Relative energetics of acetyl-histidine protomers with and without Zn²⁺ and a benchmark of energy methods

We studied acetylhistidine (AcH), bare or microsolvated with a zinc cation by simulations in isolation. First, a global search for minima of the potential energy surface combining both, empirical and first-principles methods, is performed individually for either one of five possible protonation states. Comparing the most stable structures between tautomeric forms of negatively charged AcH shows a clear preference for conformers with the neutral imidazole ring protonated at the N-epsilon-2 atom. When adding a zinc cation to the system, the situation is reversed and N-delta-1-protonated structures are energetically more favorable. Obtained minima structures then served as basis for a benchmark study to examine the goodness of commonly applied levels of theory, i.e. force fields, semi-empirical methods, density-functional approximations (DFA), and wavefunction-based methods with respect to high-level coupled-cluster calculations, i.e. the DLPNO-CCSD(T) method. All tested force fields and semi-empirical methods show a poor performance in reproducing the energy hierarchies of conformers, in particular of systems involving the zinc cation. Meta-GGA, hybrid, double hybrid DFAs, and the MP2 method are able to describe the energetics of the reference method within chemical accuracy, i.e. with a mean absolute error of less than 1kcal/mol. Best performance is found for the double hybrid DFA B3LYP+XYG3 with a mean absolute error of 0.7 kcal/mol and a maximum error of 1.8 kcal/mol. While MP2 performs similarly as B3LYP+XYG3, computational costs, i.e. timings, are increased by a factor of 4 in comparison due to the large basis sets required for accurate results

The upper-atmosphere extension of the ICON general circulation model (version: Ua-icon-1.0)

How the upper-atmosphere branch of the circulation contributes to and interacts with the circulation of the middle and lower atmosphere is a research area with many open questions. Inertia-gravity waves, for instance, have moved in the focus of research as they are suspected to be key features in driving and shaping the circulation. Numerical atmospheric models are an important pillar for this research. We use the ICOsahedral Non-hydrostatic (ICON) general circulation model, which is a joint development of the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD), and provides, e.g., local mass conservation, a flexible grid nesting option, and a non-hydrostatic dynamical core formulated on an icosahedral-triangular grid. We extended ICON to the upper atmosphere and present here the two main components of this new configuration named UA-ICON: an extension of the dynamical core from shallow- to deep-atmosphere dynamics and the implementation of an upper-atmosphere physics package. A series of idealized test cases and climatological simulations is performed in order to evaluate the upper-atmosphere extension of ICON. © Author(s) 2019

Going clean: structure and dynamics of peptides in the gas phase and paths to solvation

The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field

Better force fields start with better data: A data set of cation dipeptide interactions

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids – including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology

Evidence for Quadratic Tidal Tensor Bias from the Halo Bispectrum

The relation between the clustering properties of luminous matter in the form of galaxies and the underlying dark matter distribution is of fundamental importance for the interpretation of ongoing and upcoming galaxy surveys. The so called local bias model, where galaxy density is a function of local matter density, is frequently discussed as a means to infer the matter power spectrum or correlation function from the measured galaxy correlation. However, gravitational evolution generates a term quadratic in the tidal tensor and thus non-local in the density field, even if this term is absent in the initial conditions (Lagrangian space). Because the term is quadratic, it contributes as a loop correction to the power spectrum, so the standard linear bias picture still applies on large scales, however, it contributes at leading order to the bispectrum for which it is significant on all scales. Such a term could also be present in Lagrangian space if halo formation were influenced by the tidal field. We measure the corresponding coupling strengths from the matter-matter-halo bispectrum in numerical simulations and find a non-vanishing coefficient for the tidal tensor term. We find no scale dependence of the bias parameters up to k=0.1 h/Mpc and that the tidal effect is increasing with halo mass. While the Lagrangian bias picture is a better description of our results than the Eulerian bias picture, our results suggest that there might be a tidal tensor bias already in the initial conditions. We also find that the coefficients of the quadratic density term deviate quite strongly from the theoretical predictions based on the spherical collapse model and a universal mass function. Both quadratic density and tidal tensor bias terms must be included in the modeling of galaxy clustering of current and future surveys if one wants to achieve the high precision cosmology promise of these datasets.Comment: 14 pages, 4 figures, 1 tabl

On the use of robust regression in econometrics

The use of robust regression estimators has gained popularity among applied econometricians. The main argument invoked to justify the use of the robust estimators is that they provide efficiency gains in the presence of outliers or non-normal errors. Unfortunately, most practitioners seem to be unaware of the fact that heteroskedastic and skewed errors can dramatically affect the properties of these estimators. In this paper we reconsider the interpretation of the specific robust estimator that has become popular in applied econometrics, and conclude that its use in this context cannot be generally recommended

Manoeuvring simulation on the bridge for predicting motion of real ships and as training tool in ship handling simulators

International sea transport has growing rapidly dur-ing the period of the last decade. Ships became larg-er and wider and its container capacity is still in-creasing to 12.000 TEU and even more. To navigat

Context-aware and automatic configuration of mobile devices in cloud-enabled ubiquitous computing

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s00779-013-0698-3. Copyright @ Springer-Verlag London 2013.Context-sensitive (or aware) applications have, in recent years, moved from the realm of possibilities to that of ubiquity. One exciting research area that is still very much in the realm of possibilities is that of cloud computing, and in this paper, we present our work, which explores the overlap of these two research areas. Accordingly, this paper explores the notion of cross-source integration of cloud-based, context-aware information in ubiquitous computing through a developed prototypical solution. Moreover, the described solution incorporates remote and automatic configuration of Android smartphones and advances the research area of context-aware information by harvesting information from several sources to build a rich foundation on which algorithms for context-aware computation can be based. Evaluation results show the viability of integrating and tailoring contextual information to provide users with timely, relevant and adapted application behaviour and content

Norms and varieties of English and TESOL teacher agency

The growing recognition of the plurality of English underling the World Englishes (WE) paradigm has problematised the conventional second language acquisition (SLA) views of errors. If English use in emerging English-speaking contexts is to be judged by local norms, as argued by WE scholars, applying exocentric norms in these contexts can be inappropriate. On the other hand, despite the significant growth of WE, varieties of new Englishes have yet to develop widely acceptable endocentric norms. These developments have raised a critical question: How can TESOL teachers distinguish between errors in the SLA sense and varietal features in the WE sense? Framed around language management theory (LMT) and teacher agency, this paper investigates how a group of global TESOL practitioners in an Australian university evaluated usages of English as a second language, what criteria they used and what implications their judgments and decision-making processes have for TESOL pedagogy and WE research