A Genetic Algorithm For Convex Hull Optimisation

Computationally efficient and automated generation of convex hulls is desirable for high throughput materials discovery of thermodynamically stable multi-species crystal structures. A convex hull genetic algorithm is proposed that uses methodology adapted from multi-objective optimisation techniques to optimise the convex hull itself as an object, enabling efficient discovery of convex hulls for N >= 2 species. This method, when tested on a LiSi system utilising pre-trained machine learned potentials, was found to be able to efficiently discover reported structures as well as new potential LiSi candidate structures

Systematic Comparison of Genetic Algorithm and Basin Hopping Approaches to the Global Optimization of Si(111) Surface Reconstructions

We present a systematic study of two widely used material structure prediction methods, the Genetic Algorithm and Basin Hopping approaches to global optimization, in a search for the 3 × 3, 5 × 5, and 7 × 7 reconstructions of the Si(111) surface. The Si(111) 7 × 7 reconstruction is the largest and most complex surface reconstruction known, and finding it is a very exacting test for global optimization methods. In this paper, we introduce a modification to previous Genetic Algorithm work on structure search for periodic systems, to allow the efficient search for surface reconstructions, and present a rigorous study of the effect of the different parameters of the algorithm. We also perform a detailed comparison with the recently improved Basin Hopping algorithm using Delocalized Internal Coordinates. Both algorithms succeeded in either resolving the 3 × 3, 5 × 5, and 7 × 7 DAS surface reconstructions or getting “sufficiently close”, i.e., identifying structures that only differ for the positions of a few atoms as well as thermally accessible structures within kBT/unit area of the global minimum, with T = 300 K. Overall, the Genetic Algorithm is more robust with respect to parameter choice and in success rate, while the Basin Hopping method occasionally exhibits some advantages in speed of convergence. In line with previous studies, the results confirm that robustness, success, and speed of convergence of either approach are strongly influenced by how much the trial moves tend to preserve favorable bonding patterns once these appear

The emergence of sequence-dependent structural motifs in stretched, torsionally 2 constrained DNA

The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20–30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells

Magnetic Transition State Searching : Beyond the Static Ion Approximation

The effect of structural relaxations on the magnetocrystalline anisotropy energy (MAE) was investigated by using density functional theory (DFT). The theory of the impact of magnetostructural coupling on the MAE was discussed, including the effects on attempt frequency. The MAE for ferromagnetic FePt (3.45 meV/formula unit) and antiferromagnetic PtMn (0.41 meV/formula unit) were calculated within the local density approximation (LDA). The effects of the structural relaxation were calculated and found to give

Atomistic dynamics of sulfur-deficient high-symmetry grain boundaries in molybdenum disulfide

As a common type of structural defect, grain boundaries (GBs) play an important role in tailoring the physical and chemical properties of bulk crystals and their two-dimensional (2D) counterparts such as graphene and molybdenum disulfide (MoS2). In this study, we explore the atomic structures and dynamics of three kinds of high-symmetry GBs (α, β and γ) in monolayer MoS2. Atomic-resolution transmission electron microscopy (TEM) is used to characterize their formation and evolutionary dynamics, and atomistic simulation based analysis explains the size distribution of α-type GBs observed under TEM and the inter-GB interaction, revealing the stabilization mechanism of GBs by pre-existing sulfur vacancies. The results elucidate the correlation between the observed GB dynamics and the migration of sulfur atoms across GBs via a vacancy-mediated mechanism, offering a new perspective for GB engineering in monolayer MoS2, which may be generalized to other transition metal dichalcogenides

Cr2AlN and the search for the highest temperature superconductor in the M2AX family

We have developed a high-throughput computational method to predict the superconducting transition temperature in stable hexagonal M 2AX phases, and applied it to all the known possible choices for M (M: Sc, Ti, V, Cr, Mn, Fe, Y, Zr, Nb, Mo, Lu, Hf and Ta). We combine this with the best candidates for A (A: Al, Cu, Ge and Sn ) and X (X: C and N) from our previous work, and predict T c for 60 M2AX-phase materials, 53 of which have never been studied before. From all of these, we identify Cr2AlN as the best candidate for the highest T c , and confirm its high T c with more detailed density functional theory electron-phonon coupling calculations. Our detailed calculations predict Tc = 14.8 K for Cr2AlN, which is significantly higher than any Tc value known or predicted for any material in the M2AX family to date

Off-the-shelf DFT-DISPersion methods : Are they now “on-trend” for organic molecular crystals?

Organic molecular crystals contain long-range dispersion interactions that can be challenging for solid-state methods such as density functional theory (DFT) to capture, and in some industrial sectors are overlooked in favor of classical methods to calculate atomistic properties. Hence, this publication addresses the critical question of whether dispersion corrected DFT calculations for organic crystals can reproduce the structural and energetic trends seen from experiment, i.e., whether the calculations can now be said to be truly “on-trend.” In this work, we assess the performance of three of the latest dispersion-corrected DFT methods, in calculating the long-range, dispersion energy: the pairwise methods of D3(0) and D3(BJ) and the many-body dispersion method, MBD@rsSCS. We calculate the energetics and optimized structures of two homologous series of organic molecular crystals, namely, carboxylic acids and amino acids. We also use a classical force field method (using COMPASS II) and compare all results to experimental data where possible. The mean absolute error in lattice energies is 9.59 and 343.85 kJ/mol (COMPASS II), 10.17 and 16.23 kJ/mol (MBD@rsSCS), 10.57 and 18.76 kJ/mol [D3(0)], and 8.52 and 14.66 kJ/mol [D3(BJ)] for the carboxylic acids and amino acids, respectively. MBD@rsSCS produces structural and energetic trends that most closely match experimental trends, performing the most consistently across the two series and competing favorably with COMPASS II