Regression based D-optimality experimental design for sparse kernel density estimation

This paper derives an efficient algorithm for constructing sparse kernel density (SKD) estimates. The algorithm first selects a very small subset of significant kernels using an orthogonal forward regression (OFR) procedure based on the D-optimality experimental design criterion. The weights of the resulting sparse kernel model are then calculated using a modified multiplicative nonnegative quadratic programming algorithm. Unlike most of the SKD estimators, the proposed D-optimality regression approach is an unsupervised construction algorithm and it does not require an empirical desired response for the kernel selection task. The strength of the D-optimality OFR is owing to the fact that the algorithm automatically selects a small subset of the most significant kernels related to the largest eigenvalues of the kernel design matrix, which counts for the most energy of the kernel training data, and this also guarantees the most accurate kernel weight estimate. The proposed method is also computationally attractive, in comparison with many existing SKD construction algorithms. Extensive numerical investigation demonstrates the ability of this regression-based approach to efficiently construct a very sparse kernel density estimate with excellent test accuracy, and our results show that the proposed method compares favourably with other existing sparse methods, in terms of test accuracy, model sparsity and complexity, for constructing kernel density estimates.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Algorithmic statistical analysis of electrophysiological data for the investigation of structure-activity relationship in single neurons

We are developing computational tools supporting the detailed analysis of the dependence of neural electrophysiological response on dendritic morphology. We approach this problem by combining simulations of faithful models of neurons (experimental real life morphological data with known models of channel kinetics) with algorithmic extraction of morphological and physiological parameters and statistical analysis. In this paper, we present the novel method for an automatic recognition of spike trains in voltage traces, which eliminates the need for human intervention. This enables classification of waveforms with consistent criteria across all the analyzed traces and so it amounts to reduction of the noise in the data. This method allows for an automatic extraction of relevant physiological parameters necessary for further statistical analysis. In order to illustrate the usefulness of this procedure to analyze voltage traces, we characterized the influence of the somatic current injection level on several electrophysiological parameters in a set of modeled neurons. This application suggests that such an algorithmic processing of physiological data extracts parameters in a suitable form for further investigation of structure-activity relationship in single neurons.

Investigation of the factors influencing the survival of Bifidobacterium longum in model acidic solutions and fruit juices

The survival of Bifidobacterium longum NCIMB 8809 was studied during refrigerated storage for 6 weeks in model solutions, based on which a mathematical model was constructed describing cell survival as a function of pH, citric acid, protein and dietary fibre. A Central Composite Design (CCD) was developed studying the influence of four factors at three levels, i.e., pH (3.2–4), citric acid (2–15 g/l), protein (0–10 g/l), and dietary fibre (0–8 g/l). In total, 31 experimental runs were carried out. Analysis of variance (ANOVA) of the regression model demonstrated that the model fitted well the data. From the regression coefficients it was deduced that all four factors had a statistically significant (P < 0.05) negative effect on the log decrease [log10N0 week−log10N6 week], with the pH and citric acid being the most influential ones. Cell survival during storage was also investigated in various types of juices, including orange, grapefruit, blackcurrant, pineapple, pomegranate and strawberry. The highest cell survival (less than 0.4 log decrease) after 6 weeks of storage was observed in orange and pineapple, both of which had a pH of about 3.8. Although the pH of grapefruit and blackcurrant was similar (pH ∼3.2), the log decrease of the former was ∼0.5 log, whereas of the latter was ∼0.7 log. One reason for this could be the fact that grapefruit contained a high amount of citric acid (15.3 g/l). The log decrease in pomegranate and strawberry juices was extremely high (∼8 logs). The mathematical model was able to predict adequately the cell survival in orange, grapefruit, blackcurrant, and pineapple juices. However, the model failed to predict the cell survival in pomegranate and strawberry, most likely due to the very high levels of phenolic compounds in these two juices.

