03 Fakultät Chemie
Permanent URI for this collectionhttps://elib.uni-stuttgart.de/handle/11682/4
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Item Open Access Efficient approach to compute melting properties fully from ab initio with application to Cu(2017) Zhu, Li-Fang; Grabowski, Blazej; Neugebauer, JörgApplying thermodynamic integration within an ab initio-based free-energy approach is a state-of-the-art method to calculate melting points of materials. However, the high computational cost and the reliance on a good reference system for calculating the liquid free energy have so far hindered a general application. To overcome these challenges, we propose the two-optimized references thermodynamic integration using Langevin dynamics (TOR-TILD) method in this work by extending the two-stage upsampled thermodynamic integration using Langevin dynamics (TU-TILD) method, which has been originally developed to obtain anharmonic free energies of solids, to the calculation of liquid free energies. The core idea of TOR-TILD is to fit two empirical potentials to the energies from density functional theory based molecular dynamics runs for the solid and the liquid phase and to use these potentials as reference systems for thermodynamic integration. Because the empirical potentials closely reproduce the ab initio system in the relevant part of the phase space the convergence of the thermodynamic integration is very rapid. Therefore, the proposed approach improves significantly the computational efficiency while preserving the required accuracy. As a test case, we apply TOR-TILD to fcc Cu computing not only the melting point but various other melting properties, such as the entropy and enthalpy of fusion and the volume change upon melting. The generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the local-density approximation (LDA) are used. Using both functionals gives a reliable ab initio confidence interval for the melting point, the enthalpy of fusion, and entropy of fusion.Item Open Access Functional role of lanthanides in enzymatic activity and transcriptional regulation of Pyrroloquinoline quinone-dependent alcohol dehydrogenases in Pseudomonas putida KT2440(2017) Wehrmann, Matthias; Billard, Patrick; Martin-Meriadec, Audrey; Zegeye, Asfaw; Klebensberger, JanoschThe oxidation of alcohols and aldehydes is crucial for detoxification and efficient catabolism of various volatile organic compounds (VOCs). Thus, many Gram-negative bacteria have evolved periplasmic oxidation systems based on pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) that are often functionally redundant. Here we report the first description and characterization of a lanthanide-dependent PQQ-ADH (PedH) in a nonmethylotrophic bacterium based on the use of purified enzymes from the soil-dwelling model organism Pseudomonas putida KT2440. PedH (PP_2679) exhibits enzyme activity on a range of substrates similar to that of its Ca2+-dependent counterpart PedE (PP_2674), including linear and aromatic primary and secondary alcohols, as well as aldehydes, but only in the presence of lanthanide ions, including La3+, Ce3+, Pr3+, Sm3+, or Nd3+. Reporter assays revealed that PedH not only has a catalytic function but is also involved in the transcriptional regulation of pedE and pedH, most likely acting as a sensory module. Notably, the underlying regulatory network is responsive to as little as 1 to 10 nM lanthanum, a concentration assumed to be of ecological relevance. The present study further demonstrates that the PQQ-dependent oxidation system is crucial for efficient growth with a variety of volatile alcohols. From these results, we conclude that functional redundancy and inverse regulation of PedE and PedH represent an adaptive strategy of P. putida KT2440 to optimize growth with volatile alcohols in response to the availability of different lanthanides.Item Open Access Magnetic and structural properties of barium hexaferrite BaFe12O19 from various growth techniques(2017) Vinnik, Denis A.; Tarasova, Aleksandra Yu.; Zherebtsov, Dmitry A.; Gudkova, Svetlana A.; Galimov, Damir M.; Zhivulin, Vladimir E.; Trofimov, Evgeny A.; Nemrava, Sandra; Perov, Nikolai S.; Isaenko, Ludmila I.; Niewa, RainerBarium hexaferrite powder samples with grains in the m-range were obtained from solid-state sintering, and crystals with sizes up to 5 mm grown from PbO, Na2CO3, and BaB2O4 fluxes, respectively. Carbonate and borate fluxes provide the largest and structurally best crystals at significantly lower growth temperatures of 1533 K compared to flux-free synthesis (1623 K). The maximum synthesis temperature can be further reduced by the application of PbO-containing fluxes (down to 1223 K upon use of 80 at % PbO), however, Pb-substituted crystals Ba1-xPbxFe12O19 with Pb contents in the range of 0.23(2) x 0.80(2) form, depending on growth temperature and flux PbO content. The degree