An efficient genetic algorithm for structure prediction at the nanoscale

We have developed and implemented a new global optimization technique based on a Lamarckian genetic algorithm with the focus on structure diversity. The key process in the efficient search on a given complex energy landscape proves to be the removal of duplicates that is achieved using a topological analysis of candidate structures. The careful geometrical prescreening of newly formed structures and the introduction of new mutation move classes improve the rate of success further. The power of the developed technique, implemented in the Knowledge Led Master Code, or KLMC, is demonstrated by its ability to locate and explore a challenging double funnel landscape of a Lennard-Jones 38 atom system (LJ₃₈). We apply the redeveloped KLMC to investigate three chemically different systems: ionic semiconductor (ZnO)_1-32, metallic Ni₁₃ and covalently bonded C₆₀. All four systems have been systematically explored on the energy landscape defined using interatomic potentials. The new developments allowed us to successfully locate the double funnels of LJ₃₈, find new local and global minima for ZnO clusters, extensively explore the Ni₁₃ and C₆₀ (the buckminsterfullerene, or buckyball) potential energy surfaces.

A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide

We present a scheme, called the threshold-minimization method, for globally exploring the energy landscapes of small systems of biomolecular interest where typical exploration moves always require a certain degree of subsequent structural relaxation in order to be efficient, e.g., systems containing small or large circular carbon chains such as cyclic peptides or carbohydrates. We show that using this threshold-minimization method we can not only reproduce the global minimum and relevant local minima but also overcome energetic barriers associated with different types of isomerism for the example of a cyclic peptide, cyclo-(Gly)4. We then apply the new method to the disaccharide α-d-glucopyranose-1-2-β-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.

Prediction and clarification of structures of (bio)molecules on surfaces

The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.

Pushing the limits in accurate vibrational structure calculations: anharmonic frequencies of lithium fluoride clusters (LiF)n, n = 2-10

The vibrational spectra of a series of small lithium fluoride clusters, i.e. (LiF)n, n = 2-10, were studied by vibrational configuration interaction (VCI) calculations relying on potential energy surfaces including three-mode coupling terms and being obtained from explicitly correlated local coupled cluster calculations. Due to the account for anharmonicity effects, the simulated spectra allow for a direct comparison with experimental data and may thus help to identify clusters in the experiments. Even structurally closely related clusters can clearly be distinguished by infrared spectroscopy. The largest system in this study required more than 1000 basis functions in the electronic structure calculations and more than 10(7) configurations in the vibrational structure calculations and became computationally feasible only due to a combination of different approximations and highly parallelized algorithms.

Atomistic modeling of the low-temperature atom-beam deposition of magnesium fluoride

We model the deposition and growth of MgF(2) on a sapphire substrate as it occurs in a low-temperature atom-beam-deposition experiment. In the experiment, an (X-ray) amorphous film of MgF(2) is obtained at low temperatures of 170-180 K, and upon heating, this transforms to the expected rutile phase via the CaCl(2)-type structure. We confirm this from our simulations and propose a mechanism for this transformation. The growth process is analyzed as a function of the synthesis parameters, which include the substrate temperature, deposition rate of clusters, and types of clusters deposited. Upon annealing an initially amorphous deposit, we observe the formation of two competing nanocrystalline modifications during this process, which exhibit the CaCl(2) and CdI(2) structure types, respectively. We argue that this joint growth of the two nanocrystalline polymorphs stabilizes the kinetically unstable CaCl(2)-type structure on the macroscopic level long enough to be observed in the experiment.

Evolution of order in amorphous-to-crystalline phase transformation of MgF2

Structural disorder and distortion play a significant role in phase transformations. Experimentally, electron diffraction in the transmission electron microscope offers the ability to characterize disorderviathe pair distribution function (PDF) at high spatial resolution. In this work, energy-filteredin situelectron diffraction is applied to measure PDFs of different phases of MgF2from the amorphous deposit through metastable modifications to the thermodynamically stable phase. Despite the restriction of thick specimens resulting in multiple electron scattering, elaborate data analysis enabled experimental and molecular dynamics simulation data to be matched, thus allowing analysis of the evolution of short-range ordering. In particular, it is possible to explain the theoretically not predicted existence of a metastable phase by the presence of atomic disorder and distortion. The short-range ordering in the amorphous and crystalline phases is elucidated as three steps: (i) an initial amorphous phase exhibiting CaCl2-type short-range order which acts as a crystallization nucleus to guide the phase transformation to the metastable CaCl2-type phase and thus suppresses the direct appearance of the rutile-type phase; (ii) a metastable CaCl2-type phase containing short-range structural features of the stable rutile type; and (iii) the formation of a large volume fraction of disordered intergranular regions which stabilize the CaCl2-type phase. The structure evolution is described within the energy landscape concept.