Optimizing the methods of synthesis for barium hexagonal ferrite: an experimental and theoretical study

M-type barium hexaferrite (BaM) is a hard ferrite, crystallizing in space group P6(3)/mmc possessing a hexagonal magneto-plumbite structure, which consists of alternate hexagonal and spinel blocks. The structure of BaM is thus related to those of garnet and spinel ferrite. However the material has proved difficult to synthesize. By taking into account the presence of the spinel block in barium hexagonal ferrite, highly efficient new synthetic methods were devised with routes significantly different from existing ones. These successful variations in synthetic methods have been derived by taking into account a detailed investigation of the structural features of barium hexagonal ferrite and the least change principle whereby configuration changes are kept to a minimum. Thus considering the relevant mechanisms has helped to improve the synthesis efficiencies for both hydrothermal and co-precipitation methods by choosing conditions that invoke the formation of the cubic block or the less stable Fe3O4. The role played by BaFe2O4 in the synthesis is also discussed. The distribution of iron from reactants or intermediates among different sites was also successfully explained. The proposed mechanisms are based on the principle that the cubic block must be self-assembled to form the final product. Thus, it is believed that these formulated mechanisms should be helpful in designing experiments to obtain a deeper understanding of the synthesis process and to investigate the substitution of magnetic ions with doping ions.

Experimental economics and the artificiality of alteration

A neglected critique of social science laboratories alleges that they implement phenomena different to those supposedly under investigation. The critique purports to be conceptual and so invulnerable to a technical solution. I argue that it undermines some economics designs seeking to implement features of real societies, and counsels more modesty in experimental write‐ups. It also constitutes a plausible argument that laboratory economics experiments are necessarily less demonstrative than natural scientific ones. More radical sceptical conclusions are unwarranted.

Structure and viscoelasticity of an electrorheological fluid in oscillatory shear: computer simulation investigation

The three-dimensional molecular dynamics simulation method has been used to study the dynamic responses of an electrorheological (ER) fluid in oscillatory shear. The structure and related viscoelastic behaviour of the fluid are found to be sensitive to the amplitude of the strain. With the increase of the strain amplitude, the structure formed by the particles changes from isolated columns to sheet-like structures which may be perpendicular or parallel to the oscillating direction. Along with the structure evolution, the field-induced moduli decrease significantly with an increase in strain amplitude. The viscoelastic behaviour of the structures obtained in the cases of different strain amplitudes was examined in the linear response regime and an evident structure dependence of the moduli was found. The reason for this lies in the anisotropy of the arrangement of the particles in these structures. Short-range interactions between the particles cannot be neglected in determining the viscoelastic behaviour of ER fluids at small strain amplitude, especially for parallel sheets. The simulation results were compared with available experimental data and good agreement was reached for most of them.

Engineering the electronic bandgaps and band edge positions in carbon-substituted 2D boron nitride: a first-principles investigation

Modification of graphene to open a robust gap in its electronic spectrum is essential for its use in field effect transistors and photochemistry applications. Inspired by recent experimental success in the preparation of homogeneous alloys of graphene and boron nitride (BN), we consider here engineering the electronic structure and bandgap of C2xB1−xN1−x alloys via both compositional and configurational modification. We start from the BN end-member, which already has a large bandgap, and then show that (a) the bandgap can in principle be reduced to about 2 eV with moderate substitution of C (x < 0.25); and (b) the electronic structure of C2xB1−xN1−x can be further tuned not only with composition x, but also with the configuration adopted by C substituents in the BN matrix. Our analysis, based on accurate screened hybrid functional calculations, provides a clear understanding of the correlation found between the bandgap and the level of aggregation of C atoms: the bandgap decreases most when the C atoms are maximally isolated, and increases with aggregation of C atoms due to the formation of bonding and anti-bonding bands associated with hybridization of occupied and empty defect states. We determine the location of valence and conduction band edges relative to vacuum and discuss the implications on the potential use of 2D C2xB1−xN1−x alloys in photocatalytic applications. Finally, we assess the thermodynamic limitations on the formation of these alloys using a cluster expansion model derived from first-principles.

Perennial legumes native to Australia: a preliminary investigation of nutritive value and response to cutting

