Bayesian comparison of latent variable models: Conditional vs marginal likelihoods

Typical Bayesian methods for models with latent variables (or random effects) involve directly sampling the latent variables along with the model parameters. In high-level software code for model definitions (using, e.g., BUGS, JAGS, Stan), the likelihood is therefore specified as conditional on the latent variables. This can lead researchers to perform model comparisons via conditional likelihoods, where the latent variables are considered model parameters. In other settings, however, typical model comparisons involve marginal likelihoods where the latent variables are integrated out. This distinction is often overlooked despite the fact that it can have a large impact on the comparisons of interest. In this paper, we clarify and illustrate these issues, focusing on the comparison of conditional and marginal Deviance Information Criteria (DICs) and Watanabe-Akaike Information Criteria (WAICs) in psychometric modeling. The conditional/marginal distinction corresponds to whether the model should be predictive for the clusters that are in the data or for new clusters (where "clusters" typically correspond to higher-level units like people or schools). Correspondingly, we show that marginal WAIC corresponds to leave-one-cluster out (LOcO) cross-validation, whereas conditional WAIC corresponds to leave-one-unit out (LOuO). These results lead to recommendations on the general application of the criteria to models with latent variables.Comment: Manuscript in press at Psychometrika; 31 pages, 8 figure

Ideal barriers to polarization reversal and domain-wall motion in strained ferroelectric thin films

The ideal intrinsic barriers to domain switching in c-phase PbTiO_3 (PTO), PbZrO_3 (PZO), and PbZr_{1-x}Ti_xO_3 (PZT) are investigated via first-principles computational methods. The effects of epitaxial strain on the atomic structure, ferroelectric response, barrier to coherent domain reversal, domain-wall energy, and barrier to domain-wall translation are studied. It is found that PTO has a larger polarization, but smaller energy barrier to domain reversal, than PZO. Consequentially the idealized coercive field is over two times smaller in PTO than PZO. The Ti--O bond length is more sensitive to strain than the other bonds in the crystals. This results in the polarization and domain-wall energy in PTO having greater sensitivity to strain than in PZO. Two ordered phases of PZT are considered, the rock-salt structure and a (100) PTO/PZO superlattice. In these simple structures we find that the ferroelectric properties do not obey Vergard's law, but instead can be approximated as an average over individual 5-atom unit cells.Comment: 9 pages, 13 figure

Multiferroic BiFeO3-BiMnO3 Nanocheckerboard From First Principles

We present a first principles study of an unusual heterostructure, an atomic-scale checkerboard of BiFeO3-BiMnO3, and compare its properties to the two bulk constituent materials, BiFeO3 and BiMnO3. The "nanocheckerboard" is found to have a multiferroic ground state with the desired properties of each constituent: polar and ferrimagnetic due to BiFeO3 and BiMnO3, respectively. The effect of B-site cation ordering on magnetic ordering in the BiFeO3-BiMnO3 system is studied. The checkerboard geometry is seen to give rise to a a novel magnetostructural effect that is neither present in the bulk constituent materials, nor in the layered BiFeO3-BiMnO3 superlattice.Comment: 15 pages, 14 figure

Enhancement of piezoelectricity in a mixed ferroelectric

We use first-principles density-functional total energy and polarization calculations to calculate the piezoelectric tensor at zero temperature for both cubic and simple tetragonal ordered supercells of Pb_3GeTe_4. The largest piezoelectric coefficient for the tetragonal configuration is enhanced by a factor of about three with respect to that of the cubic configuration. This can be attributed to both the larger strain-induced motion of cations relative to anions and higher Born effective charges in the tetragonal case. A normal mode decomposition shows that both cation ordering and local relaxation weaken the ferroelectric instability, enhancing piezoelectricity.Comment: 5 pages, revtex, 2 eps figure

Selective Covalent Conjugation of Phosphorothioate DNA Oligonucleotides with Streptavidin

