Energy landscapes-Past, present, and future: A perspective.

Energy landscapes and the closely related cost function landscapes have been recognized in science, mathematics, and various other fields such as economics as being highly useful paradigms and tools for the description and analysis of the properties of many systems, ranging from glasses, proteins, and abstract global optimization problems to business models. A multitude of algorithms for the exploration and exploitation of such landscapes have been developed over the past five decades in the various fields of applications, where many re-inventions but also much cross-fertilization have occurred. Twenty-five years ago, trying to increase the fruitful interactions between workers in different fields led to the creation of workshops and small conferences dedicated to the study of energy landscapes in general instead of only focusing on specific applications. In this perspective, I will present some history of the development of energy landscape studies and try to provide an outlook on in what directions the field might evolve in the future and what larger challenges are going to lie ahead, both from a conceptual and a practical point of view, with the main focus on applications of energy landscapes in chemistry and physics.

Dependence of lactose adsorption on the exposed crystal facets of metals: a comparative study of gold, silver and copper.

In this theoretical work, we investigated the adsorption of a lactose molecule on metal-based surfaces, with a focus on the influence of the nature of the metal and of the type of exposed crystal facet on the adsorbed structures and energetics. More precisely, we considered three flat crystallographic facets of three face-centered cubic metals (gold, silver, and copper). For the global exploration of the energy landscape, we employed a multi-stage procedure where high-throughput searches, using a stochastic method that performs global optimization by iterating local searches, are followed by a refinement of the most probable adsorption conformations of the molecule at the ab initio level. We predicted the optimal conformation of lactose on each of the nine metal-surface combinations, classified the many low-energy minima into possible adsorption modes, and analyzed the structural, electronic and energetic aspects of the lactose molecule on the surface, as well as their dependence on the type of metal and exposed crystal facet. We observed structural similarities between the various minimum-energy conformations of lactose in vacuum and on the surface, a rough correlation between adsorption and interaction energies of the molecule, and a small charge transfer between molecule and surface whose direction is metal-dependent. During adsorption, an electronic reorganization occurs at the metal-molecule interface only, without affecting the vacuum-pointing atoms of the lactose molecule. For all types of surfaces, lactose exhibits the weakest adsorption on silver substrates, while for each coinage metal the adsorption is strongest on the (110) crystal facet. This study demonstrates that the control of exposed facets can allow to modulate the interaction between metals and small saccharides.

Low-Energy Transformation Pathways between Naphthalene Isomers.

The transformation pathways between low-energy naphthalene isomers are studied by investigating the topology of the energy landscape of this astrophysically relevant molecule. The threshold algorithm is used to identify the minima basins of the isomers on the potential energy surface of the system and to evaluate the probability flows between them. The transition pathways between the different basins and the associated probabilities were investigated for several lid energies up to 11 eV, this value being close to the highest photon energy in the interstellar medium (13.6 eV). More than a hundred isomers were identified and a set of 23 minima was selected among them, on the basis of their energy and probability of occurrence. The return probabilities of these 23 minima and the transition probabilities between them were computed for several lid energies up to 11 eV. The first connection appeared at 3.5 eV while all minima were found to be connected at 9.5 eV. The local density of state was also sampled inside their respective basins. This work gives insight into both energy and entropic barriers separating the different basins, which also provides information about the transition regions of the energy landscape.

Structure prediction in low dimensions: concepts, issues and examples.

Structure prediction of stable and metastable polymorphs of chemical systems in low dimensions has become an important field, since materials that are patterned on the nano-scale are of increasing importance in modern technological applications. While many techniques for the prediction of crystalline structures in three dimensions or of small clusters of atoms have been developed over the past three decades, dealing with low-dimensional systems-ideal one-dimensional and two-dimensional systems, quasi-one-dimensional and quasi-two-dimensional systems, as well as low-dimensional composite systems-poses its own challenges that need to be addressed when developing a systematic methodology for the determination of low-dimensional polymorphs that are suitable for practical applications. Quite generally, the search algorithms that had been developed for three-dimensional systems need to be adjusted when being applied to low-dimensional systems with their own specific constraints; in particular, the embedding of the (quasi-)one-dimensional/two-dimensional system in three dimensions and the influence of stabilizing substrates need to be taken into account, both on a technical and a conceptual level. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Synthesis, Characterization, and Electronic Properties of ZnO/ZnS Core/Shell Nanostructures Investigated Using a Multidisciplinary Approach.

