Browsing Science (Faculty of) by Title
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Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles
(University of Waterloo, 20170420)DNAfunctionalized gold nanoparticles (AuNPs) have been extensively used in sensing, drug delivery, and materials science. A key step is to attach DNA onto AuNPs forming a stable and functional conjugate. While the traditional ... 
A parallelized molecular collision cross section package with optimized accuracy and efficiency
(Royal Society of Chemistry, 2019)Ion mobilitybased separation prior to mass spectrometry has become an invaluable tool in the structural elucidation of gasphase ions and in the characterization of complex mixtures. Application of ion mobility to structural ... 
Parallelizing quantum circuit synthesis
(University of Waterloo, 20150424)We present an algorithmic framework for parallel quantum circuit synthesis using meetinthemiddle synthesis techniques. We also present two implementations thereof, using both threaded and hybrid parallelization ... 
Parameterization of In Silico Oral Disposition Models: Focus on Pediatrics
(University of Waterloo, 20170316)Owing to their biologically relevant design, physiologicallybased pharmacokinetic (PBPK) models require quantitative knowledge of organism anatomy and physiology to facilitate appropriate parameterization. Within such ... 
Part 1: Towards the Synthesis of Pyrene Zigzag Cyclacenes, Part 2: New Methods for the Synthesis of Conjugated Polymers
(University of Waterloo, 20210930)Part 1: Carbon nanotubes (CNTs) are allotropes of carbon that have emerged as candidates for implementation in electronic devices ranging from transistors to solar cells. Unfortunately, the behavior of CNTs is highly ... 
Partial oligomerization of pyolysin induced by a disulfidetethered mutant
(NRC Research Press, 201212)The bacterial toxin pyolysin (PLO) belongs to the family of cholesteroldependent cytolysins (CDCs), which form large, ringshaped oligomeric pores in cholesterolcontaining membranes. Monomeric CDC molecules have a structure ... 
Particle Distributions in a Block Copolymer Nanocomposite
(American Chemical Society, 2008)Selfconsistentfield theory is used to predict the centerofmass distribution of spherical nanoparticles embedded in the lamellar phase of a diblock copolymer melt. The calculation is performed in the dilute limit, where ... 
PartsperMillion of Polyethylene Glycol as a NonInterfering Blocking Agent for Homogeneous Biosensor Development
(American Chemical Society, 20131105)Many homogeneous assays are complicated by the adsorption of probe molecules by the surface of reaction vessels, which are often made of polypropylene or polystyrenebased plastics. To solve this problem, many protein and ... 
Passive In Situ Treatment of Acidic and Neutral Mine Drainage: Field and Laboratory Investigations
(University of Waterloo, 20091216)Water quality degradation is the foremost environmental issue faced by the mining industry. Negative impacts on water quality are commonly associated with unmitigated drainage emanating from sulfidebearing mine waste ... 
Passive sampling to understand and predict sources of wastewater and agricultural contamination in rural watersheds
(University of Waterloo, 20230712)Passive sampling techniques have emerged as valuable tools in environmental monitoring, offering distinct advantages over traditional discrete sampling methods. Discrete sampling techniques are only representative of the ... 
Path Integral Approaches and Graphics Processing Unit Tools for Quantum Molecular Dynamics Simulations
(University of Waterloo, 20120821)This thesis details both the technical and theoretical aspects of performing path integrals through classical Molecular Dynamics (MD) simulations. In particular, Graphics Processing Unit (GPU) computing is used to augment ... 
Path integral ground state approaches for the study of weakly bound clusters and confined molecules
(University of Waterloo, 20180921)This thesis presents the study of weakly bound clusters in the ground state (or the zerotemperature limit) using path integral molecular dynamics. Specifically, we look individually at the quantum properties of small ... 
A path integral ground state replica trick approach for the computation of entanglement entropy of dipolar linear rotors
(AIP Publishing, 20200514)We calculate the second Rényi entanglement entropy for systems of interacting linear rotors in their ground state as a measure of entanglement for continuous rotational degrees of freedom. The entropy is defined in relation ... 
Path integral Langevin dynamics of complex molecular systems: from lowtemperature quantum clusters to biomolecules
(University of Waterloo, 20110831)This thesis presents an implementation of path integral molecular dynamics (PIMD) for sampling equilibrium and dynamical properties within the molecular modelling toolkit (MMTK) [J. Comp. Chem. 21, 79 (2000)], an open ... 
A path integral methodology for obtaining thermodynamic properties of nonadiabatic systems using Gaussian mixture distributions
(American Institute of Physics, 201805)We introduce a new path integral Monte Carlo method for investigating nonadiabatic systems in thermal equilibrium and demonstrate an approach to reducing stochastic error. We derive a general path integral expression for ... 
A path integral Monte Carlo method for obtaining thermodynamic properties of nonadiabatic systems
(University of Waterloo, 20170922)The calculation of thermochemical properties is an important goal of quantum chemistry. Calculation techniques are well established for stable molecules. They are used routinely to calculate Gibbs energy (G) for stable ... 
Path Integrals in the Sky: Classical and Quantum Problems with Minimal Assumptions
(University of Waterloo, 20191024)Cosmology has, after the formulation of general relativity, been transformed from a branch of philosophy into an active field in physics. Notwithstanding the significant improvements in our understanding of our Universe, ... 
Patient compliance with contemporary contact lenses: Impact on successful contact lens wear
(University of Waterloo, 20130415)Purpose: Contact lens (CL) materials, modalities of wear and replacement, and care systems have changed considerably since the early studies of CL compliance were first conducted. Silicone hydrogel (SiHy) and daily disposable ... 
Patterns in stream biofilm communities and organic matter processing in an agricultural stream network: A multiscale assessment of the influence of groundwater
(University of Waterloo, 20240603)Benthic stream biofilm communities support stream ecosystem structure and function by mediating nutrient and carbon cycling. Understanding how environmental factors shape biofilm communities in stream ecosystems is therefore ... 
Peculiar Velocities and Large Scale Flows as Probes of Gravity, ΛCDM and the Growth of Structure over Cosmic Time
(University of Waterloo, 20120928)Peculiar velocities are possibly the most powerful probes of very largescale mass density fluctuations in the nearby Universe. When coupled with a density field they also can constrain the growth factor of the universe ...