Six Australian native herbaceous perennial legumes (Lotus australis, Swainsona colutoides, Swainsona swainsonioides, Cullen tenax, Glycine tabacina and Kennedia prorepens) were assessed in the glasshouse for nutritive value, soluble condensed tannins and production of herbage in response to three cutting treatments (regrowth harvested every 4 and 6 weeks and plants left uncut for 12 weeks). The Mediterranean perennial legumes Medicago sativa and Lotus corniculatus were also included. Dry matter (DM) yield of some native legumes was comparable to L. corniculatus, but M. sativa produced more DM than all species except S. swainsonioides after 12 weeks of regrowth. Dry matter yield of all native legumes decreased with increased cutting frequency, indicating a susceptibility to frequent defoliation. Shoot in vitro dry matter digestibility (DMD) was high (>70%) in most native legumes, except G. tabacina (65%) and K. prorepens (55%). Crude protein ranged from 21-28% for all legumes except K. prorepens (12%). More frequent cutting resulted in higher DMD and crude protein in all species, except for the DMD of C. tenax and L. australis, which did not change. Concentrations of soluble condensed tannins were 2-9 g/kg DM in the Lotus spp., 10-18 g/kg DM in K. prorepens and negligible (<1 g/kg) in the other legumes. Of the native species, C. tenax, S. swainsonioides and L. australis showed the most promise for use as forage plants and further evaluation under field conditions is now warranted.

Investigation and optimization of parameters affecting the multiply charged ion yield in AP-MALDI MS

Liquid matrix-assisted laser desorption/ionization (MALDI) allows the generation of predominantly multiply charged ions in atmospheric pressure (AP) MALDI ion sources for mass spectrometry (MS) analysis. The charge state distribution of the generated ions and the efficiency of the ion source in generating such ions crucially depend on the desolvation regime of the MALDI plume after desorption in the AP-tovacuum inlet. Both high temperature and a flow regime with increased residence time of the desorbed plume in the desolvation region promote the generation of multiply charged ions. Without such measures the application of an electric ion extraction field significantly increases the ion signal intensity of singly charged species while the detection of multiply charged species is less dependent on the extraction field. In general, optimization of high temperature application facilitates the predominant formation and detection of multiply charged compared to singly charged ion species. In this study an experimental setup and optimization strategy is described for liquid AP-MALDI MS which improves the ionization effi- ciency of selected ion species up to 14 times. In combination with ion mobility separation, the method allows the detection of multiply charged peptide and protein ions for analyte solution concentrations as low as 2 fmol/lL (0.5 lL, i.e. 1 fmol, deposited on the target) with very low sample consumption in the low nL-range.

NMR Chemical Shielding and Spin-Spin Coupling Constants of Liquid NH(3): A Systematic Investigation using the Sequential QM/MM Method

The NMR spin coupling parameters, (1)J(N,H) and (2)J(H,H), and the chemical shielding, sigma((15)N), of liquid ammonia are studied from a combined and sequential QM/MM methodology. Monte Carlo simulations are performed to generate statistically uncorrelated configurations that are submitted to density functional theory calculations. Two different Lennard-Jones potentials are used in the liquid simulations. Electronic polarization is included in these two potentials via an iterative procedure with and without geometry relaxation, and the influence on the calculated properties are analyzed. B3LYP/aug-cc-pVTZ-J calculations were used to compute the V(N,H) constants in the interval of -67.8 to -63.9 Hz, depending on the theoretical model used. These can be compared with the experimental results of -61.6 Hz. For the (2)J(H,H) coupling the theoretical results vary between -10.6 to -13.01 Hz. The indirect experimental result derived from partially deuterated liquid is -11.1 Hz. Inclusion of explicit hydrogen bonded molecules gives a small but important contribution. The vapor-to-liquid shifts are also considered. This shift is calculated to be negligible for (1)J(N,H) in agreement with experiment. This is rationalized as a cancellation of the geometry relaxation and pure solvent effects. For the chemical shielding, U(15 N) Calculations at the B3LYP/aug-pcS-3 show that the vapor-to-liquid chemical shift requires the explicit use of solvent molecules. Considering only one ammonia molecule in an electrostatic embedding gives a wrong sign for the chemical shift that is corrected only with the use of explicit additional molecules. The best result calculated for the vapor to liquid chemical shift Delta sigma((15)N) is -25.2 ppm, in good agreement with the experimental value of -22.6 ppm.

Boron and nitrogen functionalized diamondoids: A first principles investigation

Chemically functionalized adamantane molecules have been investigated by first principles total energy calculations. Boron and nitrogen functionalized molecules were found to be very stable, consistent with available experimental data. Two hypothetical molecular crystals, involving functionalized adamantane, were investigated. These molecular crystals presented direct electronic bandgaps and large bulk moduli, which suggested a possible road for molecular self-assembly using functionalized diamondoids. (C) 2010 Elsevier B.V. All rights reserved.