ZnO/ZnS core/shell nanostructures, which are studied for diverse possible applications, ranging from semiconductors, photovoltaics, and light-emitting diodes (LED), to solar cells, infrared detectors, and thermoelectrics, were synthesized and characterized by XRD, HR-(S)TEM, and analytical TEM (EDX and EELS). Moreover, band-gap measurements of the ZnO/ZnS core/shell nanostructures have been performed using UV/Vis DRS. The experimental results were combined with theoretical modeling of ZnO/ZnS (hetero)structures and band structure calculations for ZnO/ZnS systems, yielding more insights into the properties of the nanoparticles. The ab initio calculations were performed using hybrid PBE0 and HSE06 functionals. The synthesized and characterized ZnO/ZnS core/shell materials show a unique three-phase composition, where the ZnO phase is dominant in the core region and, interestingly, the auxiliary ZnS compound occurs in two phases as wurtzite and sphalerite in the shell region. Moreover, theoretical ab initio calculations show advanced semiconducting properties and possible band-gap tuning in such ZnO/ZnS structures.

Suitability of semen stress tests for predicting fertilizing capacity of boar ejaculates.

Besides classical semen parameters, semen stress tests (SSTs) are helpful tools to assess the fertilizing capacity of sperm. However, valid studies on SSTs in relation to fertility are rare because several corrections of common fertility parameters for female and male effects are required. Therefore, over a one-year period, we analyzed semen parameters of 260 ejaculates obtained from 130 Pietrain boars aged between 8 and 9 months in one AI center as well as 1521 corresponding insemination records for these ejaculates. Two consecutive ejaculates (4th and 5th) were collected from each boar and extended in DiluPorc™ BTS. In addition to routine semen evaluation, sperm motility was assessed after heat-resistance test (300 min incubation at 38 °C after seven days storage at 16 °C, HRT) and cold-resistance test (10 min incubation at 38 °C after three days storage at 6 °C, CRT). Generalized linear models (GLMs) were applied to analyze effects for the following predictors of farrowing rate (FR), number of total born (NTB) and live born (NLB) piglets: farm (P = 0.013 [FR], P = 0.001 [NTB], P = 0.023 [NLB]), parity (P = 0.679, P = 0.01, P < 0.001), weekday (P = 0.012, P = 0.08, P = 0.009) and year × season (P < 0.001, P = 0.688, P = 0.574). On boar level, GLMs revealed significant effects on FR, NTB and NLB for the predictors sow (all P < 0.001), total sperm number per dose (P = 0.007, P = 0.002, P < 0.001), total sperm motility (P = 0.002, P = 0.2, P = 0.003) and mitochondrial activity (P = 0.004, P < 0.001, P = 0.002). Moreover, FR and NTB were influenced by membrane integrity (both P < 0.001), FR and NLB by cold-resistance (P < 0.001, P = 0.043), and NTB and NLB by sperm morphology (P = 0.001, P < 0.001) and boar (both P < 0.001). NLB was additionally influenced by heat-resistance (P = 0.004) and farm (P = 0.018) and solely NTB was influenced by sperm output (P = 0.03). Boar and semen related factors explained 9% of the total variation in NTB and 7% of the total variation in NLB. Only 14.2% (n = 37) of the samples were both cold- and heat-resistant (≥65% of motile sperm). Cold- and heat-resistance were dependent factors (Chi-square, P = 0.001) and sperm motility after CRT and HRT showed a moderate positive correlation (rs = 0.40, P < 0.001, Spearman's rho). Finally, ROC curves demonstrated that neither SST can be used as a sole test for predicting the fertilizing capacity of boar ejaculates.

Short-Range Structural Correlations in Amorphous 2D Polymers.

Many 2D covalent polymers synthesized as single layers on surfaces show inherent disorder, expressed for example in their ring-size distribution. Systems which are expected to form the thermodynamically favored hexagonal lattice usually deviate from crystallinity and include high numbers of pentagons, heptagons, and rings of other sizes. The amorphous structure of two different covalent polymers in real space using scanning tunneling microscopy is investigated. Molecular dynamics simulations are employed to extract additional information. We show that short-range correlations exist in the structure of one polymer, i. e. that polygons are not tessellating the surface randomly but that ring neighborhoods have preferential compositions. The correlation is dictated by the energy of formation of the ring neighborhoods.

Carbohydrate Self-Assembly at Surfaces: STM Imaging of Sucrose Conformation and Ordering on Cu(100).

Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self-assembly of the disaccharide sucrose on a Cu(100) surface with subunit-level imaging. By employing a multistage modeling approach in combination with the experimental data, we can rationalize the conformation on the surface as well as the interactions between the sucrose molecules, thereby yielding models of the observed self-assembled patterns on the surface.

Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu(100).

