Waterloo Research

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Now showing 1 - 20 of 2921

2-Aminopurine Fluorescence Spectroscopy for Probing a Glucose Binding Aptamer
(Chemistry Europe: European Chemical Societies Publishing, 2022-04-25) Lu, Chang; Huang, Po-Jung Jimmy; Zheng, Jingkai; Liu, Juewen
Glucose is the most important analyte for biosensors. Recently a DNA aptamer was reported allowing binding-based detection. However, due to a relatively weak binding affinity, it is difficult to perform binding assays to understand the property of this aptamer. In this work, we replaced the only adenine base in the aptamer binding pocket with a 2-aminopurine (2AP) and used fluorescence spectroscopy to study glucose binding. In the selection buffer, glucose increased the 2AP fluorescence with a Kd of 15.0 mM glucose, which was comparable with the 10 mM Kd previously reported using the strand displacement assay. The binding required two Na+ ions or one Mg2+ that cannot be replaced by Li+ or K+. The binding was weaker at higher temperature and its van't Hoff plot indicated enthalpy-driven binding. While other monosaccharides failed to achieve saturated binding even at high concentrations, two glucose-containing disaccharides, namely trehalose and sucrose, reached a similar fluorescence level as glucose although with over 10-fold higher Kd values. Detection limits in both the selection buffer (0.9 mM) and in artificial interstitial fluids (6.0 mM) were measured.
2-Aminopurine-modified DNA homopolymers for robust and sensitive detection of mercury and silver
(Elsevier, 2017-01-15) Zhou, Wenhu; Ding, Jinsong; Liu, Juewen
Heavy metal detection is a key topic in analytical chemistry. DNA-based metal recognition has advanced significantly producing many specific metal ligands, such as thymine for Hg2+ and cytosine for Ag+. For practical applications, however, robust sensors that can work in a diverse range of salt concentrations need to be developed, while most current sensing strategies cannot meet this requirement. In this work, 2-aminopurine (2AP) is used as a fluorescence label embedded in the middle of four 10-mer DNA homopolymers. 2AP can be quenched up to 98% in these DNA without an external quencher. The interaction between 2AP and all common metal ions is studied systematically for both free 2AP base and 2AP embedded DNA homopolymers. With such low background, Hg2+ induces up to 14-fold signal enhancement for the poly-T DNA, and Ag+ enhances up to 10-fold for the poly-C DNA. A detection limit of 3 nM is achieved for both metals. With these four probes, silver and mercury can be readily discriminated from the rest. A comparison with other signaling methods was made using fluorescence resonance energy transfer, graphene oxide, and SYBR Green I staining, respectively, confirming the robustness of the 2AP label. Detection of Hg2+ in Lake Huron water was also achieved with a similar sensitivity. This work has provided a comprehensive fundamental understanding of using 2AP as a label for metal detection, and has achieved the highest fluorescence enhancement for non-protein targets. (C) 2016 Elsevier B.V. All rights reserved.
A 2-class maintenance model with dynamic server behavior
(Springer, 2019-04-29) Granville, Kevin; Drekic, Steve
We analyze a 2-class maintenance system within a single-server polling model framework. There are C+f machines in the system, where C is the cap on the number of machines that can be turned on simultaneously (and hence, be at risk of failure), and the excess f machines comprise a maintenance float which can be used to replace machines that are taken down for repair. The server’s behavior is dynamic, capable of switching queues upon a machine failure or service completion depending on both queue lengths. This generalized server behavior permits the analysis of several classic service policies, including preemptive resume priority, non-preemptive priority, and exhaustive. More complicated polices can also be considered, such as threshold-based ones and a version of the Bernoulli service rule. The system is modeled as a level-dependent quasi-birth-and-death process and matrix analytic methods are used to find the steady-state joint queue length distribution, as well as the distribution for the sojourn time of a broken machine. An upper bound on the expected number of working machines as a function of C is derived, and Little’s Law is used to find the relationship between the expected number of working machines and the expected sojourn time of a failed machine when f=0 or f≥1. Several numerical examples are presented, including how one might optimize an objective function depending on the mean number of working machines, with penalty costs attributed to increasing C or f.
