Nicholas Charles Handy. 17 June 1941 - 2 October 2012

Nicholas Handy made significant contributions in the applications of quantum mechanics to molecules. In an academic career at Cambridge University he was involved with many advances in the computational methods that have turned quantum chemistry into a central tool for understanding modern molecular science

Antibiotics Alter Pocillopora Coral-Symbiodiniaceae-Bacteria Interactions and Cause Microbial Dysbiosis During Heat Stress

Symbioses between eukaryotes and their associated microbial communities are fundamental processes that affect organisms’ ecology and evolution. A unique example of this is reef-building corals that maintain symbiotic associations with dinoflagellate algae (Symbiodiniaceae) and bacteria that affect coral health through various mechanisms. However, little is understood about how coral-associated bacteria communities affect holobiont heat tolerance. In this study, we investigated these interactions in four Pocillopora coral colonies belonging to three cryptic species by subjecting fragments to treatments with antibiotics intended to suppress the normal bacteria community, followed by acute heat stress. Separate treatments with only antibiotics or heat stress were conducted to compare the effects of individual stressors on holobiont transcriptome responses and microbiome shifts. Across all Pocillopora species examined, combined antibiotics and heat stress treatment significantly altered coral-associated bacteria communities and caused major changes in both coral and Cladocopium algal symbiont gene expression. Individually, heat stress impaired Pocillopora protein translation and activated DNA repair processes, while antibiotics treatments caused downregulation of Pocillopora amino acid and inorganic ion transport and metabolism genes and Cladocopium photosynthesis genes. Combined antibiotics-heat stress treatments caused synergistic effects on Pocillopora and Cladocopium gene expression including enhanced expression of oxidative stress response genes, programed cell death pathways and proteolytic enzymes that indicate an exacerbated response to heat stress following bacteria community suppression. Collectively, these results provide further evidence that corals and their Symbiodiniaceae and bacteria communities engage in highly coordinated metabolic interactions that are crucial for coral holobiont health, homeostasis, and heat tolerance

Correlation effects in ionic crystals: I. The cohesive energy of MgO

High-level quantum-chemical calculations, using the coupled-cluster approach and extended one-particle basis sets, have been performed for (Mg2+)n (O2-)m clusters embedded in a Madelung potential. The results of these calculations are used for setting up an incremental expansion for the correlation energy of bulk MgO. This way, 96% of the experimental cohesive energy of the MgO crystal is recovered. It is shown that only 60% of the correlation contribution to the cohesive energy is of intra-ionic origin, the remaining part being caused by van der Waals-like inter-ionic excitations.Comment: LaTeX, 20 pages, no figure

Ground state properties of heavy alkali halides

We extend previous work on alkali halides by calculations for the heavy-atom species RbF, RbCl, LiBr, NaBr, KBr, RbBr, LiI, NaI, KI, and RbI. Relativistic effects are included by means of energy-consistent pseudopotentials, correlations are treated at the coupled-cluster level. A striking deficiency of the Hartree-Fock approach are lattice constants deviating by up to 7.5 % from experimental values which is reduced to a maximum error of 2.4 % by taking into account electron correlation. Besides, we provide ab-initio data for in-crystal polarizabilities and van der Waals coefficients.Comment: accepted by Phys. Rev.

Three-body non-additive forces between spin-polarized alkali atoms

Three-body non-additive forces in systems of three spin-polarized alkali atoms (Li, Na, K, Rb and Cs) are investigated using high-level ab initio calculations. The non-additive forces are found to be large, especially near the equilateral equilibrium geometries. For Li, they increase the three-atom potential well depth by a factor of 4 and reduce the equilibrium interatomic distance by 0.9 A. The non-additive forces originate principally from chemical bonding arising from sp mixing effects.Comment: 4 pages, 3 figures (in 5 files

Manipulating Permeability as a Process for Controlling Crime: Balancing Security and Sustainability in Local Contexts