Protein-DNA conjugates have found numerous applications in the field of diagnostics and nanobiotechnology, however, their intrinsic susceptibility to DNA degradation by nucleases represents a major obstacle for many applications. We here report the selective covalent conjugation of the protein streptavidin (STV) with phosphorothioate oligonucleotides (psDNA) containing a terminal alkylthiolgroup as the chemically addressable linking unit, using a heterobifunctional NHS-/maleimide crosslinker. The psDNA-STV conjugates were synthesized in about 10% isolated yields. We demonstrate that the terminal alkylthiol group selectively reacts with the maleimide while the backbone sulfur atoms are not engaged in chemical conjugation. The novel psDNA-STV conjugates retain their binding capabilities for both biotinylated macromolecules and the complementary nucleic acid. Moreover, the psDNA-STV conjugate retained its binding capacity for complementary oligomers even after a nuclease digestion step, which effectively degrades deoxyribonucleotide oligomers and thus the binding capability of regular DNA-STV conjugates. The psDNA-STV therefore hold particular promise for applications e.g. in proteome research and novel biosensing devices, where interfering endogenous nucleic acids need to be removed from analytes by nuclease digestion

Conflict Between Doing Well And Doing Good? Capital Budgeting Case Study - Coors

Considering the paradox of drinking what you drive and driving what you drink, Coors Brewing Company’s conversion of spilt beer into ethanol is interesting and timely because of today’s intensified need for alternate fuels. The decision of investment in a sustainable project was present in 1996 as well as today. It is evident that Coors considered sustainability before it became popular. Their ethanol project allows an examination of several business issues that pertain to finance, accounting, operations management and environmental management students. This case has provided students sufficient information to practice the whole capital budgeting process which includes identifying and forecasting cash flows, applying capital budgeting tools and performing sensitivity and scenario analysis. Finance students will focus on cash flows and the capital budgeting aspect of the case. The potential reduction of waste disposal cost and generation of revenues from ethanol production will also be of interest to cost accounting students who focus on cutting costs in the production process. From a management standpoint, the Coors Brewing Company and Merrick’s ethanol project serves as an example of how a company can make a profit while engaging in environmentally safe projects. This illustrates the coexistence of company performance and ethicality.&nbsp

Piezoelectric control of the magnetic anisotropy via interface strain coupling in a composite multiferroic structure

We investigate theoretically the magnetic dynamics in a ferroelectric/ferromagnetic heterostructure coupled via strain-mediated magnetoelectric interaction. We predict an electric field-induced magnetic switching in the plane perpendicular to the magneto-crystalline easy axis, and trace this effect back to the piezoelectric control of the magnetoelastic coupling. We also investigate the magnetic remanence and the electric coercivity

Dynamic Behavior in Piezoresponse Force Microscopy

Frequency dependent dynamic behavior in Piezoresponse Force Microscopy (PFM) implemented on a beam-deflection atomic force microscope (AFM) is analyzed using a combination of modeling and experimental measurements. The PFM signal comprises contributions from local electrostatic forces acting on the tip, distributed forces acting on the cantilever, and three components of the electromechanical response vector. These interactions result in the bending and torsion of the cantilever, detected as vertical and lateral PFM signals. The relative magnitudes of these contributions depend on geometric parameters of the system, the stiffness and frictional forces of tip-surface junction, and operation frequencies. The dynamic signal formation mechanism in PFM is analyzed and conditions for optimal PFM imaging are formulated. The experimental approach for probing cantilever dynamics using frequency-bias spectroscopy and deconvolution of electromechanical and electrostatic contrast is implemented.Comment: 65 pages, 15 figures, high quality version available upon reques

First-principles study of epitaxial strain in perovskites

Using an extension of a first-principles method developed by King-Smith and Vanderbilt [Phys. Rev. B {\bf 49}, 5828 (1994)], we investigate the effects of in-plane epitaxial strain on the ground-state structure and polarization of eight perovskite oxides: BaTiO$_3$, SrTiO$_3$, CaTiO$_3$, KNbO$_3$, NaNbO$_3$, PbTiO$_3$, PbZrO$_3$, and BaZrO$_3$. In addition, we investigate the effects of a nonzero normal stress. The results are shown to be useful in predicting the structure and polarization of perovskite oxide thin films and superlattices.Comment: 10 page