title: Finding the good vibes of life, man: Identifying catalytic vibrations in enzyme catalysis

authors: Schipper, Daniel-Albert

subjects: MMRT

abstract: Enzyme catalysis is one of the most vital components of life. As such the elucidation of the exact mechanics of this kind of catalysis is important. The aim of this work is to look into enzyme catalysis though the lens of macromolecular rate theory (MMRT). MMRT is an idea focused around the heat capacity of an enzyme changing over the course of a reaction. Our hypothesis is that this change in heat capacity is strongly tied to the nature of enzyme catalysis. As such, the focus of this thesis is to determine what a large change in heat capacity at the transition state on the reaction pathway means and why it happens.     
			
From previous work I know that there is a difference in heat capacity when an enzyme is bound to a reaction state compared to a transition state analog. One of the components of this project is to investigate the causes of this difference using all-atom molecular dynamics (MD) and calculations based on the MD trajectories.
			
In the harmonic case, it was found that there was no significant difference between our chosen enzyme in the reaction state and it in a transition state analog; which was possibly either due to insufficient simulation time or higher order anharmonic behavior driving the change in heat capacity. I computed the vibrational frequencies used to test this from the trajectories of a molecular dynamics simulation. 
			
			
In addition, the patterns of how the change in heat capacity evolves with temperature acts similarly to how changes in heat capacity act during phase transitions. These transitions are characterized by long range fluctuations, which I aimed to detect; however, no change in the distance of fluctuations was detected in the harmonic case in the simulations. 
			
Finally, I looked into computing heat capacities for a large system using the variance in energies. Previous attempts at doing this found reasonable values for the change in heat capacity when looking at an enzyme bound to a transition state analog vs bound to the reactant state. However, the absolute values of the heat capacities were an order of magnitude too high for each state. I investigated why this was the case and concluded that it was almost entirely due to not including quantum effects and the fact that interaction energies between the system and the solvent are dynamic.

text: Finding the good vibes of life, man: Identifying catalytic vibrations in enzyme catalysis Enzyme catalysis is one of the most vital components of life. As such the elucidation of the exact mechanics of this kind of catalysis is important. The aim of this work is to look into enzyme catalysis though the lens of macromolecular rate theory (MMRT). MMRT is an idea focused around the heat capacity of an enzyme changing over the course of a reaction. Our hypothesis is that this change in heat capacity is strongly tied to the nature of enzyme catalysis. As such, the focus of this thesis is to determine what a large change in heat capacity at the transition state on the reaction pathway means and why it happens.     
			
From previous work I know that there is a difference in heat capacity when an enzyme is bound to a reaction state compared to a transition state analog. One of the components of this project is to investigate the causes of this difference using all-atom molecular dynamics (MD) and calculations based on the MD trajectories.
			
In the harmonic case, it was found that there was no significant difference between our chosen enzyme in the reaction state and it in a transition state analog; which was possibly either due to insufficient simulation time or higher order anharmonic behavior driving the change in heat capacity. I computed the vibrational frequencies used to test this from the trajectories of a molecular dynamics simulation. 
			
			
In addition, the patterns of how the change in heat capacity evolves with temperature acts similarly to how changes in heat capacity act during phase transitions. These transitions are characterized by long range fluctuations, which I aimed to detect; however, no change in the distance of fluctuations was detected in the harmonic case in the simulations. 
			
Finally, I looked into computing heat capacities for a large system using the variance in energies. Previous attempts at doing this found reasonable values for the change in heat capacity when looking at an enzyme bound to a transition state analog vs bound to the reactant state. However, the absolute values of the heat capacities were an order of magnitude too high for each state. I investigated why this was the case and concluded that it was almost entirely due to not including quantum effects and the fact that interaction energies between the system and the solvent are dynamic.

year: 2020

title: The climatic character of the Auckland rural area

authors: Sparrow, Christopher J.

subjects: New Zealand

abstract: The characteristics of the climate of the rural area surrounding the Auckland urban area are discussed. Data used, is predominantly from published reports of the New Zealand Meteorological Service giving annual summaries of observations made at the various climatological, synoptic and rainfall recording stations. The mean characteristics of the area's climatic elements are considered together with their extremes. It is concluded that warm temperatures throughout the year, high humidity, variations in amount and. intensity of rainfall, prevailing westerly and infrequent easterly winds and high sunshine hours characterise the climate of this part of northern New Zealand.

text: The climatic character of the Auckland rural area The characteristics of the climate of the rural area surrounding the Auckland urban area are discussed. Data used, is predominantly from published reports of the New Zealand Meteorological Service giving annual summaries of observations made at the various climatological, synoptic and rainfall recording stations. The mean characteristics of the area's climatic elements are considered together with their extremes. It is concluded that warm temperatures throughout the year, high humidity, variations in amount and. intensity of rainfall, prevailing westerly and infrequent easterly winds and high sunshine hours characterise the climate of this part of northern New Zealand.

year: 1968

title: Modelling loanword success a sociolinguistic quantitative study of Māori loanwords in New Zealand English

authors: Calude, Andreea S.

subjects: loanwords

abstract: Loanword use has dominated the literature on language contact and its salient nature continues to draw interest from linguists and non-linguists. Traditionally, loanwords were investigated by means of raw frequencies, which are at best uninformative and at worst misleading. Following a new wave of studies which look at loans from a quantitatively more informed standpoint, modelling “success” by taking into account frequency of the counterparts avail- able in the language adopting the loanwords, we propose a similar model of loan-use and demonstrate its benefits in a case study of loanwords from Māori into (New Zealand) English. Our model contributes to previous work in this area by combining both the success measure mentioned above with a rich range of linguistic characteristics of the loanwords (such as loan length and word class), as well as a similarly detailed group of sociolinguistic characteristics of the speakers using them (gender, age and ethnicity of both, speakers and addresses). Our model is unique in bringing together of all these factors at the same time. The findings presented here illustrate the benefit of a quantitatively balanced approach to modelling loanword use. Furthermore, they illustrate the complex interaction between linguistic and sociolinguistic factors in such lan- guage contact scenarios.

text: Modelling loanword success a sociolinguistic quantitative study of Māori loanwords in New Zealand English Loanword use has dominated the literature on language contact and its salient nature continues to draw interest from linguists and non-linguists. Traditionally, loanwords were investigated by means of raw frequencies, which are at best uninformative and at worst misleading. Following a new wave of studies which look at loans from a quantitatively more informed standpoint, modelling “success” by taking into account frequency of the counterparts avail- able in the language adopting the loanwords, we propose a similar model of loan-use and demonstrate its benefits in a case study of loanwords from Māori into (New Zealand) English. Our model contributes to previous work in this area by combining both the success measure mentioned above with a rich range of linguistic characteristics of the loanwords (such as loan length and word class), as well as a similarly detailed group of sociolinguistic characteristics of the speakers using them (gender, age and ethnicity of both, speakers and addresses). Our model is unique in bringing together of all these factors at the same time. The findings presented here illustrate the benefit of a quantitatively balanced approach to modelling loanword use. Furthermore, they illustrate the complex interaction between linguistic and sociolinguistic factors in such lan- guage contact scenarios.

year: 2017