unDrift: A versatile software for fast offline SPM image drift correction

• Tobias Dickbreder,
• Franziska Sabath,
• Lukas Höltkemeier,
• Ralf Bechstein and
• Angelika Kühnle

Beilstein J. Nanotechnol. 2023, 14, 1225–1237, doi:10.3762/bjnano.14.101

• distorted by a very high drift velocity, only partly usable images, and images exhibiting an overall weak contrast. Moreover, we show that the semi-automatic analysis of periodic images can be applied to a long series containing hundreds of images measured at the calcite–water interface. Keywords: atomic

• used for evaluation. To demonstrate that unDrift can drift-correct these images by only considering (small) parts of an image, we show example images recorded at the calcite–water interface in Figure 4e,f. In our example, the sample drifted out of the scanner’s z range after the first third of the

• (distance accuracy: ±0.3 × 10−10 m, angle accuracy: ±2°; see below). Third, we discuss the arguably most challenging situation for drift correction, images with an overall weak contrast and low signal-to-noise ratio. The periodic structures of the calcite–water interface in Figure 4j,k are very faint and

Molecular assemblies on surfaces: towards physical and electronic decoupling of organic molecules

• Sabine Maier and
• Meike Stöhr

Beilstein J. Nanotechnol. 2021, 12, 950–956, doi:10.3762/bjnano.12.71

• sufficient to truly electronically insulate molecular structures. For this, the usage of either thicker insulating films (mostly alkali halides) or bulk insulators is required. For studying molecules on bulk insulators, ionic crystals (e.g., KBr, NaCl, CaF2, and calcite) have mostly served as model systems

• monitor the STM-induced nucleation, growth, and ripening of self-assembled monolayers in a more controlled fashion. Söngen et al. [77] provide insight into the interaction of organic molecules with bulk insulators by discussing the adsorption of ethanol on both calcite and magnesite using three

• -dimensional AFM experiments. Although molecules adsorbed on bulk insulators are electronically decoupled, molecular self-assemblies can experience a substrate templating effect due to the presence of heterogeneous adsorption sites. Therefore, Söngen et al. [77] found on bulk calcite and magnesite that the

Protruding hydrogen atoms as markers for the molecular orientation of a metallocene

• Linda Laflör,
• Michael Reichling and
• Philipp Rahe

Beilstein J. Nanotechnol. 2020, 11, 1432–1438, doi:10.3762/bjnano.11.127

• ), Cu(110), and Cu3N/Cu(110) surfaces [20] as well as on the insulator surfaces calcite(104) [21] and CaF2(111) [22]. An eclipsed ferrocene conformation was found to be predominant on the metallic surfaces [20] and on calcite(104) [21]. On CaF2(111) surfaces, density functional theory (DFT) calculations

Three-dimensional solvation structure of ethanol on carbonate minerals

• Hagen Söngen,
• Ygor Morais Jaques,
• Peter Spijker,
• Christoph Marutschke,
• Stefanie Klassen,
• Ilka Hermes,
• Ralf Bechstein,
• Lidija Zivanovic,
• John Tracey,
• Adam S. Foster and
• Angelika Kühnle

Beilstein J. Nanotechnol. 2020, 11, 891–898, doi:10.3762/bjnano.11.74

• ), Kanazawa University, Kakumamachi, Kanazawa 920-1192, Japan 10.3762/bjnano.11.74 Abstract Calcite and magnesite are important mineral constituents of the earth’s crust. In aqueous environments, these carbonates typically expose their most stable cleavage plane, the (10.4) surface. It is known that these

• resolution. However, the majority of 3D AFM studies have been focused on the arrangement of water at carbonate surfaces. Here, we present an analysis of the assembly of ethanol – an organic molecule with a single hydroxy group – at the calcite and magnesite (10.4) surfaces by using high-resolution 3D AFM and

• molecular dynamics (MD) simulations. Within a single AFM data set we are able to resolve both the first laterally ordered solvation layer of ethanol on the calcite surface as well as the following solvation layers that show no lateral order. Our experimental results are in excellent agreement with MD

Facile biogenic fabrication of hydroxyapatite nanorods using cuttlefish bone and their bactericidal and biocompatibility study

• Satheeshkumar Balu,
• Manisha Vidyavathy Sundaradoss,
• Swetha Andra and
• Jaison Jeevanandam

