Molecular and Electronic Structure of the Peptide Subunit of Geobacter sulfurreducens Conductive Phi from First Principles

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved a-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pain was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's alpha-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Investigation of the optical absorption of a magnetic colloid from the thermal to the electronic time-scale regime: measurement of the free-carrier absorption cross-section

The free-carrier absorption cross-section sigma of a magnetic colloid composed of magnetite nanoparticles dispersed in oil is obtained by using the Z-scan technique in different experimental conditions of the laser beam. We show that it is possible to obtain sigma with picosecond pulsed and millisecond chopped beams with pulse frequencies smaller than about 30 Hz. For higher pulse frequencies, the heating of the colloidal system triggers the appearance of the Soret effect. This effect artificially increases the value of sigma calculated from the experimental results. The limits of the different experimental setups are discussed. (C) 2012 Optical Society of America

Effect of pre-flaring and file size on the accuracy of two electronic apex locators

Objective: This ex vivo study evaluated the effect of pre-flaring and file size on the accuracy of the Root ZX and Novapex electronic apex locators (EALs). Material and methods: The actual working length (WL) was set 1 mm short of the apical foramen in the palatal root canals of 24 extracted maxillary molars. The teeth were embedded in an alginate mold, and two examiners performed the electronic measurements using #10, #15, and #20 K-files. The files were inserted into the root canals until the "0.0" or "APEX" signals were observed on the LED or display screens for the Novapex and Root ZX, respectively, retracting to the 1.0 mark. The measurements were repeated after the pre-flaring using the S1 and SX Pro-Taper instruments. Two measurements were performed for each condition and the means were used. Intra-class correlation coefficients (ICCs) were calculated to verify the intra-and inter-examiner agreement. The mean differences between the WL and electronic length values were analyzed by the three-way ANOVA test (p<0.05). Results: ICCs were high (>0.8) and the results demonstrated a similar accuracy for both EALs (p>0.05). Statistically significant accurate measurements were verified in the pre-flared canals, except for the Novapex using a #20 K-file. Conclusions: The tested EALs showed acceptable accuracy, whereas the pre-flaring procedure revealed a more significant effect than the used file size.

Electronic stopping cross sections for protons in Al2O3: an experimental and theoretical study

The electronic stopping cross section (SCS) of Al2O3 for proton beams is studied both experimentally and theoretically. The measurements are made for proton energies from 40 keV up to 1 MeV, which cover the maximum stopping region, using two experimental methods, the transmission technique at low energies (similar to 40-175 keV) and the Rutherford backscattering at high energies (approximate to 190-1000 keV). These new data reveal an increment of 16% in the SCS around the maximum stopping with respect to older measurements. The theoretical study includes electronic stopping power calculations based on the dielectric formalism and on the transport cross section (TCS) model to describe the electron excitations of Al2O3. The non-linear TCS calculations of the SCS for valence electrons together with the generalized oscillator strengths (GOS) model for the core electrons compare well with the experimental data in the whole range of energies considered.

The Structural and Electronic Properties of Tin Oxide Nanowires: An Ab Initio Investigation

We performed an ab initio investigation on the properties of rutile tin oxide (SnOx) nanowires. We computed the wire properties determining the equilibrium geometries, binding energies, and electronic band structures for several wire dimensions and surface facet configurations. The results allowed us to establish scaling laws for the structural properties, in terms of the nanowire perimeters. The results also showed that the surface states control most of the electronic properties of the nanowires. Oxygen incorporation in the nanowire surfaces passivated the surface-related electronic states, and the resulting quantum properties and scaling laws were fully consistent with electrons confined inside the nanowire. Additionally, oxygen incorporation in the wire surfaces generated an unbalanced concentration of spin up and down electrons, leading to magnetic states for the nanowires.

Using Machine Learning Classifiers to Assist Healthcare-Related Decisions: Classification of Electronic Patient Records

Surveillance Levels (SLs) are categories for medical patients (used in Brazil) that represent different types of medical recommendations. SLs are defined according to risk factors and the medical and developmental history of patients. Each SL is associated with specific educational and clinical measures. The objective of the present paper was to verify computer-aided, automatic assignment of SLs. The present paper proposes a computer-aided approach for automatic recommendation of SLs. The approach is based on the classification of information from patient electronic records. For this purpose, a software architecture composed of three layers was developed. The architecture is formed by a classification layer that includes a linguistic module and machine learning classification modules. The classification layer allows for the use of different classification methods, including the use of preprocessed, normalized language data drawn from the linguistic module. We report the verification and validation of the software architecture in a Brazilian pediatric healthcare institution. The results indicate that selection of attributes can have a great effect on the performance of the system. Nonetheless, our automatic recommendation of surveillance level can still benefit from improvements in processing procedures when the linguistic module is applied prior to classification. Results from our efforts can be applied to different types of medical systems. The results of systems supported by the framework presented in this paper may be used by healthcare and governmental institutions to improve healthcare services in terms of establishing preventive measures and alerting authorities about the possibility of an epidemic.

