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    A classical trajectory study of the photodissociation of T1 acetaldehyde: The transition from impulsive to statistical dynamics

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    Previous experimental and theoretical studies of the radical dissociation channel of T1 acetaldehyde show conflicting behavior in the HCO and CH3 product distributions. To resolve these conflicts, a full-dimensional potential-energy surface for the dissociation of CH3CHO into HCO and CH3 fragments over the barrier on the T1 surface is developed based on RO-CCSDT/cc-pVTZDZ ab initio calculations. 20 000 classical trajectories are calculated on this surface at each of five initial excess energies, spanning the excitation energies used in previous experimental studies, and translational, vibrational, and rotational distributions of the radical products are determined. For excess energies near the dissociation threshold, both the HCO and CH3 products are vibrationally cold; there is a small amount of HCO rotational excitation and little CH3 rotational excitation, and the reaction energy is partitioned dominantly 90% at threshold into relative translational motion. Close to threshold the HCO and CH3 rotational distributions are symmetrically shaped, resembling a Gaussian function, in agreement with observed experimental HCO rotational distributions. As the excess energy increases the calculated HCO and CH3 rotational distributions are observed to change from a Gaussian shape at threshold to one more resembling a Boltzmann distribution, a behavior also seen by various experimental groups. Thus the distribution of energy in these rotational degrees of freedom is observed to change from nonstatistical to apparently statistical, as excess energy increases. As the energy above threshold increases all the internal and external degrees of freedom are observed to gain population at a similar rate, broadly consistent with equipartitioning of the available energy at the transition state. These observations generally support the practice of separating the reaction dynamics into two reservoirs: an impulsive reservoir, fed by the exit channel dynamics, and a statistical reservoir, supported by the random distribution of excess energy above the barrier. The HCO rotation, however, is favored by approximately a factor of 3 over the statistical prediction. Thus, at sufficiently high excess energies, although the HCO rotational distribution may be considered statistical, the partitioning of energy into HCO rotation is not

    On Peace

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    On the separability of large-amplitude motions in anharmonic frequency calculations

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    Nuclear vibrational theories based upon the Watson Hamiltonian are ubiquitous in quantum chemistry, but are generally unable to model systems in which the wavefunction can delocalise over multiple energy minima, i.e. molecules that have low-energy torsion and inversion barriers. In a 2019 Chemical Reviews article, Puzzarini et al. note that a common workaround is to simply decouple these problematic modes from all other vibrations in the system during anharmonic frequency calculations. They also point out that this approximation can be "ill-suited", but do not quantify the errors introduced. In this work, we present the first systematic investigation into how separating out or constraining torsion and inversion vibrations within potential energy surface (PES) expansions affects the accuracy of computed fundamental wavenumbers for the remaining vibrational modes, using a test set of 19 tetratomic molecules for which high quality analytic potential energy surfaces and fully-coupled anharmonic reference fundamental frequencies are available. We find that the most effective and efficient strategy is to remove the mode in question from the PES expansion entirely. This introduces errors of up to +10 cm-1 in stretching fundamentals that would otherwise couple to the dropped mode, and ±5 cm-1 in all other fundamentals. These errors are approximately commensurate with, but not necessarily additional to, errors due to the choice of electronic structure model used in constructing spectroscopically accurate PES

    Not War, nor Peace. Are War and Peace Mutually Exclusive Alternatives?

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    Insight into the effectomes of Aotearoa Phytophthora cinnamomi isolates by comparative genomics.