Beilstein J. Nanotechnol. 2020, 11, 285–295, doi:10.3762/bjnano.11.21

• into calcite CaCO3 (JCPDS file 71-2396) after 3 h of reaction time. The reflection peaks observed at 23°, 29°, 35°, 39°, 43°, 47°, 48°, 56° and 57° correspond to the (012), (104), (110), (113), (202), (018), (116), (211), and (122) planes, which indicates the rhombohedral structure of calcite [23

• ]. Thus, it is evident that the reaction at basic pH conditions and a temperature of 80 °C supports the relaxation of aragonite calcium carbonate bonds to form calcite structure in 3 h [24]. It can be noted from the diffraction peaks that the formation of Hap crystal growth was initiated at 6 h of

• reaction time along with certain traces of calcite. Moreover, the intensity of the calcite at peak positions of 23° and 29° significantly decreased with increasing reaction time. This reveals that prolonged heating of calcite crystal relaxes the lattice of calcite to facilitate the formation of Hap [25

Quantitative comparison of wideband low-latency phase-locked loop circuit designs for high-speed frequency modulation atomic force microscopy

• Kazuki Miyata and
• Takeshi Fukuma

Beilstein J. Nanotechnol. 2018, 9, 1844–1855, doi:10.3762/bjnano.9.176

• imaging of calcite dissolution in water at 0.5 s/frame with true atomic resolution. The high-speed and high-resolution imaging capabilities of the proposed design will enable a wide range of studies to be conducted on various atomic-scale dynamic phenomena at solid–liquid interfaces. Keywords: calcite

• same digital signal-processing platform to conduct quantitative and direct performance comparisons. We also present the result of high-speed FM-AFM imaging of calcite dissolution with atomic-scale resolution to demonstrate the applicability of the proposed PLL design to practical experiments

• preparation and imaging conditions A 5 × 5 × 2 mm3 calcite crystal (Crystal Base Co., Ltd.) was used for the FM-AFM experiment. The sample was glued onto the sample holder. Immediately after cleavage of the sample with a razor blade, 50 μL of Milli-Q water was deposited onto the sample surface. Then, high

Review on nanoparticles and nanostructured materials: history, sources, toxicity and regulations

• Jaison Jeevanandam,
• Ahmed Barhoum,
• Yen S. Chan,
• Alain Dufresne and
• Michael K. Danquah

Beilstein J. Nanotechnol. 2018, 9, 1050–1074, doi:10.3762/bjnano.9.98

• and protein that are aligned in a column and layers of calcite, forms the thin and strong eggshell. During the eggshell formation, the CaCO3 NPs begin as an amorphous mineral which is transformed by the c-type lectin proteins into ordered crystals. The crystal transformation is initiated by the

Multifunctional layered magnetic composites

• Maria Siglreitmeier,
• Baohu Wu,
• Tina Kollmann,
• Martin Neubauer,
• Gergely Nagy,
• Dietmar Schwahn,
• Vitaliy Pipich,
• Damien Faivre,
• Dirk Zahn,
• Andreas Fery and
• Helmut Cölfen

Beilstein J. Nanotechnol. 2015, 6, 134–148, doi:10.3762/bjnano.6.13

• before usage. Preparation of insoluble organic nacre matrix Shells of Haleotis laevigata were sand-blasted to remove the calcite layer. After thorough washing with deionized water, the shells were dried overnight at room temperature and cut into pieces with an area of around 1 cm × 1 cm. The nacre pieces

Real-time monitoring of calcium carbonate and cationic peptide deposition on carboxylate-SAM using a microfluidic SAW biosensor

• Anna Pohl and
• Ingrid M. Weiss

Beilstein J. Nanotechnol. 2014, 5, 1823–1835, doi:10.3762/bjnano.5.193

• 10−11 mol. One microfluidic channel has a flow cell height of 2 × 105 nm and a volume of 1.2 µL. The sensitive area of the chip is 5 × 106 nm × 1.2 × 106 nm and the cross-sectional area of the flow channel is 0.24 mm2. This would correspond to ~2 × 1013 to 3 × 1013 elementary cells of calcite

Direct nanoscale observations of the coupled dissolution of calcite and dolomite and the precipitation of gypsum

