Modelling photoreactions in proteins by density functional theory

Photoactive proteins are an important class of biomolecules that, apart from their biological relevance, offer potential technological applications in the field of molecular electronics. In the first hundreds of femtoseconds of their photocycle, light absorption produces conformational changes that trigger a cascade of chemical reactions culminating in a specific biological signal. The extremely short time of the initial photoreaction makes an accurate experimental characterisation of these processes very difficult. Computer simulations could therefore complement the experimental information and help provide a microscopic picture of the initial events of protein photocycles. We present here some attempts to use a density functional theory based method to investigate photochemical reactions in proteins. Results for the photoisomerisation of the rhodopsin chromophore are discussed.     

RETRACTED ARTICLE: Predatory publishing in Scopus: evidence on cross-country differences

Scientometrics - Predatory publishing represents a major challenge to scholarly communication. This paper maps the infiltration of journals suspected of predatory practices into the citation...     

RETRACTED ARTICLE: Functionalization of titanium based metallic biomaterials for implant applications

Surface immobilization with active functional molecules (AFMs) on a nano-scale is a main field in the current biomaterial research. The functionalization of a vast number of substances and molecules, ranging from inorganic calcium phosphates, peptides and proteins, has been investigated throughout recent decades. However, in vitro and in vivo results are heterogeneous. This may be attributed partially to the limits of the applied immobilization methods. Therefore, this paper highlights the advantages and limitations of the currently applied methods for the biological nano-functionalization of titanium-based biomaterial surfaces. The second part describes a newer immobilization system, using the nanomechanical fixation of at least partially single-stranded nucleic acids (NAs) into an anodic titanium oxide layer as an immobilization principle and their hybridization ability for the functionalization of the surface with active functional molecules conjugated to the respective complementary NA strands.     

Magnetism in non-transition-metal doped CdS studied by density functional theory

The electronic structure of non-transition-metal element (Be, B, C, N, O and F)-doped CdS is studied based on spin-polarized density function theory within the generalized gradient approximation. Our results show that the substitutional Be, B and C for S in CdS induces spin polarized localized states in the gap or near the valence band and generates local magnetic moments 2.0 μ_B, 3.0 μ_B and 2.0 μ_B with one dopant atom, respectively. Whereas doping with N, O and F in CdS does not induce spin polarization. It is found the magnetic states in these systems are related to the difference between the electronegativities of the dopant and the anion in the host. Long-range ferromagnetic coupling may occur in Be, B and C-doped CdS, which can be explained by the p–d exchange-like p–p coupling interaction involving holes.     

RETRACTED ARTICLE: Characteristics of porous zirconia coated with hydroxyapatite as human bones

Since hydroxyapatite has excellent biocompatibility and bone bonding ability, porous hydroxyapatite ceramics have been intensively studied. However, porous hydroxyapatite bodies are mechanically weak and brittle, which makes shaping and implantation difficult. One way to solve this problem is to introduce a strong porous network onto which hydroxyapatite coating is applied. In this study, porous zirconia and alumina-added zirconia ceramics were prepared by ceramic slurry infiltration of expanded polystyrene bead compacts, followed by firing at 1500°C. Then slurry of hydroxyapatite-borosilicate glass mixed powder was used to coat the porous ceramics, followed by firing at 1200°C. The porous structures without the coating had high porosities of 51–69%, high pore interconnectivity, and sufficiently large pore window sizes (300–500 μm). The porous ceramics had compressive strengths of 5·3∼36·8 MPa, favourably comparable to the mechanical properties of cancellous bones. In addition, porous hydroxyapatite surface was formed on the top of the composite coating, whereas a borosilicate glass layer was found on the interface. Thus, porous zirconia-based ceramics were modified with a bioactive composite coating for biomedical applications.     

