Optoelectronics and defect levels in hydroxyapatite by first-principles.

Hydroxyapatite (HAp) is an important component of mammal bones and teeth, being widely used in prosthetic implants. Despite the importance of HAp in medicine, several promising applications involving this material (e.g., in photo-catalysis) depend on how well we understand its fundamental properties. Among the ones that are either unknown or not known accurately, we have the electronic band structure and all that relates to it, including the bandgap width. We employ state-of-the-art methodologies, including density hybrid-functional theory and many-body perturbation theory within the dynamically screened single-particle Green's function approximation, to look at the optoelectronic properties of HAp. These methods are also applied to the calculation of defect levels. We find that the use of a mix of (semi-)local and exact exchange in the exchange-correlation functional brings a drastic improvement to the band structure. Important side effects include improvements in the description of dielectric and optical properties not only involving conduction band (excited) states but also the valence. We find that the highly dispersive conduction band bottom of HAp originates from anti-bonding σ* states along the ⋯OH-OH-⋯ infinite chain, suggesting the formation of a conductive 1D-ice phase. The choice of the exchange-correlation treatment to the calculation of defect levels was also investigated by using the OH-vacancy as a testing model. We find that donor and acceptor transitions obtained within semi-local density functional theory (DFT) differ from those of hybrid-DFT by almost 2 eV. Such a large discrepancy emphasizes the importance of using a high-quality description of the electron-electron interactions in the calculation of electronic and optical transitions of defects in HAp.

Influence of Magnesium Source on the Mechanochemical Synthesis of Magnesium-Substituted Hydroxyapatite.

Magnesium, as one of the most abundant cations in the human body, plays an important role in both physiological and pathological processes. In this study, it was shown that a promising biomedical material, Mg-substituted hydroxyapatite (Mg-HA), can be synthesized via a fast mechanochemical method. For this method, the nature of magnesium-containing carriers was shown to be important. When using magnesium oxide as a source of magnesium, the partial insertion of magnesium cations into the apatite structure occurs. In contrast, when magnesium hydroxide or monomagnesium phosphate is used, single-phase Mg-HA is formed. Both experimental and theoretical investigations showed that an increase in the Mg content leads to a decrease in the lattice parameters and unit cell volume of Mg-HA. Density functional theory calculations showed the high sensitivity of the lattice parameters to the crystallographic position of the calcium site substituted by magnesium. It was shown experimentally that the insertion of magnesium cations decreases the thermal stability of hydroxyapatite. The thermal decomposition of Mg-HA leads to the formation of a mixture of stoichiometric HA, magnesium oxide, and Mg-substituted tricalcium phosphate phases.

Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality.

In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of a phenylalanine helical nanotube. Now, a new application of the algorithm has been developed for implementing a similar molecular dynamic self-assembly into helical structures of peptide nanotubes (PNTs) based on other peptide molecules-namely diphenylalanine (FF) molecules of different chirality L-FF and D-FF. In this work, helical nanotubes were assembled from linear sequences of FF molecules with these initially different chiralities. The chirality of the obtained nanotubes was calculated by various methods, including calculation by dipole moments. In addition, a statistical analysis of the results obtained was performed. A comparative analysis of the structures of nanotubes was also performed using the method of visual differential analysis. It was found that FF PNTs obtained by the MD self-assembly method form helical nanotubes of different chirality. The regimes that form nanotubes of right chirality D from initial L-FF dipeptides and nanotubes of left chirality L from D-FF dipeptides are revealed. This corresponds to the law of changing the sign of the chirality of molecular helical structures as the level of their hierarchical organization becomes more complicated.

Effect of Magnesium Substitution on Structural Features and Properties of Hydroxyapatite.

Hydroxyapatite (HAP) is the main mineral component of bones and teeth. It is widely used in medicine as a bone filler and coating for implants to promote new bone growth. Ion substitutions into the HAP structure highly affect its properties. One of the most important substituents is magnesium. This paper presents new results obtained using high-precision hybrid density functional theory calculations for Mg/Ca substitutions in HAP in a wide magnesium concentration range within a 2 × 2 × 2 supercell model. Experimental data on the mechanochemical synthesis of HAP-Mg samples with different Mg concentrations are also presented. A comparison between the experiment and the theory showed good agreement: the HAP-Mg unit cell parameters and volume decreased with increasing degree of Mg/Ca substitution. The changes in the distances between the Ca and O, Ca and H, and Mg and O ions upon Mg/Ca substitution in different calcium positions was analyzed. The resulting asymmetry and distortion of the cell parameters were evaluated. It was shown that bulk modulus, energy levels, and band gap depend on the degree of Mg substitutions in the Ca1 and Ca2 positions. The formation energies of Mg/Ca substitutions showed non-monotonic behavior that was different for Ca1 and Ca2 positions. The Ca2 position had a slightly higher probability (~5 meV/f.u.) of substitution than Ca1 position at a Mg concentration x = 0.5. At x = 1, substitution in both positions can coexist. The simulated IR spectra for different Mg/Ca substitutions showed that Mg in the Ca2 position changes the IR spectrum more significantly than Mg in the Ca1 position. Similar changes were recorded in the IR spectra of the synthesized samples. The electronic structure is shown to be sensitive to the number and position of substitutions, which may be used to tweak the optical properties of the HAP-Mg material.