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    Phytophthora cinnamomi is an extremely destructive phytopathogen that is the causative agent of dieback and root rot diseases in thousands of plant species worldwide. This fungi-like oomycete is a highly invasive endophyte, whose infections poses a serious threat to native biodiversity, forestry and agriculture. Exacerbation of its virulence and transmission is expected in a warming climate, increasing the need for the development of countermeasures against it, as current ones are largely ineffective. P. cinnamomi’s pathogenicity is dependent on its effector proteins that are secreted into the host’s tissues and allow for the establishment of a niche. The effectome is the collection of all effector proteins present in a genome, and they are under constant selective pressure, as the host species are in a race to develop resistance and co-evolve defences against the parasite. Therefore, understanding P. cinnamomi’s mechanisms of pathogenicity requires the identification of its rapidly evolving effectome. To investigate the results of constant co-evolution in such an effective plant pathogen, genome assembly and annotation were used for effectome identification. By understanding the basis of P. cinnamomi’s pathogenicity, we hope to provide insights into the evolution of susceptibility and resistance in hosts which will contribute to the development of treatments. Specifically, this will be done by analysing the variation between effectomes of P. cinnamomi that have been isolated from different host species. Here the genomes of 10 isolates of P. cinnamomi that were obtained from various hosts in Aotearoa were assembled using long-read sequencing. The annotation of genomic information obtained through reference guided assembly of long sequence reads allows for the identification of effectomes present in these genomes. By comparing the 10 genomes and their annotated effectomes a deeper understanding into the co-evolution of P. cinnamomi and it hosts, as well as its mechanisms of pathogenicity

    Hydrogenation-coupled water-gas shift reaction for simultaneous hydrogen generation and chemical storage.

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    The water–gas shift reaction (WGSR) is an important route for hydrogen (H₂) generation from syngas in biomass conversion processes such as gasification. Due to the exothermic nature of the reaction, a high reaction temperature hinders the equilibrium from moving towards hydrogen production. As a compromise, industrial plants often use a combination of a high-temperature and low-temperature WGS steps connected in series to maximize the hydrogen yield and productivity. In addition to hydrogen, the product gas contains CO residuals (approximately 1–10% due to incomplete conversion) and significant quantities of CO₂, which require costly processes of separation and purification. In this study, a system of hydrogenation-coupled WGSR (HC-WGSR) for simultaneous hydrogen production and in situ chemical storage is reported. The performance of the HC-WGSR system was first predicted through thermodynamic simulation. The proof-of-concept tandem WGSR and propene hydrogenation (model) reaction was successfully demonstrated using a low-temperature WGSR catalyst of CuO/ZnO/Al₂O₃. The results verified that the H₂ produced from the WGSR was successfully stored in propane simultaneously. An overall CO conversion of nearly 100% overcame the equilibrium limitation of the WGSR over a wide range of space velocities (3000-9000 h⁻¹) at 200 °C. Of particular industrial relevance, this study explicitly demonstrated that the in situ removal/storage of H₂ using the hydrogenation-coupling approach is promising even in a CO₂-rich environment (20% CO₂). A CO₂-rich syngas is commonly present in many plants, hindering WGSR for H₂ generation. This study also offers a new approach for using the underutilized CuO/ZnO/Al₂O₃ formulation in a commercial WGS catalyst. The new approach shall see a great opportunity in using organic hydrogen carriers, such as benzene, toluene, naphthalene, N-ethylcarbazole, to expand the industrial applications. Chapters 3 and 5 are based on a journal paper published in the International Journal of Hydrogen Energy: "A new hydrogenation-coupling approach for supra-equilibrium conversion in a water–gas shift reaction: simultaneous hydrogen generation and chemical storage" by Michael H. K. Lee et al. (Accepted on the 6th of February 2023)

    A theoretical and numerical investigation of large array of cantilever beams in fluids.

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    Over the last decade, several studies have been conducted involving a single cantilever beam oscillating in an unbounded fluid and close to a rigid surface. The purpose of these studies was to understand how the surrounding fluid and a rigid surface influence vibrating beams. In particular, these studies are relevant to applications such as atomic force microscopy (AFM), micro-electromechanical systems (MEMS), and energy harvesting. However, investigations based on multiple beams or a large array of beams in fluids remain unexplored. In addition, applications based on single beams can improve their efficiency by considering the array of beams (for example AFM). In this work, a two-dimensional boundary integral method (BIM) is employed to investigate the fluid dynamics of a large array of beams, for the first time taking into account the effects of neighbouring and non-neighbouring members. In order to gain a better understanding of the array dynamics we used a semi-analytical approach involving linearized Navier-Stokes equations. We analyze array sizes from 5 to 25 beams by comparing transverse hydrodynamic force and velocity profiles. An array of beams is studied parametrically by considering various parameters, including the gap between the beams, the height from the rigid surface, the Reynolds number, and the number of beams. BIM is a linearized model which is applicable to small amplitude ratios. A two-dimensional computational fluid dynamic analysis (CFD) has also been conducted for 3 to 11 beams in the fluid environment for both unbounded and bounded domains, in order to understand the effect of the fluid on a large array at various amplitude ratios and understand the onset, presence and influence of any nonlinearities. Novel results, directly related to the array configuration or size of the array include an overall increase in hydrodynamic force with an increase in array size, array effects highly coupled to the size of viscous layers, and interesting jump phenomena in hydrodynamic force close to the rigid surface. CFD analysis indicates the dominance of convection-driven nonlinearities. Further, we have compared and validated both the results of BIM and CFD analysis