• Francesco G. Offeddu,
• Jordi Cama,
• Josep M. Soler and
• Christine V. Putnis

Beilstein J. Nanotechnol. 2014, 5, 1245–1253, doi:10.3762/bjnano.5.138

• /bjnano.5.138 Abstract In-situ atomic force microscopy (AFM) experiments were performed to study the overall process of dissolution of common carbonate minerals (calcite and dolomite) and precipitation of gypsum in Na2SO4 and CaSO4 solutions with pH values ranging from 2 to 6 at room temperature (23 ± 1

• -equilibrium conditions with respect to calcite. The calculated dissolution rates of calcite at pH 4.8 and 5.6 agreed with the values reported in the literature. When using solutions previously equilibrated with respect to gypsum, gypsum precipitation coupled with calcite dissolution showed short gypsum

• nucleation induction times. The gypsum precipitate quickly coated the calcite surface, forming arrow-like forms parallel to the crystallographic orientations of the calcite etch pits. Gypsum precipitation coupled with dolomite dissolution was slower than that of calcite, indicating the dissolution rate to be

Biocalcite, a multifunctional inorganic polymer: Building block for calcareous sponge spicules and bioseed for the synthesis of calcium phosphate-based bone

• Xiaohong Wang,
• Heinz C. Schröder and
• Werner E. G. Müller

Beilstein J. Nanotechnol. 2014, 5, 610–621, doi:10.3762/bjnano.5.72

• for the precipitation of calcium phosphate mineral onto bone-forming osteoblasts. Two different calcium carbonate phases have been found during CA-driven enzymatic calcium carbonate deposition in in vitro assays: calcite crystals and round-shaped vaterite deposits. The CA provides a new target of

• built of calcite [5]. The selection of the mineral appears to parallel the levels of silicate and carbonate in the marine environment [6]. The distinguished feature of biosilica-based skeletons is the fact that this polymer is formed enzymatically, a finding that resulted in the introduction of a new

• this enzyme is secreted by the sponge cells or bound to the cell membrane. The spicules from the calcareous sponges (Figure 2B), e.g., Sycon used in our studies [38][42], consists of almost pure calcium carbonate (calcite). In a first approach to investigate the formation of the calcareous spicules on

Nano-FTIR chemical mapping of minerals in biological materials

• Sergiu Amarie,
• Paul Zaslansky,
• Yusuke Kajihara,
• Erika Griesshaber,
• Wolfgang W. Schmahl and
• Fritz Keilmann

Beilstein J. Nanotechnol. 2012, 3, 312–323, doi:10.3762/bjnano.3.35

• calcite layer and an inner aragonite layer is readily located with the help of an overview microscope (0.7 µm resolution) built into the commercial s-SNOM used (neaspec.com). On the inner side there is an interlayer, ca. 2 µm wide, with modified bioaragonite crystals [34]. Three adjoining s-SNOM images of

• shown in Figure 5). The spectra in Figure 3b and Figure 3c (and also the extracted averaged spectral profiles in Figure 4) are dominated by a single, sharp resonance, which differs in frequency position for orthorhombic aragonite (855 cm−1) and trigonal calcite (873 cm−1), and thus both calcium

• Figure 3b, Figure 4 and Figure 5b). "Phosphate" occurs at a few spots only, in the calcite region up to and including the interlayer, but not further out in the aragonite region; in the calcite region its occurrence diminishes with distance from the interface (Figure 6). Additional zoomed images such as

Detection of interaction between biomineralising proteins and calcium carbonate microcrystals

• Hanna Rademaker and
• Malte Launspach

Beilstein J. Nanotechnol. 2011, 2, 222–227, doi:10.3762/bjnano.2.26

• interacting with minerals from the totality of proteins contained in nacre. Here, we adopted and modified a recently published approach given by Suzuki et al. [1] that gives a hint of specific protein–mineral interactions. Synthesised aragonite or calcite microcrystals were incubated with a protein mixture

• extracted from nacre of Haliotis laevigata. After incubation the mineral phase was dissolved and investigated for attached proteins. The results give a hint of one protein that seems to bind specifically to aragonite and not to calcite. The presented protocol seems to be suitable to detect mineral binding

• formation. Recently, Suzuki and co-workers [1] described an assay to detect whether a protein binds to aragonite or calcite microcrystals specifically. Here, we wish to report how to modify the protocol given by Suzuki et al. and apply it to a mixture of soluble proteins extracted from nacre from Haliotis