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: How topography-dependent are topographic effects? Complementary numerical modeling of centrifuge experiments

authors: Jeong, Seokho

subjects: Science & Technology

abstract: Topographic effects, the modification of seismic shaking by irregular topographies compared to flat ground, have been extensively studied. Very few studies, however, have investigated the effects of the stratigraphy and nonlinear response of the underlying geology on topographic amplification. Furthermore, most experimental studies have been performed in the field, where it is often difficult to establish an ideal flat-ground reference station, as well as to characterize the soil properties and their spatial variability in sufficient detail. Dafni [1] recently tested the seismic response of step-like slopes in a series of centrifuge experiments, where the incident motion, reference station and material properties were characterized in detail. In this study, we investigated the influence of the container boundary on topographic effects observed in the centrifuge experiments by performing numerical simulations with and without the container boundary. Our analysis suggested that the rigid-body rocking motion of the centrifuge container likely increased the experimental topographic spectral ratios, contributing to the discrepancy between the simulated and observed spectral ratios. We also found that although the laminar box lateral boundaries caused spurious reflections, they didn’t qualitatively affect the ground surface amplification pattern compared to numerical predictions of the same configuration without boundaries. At the same time, and most importantly, however, we found that the baseplate –by trapping waves scattered and distracted by the slope– amplified the ground motion at the crest up to one order of magnitude compared to numerical predictions of the response in absence of the baseplate. Our results show that topographic effects can be significantly affected by the underlying soil stratigraphy; and allude to the potentially significant role of this phenomenon in elevating seismic risk in regions with strong topographic relief. The findings of this study also suggest that future studies will benefit from clear understanding and careful considerations of capabilities and limitations of different investigation methods and that the numerical modelling and the lab testing (or the field testing) methods should complement each other.

text: How topography-dependent are topographic effects? Complementary numerical modeling of centrifuge experiments Topographic effects, the modification of seismic shaking by irregular topographies compared to flat ground, have been extensively studied. Very few studies, however, have investigated the effects of the stratigraphy and nonlinear response of the underlying geology on topographic amplification. Furthermore, most experimental studies have been performed in the field, where it is often difficult to establish an ideal flat-ground reference station, as well as to characterize the soil properties and their spatial variability in sufficient detail. Dafni [1] recently tested the seismic response of step-like slopes in a series of centrifuge experiments, where the incident motion, reference station and material properties were characterized in detail. In this study, we investigated the influence of the container boundary on topographic effects observed in the centrifuge experiments by performing numerical simulations with and without the container boundary. Our analysis suggested that the rigid-body rocking motion of the centrifuge container likely increased the experimental topographic spectral ratios, contributing to the discrepancy between the simulated and observed spectral ratios. We also found that although the laminar box lateral boundaries caused spurious reflections, they didn’t qualitatively affect the ground surface amplification pattern compared to numerical predictions of the same configuration without boundaries. At the same time, and most importantly, however, we found that the baseplate –by trapping waves scattered and distracted by the slope– amplified the ground motion at the crest up to one order of magnitude compared to numerical predictions of the response in absence of the baseplate. Our results show that topographic effects can be significantly affected by the underlying soil stratigraphy; and allude to the potentially significant role of this phenomenon in elevating seismic risk in regions with strong topographic relief. The findings of this study also suggest that future studies will benefit from clear understanding and careful considerations of capabilities and limitations of different investigation methods and that the numerical modelling and the lab testing (or the field testing) methods should complement each other.

year: 2019

title: Taku Rāta Tūtahi (composed 28 Oct 2013)

authors: Maxwell, Te Kahautu

abstract: Taku Rāta Tūtahi is a lament dedicated to my daughter Kaaterina Ataria Ariha Maxwell who passed away suddenly on the 23 March 2013. This composition talks about the pain of a father for his daughter and how at times life is unbearable because of this undiscribable pain. This composition was performed by Ōpōtiki Mai Tawhiti Kapa Haka at the Mātaatua Kapa Haka Regional Competition. This composition placed 2nd in the Whakaeke discipline.

text: Taku Rāta Tūtahi (composed 28 Oct 2013) Taku Rāta Tūtahi is a lament dedicated to my daughter Kaaterina Ataria Ariha Maxwell who passed away suddenly on the 23 March 2013. This composition talks about the pain of a father for his daughter and how at times life is unbearable because of this undiscribable pain. This composition was performed by Ōpōtiki Mai Tawhiti Kapa Haka at the Mātaatua Kapa Haka Regional Competition. This composition placed 2nd in the Whakaeke discipline.

year: 2014