    Documenting Horror in Häxan

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    AI's Promise: Our post-human future

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    In celebration of the centenary of Alan Turing’s birth, and motivated by the possibility of living forever in a cyborg body, we’ve given this forum over to refl ection on the future of machine intelligence. Turing is rightly called the father of computing, but just what did he accomplish, and what is his legacy? We begin to answer these questions with a rousing bit of speculation (and calls for restraint) by Jack Copeland and Diane Proudfoot, who consider the real promise of artifi cial intelligence. Next, John Preston gives us pause with an argument for the view that, Turing’s enthusiasm notwithstanding, computers will never really be thinking things. The famous Turing Test for machine intelligence gets a lot of attention, but Georges Rey argues that it’s small fry compared to Turing’s lesser known and much more profound ideas. Selmer Bringsjord and Joe Johnson warn of social upheaval ahead, owed to advances in robotics. We conclude with Luciano Floridi’s thoughts not just on Turing, but on the information revolution we fi nd ourselves in. Perhaps Turing’s ideas are transforming our conception of the universe and our place in it, in ways we have yet to understand fully. Floridi argues that Turing is still with us, and his legacy is very much alive.In celebration of the centenary of Alan Turing’s birth, and motivated by the possibility of living forever in a cyborg body, we’ve given this forum over to refl ection on the future of machine intelligence. Turing is rightly called the father of computing, but just what did he accomplish, and what is his legacy? We begin to answer these questions with a rousing bit of speculation (and calls for restraint) by Jack Copeland and Diane Proudfoot, who consider the real promise of artifi cial intelligence. Next, John Preston gives us pause with an argument for the view that, Turing’s enthusiasm notwithstanding, computers will never really be thinking things. The famous Turing Test for machine intelligence gets a lot of attention, but Georges Rey argues that it’s small fry compared to Turing’s lesser known and much more profound ideas. Selmer Bringsjord and Joe Johnson warn of social upheaval ahead, owed to advances in robotics. We conclude with Luciano Floridi’s thoughts not just on Turing, but on the information revolution we fi nd ourselves in. Perhaps Turing’s ideas are transforming our conception of the universe and our place in it, in ways we have yet to understand fully. Floridi argues that Turing is still with us, and his legacy is very much alive

    An Analysis of Agricultural Systems Modelling Approaches and Examples to Support Future Policy Development under Disruptive Changes in New Zealand

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    Agricultural systems have entered a period of significant disruption due to impacts from change drivers, increasingly stringent environmental regulations and the need to reduce unwanted discharges, and emerging technologies and biotechnologies. Governments and industries are developing strategies to respond to the risks and opportunities associated with these disruptors. Modelling is a useful tool for system conceptualisation, understanding, and scenario testing. Today, New Zealand and other nations need integrated modelling tools at the national scale to help industries and stakeholders plan for future disruptive changes. In this paper, following a scoping review process, we analyse modelling approaches and available agricultural systems’ model examples per thematic applications at the regional to national scale to define the best options for the national policy development. Each modelling approach has specificities, such as stakeholder engagement capacity, complex systems reproduction, predictive or prospective scenario testing, and users should consider coupling approaches for greater added value. The efficiency of spatial decision support tools working with a system dynamics approach can help holistically in stakeholders’ participation and understanding, and for improving land planning and policy. This model combination appears to be the most appropriate for the New Zealand national context

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