Mechanistic Insights of Amino Acid Binding to Hydroxyapatite: Molecular Dynamics Charts Future Directions in Biomaterial Design.

Extensive efforts have been made to improve the understanding of hard tissue regeneration, essential for advancing medical applications like bone graft materials. However, the mechanisms of bone biomineralization, particularly the regulation of hydroxyapatite growth by proteins/peptides, remain debated. Small biomolecules such as amino acids are ideal for studying these mechanisms due to their simplicity and relevance as protein/peptide building blocks.

Atomistic insight into salinity dependent preferential binding of polar aromatics to calcite/brine interface: implications to low salinity waterflooding.

This paper resolve the salinity-dependent interactions of polar components of crude oil at calcite-brine interface in atomic resolution. Molecular dynamics simulations carried out on the present study showed that ordered water monolayers develop immediate to a calcite substrate in contact with a saline solution. Carboxylic compounds, herein represented by benzoic acid (BA), penetrate into those hydration layers and directly linking to the calcite surface.

Ion-specific interactions at calcite-brine interfaces: a nano-scale study of the surface charge development and preferential binding of polar hydrocarbons.

This research provides an atomic-level insight into the synergic contribution of mono- and divalent ions to interfacial characteristics of calcite surfaces exposed to electrolyte solution containing organic compounds. The emphasis was placed on the ionic interactions responsible for charge developing mechanisms of calcite surfaces and also the capacity for adsorption of polar hydrocarbons, represented by benzoic acid (BA), at different brine compositions. For this purpose, molecular dynamics (MD) simulations were employed to explore the interplay of the main constituent ions of natural brines (Na+, Cl-, Mg2+, and SO42-) and BA at the interface of CaCO3.

A Deep Look into the Dynamics of Saltwater Imbibition in a Calcite Nanochannel: Temperature Impacts Capillarity Regimes.

This research concerns fundamentals of spontaneous transport of saltwater (1 mol·dm NaCl solution) in nanopores of calcium carbonates. A fully atomistic model was adopted to scrutinize the temperature dependence of flow regimes during solution transport under CaCO nanoconfinement. The early time of capillary filling is inertia-dominated, and the solution penetrates with a near-planar meniscus at constant velocity.

How do ions contribute to brine-hydrophobic hydrocarbon Interfaces? An in silico study.

Hypothesis: The saltwater-oil interface is of broad implication in geochemistry and petroleum disciplines. To date, the main focus has been on the surface contribution of polar, heavy compounds of crude oil, widely neglecting the role of non-polar hydrocarbons. However, non-polar compounds are expected to contribute to characteristics of oil-brine interfaces.

The Impact of Salinity on the Interfacial Structuring of an Aromatic Acid at the Calcite/Brine Interface: An Atomistic View on Low Salinity Effect.

This study aims to elucidate the impact of salinity on the interactions governing the adsorption of polar aromatic oil compounds onto calcite. To this end, molecular dynamics simulations were employed to assess adsorption of a model polar organic molecule (deprotonated benzoic acid, benzoate) on the calcite surface in NaCl brines of different concentration levels, namely, deionized water (DW), low-salinity water (LS, 5000 ppm), and sea water (SW; 45,000 ppm). Calcite was found to be completely covered by several well-ordered water layers.

Graphene-Subgrain-Defined Oxidation of Copper.

The correlation between the crystal structure of chemical vapor deposition (CVD)-grown graphene and the crystal structure of the Cu growth substrate and their mutual effect on the oxidation of the underlying Cu are systematically explored. We report that natural oxygen or water intercalation along the graphene-Cu interface results in an orientation-dependent oxidation rate of the Cu surface, particularly noticeable for bicrystal graphene domains on the same copper grain, suggesting that the relative crystal orientation of subgrains determines the degree of Cu oxidation. Atomistic force field calculations support these observations, showing that graphene domains have preferential alignment with the Cu(111) with a smaller average height above the global Cu surface as compared to intermediate orientations, and that this is the origin of the heterogeneous oxidation rate of Cu.

Multi-scale approach to first-principles electron transport beyond 100 nm.