A 30-Year Study of Impacts, Recovery, and Development of Critical Effect Sizes for Endocrine Disruption in White Sucker (Catostomus commersonii) Exposed to Bleached-Kraft Pulp Mill Effluent at Jackfish Bay, Ontario, Canada
(Frontiers, 2021-04-22) Ussery, Erin J.; McMaster, Mark E.; Servos, Mark. R.; Miller, David H.; Munkittrick, Kelly R.
Jackfish Bay is an isolated bay on the north shore of Lake Superior, Canada that has received effluent from a large bleached-kraft pulp mill since the 1940s. Studies conducted in the late 1980s found evidence of reductions in sex steroid hormone levels in multiple fish species living in the Bay, and increased growth, condition and relative liver weights, with a reduction in internal fat storage, reduced gonadal sizes, delayed sexual maturation, and altered levels of circulating sex steroid hormones in white sucker (Catostomus commersonii). These early studies provided some of the first pieces of evidence of endocrine disruption in wild animals. Studies on white sucker have continued at Jackfish Bay, monitoring fish health after the installation of secondary waste treatment (1989), changes in the pulp bleaching process (1990s), during facility maintenance shutdowns and during a series of facility closures associated with changing ownership (2000s), and were carried through to 2019 resulting in a 30-year study of fish health impacts, endocrine disruption, chemical exposure, and ecosystem recovery. The objective of the present study was to summarize and understand more than 75 physiological, endocrine, chemical and whole organism endpoints that have been studied providing important context for the complexity of endocrine responses, species differences, and challenges with extrapolation. Differences in body size, liver size, gonad size and condition persist, although changes in liver and gonad indices are much smaller than in the early years. Population modeling of the initial reproductive alterations predicted a 30% reduction in the population size, however with improvements over the last couple of decades those population impacts improved considerably. Reflection on these 30 years of detailed studies, on environmental conditions, physiological, and whole organism endpoints, gives insight into the complexity of endocrine responses to environmental change and mitigation.
3D bioprinting of liver-mimetic construct with alginate/cellulose nanocrystal hybrid bioink
(Elsevier, 2018-03-01) Wu, Yun; Lin, Zhi Yuan (William); Wenger, Andrew; Tam, Kam C.; Tang, Xiaowu (Shirley)
3D bioprinting is a novel platform for engineering complex, three-dimensional (3D) tissues that mimic real ones. The development of hybrid bioinks is a viable strategy that integrates the desirable properties of the constituents. In this work, we present a hybrid bioink composed of alginate and cellulose nanocrystals (CNCs) and explore its suitability for extrusion-based bioprinting. This bioink possesses excellent shear-thinning property, can be easily extruded through the nozzle, and provides good initial shape fidelity. It has been demonstrated that the viscosities during extrusion were at least two orders of magnitude lower than those at small shear rates, enabling the bioinks to be extruded through the nozzle (100µm inner diameter) readily without clogging. This bioink was then used to print a liver-mimetic honeycomb 3D structure containing fibroblast and hepatoma cells. The structures were crosslinked with CaCl2 and incubated and cultured for 3 days. It was found that the bioprinting process resulted in minimal cell damage making the alginate/CNC hybrid bioink an attractive bioprinting material.
A 3D ellipsoidal volumetric foot–ground contact model for forward dynamics
(Springer, 2018-04-01) Brown, Peter; McPhee, John
Foot–ground contact models are an important part of forward dynamic biomechanic models, particularly those used to model gait, and have many challenges associated with them. Contact models can dramatically increase the complexity of the multibody system equations, especially if the contact surface is relatively large or conforming. Since foot–ground contact has a large potential contact area, creating a computationally efficient model is challenging. This is particularly problematic in predictive simulations, which may determine optimal performance by running a model simulation thousands of times. An ideal contact model must find a balance between accuracy for large, conforming surfaces, and computational efficiency.Volumetric contact modelling is explored as a computationally efficient model for foot–ground contact. Previous foot models have used volumetric contact before, but were limited to 2D motion and approximated the surfaces as spheres or 2D shapes. The model presented here improves on current work by using ellipsoid contact geometry and considering 3D motion and geometry. A gait experiment was used to parametrise and validate the model. The model ran over 100 times faster than real-time (in an inverse simulation at 128 fps) and matched experimental normal force and centre of pressure location with less than 7% root-mean-square error.In most gait studies, only the net reaction forces, centre of pressure, and body motions are recorded and used to identify parameters. In this study, contact pressure was also recorded and used as a part of the identification, which was found to increase parameter optimisation time from 10 to 164 s (due to the additional time needed to calculate the pressure distribution) but helped the results converge to a more realistic model. The model matched experimental pressures with 33–45% root-mean-square error, though some of this was due to measurement errors.The same parametrisation was done with friction included in the foot model. It was determined that the velocity-based friction model that was used was inappropriate for use in an inverse-dynamics simulation. Attempting to optimise the model to match experimental friction resulted in a poor match to the experimental friction forces, inaccurate values for the coefficient of friction, and a poorer match to the experimental normal force.
