title: Use of computer simulation in the interpretation of elastic neutron scattering in complex molecular systems: a small protein in various environments

authors: Hayward, Jennifer A.

subjects: biology

abstract: Elastic and quasielastic neutron scattering experiments on complex systems are often difficult to interpret unambiguously directly using analytical dynamical models. In such cases computer simulations can be used to provide information at atomic detail. Here we report on the use of normal mode analysis (NMA) and molecular dynamics (MD) simulations of a small protein, bovine pancreatic trypsin inhibitor (BPTI) in vacuum and in various solvents. The simulations were performed over a range of temperatures (80–300 K). The vacuum simulation data are used to investigate neutron scattering properties. Effects are determined of instrumental energy resolution and of approximations commonly used to extract mean-square displacement data from elastic scattering experiments. Both the presence of a distribution of mean-square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean-square displacement obtained. Variation of the environment of the protein shows that the dry protein has higher fluctuations at lower temperatures than in the solvated protein, in agreement with recent experiments [1 and 2], that the dynamical transition is solvent-independent on short timescales (also in agreement with experiment [3]), and that at longer timescales it is strongly activated by water.

text: Use of computer simulation in the interpretation of elastic neutron scattering in complex molecular systems: a small protein in various environments Elastic and quasielastic neutron scattering experiments on complex systems are often difficult to interpret unambiguously directly using analytical dynamical models. In such cases computer simulations can be used to provide information at atomic detail. Here we report on the use of normal mode analysis (NMA) and molecular dynamics (MD) simulations of a small protein, bovine pancreatic trypsin inhibitor (BPTI) in vacuum and in various solvents. The simulations were performed over a range of temperatures (80–300 K). The vacuum simulation data are used to investigate neutron scattering properties. Effects are determined of instrumental energy resolution and of approximations commonly used to extract mean-square displacement data from elastic scattering experiments. Both the presence of a distribution of mean-square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean-square displacement obtained. Variation of the environment of the protein shows that the dry protein has higher fluctuations at lower temperatures than in the solvated protein, in agreement with recent experiments [1 and 2], that the dynamical transition is solvent-independent on short timescales (also in agreement with experiment [3]), and that at longer timescales it is strongly activated by water.

year: 2003

title: Moving beyond panaceas in fisheries governance

authors: Young, Oran R.

subjects: Science & Technology

abstract: In fisheries management—as in environmental governance more generally—regulatory arrangements thatare thought to be helpful in some contexts frequently become panaceas or, in other words, simpleformulaic policy prescriptions believed to solve a given problem in a wide range of contexts, regardlessof their actual consequences. When this happens, management is likely to fail, and negative side effectsare common. We focus on the case of individual transferable quotas to explore the panacea mindset, a setof factors that promote the spread and persistence of panaceas. These include conceptual narratives thatmake easy answers like panaceas seem plausible, power disconnects that create vested interests in pan-aceas, and heuristics and biases that prevent people from accurately assessing panaceas. Analysts havesuggested many approaches to avoiding panaceas, but most fail to conquer the underlying panaceamindset. Here, we suggest the codevelopment of an institutional diagnostics toolkit to distill the vastamount of information on fisheries governance into an easily accessible, open, on-line database of check-lists, case studies, and related resources. Toolkits like this could be used in many governance settings tochallenge users’understandings of a policy’s impacts and help them develop solutions better tailored totheir particular context. They would not replace the more comprehensive approaches found in the liter-ature but would rather be an intermediate step away from the problem of panaceas.

text: Moving beyond panaceas in fisheries governance In fisheries management—as in environmental governance more generally—regulatory arrangements thatare thought to be helpful in some contexts frequently become panaceas or, in other words, simpleformulaic policy prescriptions believed to solve a given problem in a wide range of contexts, regardlessof their actual consequences. When this happens, management is likely to fail, and negative side effectsare common. We focus on the case of individual transferable quotas to explore the panacea mindset, a setof factors that promote the spread and persistence of panaceas. These include conceptual narratives thatmake easy answers like panaceas seem plausible, power disconnects that create vested interests in pan-aceas, and heuristics and biases that prevent people from accurately assessing panaceas. Analysts havesuggested many approaches to avoiding panaceas, but most fail to conquer the underlying panaceamindset. Here, we suggest the codevelopment of an institutional diagnostics toolkit to distill the vastamount of information on fisheries governance into an easily accessible, open, on-line database of check-lists, case studies, and related resources. Toolkits like this could be used in many governance settings tochallenge users’understandings of a policy’s impacts and help them develop solutions better tailored totheir particular context. They would not replace the more comprehensive approaches found in the liter-ature but would rather be an intermediate step away from the problem of panaceas.