A high-throughput infrastructure for density functional theory calculations

The use of high-throughput density functional theory (DFT) calculations to screen for new materials and conduct fundamental research presents an exciting opportunity for materials science and materials innovation. High-throughput DFT typically involves computations on hundreds, thousands, or tens of thousands of compounds, and such a change of scale requires new calculation and data management methodologies. In this article, we describe aspects of the necessary data infrastructure for such projects to handle data generation and data analysis in a scalable way. We discuss the problem of accurately computing properties of compounds across diverse chemical spaces with a single exchange correlation functional, and demonstrate that errors in the generalized gradient approximation are highly dependent on chemical environment.     

RETRACTED ARTICLE: Cooperative Time-Reversal Symmetry Breaking Induced by a Magnetic Field in a Quasi-2D d-Wave Superconductor

A model of quasi-two-dimensional d-wave superconductor, with strong nesting properties of the Fermi surface is considered. The orbital effect of a moderate magnetic field applied perpendicularly to the conducting planes is studied in the mean field approximation. It is shown that the field can induce a time-reversal symmetry-breaking spin density wave order coexisting with the superconducting order and can open a gap over the whole Fermi surface. The anomalies recently observed in the heat conductivity, penetration depth, and zero-bias conduction in cuprates might be ascribed to this effect.     

RETRACTED ARTICLE: The effects of ZnO2 nanoparticles on split tensile strength of self-compacting concrete

We the Editor and Publisher of Journal of Experimental Nanoscience retract the following three articles: 1. Nazari, Ali, and Shadi Riahi. “The effects of ZnO2 nanoparticles on split tensile strength of self-compacting concrete.” Journal of Experimental Nanoscience 7.5 (2012): 491-512, https://www.tandfonline.com/doi/full/10.1080/17458080.2010.524669

2. Nazari, Ali, and Shadi Riahi. “The effects of SnO2 nanoparticles on physical and mechanical properties of high-strength self-compacting concrete.” Journal of Experimental Nanoscience 7.5 (2012): 559-577, https://www.tandfonline.com/doi/full/10.1080/17458080.2010.543991

3. Nazari, Ali, and Shadi Riahi. “The effects of ZrO2 nanoparticles on strength assessments and water permeability of concrete in different curing media.” Journal of Experimental Nanoscience 8.4 (2013): 413-433, https://www.tandfonline.com/doi/full/10.1080/17458080.2011.586369

Since publication it has come to our attention that these articles duplicate significant parts of other papers published elsewhere and that these were not referenced within these articles (listed above). Following COPE guidelines, Taylor & Francis has tried numerous times to contact the authors as well as their affiliated institutes with a request for clarification, however, we failed to receive a response.

As we have been able to verify that unreferenced content has been duplicated, we have decided to retract these articles. We apologize to the readers that this was not detected during the submission process.

We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions.

The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as “Retracted”.     

RETRACTED ARTICLE: The influence of surface cleaning on the stability of Pd/GaAs contacts

The thermal stability of –GaAs ohmic contacts with Ge and Sn layers was investigated at 300 and 400 °C. The majority of contact structures are possible to anneal according to the annealing optimization at one temperature, but the dependence of the contact resistivity on the annealing temperature show two minima in the case of the Ge(20 nm)/Pd(10 nm) structure. The thermal stability of the structure is better after the annealing at temperatures from the higher temperature minimum. Etching of GaAs wafers before the metal deposition in the solution of (1 : 8 : 500) followed by (1 : 1) or in concentrate HCl produces the best thermal stability. The Ge/Pd contact structures are based on the solid phase regrowth mechanisms but the annealing mechanism is completely different for the Sn/Pd contact structures.     

Peptide synthesis of gold nanoparticles: the early steps of gold reduction investigated by density functional theory

Gold nanoparticles can be synthesized by reducing chloroaurate(III) ions in the presence of peptides. Here, such reduction for serine and tyrosine is studied by density functional theory including solvent effects. We find that the formation of chloroaurate complexes of these amino acids is thermodynamically viable and facilitates the reduction of Au(III), to a greater degree for tyrosine as found in experiments. Our results also suggest a rationale for the behavior of tyrosine-intercalated peptides.