of Pb-substitution has only a minor influence on unit cell and magnetic parameters, although the values for Curie temperature, saturation magnetization, as well as the coercivity of these samples are significantly reduced in comparison with those from samples obtained from the other fluxes. Due to the lowest level of impurities, the samples from carbonate flux show superior quality compared to materials obtained using other methods.Item Open Access Migration mechanisms of a faceted grain boundary(2018) Hadian, Raheleh; Grabowski, Blazej; Finnis, Michael W.; Neugebauer, JörgWe report molecular dynamics simulations and their analysis for a mixed tilt and twist grain boundary vicinal to the Σ7 symmetric tilt boundary of the type {123} in aluminum. When minimized in energy at 0K, a grain boundary of this type exhibits nanofacets that contain kinks. We observe that at higher temperatures of migration simulations, given extended annealing times, it is energetically favorable for these nanofacets to coalesce into a large terrace-facet structure. Therefore, we initiate the simulations from such a structure and study as a function of applied driving force and temperature how the boundary migrates. We find the migration of a faceted boundary can be described in terms of the flow of steps. The migration is dominated at lower driving force by the collective motion of the steps incorporated in the facet, and at higher driving forces by the step detachment from the terrace-facet junction and propagation of steps across the terraces. The velocity of steps on terraces is faster than their velocity when incorporated in the facet, and very much faster than the velocity of the facet profile itself, which is almost stationary. A simple kinetic Monte Carlo model matches the broad kinematic features revealed by the molecular dynamics. Since the mechanisms seem likely to be very general on kinked grain-boundary planes, the step-flow description is a promising approach to more quantitative modeling of general grain boundaries.Item Open Access Ab initio based method to study structural phase transitions in dynamically unstable crystals, with new insights on the β to ω transformation in titanium(2019) Korbmacher, Dominique; Glensk, Albert; Duff, Andrew Ian; Finnis, Michael W.; Grabowski, Blazej; Neugebauer, JörgWe present an approach that enables an efficient and accurate study of dynamically unstable crystals over the full temperature range. The approach is based on an interatomic potential fitted to ab initio molecular dynamics energies for both the high- and low-temperature stable phases. We verify by comparison to explicit ab initio simulations that such a bespoke potential, for which we use here the functional form of the embedded atom method, provides accurate transformation temperatures and atomistic features of the transformation. The accuracy of the potential makes it an ideal tool to study the important impact of finite size and finite time effects. We apply our approach to the dynamically unstable β (bcc) titanium phase and study in detail the transformation to the low-temperature stable hexagonal ω phase. We find a large set of previously unreported linear-chain disordered (LCD) structures made up of three types of [111]β linear-chain defects that exhibit randomly disordered arrangements in the (111)β plane.Item Open Access Phonon lifetimes throughout the Brillouin zone at elevated temperatures from experiment and ab Initio(2019) Glensk, Albert; Grabowski, Blazej; Hickel, Tilmann; Neugebauer, Jörg; Neuhaus, Jürgen; Hradil, Klaudia; Petry, Winfried; Leitner, MichaelWe obtain phonon lifetimes in aluminium by inelastic neutron scattering experiments, by ab initio molecular dynamics, and by perturbation theory. At elevated temperatures significant discrepancies are found between experiment and perturbation theory, which disappear when using molecular dynamics due to the inclusion of full anharmonicity and the correct treatment of the multiphonon background. We show that multiple-site interactions are small and that local pairwise anharmonicity dominates phonon-phonon interactions, which permits an efficient computation of phonon lifetimes.Item Open Access Analysis of the substrate specificity of the SMYD2 protein lysine methyltransferase and discovery of novel non-histone substrates(2019) Weirich, Sara; Schuhmacher, Maren Kirstin; Kudithipudi, Srikanth; Lungu, Cristiana; Ferguson, Andrew D.; Jeltsch, AlbertThe SMYD2 protein lysine methyltransferase methylates various histone and non-histone proteins and is overexpressed in several cancers. Using peptide arrays, we investigated the substrate specificity of the enzyme, revealing a recognition of leucine (or weaker phenylalanine) at the -1 peptide site and disfavor of acidic residues at the +1 to +3 sites. Using this motif, novel SMYD2 peptide substrates were identified, leading to the discovery of 