title: A dynamic look into hydrogen bonding In proteins

authors: Van Tiel, Troy

subjects: Hydrogen bonding

abstract: This thesis aims to highlight the importance of analysing the dynamic nature of hydrogen bonds and their temporal variation. We also evaluate whether distance alone can and should be used as the main estimator for hydrogen bond strength. Molecular dynamics simulations of three common protein building blocks were conducted in triplicate to provide temporal data for our investigation. This data was then run through a newly developed program called Hybond, which analyses a given hydrogen bonding interaction as a function of time based on the reduced electron density gradient. The results found were promising and showed that the strength of a given hydrogen bond changes significantly throughout each simulation trajectory.  This demonstrates the dynamic nature of these hydrogen bonds, and we provide a workflow to efficiently characterise individual interactions as a function of time. We found that distance correlates well with kinetic energy density however there are points that do not fit this correlation. In these cases, hydrogen bond strength cannot be estimated through distance alone. Other properties that Hybond outputs have also shown promising correlations with kinetic energy density, and these can be used in place of distance to estimate the strength of the interaction. Finally, we investigated some of the challenges that arise when trying to determine the time-averaged strength of a given hydrogen bond and how different averaging approaches might be more appropriate than others, depending on the underlying science question that is being asked.

text: A dynamic look into hydrogen bonding In proteins This thesis aims to highlight the importance of analysing the dynamic nature of hydrogen bonds and their temporal variation. We also evaluate whether distance alone can and should be used as the main estimator for hydrogen bond strength. Molecular dynamics simulations of three common protein building blocks were conducted in triplicate to provide temporal data for our investigation. This data was then run through a newly developed program called Hybond, which analyses a given hydrogen bonding interaction as a function of time based on the reduced electron density gradient. The results found were promising and showed that the strength of a given hydrogen bond changes significantly throughout each simulation trajectory.  This demonstrates the dynamic nature of these hydrogen bonds, and we provide a workflow to efficiently characterise individual interactions as a function of time. We found that distance correlates well with kinetic energy density however there are points that do not fit this correlation. In these cases, hydrogen bond strength cannot be estimated through distance alone. Other properties that Hybond outputs have also shown promising correlations with kinetic energy density, and these can be used in place of distance to estimate the strength of the interaction. Finally, we investigated some of the challenges that arise when trying to determine the time-averaged strength of a given hydrogen bond and how different averaging approaches might be more appropriate than others, depending on the underlying science question that is being asked.

year: 2022

title: Gender and sexuality III: Precarious places

authors: Johnston, Lynda

subjects: social sciences

abstract: This progress report considers precarious geographies of genders and sexualities at a range of intersecting scales. In a time currently characterised as precarious, anxious and insecure, feminist and queer geographers are well placed to examine vulnerable geographies - including their own - of bodies, lives and labours. The review considers the ways precarity operates as a concept, condition and experience by first, asking what and where is precarity? Second, a recurring theme throughout feminist and queer precarious geographical literature is the importance of foregrounding relationality, the multiscalar, and marginalised bodies. Ultimately, what it means to feel ‘secure’ shifts and changes across places, genders and sexualities.

text: Gender and sexuality III: Precarious places This progress report considers precarious geographies of genders and sexualities at a range of intersecting scales. In a time currently characterised as precarious, anxious and insecure, feminist and queer geographers are well placed to examine vulnerable geographies - including their own - of bodies, lives and labours. The review considers the ways precarity operates as a concept, condition and experience by first, asking what and where is precarity? Second, a recurring theme throughout feminist and queer precarious geographical literature is the importance of foregrounding relationality, the multiscalar, and marginalised bodies. Ultimately, what it means to feel ‘secure’ shifts and changes across places, genders and sexualities.

year: 2018

title: The “standard story” of anti-Māori talk in Pae Ora (Healthy Futures) Bill submissions

authors: Black, Rose

abstract: AIM: To review some common patterns of race talk in a sample of submissions made to the Pae Ora (Healthy Futures) Bill. This bill proposed a structural reform of the health system in Aotearoa New Zealand to address long-standing health inequities experienced by Māori, the Indigenous peoples, and other priority populations. METHOD: In a sample of 3,000 individual submissions made in late 2021, we found 2,536 explicit references to race. Utilising the “stan-dard story” frame of Pākehā/non-Maori race talk, five longer submissions that inferred that the Pae Ora bill was “racist” were analysed in detail. RESULTS: Many “standard story” race discourses were identified in the Pae Ora submissions. Three derived discourses included in this paper are: Pākehā as norm (monoculturalism or not seeing Pākehā as a culture), equality and the “Treaty” (equality for all to access healthcare), and one people (we are all New Zealanders). Sources such as the Waitangi Tribunal Wai 2575 Hauora report were drawn on to provide alternative discourses. CONCLUSION: Identifying Pākehā standard story discourses enables learning about language patterns systems draw on, and the development of tools and procedures to improve equity for Māori and eliminate institutional racism.

text: The “standard story” of anti-Māori talk in Pae Ora (Healthy Futures) Bill submissions AIM: To review some common patterns of race talk in a sample of submissions made to the Pae Ora (Healthy Futures) Bill. This bill proposed a structural reform of the health system in Aotearoa New Zealand to address long-standing health inequities experienced by Māori, the Indigenous peoples, and other priority populations. METHOD: In a sample of 3,000 individual submissions made in late 2021, we found 2,536 explicit references to race. Utilising the “stan-dard story” frame of Pākehā/non-Maori race talk, five longer submissions that inferred that the Pae Ora bill was “racist” were analysed in detail. RESULTS: Many “standard story” race discourses were identified in the Pae Ora submissions. Three derived discourses included in this paper are: Pākehā as norm (monoculturalism or not seeing Pākehā as a culture), equality and the “Treaty” (equality for all to access healthcare), and one people (we are all New Zealanders). Sources such as the Waitangi Tribunal Wai 2575 Hauora report were drawn on to provide alternative discourses. CONCLUSION: Identifying Pākehā standard story discourses enables learning about language patterns systems draw on, and the development of tools and procedures to improve equity for Māori and eliminate institutional racism.

year: 2023-07-21