In response to the sustainability agenda, planning policy in the UK, USA and Australia has shifted to promote compact, high-density, mixed-used residential developments in walkable and permeable street networks close to public transport (Commonwealth of Australia, 1995; DETR, 1998; American Planning Association, 2007). This is to encourage walking and the use of public transport and to reduce car-use, energy use, pollution, congestion and urban sprawl. However, although permeability is assumed to represent a positive built environment feature which reduces crime by promoting more "eyes on the street" (Jacobs, 1961), a significant body of research in the field of environmental criminology challenges this assumptions. This paper reviews the theories and evidence associated with permeability and crime.Pedestrian access ways (PAWs) are often associated with crime and this paper discusses research which was directed at providing practical guidance to local governments on how they could better manage existing PAWs in Western Australia (WA). A morphological analysis of existing PAWs was undertaken which analysed the purposes, roles, functionality, users and dynamics of PAWs in a variety of different settings. In addition to crime (which had commonly be used as an excuse to close PAWs), the research considered issues such as amenity, walkability, equity and sustainability. A suite of five tools for assessing and reducing crime risk were developed, which attempt to balance security and sustainability issues. Contrary to assumptions, most PAWs were not subject to high levels of crime and many were vital to the community. Intriguingly, findings indicated that neighbourhood permeability can potentially be manipulated (via the management, closure or construction of new PAWs) to achieve the desired outcomes of reducing crime and of enhancing walkability, liveability and ultimately, the sustainability and well-being of communities

Human peritoneal mesothelial cells display phagocytic and antigen-presenting functions to contribute to intraperitoneal immunity

Mesothelial cells lining the peritoneal cavity are strategically positioned to respond to and counter intraperitoneal infections, cancer cells, and other challenges. We have investigated human peritoneal mesothelial cells (HPMCs) for phagocytic activity, expression of surface MHC Class II and accessory molecules involved in antigen presentation, and the ability to present recall antigens to T cells. Phagocytosis of dextran, latex beads and Escherichia coli was observed by flow cytometry, and internalization was visualised using confocal and electron microscopy. Flow cytometry and/or cellular ELISA showed constitutive expression of ICAM-I, LFA-3, and B7-1, but not B7-2 or MHC II. Interferon-gamma induced MHC II and ICAM-1 expression in a dose- and time-dependent manner. Importantly, HPMCs induced autologous CD3+ T lymphocyte proliferation (3H-incorporation) after pulse with recall antigen. HPMCs equipped with phagocytic and antigen-presenting machinery are anticipated to have an integral role in intraperitoneal immune surveillance

Sensory fusion in Physarum polycephalum and implementing multi-sensory functional computation

Surface electrical potential and observational growth recordings were made of a protoplasmic tube of the slime mould Physarum polycephalum in response to a multitude of stimuli with regards to sensory fusion or multisensory integration. Each stimulus was tested alone and in combination in order to evaluate for the first time the effect that multiple stimuli have on the frequency of streaming oscillation. White light caused a decrease in frequency whilst increasing the temperature and applying a food source in the form of oat flakes both increased the frequency. Simultaneously stimulating P. polycephalum with light and oat flake produced no net change in frequency, while combined light and heat stimuli showed an increase in frequency smaller than that observed for heat alone. When the two positive stimuli, oat flakes and heat, were combined, there was a net increase in frequency similar to the cumulative increases caused by the individual stimuli. Boolean logic gates were derived from the measured frequency change. © 2014

A gradient approach to localization of deformation. I. Hyperelastic materials

By utilizing methods recently developed in the theory of fluid interfaces, we provide a new framework for considering the localization of deformation and illustrate it for the case of hyperelastic materials. The approach overcomes one of the major shortcomings in constitutive equations for solids admitting localization of deformation at finite strains, i.e. their inability to provide physically acceptable solutions to boundary value problems in the post-localization range due to loss of ellipticity of the governing equations. Specifically, strain-induced localized deformation patterns are accounted for by adding a second deformation gradient-dependent term to the expression for the strain energy density. The modified strain energy function leads to equilibrium equations which remain always elliptic. Explicit solutions of these equations can be found for certain classes of deformations. They suggest not only the direction but also the width of the deformation bands providing for the first time a predictive unifying method for the study of pre- and post-localization behavior. The results derived here are a three-dimensional extension of certain one-dimensional findings reported earlier by the second author for the problem of simple shear.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42674/1/10659_2004_Article_BF00040814.pd