Molecular Dynamics Simulation of the Thermal Behavior of Hydroxyapatite.

Hydroxyapatite (HAP) is the main mineral component of bones and teeth. Due to its biocompatibility, HAP is widely used in medicine as a filler that replaces parts of lost bone and as an implant coating that promotes new bone growth. The modeling and calculations of the structure and properties of HAP showed that various structural defects have a significant effect on the properties of the material. By varying these structural heterogeneities, it is possible to increase the biocompatibility of HAP. An important role here is played by OH group vacancies, which are easily formed when these hydroxyl groups leave OH channels of HAP. In this case, the temperature dependence of the concentration of OH ions, which also determines the thermal behavior of HAP, is important. To study the evaporation of OH ions from HAP structures with increasing temperatures, molecular dynamics simulation (MDS) methods were used in this work. As a program for MDS modeling, we used the PUMA-CUDA software package. The initial structure of HAP, consisting of 4 × 4 × 2 = 32 unit cells of the hexagonal HAP phase, surrounded by a 15-Å layer of water was used in the modelling. Multiple and statistically processed MDS, running calculations in the range of 700-1400 K, showed that active evaporation of OH ions begins at the temperature of 1150 K. The analysis of the obtained results in comparison with those available in the literature data shows that these values are very close to the experiments. Thus, this MDS approach demonstrates its effective applicability and shows good results in the study of the thermal behavior of HAP.

Simulation and Computer Study of Structures and Physical Properties of Hydroxyapatite with Various Defects.

Simulation and computer studies of the structural and physical properties of hydroxyapatite (HAP) with different defects are presented in this review. HAP is a well-known material that is actively used in various fields of medicine, nanotechnology, and photocatalytic processes. However, all HAP samples have various defects and are still insufficiently studied. First of all, oxygen and OH group vacancies are important defects in HAP, which significantly affect its properties. The properties of HAP are also influenced by various substitutions of atoms in the HAP crystal lattice. The results of calculations by modern density functional theory methods of HAP structures with these different defects, primarily with oxygen and hydroxyl vacancies are analyzed in this review. The results obtained show that during the structural optimization of HAP with various defects, both the parameters of the crystallographic cells of the HAP change and the entire band structure of the HAP changes (changes in the band gap). This affects the electronic, optical, and elastic properties of HAP. The review considers the results of modeling and calculation of HAP containing various defects, the applied calculation methods, and the features of the effect of these defects on the properties of HAP, which is important for many practical applications.

Iron in Hydroxyapatite: Interstitial or Substitution Sites?

Iron-doped hydroxyapatite (Fe-HAp) is regarded as a promising magnetic material with innate biocompatibility. Despite the many studies reported in the literature, a detailed theoretical description of Fe inclusions is still missing. There is even no consensual view on what kind of Fe defects take place in Fe-HAp-iron interstitial or calcium substitutions? In order to address these questions, we employ modern first-principles methodologies, including hybrid density functional theory, to find the geometry, electronic, magnetic and thermodynamic properties of iron impurities in Fe-HAp. We consider a total of 26 defect configurations, including substitutional (phosphorus and calcium sites) and interstitial defects. Formation energies are estimated considering the boundaries of chemical potentials in stable hydroxyapatite. We show that the most probable defect configurations are: Fe3+ and Fe2+ substitutions of Ca(I) and Ca(II) sites under Ca-poor conditions. Conversely, Fe interstitials near the edge of the hydroxyl channel are favored in Ca-rich material. Substitutional Fe on the P site is also a probable defect, and unlike the other forms of Fe, it adopts a low-spin state. The analysis of Fe K-XANES spectra available in the literature shows that Fe-HAp usually contains iron in different configurations.

Polarization Switching in 2D Nanoscale Ferroelectrics: Computer Simulation and Experimental Data Analysis.