Saccharides, also commonly known as carbohydrates, are ubiquitous biomolecules, but little is known about their interaction with surfaces. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy now provides access to the molecular details of the surface assembly of this important class of bio-molecules. Among carbohydrates, the disaccharide trehalose is outstanding as it enables strong anhydrobiotic effects in biosystems. This ability is closely related to the observed polymorphism. In this work, we explore the self-assembly of trehalose on the Cu(100) surface. Molecular imaging reveals the details of the assembly properties in this reduced symmetry environment. Already at room temperature, we observe a variety of self-assembled motifs, in contrast to other disaccharides like e.g. sucrose. Using a multistage modeling approach, we rationalize the conformation of trehalose on the copper surface as well as the intermolecular interactions and the self-assembly behavior.

The threshold algorithm: Description of the methodology and new developments.

Understanding the dynamics of complex systems requires the investigation of their energy landscape. In particular, the flow of probability on such landscapes is a central feature in visualizing the time evolution of complex systems. To obtain such flows, and the concomitant stable states of the systems and the generalized barriers among them, the threshold algorithm has been developed. Here, we describe the methodology of this approach starting from the fundamental concepts in complex energy landscapes and present recent new developments, the threshold-minimization algorithm and the molecular dynamics threshold algorithm. For applications of these new algorithms, we draw on landscape studies of three disaccharide molecules: lactose, maltose, and sucrose.

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-ß-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.

Energy landscape exploration of sub-nanometre copper-silver clusters.

The energy landscapes of sub-nanometre bimetallic coinage metal clusters are explored with the Threshold Algorithm coupled with the Birmingham Cluster Genetic Algorithm. Global and energetically low-lying minima along with their permutational isomers are located for the Cu(4)Ag(4) cluster with the Gupta potential and density functional theory (DFT). Statistical tools are employed to map the connectivity of the energy landscape and the growth of structural basins, while the thermodynamics of interconversion are probed, based on probability flows between minima. Asymmetric statistical weights are found for pathways across dividing states between stable geometries, while basin volumes are observed to grow independently of the depth of the minimum. The DFT landscape is found to exhibit significantly more frustration than that of the Gupta potential, including several open, pseudo-planar geometries which are energetically competitive with the global minimum. The differences in local minima and their transition barriers between the two levels of theory indicate the importance of explicit electronic structure for even simple, closed shell clusters.

Seminal fluid promotes in vitro sperm-oviduct binding in the domestic cat (Felis catus).

From many endangered or threatened species which are expected to profit from assisted reproduction techniques, mainly epididymal sperm of dead or freshly castrated males are available. These sperm had contact to epididymal secretion products but not to seminal fluid components. Notably, products of accessory sex glands have been shown in domestic animals to condition sperm for fertilization, in particular by mediating sperm-oviduct interaction. We report for the first time that motile epididymal sperm from domestic cats are able to bind to fresh oviduct epithelial cell explants from preovulatory females (median [min, max] of 10 [8, 16] and 10 [8, 17] sperm per 0.01 mm(2) explant surface from both isthmic and ampullar regions, respectively). More sperm attach to the explants when epididymal sperm were preincubated for 30 minutes with seminal fluid separated from electroejaculates of mature tomcats (median [min, max] of 17 [13, 25] and 16 [12, 21] sperm per 0.01 mm(2) explant surface from isthmus and ampulla, respectively). The proportion of bound sperm increased from a median of 54% to 62% by seminal fluid treatment. Sperm-oviduct binding could be facilitated by the decelerated sperm motion which was observed in seminal fluid-treated samples or supported by seminal fluid proteins newly attached to the sperm surface. Seminal fluid had no effect on the proportion of sperm with active mitochondria. Extent and pattern of sperm interaction in vitro were independent of explant origin from isthmus or ampulla. Sperm were attached to both cilia and microvilli of the main epithelial cell types present in all explants. In contrast to published sperm-binding studies with porcine and bovine oviduct explants where predominantly the anterior head region of sperm was attached to ciliated cells, the tails of some cat sperm were firmly stuck to the oviduct cell surfaces, whereas the heads were wobbling. Whether this response is a preliminary step toward phagocytosis or a precondition to capacitation and fertilization remains to be determined. In conclusion, treatment of epididymal sperm with seminal fluid or particular protein components should be considered in future investigations for its potential to improve the outcome of artificial insemination in felids.

Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.

We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.

How can Databases assist with the Prediction of Chemical Compounds?

An overview is given on the ways databases can be employed to aid in the prediction of chemical compounds, in particular inorganic crystalline compounds. Methods currently employed and possible future approaches are discussed.

CCL: an algorithm for the efficient comparison of clusters.

The systematic comparison of the atomic structure of solids and clusters has become an important task in crystallography, chemistry, physics and materials science, in particular in the context of structure prediction and structure determination of nanomaterials. In this work, an efficient and robust algorithm for the comparison of cluster structures is presented, which is based on the mapping of the point patterns of the two clusters onto each other. This algorithm has been implemented as the module CCL in the structure visualization and analysis program KPLOT.