32 novel peptide substrates with a validated target site. Among them, 19 were previously reported to be methylated at the target lysine in human cells, strongly suggesting that SMYD2 is the protein lysine methyltransferase responsible for this activity. Methylation of some of the novel peptide substrates was tested at the protein level, leading to the identification of 14 novel protein substrates of SMYD2, six of which were more strongly methylated than p53, the best SMYD2 substrate described so far. The novel SMYD2 substrate proteins are involved in diverse biological processes such as chromatin regulation, transcription, and intracellular signaling. The results of our study provide a fundament for future investigations into the role of this important enzyme in normal development and cancer.Item Open Access Impact of asymmetric martensite and austenite nucleation and growth behavior on the phase stability and hysteresis of freestanding shape-memory nanoparticles(2018) Ko, Won-Seok; Grabowski, Blazej; Neugebauer, JörgMartensitic transformations in nanoscaled shape-memory alloys exhibit characteristic features absent for the bulk counterparts. Detailed understanding is required for applications in micro- and nanoelectromechanical systems, and experimental limitations render atomistic simulation an important complementary approach. Using a recently developed, accurate potential we investigate the phase transformation in freestanding Ni-Ti shape-memory nanoparticles with molecular-dynamics simulations. The results confirm that the decrease in the transformation temperature with decreasing particle size is correlated with an overstabilization of the austenitic surface energy over the martensitic surface energy. However, a detailed atomistic analysis of the nucleation and growth behavior reveals an unexpected difference in the mechanisms determining the austenite finish and martensite start temperature. While the austenite finish temperature is directly affected by a contribution of the surface energy difference, the martensite start temperature is mostly affected by the transformation strain, contrary to general expectations. This insight not only explains the reduced transformation temperature but also the reduced thermal hysteresis in freestanding nanoparticles.Item Open Access Accurate electronic free energies of the 3d, 4d, and 5d transition metals at high temperatures(2017) Zhang, Xi; Grabowski, Blazej; Körmann, Fritz; Freysoldt, Christoph; Neugebauer, JörgFree energies of bulk materials are nowadays routinely computed by density functional theory. In particular for metals, electronic excitations can significantly contribute to the free energy. For an ideal static lattice, this contribution can be obtained at low computational cost, e.g., from the electronic density of states derived at T = 0 K or by utilizing the Sommerfeld approximation. The error introduced by these approximations at elevated temperatures is rarely known. The error arising from the ideal lattice approximation is likewise unexplored but computationally much more challenging to overcome. In order to shed light on these issues we have computed the electronic free energies for all 3d, 4d, and 5d transition elements on the ideal lattices of the bcc, fcc, and hcp structures using finite-temperature density-functional theory. For a subset of elements we have explored the impact of explicit thermal vibrations on the electronic free energies by using ab initio molecular dynamics simulations. We provide an analysis of the observed chemical trends in terms of the electronic density of states and the canonical d band model and quantify the errors in the approximate methods. The electronic contribution to the heat capacities and the corresponding errors due to the different approximations are studied as well.Item Open Access A machine learning approach to model solute grain boundary segregation(2018) Huber, Liam; Hadian, Raheleh; Grabowski, Blazej; Neugebauer, JörgEven minute amounts of one solute atom per one million bulk atoms may give rise to qualitative changes in the mechanical response and fracture resistance of modern structural materials. These changes are commonly related to enrichment by several orders of magnitude of the solutes at structural defects in the host lattice. The underlying concept - segregation - is thus fundamental in materials science. To include it in modern strategies of materials design, accurate and realistic computational modelling tools are necessary. However, the enormous number of defect configurations as well as sites solutes can occupy requires models which rely on severe approximations. In the present study we combine a high-throughput study containing more than 1 million data points with machine learning to derive a computationally highly efficient framework which opens the opportunity to model this important mechanism on a routine basis.