title: Portfolio of Compositions

authors: Wragg, Jeffrey Stephen

abstract: This portfolio is made up of eight works. Et Tu mixes both acoustic and electronic instruments. In addition to traditional compositional techniques it also utilizes digital effects as a means of enhancing the composition. Following that is a collection of four short piano etudes. These pieces were composed as studies of the Tone Clock theory, primarily as a means of acquainting myself with the principles behind the Tone Clock. The first etude, Tea with Chopin, is based on the third hour and utilizes a synthetic scale which I then harmonized to create a unique harmonic palette. Coffee with Beethoven is based on the second hour of the Tone Clock and relies heavily on the octatonic scale. Absinthe with Ligeti is based on the fourth hour. Unlike the previous etudes it is atonal and uses some very complex rhythms.  The final etude, Early Morning Raindrops on a Misty Pond, is based on the ninth hour of the Tone Clock. The two hands of the piano play in a highly syncopated manner, creating a free flowing rhythmic texture. The way in which I used the Tone Clock in this piece, as well as its gesturing quality, provided the most insight into the composition of Symphony No. 2. Vengeance is a polystylist piece, blending popular and orchestral music. Through the use of vocals and spoken word it ponders the question of the nature of God and the place of religion in the world. The Call of Capistrano is a piece for solo classical guitar. It is based on sonata form and incorporates percussive elements such as striking the body of the guitar. The portfolio  concludes with Symphony No. 2. It is contemporary in style, with little reference to the symphonic writing of the Classical and Romantic periods. Instead it draws inspiration from 20th century composers such as Lutoslawski and Penderecki. While all the pitches are strictly controlled there are many aleatoric sections where certain liberties can be taken with the rhythms notated and each family of the orchestra will not always play together as a unified section.

text: Portfolio of Compositions This portfolio is made up of eight works. Et Tu mixes both acoustic and electronic instruments. In addition to traditional compositional techniques it also utilizes digital effects as a means of enhancing the composition. Following that is a collection of four short piano etudes. These pieces were composed as studies of the Tone Clock theory, primarily as a means of acquainting myself with the principles behind the Tone Clock. The first etude, Tea with Chopin, is based on the third hour and utilizes a synthetic scale which I then harmonized to create a unique harmonic palette. Coffee with Beethoven is based on the second hour of the Tone Clock and relies heavily on the octatonic scale. Absinthe with Ligeti is based on the fourth hour. Unlike the previous etudes it is atonal and uses some very complex rhythms.  The final etude, Early Morning Raindrops on a Misty Pond, is based on the ninth hour of the Tone Clock. The two hands of the piano play in a highly syncopated manner, creating a free flowing rhythmic texture. The way in which I used the Tone Clock in this piece, as well as its gesturing quality, provided the most insight into the composition of Symphony No. 2. Vengeance is a polystylist piece, blending popular and orchestral music. Through the use of vocals and spoken word it ponders the question of the nature of God and the place of religion in the world. The Call of Capistrano is a piece for solo classical guitar. It is based on sonata form and incorporates percussive elements such as striking the body of the guitar. The portfolio  concludes with Symphony No. 2. It is contemporary in style, with little reference to the symphonic writing of the Classical and Romantic periods. Instead it draws inspiration from 20th century composers such as Lutoslawski and Penderecki. While all the pitches are strictly controlled there are many aleatoric sections where certain liberties can be taken with the rhythms notated and each family of the orchestra will not always play together as a unified section.

year: 2012

title: How life uses sound to reorganise matter: The role of anharmonic phonon exchange in enzyme catalysis

authors: Batterton, Christopher

subjects: enzyme catalysis

abstract: Biological enzyme catalysis is the name for life's ability to rapidly invoke coordinated rearrangements of molecular structures using highly specialised, relatively-large functional proteins called enzymes. It is well established that enzymes reduce the activation energy barrier, which vastly accelerates the rate of reaction, however the specific dynamics and quantum mechanics are largely uncharted. Recent experimentation and modelling hints that there is a phase transition dynamic that is fundamental to enzymatic catalysis. The hypothesis that I explore in this thesis is that a mathematical model of a substrate molecule based upon anharmonic quantum vibrational modes (molecular phonons) will predict phase transition dynamics due to the presence of the appropriate enzyme. A molecular phonon is one particular individualised wave pattern in the locations of atomic nuclei from the total molecular dance that spans the low-frequency bulk swaying motions, mid-frequency bond stretches, to the high-frequency oscillations of the hydrogen bond network. 