In-plane mapping of buried InGaAs quantum rings and hybridization effects on the electronic structure

This work reports the investigation on the structural differences between InAs quantum rings and their precursor quantum dots species as well as on the presence of piezoelectric fields and asymmetries in these nanostructures. The experimental results show significant reduction in the ring dimensions when the sizes of capped and uncapped ring and dot samples are compared. The iso-lattice parameter mapped by grazing-incidence x-ray diffraction has revealed the lateral extent of strained regions in the buried rings. A comparison between strain and composition of dot and ring structures allows inferring on how the ring formation and its final configuration may affect optical response parameters. Based on the experimental observations, a discussion has been introduced on the effective potential profile to emulate theoretically the ring-shape confinement. The effects of confinement and strain field modulation on electron and hole band structures are simulated by a multiband k.p calculation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4733964]

Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method

There is a continuous search for theoretical methods that are able to describe the effects of the liquid environment on molecular systems. Different methods emphasize different aspects, and the treatment of both the local and bulk properties is still a great challenge. In this work, the electronic properties of a water molecule in liquid environment is studied by performing a relaxation of the geometry and electronic distribution using the free energy gradient method. This is made using a series of steps in each of which we run a purely molecular mechanical (MM) Monte Carlo Metropolis simulation of liquid water and subsequently perform a quantum mechanical/molecular mechanical (QM/MM) calculation of the ensemble averages of the charge distribution, atomic forces, and second derivatives. The MP2/aug-cc-pV5Z level is used to describe the electronic properties of the QM water. B3LYP with specially designed basis functions are used for the magnetic properties. Very good agreement is found for the local properties of water, such as geometry, vibrational frequencies, dipole moment, dipole polarizability, chemical shift, and spin-spin coupling constants. The very good performance of the free energy method combined with a QM/MM approach along with the possible limitations are briefly discussed.

The influence of different indium-composition profiles on the electronic structure of lens-shaped InxGa1-xAs quantum dots

We present effective-mass calculations of the bound-state energy levels of electrons confined inside lens-shaped InxGa1-xAs quantum dots (QDs) embedded in a GaAs matrix, taking into account the strain as well as the In gradient inside the QDs due to the strong In segregation and In-Ga intermixing present in the InxGa1-xAs/GaAs system. In order to perform the calculations, we used a continuum model for the strain, and the QDs and wetting layer were divided into their constituting monolayers, each one with a different In concentration, to be able to produce a specific composition profile. Our results clearly show that the introduction of such effects is very important if one desires to correctly reproduce or predict the optoelectronic properties of these nanostructures.

Local order and electronic structure of Pb1-xLaxZr0.40Ti0.60O3 materials and its relation with ferroelectric properties

The knowledge of electronic and local structures is a fundamental step towards understanding the properties of ferroelectric ceramics. X-ray absorption near-edge structure (XANES) of Pb1-xLaxZr0.40Ti0.60O3 ferroelectric samples was measured in order to know how the local order and electronic structure are related to their ferroelectric property, which was tailored by the substitution of lead by lanthanum atoms. The analysis of XANES spectra collected at Ti K- and L-edges XANES showed that the substitution of Pb by La leads to a decrement of local distortion around Ti atoms on the TiO6 octahedron. The analysis of O K-edge XANES spectra showed that the hybridization between O 2p and Pb 6sp states is related to the displacement of Ti atoms in the TiO6 octahedra. Based on these results, it is possible to determine that the degree of ferroelectricity in these samples and the manifestation of relaxor behavior are directly related to the weakening of O 2p and Pb 6sp hybridization. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4720472]

Accuracy of five electronic foramen locators with different operating systems: na ex vivo study

Objective: The aim of this study was to evaluate, ex vivo, the precision of five electronic root canal length measurement devices (ERCLMDs) with different operating systems: the Root ZX, Mini Apex Locator, Propex II, iPex, and RomiApex A-15, and the possible influence of the positioning of the instrument tips short of the apical foramen. Material and Methods: Forty-two mandibular bicuspids had their real canal lengths (RL) previously determined. Electronic measurements were performed 1.0 mm short of the apical foramen (-1.0), followed by measurements at the apical foramen (0.0). The data resulting from the comparison of the ERCLMD measurements and the RL were evaluated by the Wilcoxon and Friedman tests at a significance level of 5%. Results: Considering the measurements performed at 0.0 and -1.0, the precision rates for the ERCLMDs were: 73.5% and 47.1% (Root ZX), 73.5% and 55.9% (Mini Apex Locator), 67.6% and 41.1% (Propex II), 61.7% and 44.1% (iPex), and 79.4% and 44.1% (RomiApex A-15), respectively, considering ±0.5 mm of tolerance. Regarding the mean discrepancies, no differences were observed at 0.0; however, in the measurements at -1.0, the iPex, a multi-frequency ERCLMD, had significantly more discrepant readings short of the apical foramen than the other devices, except for the Propex II, which had intermediate results. When the ERCLMDs measurements at -1.0 were compared with those at 0.0, the Propex II, iPex and RomiApex A-15 presented significantly higher discrepancies in their readings. Conclusions: Under the conditions of the present study, all the ERCLMDs provided acceptable measurements at the 0.0 position. However, at the -1.0 position, the ERCLMDs had a lower precision, with statistically significant differences for the Propex II, iPex, and RomiApex A-15.