3D N-doped hybrid architectures assembled from 0D T-Nb2O5 embedded in carbon microtubes toward high-rate Li-ion capacitors
(Elsevier, 2019-02) Tolami Hemmati, Sahar; Li, Ge; Wang, Xiaolei; Ding, Yuanli; Pei, Yu; Yu, Aiping; Chen, Zhongwei
Herein, a unique nitrogen-doped T-Nb2O5/tubular carbon hybrid structure in which T-Nb2O5 nanoparticles are homogeneously embedded in an in-situ formed nitrogen-doped microtubular carbon is synthesized, utilizing a facile and innovative synthesis strategy. This structure addresses the poor electron conductivity and rate capability that hinder T-Nb2O5's promise as an anode for Li-ion devices. Such a distinctive structure possesses a robust framework that has ultrasmall active nanocomponents encapsulated in highly conductive carbon scaffold with hollow interior and abundant voids, enabling fast electron/ion transport and electrolyte penetration. Moreover, nitrogen-doping not only ameliorates the electronic conductivity of the heterostructure, but also induces pseudocapacitance mechanism. When evaluated in a half-cell, the as-prepared material delivers a specific capacitance of 370 F g−1 at 0.1 A g−1 within 1–3 V vs. Li/Li+ and excellent cyclability over 1100 cycles. A high energy density of 86.6 W h kg−1 and high power density of 6.09 kW kg−1 are realized. Additionally, a capacitance retention as high as 81% after 3500 cycles is achieved in an Li-ion Capacitor (LIC) with activated carbon as the cathode and nitrogen-doped T-Nb2O5/tubular carbon as the anode.
3D representation and CNC machining of 2D digital images
(Elsevier, 2018-01-01) Sood, Sumit; Duvedi, Ravinder Kumar; Bedi, Sanjeev; Mann, Stephen
In this paper a new paradigm for CNC carving of digital images in the form of lookalike three-dimensional (3D) surfaces on wooden or metallic plaques is discussed. This work is focused on development of a single page windows based console application for conversion of a two-dimensional (2D) digital image into a 3D freeform surface representation in the form of a point cloud data and STL format. Subsequently, the 3D surface data is then used for generating an efficient toolpath data for 3-axis CNC finish machining using a ball end mill tool. The results from the developed algorithm are validated using a machining simulation in the virtual environment of an Open-GL based 3D graphical simulator ToolSim [1].
A Beginner's Guide for Policymakers and Governance for a Green Hydrogen Ecosystem
(Balsillie School of International Affairs, 2024-12-04) Herdem, Munur Sacit; Nathwani, Jatin
Green hydrogen has enormous potential for advancing a low-carbon future within the hard-to-abate sectors and also for shaping the issue of energy security. In this paper, we present a beginner’s guide for policymakers and readers interested in green hydrogen.