In this thesis, I derive a generalised set of equations of motion for the anharmonic response behaviour of molecular phonons to enzyme stimulus via a dissipative quantum master equation, and I explore the phase transition dynamics by determining the stability bifurcation of the steady states. I then determine the critical minimum stimulus required for a molecular vibrational mode to exhibit a phase transition. The primary catalytic reaction of focus for this thesis is the cleavage of the glycosidic carbon-oxygen bond of the complex sugar isomaltose into two individual glucose molecules via the action of the enzyme MalL. Prior to this thesis, the atomic structure of MalL was obtained experimentally via X-ray diffraction crystallography of prepared MalL crystals, then digitised into the Gromacs software package and energy minimised in a simulated water bath to approximate the vibrational modes of the in vivo configuration. I obtain the substrate molecule's harmonic frequencies and anharmonic shifts via molecular dynamics performed using the Gaussian 09 normal mode analysis and simulated anharmonic infrared spectroscopy packages, respectively. I construct a generalised coding package in Matlab to extract the molecule and enzyme data, perform a quantum anharmonic analysis of the molecule--enzyme complex and their interactions, and then simulate the response of the molecule to stimulus from the enzyme. 

 
I determine that the vibrational modes of isomaltose that significantly contribute to stretching the glycosidic carbon-oxygen bond occur within the 21 to 35 THz (700 to 1,170 cm^{-1}) frequency bandwidth, and the dominant stretching modes are contained within 28 to 33 THz (930 to 1,100cm^{-1}), which is in agreement with the experimental literature of polysaccharides. In the final chapter, I perform numerical simulations of the equations of motion to compute the energy response spectrogram for a proxy substrate (benzene) under conditions that are informed by literature and the theoretical findings of this thesis. In lieu of anharmonic isomaltose data, I selected benzene as it is a small molecule with a high degree of symmetry which has several bond stretching modes within the aforementioned bandwidth. The results show that while the stimulus from water is insufficient, there are vibrational modes pertaining to glycosidic bond stretching that can be selectively excited to phase transition behaviour due to a reasonable stimulus from the supply of phonons from the MalL enzyme.

text: How life uses sound to reorganise matter: The role of anharmonic phonon exchange in enzyme catalysis Biological enzyme catalysis is the name for life's ability to rapidly invoke coordinated rearrangements of molecular structures using highly specialised, relatively-large functional proteins called enzymes. It is well established that enzymes reduce the activation energy barrier, which vastly accelerates the rate of reaction, however the specific dynamics and quantum mechanics are largely uncharted. Recent experimentation and modelling hints that there is a phase transition dynamic that is fundamental to enzymatic catalysis. The hypothesis that I explore in this thesis is that a mathematical model of a substrate molecule based upon anharmonic quantum vibrational modes (molecular phonons) will predict phase transition dynamics due to the presence of the appropriate enzyme. A molecular phonon is one particular individualised wave pattern in the locations of atomic nuclei from the total molecular dance that spans the low-frequency bulk swaying motions, mid-frequency bond stretches, to the high-frequency oscillations of the hydrogen bond network. 


In this thesis, I derive a generalised set of equations of motion for the anharmonic response behaviour of molecular phonons to enzyme stimulus via a dissipative quantum master equation, and I explore the phase transition dynamics by determining the stability bifurcation of the steady states. I then determine the critical minimum stimulus required for a molecular vibrational mode to exhibit a phase transition. The primary catalytic reaction of focus for this thesis is the cleavage of the glycosidic carbon-oxygen bond of the complex sugar isomaltose into two individual glucose molecules via the action of the enzyme MalL. Prior to this thesis, the atomic structure of MalL was obtained experimentally via X-ray diffraction crystallography of prepared MalL crystals, then digitised into the Gromacs software package and energy minimised in a simulated water bath to approximate the vibrational modes of the in vivo configuration. I obtain the substrate molecule's harmonic frequencies and anharmonic shifts via molecular dynamics performed using the Gaussian 09 normal mode analysis and simulated anharmonic infrared spectroscopy packages, respectively. I construct a generalised coding package in Matlab to extract the molecule and enzyme data, perform a quantum anharmonic analysis of the molecule--enzyme complex and their interactions, and then simulate the response of the molecule to stimulus from the enzyme. 