Transfer reactions in the investigation of light-nuclei nucleosynthesis

Cross sections for the (6)Li(p,gamma)(7)Be, (7)Li(n,gamma)(8)Li (8)Li(n,gamma)(9)Li and (8)Li(p,gamma)(9)Be capture reactions have been investigated in the framework of the potential model. The main ingredients of the potential model are the potentials used to generate the continuum and bound-state wave functions and spectroscopic factors of the corresponding bound systems. The spectroscopic factors for the (7)Li circle times n=(8)Li(gs), (8)Li circle times n=(9)Li(gs) bound systems were obtained from a FR-DWBA analysis of neutron transfer reactions induced by (8)Li radioactive beam on a (9)Be target, while spetroscopic factor for the (8)Li circle times n=(9)Be(gs) bound system were obained from a proton transfer reaction. From the obtained capture reaction cross section, reaction rate for the (8)Li(n,gamma)(9)Li and (8)Li(p,gamma)(9)Be direct neutron and proton capture were determined and compared with other experimental and calculated values.

Structural and spectroscopic properties of the diazocarbene radical (CNN) and its ions CNN(+) and CNN(-): a high-level theoretical investigation

The diazocarbene radical, CNN, and the ions CNN(+) and CNN(-) were investigated at a high level of theory. Very accurate structural parameters for the states X(3)Sigma(-) and A(3)Pi of CNN, and X(2)Pi of both CNN(+) and CNN(-) were obtained with the UCCSD(T) method using correlated-consistent basis functions with extrapolations to the complete basis set limit, with valence only and also with all electrons correlated. Harmonic and anharmonic frequencies were obtained for all species and the Renner parameter and average frequencies evaluated for the Pi states. At the UCCSD(T)/CBS(T-5) level of theory, Delta(f)H(0 K) = 138.89 kcal/mol and Delta(f)H(298 K) = 139.65 kcal/mol were obtained for diazocarbene; for the ionization potential and the electron affinity of CNN, 10.969 eV (252.95 kcal/mol), and 1.743 eV (40.19 kcal/mol), respectively, are predicted. Geometry optimization was also carried out with the CASSCF/MRCI/CBS(T-5) approach for the states X(3)Sigma(-) A(3)Pi, and a(1)Delta of CNN, and with the CASSCF/MRSDCI/aug-cc-pVTZ approach for the states b(1)Sigma(+), c(1)Pi, d(1)Sigma(-), and B(3)Sigma(-), and excitation energies (T(e)) evaluated. Vertical energies were calculated for 15 electronic states, thus improving on the accuracy of the five transitions already described, and allowing for a reliable overview of a manifold of other states, which is expected to guide future spectroscopic experiments. This study corroborates the experimental assignment for the vertical transition X (3)Sigma(-) <- E (3)Pi.

Spectroscopic investigation of the interactions between emeraldine base polyaniline and Eu(III) ions

The interactions of emeraldine base form of polyaniline (EB-PANI) and Eu(III) ions in 1-methyl-2-pyrrolidinone (NMP) solution and in films have been investigated by UV-vis-NIR, resonance Raman. luminescence and electron paramagnetic resonance (EPR) spectroscopies. These spectroscopic techniques allowed to characterize quinone and semiquinone segments in the polymeric chains. and the oxidation state of europium ions in Eu-PANI samples. For high values of Eu(III)/N molar ratio (24/1) the presence of a weak polaronic absorption band at 980 nm in UV-vis-NIR spectrum and the observation of bands at 1330 and 1378 (nu(center dot)(C-N+)) cm(-1) due to emeraldine salt in the Raman spectrum at 1064 nm indicate a low doping degree. Oxidation of EB-PANI to pernigraniline base (PB-PANI) occurs in diluted solutions. The experimental data showed that the solvent plays an important role on the nature of formed species. The narrow EPR signal at g = 2.006 (line width 8G) confirms the presence of PANI radical cations in Eu-PANI film. The absence of broad signal characteristic of Eu(II) in EPR spectrum suggested that europium ions are primarily at Eu(III) oxidation state. The luminescence spectra of Eu-PANI film presented emission bands at 405 and 418 nm assigned to PANI moieties and bands at 594,615 and 701 nm assigned to (5)D(0) -> (7)F(J) (J = 1, 2 and 4, respectively) transitions of Eu(III). EPR and photoluminescence data confirm that europium ions are mainly in Eu(III) oxidation state in Eu(III)/PANI films. (C) 2008 Elsevier B.V. All rights reserved.