year: 2018-09-11

title: The use of functionalised biochar to enhance phosphorus removal in woodchip bioreactors. The integration of mātauranga Māori to enhance the cultural aspects of woodchip bioreactors.

authors: Taoho, Brandon

subjects: Woodchip bioreactor

abstract: Nutrient pollution, resulting from excessive releases of nitrogen (N) and phosphorus (P) into waterways, poses a significant threat to aquatic ecosystems worldwide. Elevated nutrient levels can result in eutrophication, which can have detrimental effects on the health of waterbodies and their biota. Woodchip bioreactors are effective, edge-of-field technologies that can help mitigate nutrient pollution by lowering nutrient concentrations in agricultural drainage systems known to carry leached N and P into waterways. However, one limitation to their design is their ineffectiveness at removing P. The inclusion of functionalised biochar is one potential solution to enhance P removal in woodchip bioreactors. There is a growing need to mitigate nutrient pollution in New Zealand that does not depend on a western-centric perspective only. Integration of mātauranga Māori and western science into the design and operations of a woodchip bioreactor is one approach to incorporate both knowledge systems to the goal of mitigating nutrient pollution. In this dissertation, a column experiment was used to compare the P removal efficiencies of two treatments of functionalised biochar, and one treatment of woodchips when subjected to stream water spiked with P. Subsequently, a single phosphate extraction was done to determine the phosphate absorption capacities of each treatment. The results showed that the two functionalised biochar treatments had the highest efficacy in reducing P concentrations in the P-spiked stream water compared to the woodchip-only treatment. Both treatments also showed higher P absorption, evidenced from the Fe-P/Feox ratio, within the phosphate extraction experiment. A wānanga was organised at Matahuru Marae, Lake Waikare, to share mātauranga Māori on how to culturally enhance woodchip bioreactors from a Te Ao Māori perspective. Participants recommended that native woodchips be incorporated into woodchip bioreactors because of their inherent association to the land and people. Overall, the results implied that functionalised biochar is an effective solution to enhance P removal in woodchip bioreactors due to their biophysical properties to absorb and retain P. Secondly, incorporating native woodchips into woodchip bioreactors systems potentially offers a sustainable and culturally respected alternative to conventional wood chips, aligning with Māori values and tikanga

text: The use of functionalised biochar to enhance phosphorus removal in woodchip bioreactors. The integration of mātauranga Māori to enhance the cultural aspects of woodchip bioreactors. Nutrient pollution, resulting from excessive releases of nitrogen (N) and phosphorus (P) into waterways, poses a significant threat to aquatic ecosystems worldwide. Elevated nutrient levels can result in eutrophication, which can have detrimental effects on the health of waterbodies and their biota. Woodchip bioreactors are effective, edge-of-field technologies that can help mitigate nutrient pollution by lowering nutrient concentrations in agricultural drainage systems known to carry leached N and P into waterways. However, one limitation to their design is their ineffectiveness at removing P. The inclusion of functionalised biochar is one potential solution to enhance P removal in woodchip bioreactors. There is a growing need to mitigate nutrient pollution in New Zealand that does not depend on a western-centric perspective only. Integration of mātauranga Māori and western science into the design and operations of a woodchip bioreactor is one approach to incorporate both knowledge systems to the goal of mitigating nutrient pollution. In this dissertation, a column experiment was used to compare the P removal efficiencies of two treatments of functionalised biochar, and one treatment of woodchips when subjected to stream water spiked with P. Subsequently, a single phosphate extraction was done to determine the phosphate absorption capacities of each treatment. The results showed that the two functionalised biochar treatments had the highest efficacy in reducing P concentrations in the P-spiked stream water compared to the woodchip-only treatment. Both treatments also showed higher P absorption, evidenced from the Fe-P/Feox ratio, within the phosphate extraction experiment. A wānanga was organised at Matahuru Marae, Lake Waikare, to share mātauranga Māori on how to culturally enhance woodchip bioreactors from a Te Ao Māori perspective. Participants recommended that native woodchips be incorporated into woodchip bioreactors because of their inherent association to the land and people. Overall, the results implied that functionalised biochar is an effective solution to enhance P removal in woodchip bioreactors due to their biophysical properties to absorb and retain P. Secondly, incorporating native woodchips into woodchip bioreactors systems potentially offers a sustainable and culturally respected alternative to conventional wood chips, aligning with Māori values and tikanga

year: 2023