Multi-scale computational approaches are important for studies of novel, low-dimensional electronic devices since they are able to capture the different length-scales involved in the device operation, and at the same time describe critical parts such as surfaces, defects, interfaces, gates, and applied bias, on a atomistic, quantum-chemical level. Here we present a multi-scale method which enables calculations of electronic currents in two-dimensional devices larger than 100 nm2, where multiple perturbed regions described by density functional theory (DFT) are embedded into an extended unperturbed region described by a DFT-parametrized tight-binding model. We explain the details of the method, provide examples, and point out the main challenges regarding its practical implementation.

Bonding, structural and thermodynamic analysis of dissociative adsorption of HO ion onto calcite (101⁻4) surface: CPMD and DFT calculations.

We used density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulation to investigate the adsorption and bond formation of hydronium ion (HO) onto a [Formula: see text] calcite surface. For surface coverage of 25% to 100%, the nature of HO interaction was explored through electron density and energetics in the context of bond critical points. The adsorbate-adsorbent structure was studied by simulation of pair correlation function.

Atomic White-Out: Enabling Atomic Circuitry through Mechanically Induced Bonding of Single Hydrogen Atoms to a Silicon Surface.

We report the mechanically induced formation of a silicon-hydrogen covalent bond and its application in engineering nanoelectronic devices. We show that using the tip of a noncontact atomic force microscope (NC-AFM), a single hydrogen atom could be vertically manipulated. When applying a localized electronic excitation, a single hydrogen atom is desorbed from the hydrogen-passivated surface and can be transferred to the tip apex, as evidenced from a unique signature in frequency shift curves.

Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface.

The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface.

Time-Resolved Imaging of Negative Differential Resistance on the Atomic Scale.

Negative differential resistance remains an attractive but elusive functionality, so far only finding niche applications. Atom scale entities have shown promising properties, but the viability of device fabrication requires a fuller understanding of electron dynamics than has been possible to date. Using an all-electronic time-resolved scanning tunneling microscopy technique and a Green's function transport model, we study an isolated dangling bond on a hydrogen terminated silicon surface.

Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory.

Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules.

Gas doping on the topological insulator Bi2Se3 surface.

Gas molecule doping on the topological insulator Bi(2)Se(3) surface with existing Se vacancies is investigated using first-principles calculations. Consistent with experiments, NO(2) and O(2) are found to occupy the Se vacancy sites, remove vacancy-doped electrons, and restore the band structure of a perfect surface. In contrast, NO and H(2) do not favor passivation of such vacancies.

Strong spin-filtering and spin-valve effects in a molecular V-C(60)-V contact.

Motivated by the recent achievements in the manipulation of C(60) molecules in STM experiments, we study theoretically the structure and electronic properties of a C(60) molecule in an STM tunneljunction with a magnetic tip and magnetic adatom on a Cu(111) surface using first-principles calculations. For the case of a vanadium tip/adatom, we demonstrate how spin coupling between the magnetic V atoms, mediated by the C(60), can be observed in the electronic transport, which display a strong spin-filtering effect, allowing mainly majority-spin electrons to pass (>95%). Moreover, we find a significant change in the conductance between parallel and anti-parallel spin polarizations in the junction (86%) which suggests that STM experiments should be able to characterize the magnetism and spin coupling for these systems.

Electronic transport in natively oxidized silicon nanowires.

Silicon nanowires are widely used as active functional elements in advanced electronic devices, most notably in biological sensors. While surface oxidation of the wires occurs upon exposure to a wet environment, theoretical studies are often limited to ideally crystalline, H-terminated wire models. We present an accurate computational study of the electronic and transport properties of natively oxidized, ultrathin silicon nanowires including dopant elements.

Carbon nanostructures as catalytic support for chemiluminescence of sulfur compounds in a molecular emission cavity analysis system.

The effect of different substrates including stainless steel, activated carbon, single-walled carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs), fullerenes (C60, C70, etc.) and SWCNTs doped with iron and palladium nanoparticles were compared for catalytic chemiluminescence reaction of sulfur compounds in a flame-containing cavity of molecular emission cavity analysis (MECA) system. Different forms of CNT substrates were fabricated using electric arc-discharge method.

Efficient organometallic spin filter between single-wall carbon nanotube or graphene electrodes.

We present a theoretical study of spin transport in a class of molecular systems consisting of an organometallic benzene-vanadium cluster placed in between graphene or single-wall carbon-nanotube-model contacts. Ab initio modeling is performed by combining spin density functional theory and nonequilibrium Green's function techniques. We consider weak and strong cluster-contact bonds.