57 research outputs found
CO adsorption on Pt induced Ge nanowires
Using density functional theory, we investigate the possible adsorption sites
of CO molecules on the recently discovered Pt induced Ge nanowires on Ge(001).
Calculated STM images are compared to experimental STM images to identify the
experimentally observed adsorption sites. The CO molecules are found to adsorb
preferably onto the Pt atoms between the Ge nanowire dimer segments. This
adsorption site places the CO in between two nanowire dimers, pushing them
outward, blocking the nearest equivalent adsorption sites. This explains the
observed long-range repulsive interaction between CO molecules on these Pt
induced nanowires.Comment: 12 pages, 10 figure
Reply to 'Comment on "Extending Hirshfeld-I to bulk and periodic materials" '
The issues raised in the comment by T.A. Manz are addressed through the
presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO and
LaCeO, using our previously presented method for calculating
Hirshfeld-I charges in Solids [J. Comput. Chem.. doi: 10.1002/jcc.23088]. It is
shown that the use of pseudo-valence charges is sufficient to retrieve the full
all-electron Hirshfeld-I charges to good accuracy. Furthermore, we present
timing results of different systems, containing up to over atoms,
underlining the relatively low cost for large systems. A number of theoretical
issues is formulated, pointing out mainly that care must be taken when deriving
new atoms in molecules methods based on "expectations" for atomic charges.Comment: 7 pages, 2 Tables, 2 figure
Extending Hirshfeld-I to bulk and periodic materials
In this work, a method is described to extend the iterative Hirshfeld-I
method, generally used for molecules, to periodic systems. The implementation
makes use of precalculated pseudo-potential based charge density distributions,
and it is shown that high quality results are obtained for both molecules and
solids, such as ceria, diamond, and graphite. The use of such grids makes the
implementation independent of the solid state or quantum chemical code used for
studying the system. The extension described here allows for easy calculation
of atomic charges and charge transfer in periodic and bulk systems.Comment: 11 pages, 4 Tables, 5 Figures, pre-referee draft only, much extended
post referee version only available at publishe
Mechanical Properties from Periodic Plane Wave Quantum Mechanical Codes: The Challenge of the Flexible Nanoporous MIL-47(V) Framework
Family Businesses and Adaptation: A Dynamic Capabilities Approach
The main objective of this research was to propose a framework centred on the dynamic capabilities approach, and to be applied in the context of family businessesā adaption to their changing business environment. Data were gathered through interviews with ten FBs operating in Western Australia. Based on the findings, the clusters of activities, sensing, seizing, and transforming emerged as key factors for firmsā adaptation, and were reinforced by firmsā open culture, signature processes, idiosyncratic knowledge, and valuable, rare, inimitable and non-substitutable attributes. Thus, the usefulness of the proposed framework was confirmed. Implications and future research opportunities are presented. Ā© 2018, The Author(s)
How to verify the precision of density-functional-theory implementations via reproducible and universal workflows
In the past decades many density-functional theory methods and codes adopting
periodic boundary conditions have been developed and are now extensively used
in condensed matter physics and materials science research. Only in 2016,
however, their precision (i.e., to which extent properties computed with
different codes agree among each other) was systematically assessed on
elemental crystals: a first crucial step to evaluate the reliability of such
computations. We discuss here general recommendations for verification studies
aiming at further testing precision and transferability of
density-functional-theory computational approaches and codes. We illustrate
such recommendations using a greatly expanded protocol covering the whole
periodic table from Z=1 to 96 and characterizing 10 prototypical cubic
compounds for each element: 4 unaries and 6 oxides, spanning a wide range of
coordination numbers and oxidation states. The primary outcome is a reference
dataset of 960 equations of state cross-checked between two all-electron codes,
then used to verify and improve nine pseudopotential-based approaches. Such
effort is facilitated by deploying AiiDA common workflows that perform
automatic input parameter selection, provide identical input/output interfaces
across codes, and ensure full reproducibility. Finally, we discuss the extent
to which the current results for total energies can be reused for different
goals (e.g., obtaining formation energies).Comment: Main text: 23 pages, 4 figures. Supplementary: 68 page
Identification of stromally expressed molecules in the prostate by tag-profiling of cancer-associated fibroblasts, normal fibroblasts and fetal prostate.
The stromal microenvironment has key roles in prostate development and cancer, and cancer-associated fibroblasts (CAFs) stimulate tumourigenesis via several mechanisms including the expression of pro-tumourigenic factors. Mesenchyme (embryonic stroma) controls prostate organogenesis, and in some circumstances can re-differentiate prostate tumours. We have applied next-generation Tag profiling to fetal human prostate, normal human prostate fibroblasts (NPFs) and CAFs to identify molecules expressed in prostatic stroma. Comparison of gene expression profiles of a patient-matched pair of NPFs vs CAFs identified 671 transcripts that were enriched in CAFs and 356 transcripts whose levels were decreased, relative to NPFs. Gene ontology analysis revealed that CAF-enriched transcripts were associated with prostate morphogenesis and CAF-depleted transcripts were associated with cell cycle. We selected mRNAs to follow-up by comparison of our data sets with published prostate cancer fibroblast microarray profiles as well as by focusing on transcripts encoding secreted and peripheral membrane proteins, as well as mesenchymal transcripts identified in a previous study from our group. We confirmed differential transcript expression between CAFs and NPFs using QrtPCR, and defined protein localization using immunohistochemistry in fetal prostate, adult prostate and prostate cancer. We demonstrated that ASPN, CAV1, CFH, CTSK, DCN, FBLN1, FHL1, FN, NKTR, OGN, PARVA, S100A6, SPARC, STC1 and ZEB1 proteins showed specific and varied expression patterns in fetal human prostate and in prostate cancer. Colocalization studies suggested that some stromally expressed molecules were also expressed in subsets of tumour epithelia, indicating that they may be novel markers of EMT. Additionally, two molecules (ASPN and STC1) marked overlapping and distinct subregions of stroma associated with tumour epithelia and may represent new CAF markers
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