An in vivo radiographic evaluation of the accuracy of Apex and iPex electronic Apex locators

The aim of this study was to evaluate in vivo the clinical applicability of two electronic apex locators (EALs) - Apex (Septodont) and iPex (NSK) - in different groups of human teeth by using radiography. The working lengths (WLs) of 100 root canals were determined electronically. The EAL to be used first was chosen randomly and a K-file was inserted into the root canal until the EAL display indicated the location of the apical constriction (0 mm). The K-file was fixed to the tooth and a periapical radiograph was taken using a radiographic film holder. The K-file was removed and the WL was measured. The same procedure was repeated using the other EAL. Radiographs were examined with the aid of a light-box with lens of ×4 magnification by two blinded experienced endodontists. The distance between the file tip and the root apex was recorded as follows: (A) +1 to 0 mm, (B) -0.1 to 0.5 mm, (C) -0.6 to 1 mm, (D) -1.1 to 1.5 mm, and (E) -1.6 mm or greater. For statistical purposes, these scores were divided into 2 subgroups according to the radiographic apex: acceptable (B, C, and D) and non-acceptable (A and E). Statistically significant differences were not found between the results of Apex and iPex in terms of acceptable and non-acceptable measurements (p>0.05) or in terms of the distance recorded from file tip and the radiographic apex (p>0.05). Apex and iPex EALs provided reliable measurements for WL determination for endodontic therapy.

Three-dimensional portable document format: a simple way to present 3-dimensional data in an electronic publication

Three-dimensional (3D) models of teeth and soft and hard tissues are tessellated surfaces used for diagnosis, treatment planning, appliance fabrication, outcome evaluation, and research. In scientific publications or communications with colleagues, these 3D data are often reduced to 2-dimensional pictures or need special software for visualization. The portable document format (PDF) offers a simple way to interactively display 3D surface data without additional software other than a recent version of Adobe Reader (Adobe, San Jose, Calif). The purposes of this article were to give an example of how 3D data and their analyses can be interactively displayed in 3 dimensions in electronic publications, and to show how they can be exported from any software for diagnostic reports and communications among colleagues.

Development of a model-based transient calibration process for diesel engine electronic control module tables – Part 1: data requirements, processing, and analysis

This is the first part of a study investigating a model-based transient calibration process for diesel engines. The motivation is to populate hundreds of parameters (which can be calibrated) in a methodical and optimum manner by using model-based optimization in conjunction with the manual process so that, relative to the manual process used by itself, a significant improvement in transient emissions and fuel consumption and a sizable reduction in calibration time and test cell requirements is achieved. Empirical transient modelling and optimization has been addressed in the second part of this work, while the required data for model training and generalization are the focus of the current work. Transient and steady-state data from a turbocharged multicylinder diesel engine have been examined from a model training perspective. A single-cylinder engine with external air-handling has been used to expand the steady-state data to encompass transient parameter space. Based on comparative model performance and differences in the non-parametric space, primarily driven by a high engine difference between exhaust and intake manifold pressures (ΔP) during transients, it has been recommended that transient emission models should be trained with transient training data. It has been shown that electronic control module (ECM) estimates of transient charge flow and the exhaust gas recirculation (EGR) fraction cannot be accurate at the high engine ΔP frequently encountered during transient operation, and that such estimates do not account for cylinder-to-cylinder variation. The effects of high engine ΔP must therefore be incorporated empirically by using transient data generated from a spectrum of transient calibrations. Specific recommendations on how to choose such calibrations, how many data to acquire, and how to specify transient segments for data acquisition have been made. Methods to process transient data to account for transport delays and sensor lags have been developed. The processed data have then been visualized using statistical means to understand transient emission formation. Two modes of transient opacity formation have been observed and described. The first mode is driven by high engine ΔP and low fresh air flowrates, while the second mode is driven by high engine ΔP and high EGR flowrates. The EGR fraction is inaccurately estimated at both modes, while EGR distribution has been shown to be present but unaccounted for by the ECM. The two modes and associated phenomena are essential to understanding why transient emission models are calibration dependent and furthermore how to choose training data that will result in good model generalization.