 
I determine that the vibrational modes of isomaltose that significantly contribute to stretching the glycosidic carbon-oxygen bond occur within the 21 to 35 THz (700 to 1,170 cm^{-1}) frequency bandwidth, and the dominant stretching modes are contained within 28 to 33 THz (930 to 1,100cm^{-1}), which is in agreement with the experimental literature of polysaccharides. In the final chapter, I perform numerical simulations of the equations of motion to compute the energy response spectrogram for a proxy substrate (benzene) under conditions that are informed by literature and the theoretical findings of this thesis. In lieu of anharmonic isomaltose data, I selected benzene as it is a small molecule with a high degree of symmetry which has several bond stretching modes within the aforementioned bandwidth. The results show that while the stimulus from water is insufficient, there are vibrational modes pertaining to glycosidic bond stretching that can be selectively excited to phase transition behaviour due to a reasonable stimulus from the supply of phonons from the MalL enzyme.

year: 2024

title: An evaluation of Kaupapa Māori in Psychology at the University of Waikato

authors: McAllister, Sue

abstract: The University of Waikato’s (UOW) reputation has been built on its unique commitment to Māori aspirations and the educational success of Māori students (The University of Waikato, n.d.-c). Kaupapa Māori has made a significant contribution to this commitment, including in the School of Psychology. Kaupapa Māori prioritises Māori values and a Māori worldview which is necessary in educating culturally aware practitioners. In addition, the inclusion of kaupapa Māori within the School ensures Māori psychology students are valued and their beliefs and worldviews are acknowledged and included. Through this evaluation we aspired to gain insight into how the UOW maintains its commitment to Māori aspirations and the educational success of Māori students.
This evaluation was conducted at the request of the Māori and Psychology Research Unit (MPRU). The aim of this evaluation was to investigate the presence and practice of kaupapa Māori within the School of Psychology at the UOW. Presence and practice refers to the ways in which kaupapa Māori is included, and actively engaged in, within the School of Psychology. This might include, public notices in the School of Psychology, tutorials, workshops, laboratories, support programmes, training, or the inclusion of kaupapa Māori material in the teaching curriculum. The vision for this evaluation was to help assist in shaping practitioners who are able to engage with Māori clients in a culturally appropriate way.
Our evaluation was guided by three objectives:
(1) to consider the experiences of psychology staff in integrating kaupapa Māori into their teaching and administration,
(2) to explore the barriers experienced by Māori psychology students during their programmes of study (both undergraduate and graduate level), and
(3) to identify the practices and structures that support the implementation of kaupapa Māori in the School of Psychology, and ways of expanding these. This evaluation adds to three previous evaluations of kaupapa Māori within the School (Masters & Levy, 1995; Hunt, Morgan & Teddy, 2002; MacLennan, Namwinga, Taylor, & Theodorus, 2013). In this evaluation we investigated outcomes of the past evaluations while exploring ways to further develop kaupapa Māori within the School.
Drawing on the UOW’s Charter, Strategy, Investment Plan, and Māori Advancement Plan, which all set out specific goals and commitments to provide culturally responsive research and education that meets the needs of Māori communities, this evaluation investigates whether the goals and commitments outlined in these documents are being met. In order to do this, this evaluation has aspired to provide significant information regarding the importance and experiences of kaupapa Māori for staff and students (both current and former) within the School of Psychology.
The evaluators conducted four focus groups and 13 semi-structured qualitative interviews with current undergraduate and graduate Māori students, former Māori students, and current and former Māori and non-Māori UOW staff. In total, the voices of 23 participants are reflected in this report.
The analysis of our findings resulted in the following themes relating to staff experiences integrating kaupapa Māori into their teaching and administration: inconsistent integration of kaupapa Māori across the School, cultural incompetence, and harmful University politics. Barriers that were identified by our participants were: lack of kaupapa Māori visibility, navigating two worlds, and financial and practical barriers experienced by Māori students. Various supports for kaupapa Māori were identified and suggestions were given on ways of expanding these. These supports, which included structures and people, were: the MPRU, Te Aka Matua (a mentoring service within the Faculty of Arts and Social Sciences (FASS, now the DALPSS)), kaupapa Māori tutorials, specific staff in the School of Psychology, integration of kaupapa Māori into papers, support of Māori peers, the importance of role models, and the importance of kaupapa Māori in preparing students for the workforce. Ideas often overlapped due to the interrelated nature of experiences, barriers, and supports.
Overall, participants advocated their support for increasing kaupapa Māori support and content within the School of Psychology through the recognition of Māori worldviews. However, it is clear that there is room for development and expansion of the ways kaupapa Māori is currently supported.
Based on the evaluation findings, the recommendations are:
● Recruit more Māori staff
● Further develop kaupapa Māori Tutorials
● Re-establish the Kaupapa Māori Student Advisor position
● Implement discussion of psychology pathways
● Include more bicultural knowledge in paper content
● Include workforce preparation
● Implement kaupapa Māori training for staff
● Incorporate cultural practices into teaching
● Appoint a cultural advisor for staff
● Offer scholarships to alleviate financial barriers
● Invite a kaumatua on site
● Create a whānau space
● Increase the marketing of all Māori services within FASS (DALPSS) and the School of Psychology
● Allocate funding to all Māori support services
● Incorporate more Māori culture visually on campus

