Efficient parametrization of complex molecule-surface force fields

We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules. © 2015 Wiley Periodicals, Inc

Identification of intrinsic electron trapping sites in bulk amorphous silica from ab initio calculations

Using ab initio calculations we demonstrate that extra electrons in pure amorphous SiO2 can be trapped in deep band gap states. Classical potentials were used to generate amorphous silica models and density functional theory to characterise the geometrical and electronic structures of trapped electrons. Extra electrons can trap spontaneously on pre-existing structural precursors in amorphous SiO2 and produce ≈≈3.2 eV deep states in the band gap. These precursors comprise wide (⩾⩾130°°) O–Si–O angles and elongated Si–O bonds at the tails of corresponding distributions. The electron trapping in amorphous silica structure results in an opening of the O–Si–O angle (up to almost 180°°). We estimate the concentration of these electron trapping sites to be View the MathML source≈5×1019cm-3

Nature of intrinsic and extrinsic electron trapping in SiO 2

Using classical and ab initio calculations we demonstrate that extra electrons can be trapped in pure crystalline and amorphous SiO2 (a-SiO2) in deep band gap states. The structure of trapped electron sites in pure a-SiO2 is similar to that of Ge electron centers and so-called [SiO4/Li]0 centers in α quartz. Classical potentials were used to generate amorphous silica models and density functional theory to characterize the geometrical and electronic structures of trapped electrons in crystalline and amorphous silica. The calculations demonstrate that an extra electron can be trapped at a Ge impurity in α quartz in six different configurations. An electron in the [SiO4/Li]0 center is trapped on a regular Si ion with the Li ion residing nearby. Extra electrons can trap spontaneously on pre-existing structural precursors in amorphous SiO2, while the electron self-trapping in α quartz requires overcoming a barrier of about 0.6 eV. The precursors for electron trapping in amorphous SiO2 comprise wide (≥132∘) O–Si–O angles and elongated Si–O bonds at the tails of corresponding distributions. Using this criterion, we estimate the concentration of these electron trapping sites at ≈4×1019 cm−3

Calculating the entropy loss on adsorption of organic molecules at insulating surfaces

Although it is recognized that the dynamic behavior of adsorbing molecules strongly affects the entropic contribution to adsorption free energy, detailed studies of the adsorption entropy of large organic molecules at insulating surfaces are still rare. We compared adsorption of two different functionalized organic molecules, 1,3,5-tri(4-cyano-4,4-biphenyl)benzene (TCB) and 1,4-bis(cyanophenyl)-2,5-bis(decyloxy)benzene (CDB), on the KCl(001) surface using density functional theory (DFT) and molecular dynamics (MD) simulations. The accuracy of the van der Waals corrected DFT-D3 was benchmarked using Møller–Plesset perturbation theory calculations. Classical force fields were then parametrized for both the TCB and CDB molecules on the KCl(001) surface. These force fields were used to perform potential of mean force (PMF) calculations of adsorption of individual molecules and extract information on the entropic contributions to adsorption energy. The results demonstrate that entropy loss upon adsorption are significant for flexible molecules. Even at relatively low temperatures (e.g., 400 K), these effects can match the enthalpic contribution to adsorption energ

Hydrogen-induced rupture of strained Si─O bonds in amorphous silicon dioxide

Using ab initio modeling we demonstrate that H atoms can break strained Si─O bonds in continuous amorphous silicon dioxide (a−SiO2) networks, resulting in a new defect consisting of a threefold-coordinated Si atom with an unpaired electron facing a hydroxyl group, adding to the density of dangling bond defects, such as E′ centers. The energy barriers to form this defect from interstitial H atoms range between 0.5 and 1.3 eV. This discovery of unexpected reactivity of atomic hydrogen may have significant implications for our understanding of processes in silica glass and nanoscaled silica, e.g., in porous low-permittivity insulators, and strained variants of a−SiO2

Rationalizing meat consumption:The 4Ns

Recent theorizing suggests the 4Ns—that is, the belief that eating meat is natural, normal, necessary, and nice—are common rationalizations people use to defend their choice of eating meat. However, such theorizing has yet to be subjected to empirical testing. Six studies were conducted on the 4Ns. Studies 1a-1b demonstrated that the 4N classification captures the vast majority (83%-91%) of justifications people naturally offer in defense of eating meat. In Study 2, individuals who endorsed the 4Ns tended also to objectify (dementalize) animals and included fewer animals in their circle of moral concern, and this was true independent of social dominance orientation. Subsequent studies (Studies 3-5) showed that individuals who endorsed the 4Ns tend not to be motivated by ethical concerns when making food choices, are less involved in animal-welfare advocacy, less driven to restrict animal products from their diet, less proud of their animal-product decisions, tend to endorse Speciesist attitudes, tend to consume meat and animal products more frequently, and are highly committed to eating meat. Furthermore, omnivores who strongly endorsed the 4Ns tended to experience less guilt about their animal-product decisions, highlighting the guilt-alleviating function of the 4Ns

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity

Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient’s disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase’s ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours

Acceptability and feasibility of peer assisted supervision and support for intervention practitioners: a Q-methodology evaluation

Evidence-based interventions often include quality improvement methods to support fidelity and improve client outcomes. Clinical supervision is promoted as an effective way of developing practitioner confidence and competence in delivery; however, supervision is often inconsistent and embedded in hierarchical line management structures that may limit the opportunity for reflective learning. The Peer Assisted Supervision and Support (PASS) supervision model uses peer relationships to promote the self-regulatory capacity of practitioners to improve intervention delivery. The aim of the present study was to assess the acceptability and feasibility of PASS amongst parenting intervention practitioners. A Q-methodology approach was used to generate data and 30 practitioners volunteered to participate in the study. Data were analyzed and interpreted using standard Q-methodology procedures and by-person factor analysis yielded three factors. There was consensus that PASS was acceptable. Participants shared the view that PASS facilitated an environment of support where negative aspects of interpersonal relationships that might develop in supervision were not evident. Two factors represented the viewpoint that PASS was also a feasible model of supervision. However, the third factor was comprised of practitioners who reported that PASS could be time consuming and difficult to fit into existing work demands. There were differences across the three factors in the extent to which practitioners considered PASS impacted on their intervention delivery. The findings highlight the importance of organizational mechanisms that support practitioner engagement in supervision

Effect of electric field on migration of defects in oxides: Vacancies and interstitials in bulk MgO

Dielectric layers composed of metal oxides are routinely subjected to external electric fields during the course of normal operation of electronic devices. Many phenomenological theories suggest that electric fields strongly affect the properties and mobilities of defects in oxide films and can even facilitate the creation of new defects. Although defects in metal oxides have been studied extensively both experimentally and theoretically, the effect of applied electric fields on their structure and migration barriers is not well understood and still remains subject to speculations. Here, we investigate how static, homogeneous electric fields affect migration barriers of canonical defects—oxygen vacancies and interstitial ions—in a prototypical oxide, MgO. Using the modern theory of polarization within density functional theory (DFT), we apply electric fields to defect migration pathways in three different charge states. The effect of the field is characterized by the change of the dipole moment of the system along the migration pathway. The largest changes in the calculated barriers are observed for charged defects, while those for the neutral defects are barely significant. We show that by multiplying the dipole moment difference between the initial and the transition states, which we define as the effective dipole moment, by the field strength, one can obtain an estimate of the barrier change in excellent agreement with the DFT calculated values. These results will help to assess the applicability of phenomenological models and elucidate linear and nonlinear effects of field application in degradation of microelectronic devices, electrocatalysis, batteries, and other applications