The polarization switching kinetics of nanosized ferroelectric crystals and the transition between homogeneous and domain switching in nanoscale ferroelectric films are considered. Homogeneous switching according to the Ginzburg-Landau-Devonshire (LGD) theory is possible only in two-dimensional (2D) ferroelectrics. The main condition for the applicability of the LGD theory in such systems is its homogeneity along the polarization switching direction. A review is given of the experimental results for two-dimensional (2D) films of a ferroelectric polymer, nanosized barium titanate nanofilms, and hafnium oxide-based films. For ultrathin 2D ferroelectric polymer films, the results are confirmed by first-principle calculations. Fitting of the transition region from homogeneous to domain switching by sigmoidal Boltzmann functions was carried out. Boltzmann function fitting data enabled us to correctly estimate the region sizes of the homogeneous switching in which the LGD theory is valid. These sizes contain several lattice constants or monolayers of a nanosized ferroelectrics.

Carnitine-dependent transport of acetyl coenzyme A in Candida albicans is essential for growth on nonfermentable carbon sources and contributes to biofilm formation.

In eukaryotes, acetyl coenzyme A (acetyl-CoA) produced during peroxisomal fatty acid beta-oxidation needs to be transported to mitochondria for further metabolism. Two parallel pathways for acetyl-CoA transport have been identified in Saccharomyces cerevisiae; one is dependent on peroxisomal citrate synthase (Cit), while the other requires peroxisomal and mitochondrial carnitine acetyltransferase (Cat) activities. Here we show that the human fungal pathogen Candida albicans lacks peroxisomal Cit, relying exclusively on Cat activity for transport of acetyl units. Deletion of the CAT2 gene encoding the major Cat enzyme in C. albicans resulted in a strain that had lost both peroxisomal and mitochondrion-associated Cat activities, could not grow on fatty acids or C(2) carbon sources (acetate or ethanol), accumulated intracellular acetyl-CoA, and showed greatly reduced fatty acid beta-oxidation activity. The cat2 null mutant was, however, not attenuated in virulence in a mouse model of systemic candidiasis. These observations support our previous results showing that peroxisomal fatty acid beta-oxidation activity is not essential for C. albicans virulence. Biofilm formation by the cat2 mutant on glucose was slightly reduced compared to that by the wild type, although both strains grew at the same rate on this carbon source. Our data show that C. albicans has diverged considerably from S. cerevisiae with respect to the mechanism of intracellular acetyl-CoA transport and imply that carnitine dependence may be an important trait of this human fungal pathogen.

Molecular modeling of the piezoelectric properties of ferroelectric composites containing polyvinylidene fluoride (PVDF) and either graphene or graphene oxide.

Molecular modeling of ferroelectric composites containing polyvinylidene fluoride (PVDF) and either graphene (G) or graphene oxide (GO) were performed using the semi-empirical quantum approximation PM3 in HyperChem. The piezo properties of the composites were analyzed and compared with experimental data obtained for P(VDF-TrFE)-GO films. Qualitative agreement was obtained between the results of the modeling and the experimental results in terms of the properties of the measured effective piezoelectric coefficient d 33eff and its decrease in the presence of G/GO in comparison with the average computed piezoelectric coefficient . When models incorporating one or several G layers with 54 carbon atoms were investigated, the average piezoelectric coefficient was found to decrease to -9.8 pm/V for the one-sided model PVDF/G and to -18.98 pm/V for the sandwich model G/PVDF/G as compared with the calculated piezoelectric coefficient for pure PVDF ( = -42.2 pm/V computed in present work, and = -38.5 pm/V, obtained from J Mol Model 35 (2013) 19:3591-3602). When models incorporating one or several GO layers with 98 carbon atoms were considered, the piezoelectric coefficient was found to decrease to -14.6 pm/V for the one-sided PVDF/GO model and to -29.8 pm/V for the sandwich GO/PVDF/GO model as compared with the same calculated piezoelectric coefficient for pure PVDF.

Molecular modeling of the piezoelectric effect in the ferroelectric polymer poly(vinylidene fluoride) (PVDF).

In this work, computational molecular modeling and exploration was applied to study the nature of the negative piezoelectric effect in the ferroelectric polymer polyvinylidene fluoride (PVDF), and the results confirmed by actual nanoscale measurements. First principle calculations were employed, using various quantum-chemical methods (QM), including semi-empirical (PM3) and various density functional theory (DFT) approaches, and in addition combined with molecular mechanics (MM) methods in complex joint approaches (QM/MM). Both PVDF molecular chains and a unit cell of crystalline ß-phase PVDF were modeled. This computational molecular exploration clearly shows that the nature of the so-called negative piezo-electric effect in the ferroelectric PVDF polymer has a self-consistent quantum nature, and is related to the redistribution of the electron molecular orbitals (wave functions), leading to the shifting of atomic nuclei and reorganization of all total charges to the new, energetically optimal positions, under an applied electrical field. Molecular modeling and first principles calculations show that the piezoelectric coefficient d 33 has a negative sign, and its average values lies in the range of d 33 ~ -16.6 to -19.2 pC/N (or pm/V) (for dielectric permittivity ε = 5) and in the range of d 33 ~ -33.5 to -38.5 pC/N (or pm/V) (for ε = 10), corresponding to known data, and allowing us to explain the reasons for the negative sign of the piezo-response. We found that when a field is applied perpendicular to the PVDF chain length, as polarization increases the chain also stretches, increasing its length and reducing its height. For computed value of ε ~ 5 we obtained a value of d31 ~ +15.5 pC/N with a positive sign. This computational study is corroborated by measured nanoscale data obtained by atomic force and piezo-response force microscopy (AFM/PFM). This study could be useful as a basis for further insights into other organic and molecular ferroelectrics.

