local searches and stochastic for…
We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis…
Existing Genetic Algorithms for crystal structure and polymorph prediction can suffer from stagnation during evolution, with a consequent loss of efficiency and accuracy. An improved Genetic Algorithm (GA) is introduced herein which…
We investigate the nonlinear evolution of the Bales-Zangwill instability, responsible for the meandering of atomic steps on a growing vicinal surface. We develop an asymptotic method to derive, in the continuous limit, an evolution equation…
We present a multirate method that is particularly suited for integrating the systems of Ordinary Differential Equations (ODEs) that arise in step models of surface evolution. The surface of a crystal lattice, that is slightly miscut from a…
By taking account of the alternation of structural parameters, we study bunching of impermeable steps induced by drift of adatoms on a vicinal face of Si(001). With the alternation of diffusion coefficient, the step bunching occurs…
In this paper, we introduce a natural dynamical analogue of crystalline order, which we call choreographic order. In an ordinary (static) crystal, a high degree of symmetry may be achieved through a careful arrangement of the fundamental…
Simulations of SiC crystal growth using molecular dynamics (MD) have become popular in recent years. They, however, simulate very fast deposition rates, to reduce computational costs. Therefore, they are more akin to surface sputtering,…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
The shape of nanocrystals is crucial in determining their surface area, reactivity, optical properties, mechanical strength, and self-assembly behavior. Traditionally, shape control has been achieved through empirical methods, highlighting…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe…
The BCF theory of crystal growth has been successful in describing a wide range of phenomena in surface physics. Typical crystal surfaces are slightly misoriented with respect to a facet plane; thus, the BCF theory views such systems as…
In this paper, we study a numerical method for the solution of partial differential equations on evolving surfaces. The numerical method is built on the stabilized trace finite element method (TraceFEM) for the spatial discretization and…
Step meandering due to a deterministic morphological instability on vicinal surfaces during growth is studied. We investigate nonlinear dynamics of a step model with asymmetric step kinetics, terrace and line diffusion, by means of a…
We present a method to determine the equilibrium geometry of large atomistic systems with linear scaling. It is based on a separate treatment of long and short wavelength components of the forces. While the rapidly varying part is handled…
The growth of a crystal is usually determined by its surface. Many factors influence the growth dynamics. Energy barriers associated with the presence of steps most often decide about the emerging pattern. The height and type of…
Detection of crystal structures from particle positions of crystalline assemblies formed in computer simulations is an unsolved problem. The standard protocol, formulated in the reciprocal space, for structure determination from…
This paper investigates faceting mechanisms induced by electromigration in the regime where atomic steps are transparent. For this purpose we study several vicinal orientations by means of in-situ (optical diffraction, electronic…