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: Paleoliquefaction in Late Pleistocene alluvial sediments in Hauraki and Hamilton basins, and implications for paleoseismicity

authors: Kleyburg, Melissa Anita

abstract: Liquefaction susceptibility of the Late Pleistocene Hinuera Formation is of interest to the engineering community as it is unclear whether materials of this age will still be prone to activation by cyclic stresses. In this paper we report on rare paleoliquefaction features in the form of injection structures that we have identified at two sites near Hamilton. These structures are clearly earthquake induced, and indicate the potential for future liquefaction episodes. However, we suggest that the hazard is restricted to areas with impeded drainage that imparts a high water table. Such areas are localised, and may be recognised from the modern (pedological) soil distribution. Evaluating piezocone penetration test (CPTu) data from the sites of known paleoliquefaction indicates that the CPTu gives a meaningful indication of liquefaction potential, and questions the validity of applying aging factors to these deposits.

text: Paleoliquefaction in Late Pleistocene alluvial sediments in Hauraki and Hamilton basins, and implications for paleoseismicity Liquefaction susceptibility of the Late Pleistocene Hinuera Formation is of interest to the engineering community as it is unclear whether materials of this age will still be prone to activation by cyclic stresses. In this paper we report on rare paleoliquefaction features in the form of injection structures that we have identified at two sites near Hamilton. These structures are clearly earthquake induced, and indicate the potential for future liquefaction episodes. However, we suggest that the hazard is restricted to areas with impeded drainage that imparts a high water table. Such areas are localised, and may be recognised from the modern (pedological) soil distribution. Evaluating piezocone penetration test (CPTu) data from the sites of known paleoliquefaction indicates that the CPTu gives a meaningful indication of liquefaction potential, and questions the validity of applying aging factors to these deposits.

year: 2015-02-22

title: Culture – the foundation of Maori Governance

authors: Toki, Valmaine

abstract: The structure of a governance system specifies the distribution of rights and responsibilities among different participants dictating the mutually agreed rules and procedures for making decisions on business affairs. For Maori, an indigenous people, the unique and pivotal factor that provides the point of difference, for governance, is the importance of their culture. Notwithstanding this point of difference, there exists a paucity of governance structures that adequately cater and provide for culture.

text: Culture – the foundation of Maori Governance The structure of a governance system specifies the distribution of rights and responsibilities among different participants dictating the mutually agreed rules and procedures for making decisions on business affairs. For Maori, an indigenous people, the unique and pivotal factor that provides the point of difference, for governance, is the importance of their culture. Notwithstanding this point of difference, there exists a paucity of governance structures that adequately cater and provide for culture.

year: 2013