text: An evaluation of Kaupapa Māori in Psychology at the University of Waikato The University of Waikato’s (UOW) reputation has been built on its unique commitment to Māori aspirations and the educational success of Māori students (The University of Waikato, n.d.-c). Kaupapa Māori has made a significant contribution to this commitment, including in the School of Psychology. Kaupapa Māori prioritises Māori values and a Māori worldview which is necessary in educating culturally aware practitioners. In addition, the inclusion of kaupapa Māori within the School ensures Māori psychology students are valued and their beliefs and worldviews are acknowledged and included. Through this evaluation we aspired to gain insight into how the UOW maintains its commitment to Māori aspirations and the educational success of Māori students.
This evaluation was conducted at the request of the Māori and Psychology Research Unit (MPRU). The aim of this evaluation was to investigate the presence and practice of kaupapa Māori within the School of Psychology at the UOW. Presence and practice refers to the ways in which kaupapa Māori is included, and actively engaged in, within the School of Psychology. This might include, public notices in the School of Psychology, tutorials, workshops, laboratories, support programmes, training, or the inclusion of kaupapa Māori material in the teaching curriculum. The vision for this evaluation was to help assist in shaping practitioners who are able to engage with Māori clients in a culturally appropriate way.
Our evaluation was guided by three objectives:
(1) to consider the experiences of psychology staff in integrating kaupapa Māori into their teaching and administration,
(2) to explore the barriers experienced by Māori psychology students during their programmes of study (both undergraduate and graduate level), and
(3) to identify the practices and structures that support the implementation of kaupapa Māori in the School of Psychology, and ways of expanding these. This evaluation adds to three previous evaluations of kaupapa Māori within the School (Masters & Levy, 1995; Hunt, Morgan & Teddy, 2002; MacLennan, Namwinga, Taylor, & Theodorus, 2013). In this evaluation we investigated outcomes of the past evaluations while exploring ways to further develop kaupapa Māori within the School.
Drawing on the UOW’s Charter, Strategy, Investment Plan, and Māori Advancement Plan, which all set out specific goals and commitments to provide culturally responsive research and education that meets the needs of Māori communities, this evaluation investigates whether the goals and commitments outlined in these documents are being met. In order to do this, this evaluation has aspired to provide significant information regarding the importance and experiences of kaupapa Māori for staff and students (both current and former) within the School of Psychology.
The evaluators conducted four focus groups and 13 semi-structured qualitative interviews with current undergraduate and graduate Māori students, former Māori students, and current and former Māori and non-Māori UOW staff. In total, the voices of 23 participants are reflected in this report.
The analysis of our findings resulted in the following themes relating to staff experiences integrating kaupapa Māori into their teaching and administration: inconsistent integration of kaupapa Māori across the School, cultural incompetence, and harmful University politics. Barriers that were identified by our participants were: lack of kaupapa Māori visibility, navigating two worlds, and financial and practical barriers experienced by Māori students. Various supports for kaupapa Māori were identified and suggestions were given on ways of expanding these. These supports, which included structures and people, were: the MPRU, Te Aka Matua (a mentoring service within the Faculty of Arts and Social Sciences (FASS, now the DALPSS)), kaupapa Māori tutorials, specific staff in the School of Psychology, integration of kaupapa Māori into papers, support of Māori peers, the importance of role models, and the importance of kaupapa Māori in preparing students for the workforce. Ideas often overlapped due to the interrelated nature of experiences, barriers, and supports.
Overall, participants advocated their support for increasing kaupapa Māori support and content within the School of Psychology through the recognition of Māori worldviews. However, it is clear that there is room for development and expansion of the ways kaupapa Māori is currently supported.
Based on the evaluation findings, the recommendations are:
● Recruit more Māori staff
● Further develop kaupapa Māori Tutorials
● Re-establish the Kaupapa Māori Student Advisor position
● Implement discussion of psychology pathways
● Include more bicultural knowledge in paper content
● Include workforce preparation
● Implement kaupapa Māori training for staff
● Incorporate cultural practices into teaching
● Appoint a cultural advisor for staff
● Offer scholarships to alleviate financial barriers
● Invite a kaumatua on site
● Create a whānau space
● Increase the marketing of all Māori services within FASS (DALPSS) and the School of Psychology
● Allocate funding to all Māori support services
● Incorporate more Māori culture visually on campus

year: 2018