Micromechanics of base pair unzipping in the DNA duplex.

All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G·C content and rather distinct for the parts with A·T content. It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork.

Hyphal content determines the compression strength of Candida albicans biofilms.

Candida albicans is the most frequently isolated human fungal pathogen among species causing biofilm-related clinical infections. Mechanical properties of Candida biofilms have hitherto been given no attention, despite the fact that mechanical properties are important for selection of treatment or dispersal of biofilm organisms due to a bodily fluid flow. The aim of this study was to identify the factors that determine the compression strength of Candida biofilms. Biofilms of C. albicans wild-type parental strain Caf2-1, mutant strain Chk24 lacking Chk1p [known to be involved in regulation of morphogenesis (yeast-to-hyphae transition)] and gene-reconstructed strain Chk23 were evaluated for their resistance to compression, along with biofilms of Candida tropicalis GB 9/9 and Candida parapsilosis GB 2/8, derived from used voice prosthetic biofilms. Additionally, cell morphologies within the biofilm, cell-surface hydrophobicities and extracellular polymeric substance composition were determined. Our results suggest that the hyphae-to-yeast ratio influences the compression strength of C. albicans biofilms. Biofilms with a hyphal content >50 % possessed significantly higher compressive strength and were more difficult to destroy by vortexing and sonication than biofilms with a lower hyphal content. However, when the amount of extracellular DNA (eDNA) in biofilms of C. albicans Caf2-1 and Chk24 increased, biofilm strength declined, suggesting that eDNA may influence biofilm integrity adversely.

Low-load compression testing: a novel way of measuring biofilm thickness.

Biofilms are complex and dynamic communities of microorganisms that are studied in many fields due to their abundance and economic impact. Biofilm thickness is an important parameter in biofilm characterization. Current methods of measuring biofilm thicknesses have several limitations, including application, availability, and costs. Here, we present low-load compression testing (LLCT) as a new method for measuring biofilm thickness. With LLCT, biofilm thicknesses are measured during compression by inducing small loads, up to 5 Pa, corresponding to 0.1% deformation, making LLCT essentially a nondestructive technique. Comparison of the thicknesses of various bacterial and yeasts biofilms obtained by LLCT and by using confocal laser scanning microscopy (CLSM) resulted in the conclusion that CLSM underestimates the biofilm thickness due to poor penetration of different fluorescent dyes, especially through the thicker biofilms, whereas LLCT does not suffer from this thickness limitation.

Measurement of biocolloid collision efficiencies for granular activated carbon by use of a two-layer filtration model.

Point-of-use filters containing granular activated carbon (GAC) are an effective method for removing certain chemicals from water, but their ability to remove bacteria and viruses has been relatively untested. Collision efficiencies (alpha) were determined using clean-bed filtration theory for two bacteria (Raoutella terrigena 33257 and Escherichia coli 25922), a bacteriophage (MS2), and latex microspheres for four GAC samples. These GAC samples had particle size distributions that were bimodal, but only a single particle diameter can be used in the filtration equation. Therefore, consistent with previous reports, we used a particle diameter based on the smallest diameter of the particles (derived from the projected areas of 10% of the smallest particles). The bacterial collision efficiencies calculated using the filtration model were high (0.8 < or = alpha < or = 4.9), indicating that GAC was an effective capture material. Collision efficiencies greater than unity reflect an underestimation of the collision frequency, likely as a result of particle roughness and wide GAC size distributions. The collision efficiencies for microspheres (0.7 < or = alpha < or = 3.5) were similar to those obtained for bacteria, suggesting that the microspheres were a reasonable surrogate for the bacteria. The bacteriophage collision efficiencies ranged from > or = 0.2 to < or = 0.4. The predicted levels of removal for 1-cm-thick carbon beds ranged from 0.8 to 3 log for the bacteria and from 0.3 to 1.0 log for the phage. These tests demonstrated that GAC can be an effective material for removal of bacteria and phage and that GAC particle size is a more important factor than relative stickiness for effective particle removal.