A biomechanical analysis of ventral furrow formation in the Drosophila melanogaster embryo
(Public Library of Science (PLOS), 2012) Conte, Vito; Ulrich, Florian; Baum, Buzz; Munoz, Jose; Veldhuis, Jim; Brodland, Wayne; Miodownik, Mark
The article provides a biomechanical analysis of ventral furrow formation in the Drosophila melanogaster embryo. Ventral furrow formation is the first large-scale morphogenetic movement in the fly embryo. It involves deformation of a uniform cellular monolayer formed following cellularisation, and has therefore long been used as a simple system in which to explore the role of mechanics in force generation. Here we use a quantitative framework to carry out a systematic perturbation analysis to determine the role of each of the active forces observed. The analysis confirms that ventral furrow invagination arises from a combination of apical constriction and apical-basal shortening forces in the mesoderm, together with a combination of ectodermal forces. We show that the mesodermal forces are crucial for invagination: the loss of apical constriction leads to a loss of the furrow, while the mesodermal radial shortening forces are the primary cause of the internalisation of the future mesoderm as the furrow rises. Ectodermal forces play a minor but significant role in furrow formation: without ectodermal forces the furrow is slower to form, does not close properly and has an aberrant morphology. Nevertheless, despite changes in the active mesodermal and ectodermal forces lead to changes in the timing and extent of furrow, invagination is eventually achieved in most cases, implying that the system is robust to perturbation and therefore over-determined.
A Centralized Energy Management System for Isolated Microgrids
(Institute of Electrical and Electronics Engineers (IEEE), 2014-04-25) Olivares, Daniel E.; Canizares, Claudio A.; Kazerani, Mehrdad
This paper presents the mathematical formulation of the microgrid's energy management problem and its implementation in a centralized Energy Management System (EMS) for isolated microgrids. Using the model predictive control technique, the optimal operation of the microgrid is determined using an extended horizon of evaluation and recourse, which allows a proper dispatch of the energy storage units. The energy management problem is decomposed into Unit Commitment (UC) and Optimal Power Flow (OPF) problems in order to avoid a mixed-integer non-linear formulation. The microgrid is modeled as a three-phase unbalanced system with presence of both dispatchable and non-dispatchable distributed generation. The proposed EMS is tested in an isolated microgrid based on a CIGRE medium-voltage benchmark system. Results justify the need for detailed three-phase models of the microgrid in order to properly account for voltage limits and procure reactive power support.
A Comprehensive Evaluation of Tempering Kinetics on 3rd Generation Advanced High Strength Steels
(Elsevier, 2022-12-02) Dileep Chandran Ramachandran; Elliot Biro
Emerging third-generation advanced high strength steels (3G AHSS) grades are being increasingly considered for autobody applications owing to their complex microstructures providing an excellent combination of strength and ductility. When welded with RSW, 3G AHSS such as 3G 1180 and 3G 980, exhibits a solid-state transformation in the sub-critical-heat-affected-zone (SCHAZ) due to the heat generated during the RSW process. The resulting changes in microstructure can affect the mechanical properties of the material within and around the spot welds and thereby influence the performance of welded components in case of a vehicle crash event. To study metallurgical transformations in the SCHAZ during the RSW process, 3G 1180 and 3G 980, and a reference martensitic press hardened steel, PHS 1500, were selected. These materials were subjected to isothermal tempering experiments at temperatures ranging between 350 °C and 650 °C and different tempering times from 0.2 s to 24 h. It was shown that the Hollomon-Jaffe model accurately describes the tempering kinetics of 3G 1180 and PHS 1500 but does not predict the transformation processes in the SCHAZ of 3G 980. The PHS 1500 and 3G 1180 showed softening (tempering) for all combinations of investigated tempering times and temperatures due to the decomposition of martensite. In contrast, the 3G 980 showed a combination of softening by the formation of martensite and secondary ferrite combined with secondary hardening due to the formation of fine M2C typed plate-like carbides. Furthermore, during long tempering, the M2C particles dissolve into the matrix and were replaced by cementite particles in 3G 980.
A Decade of Change: Origins of the Nishga And Tsimshian Land Protests in the 1880s
(University of Toronto Press, 1983) Patterson II, E Palmer
The decade of the 1880s was one of ferment and change for the Nishga. Internal and external factors operated. The allotment of reserves, the coming of Indian administration, the changing role of the missionary, the conflict within the missionary community — all of these were felt and reacted to by the Nishga. Rivalries between Nishga and Tsimshian and among the Nishga contributed to the sharpened awareness of changes regarding the land. The threat to the land was keenly felt and became the public issue. It retained that position for the next one hundred years, with intermittent periods of greater or lesser intensity.
A Decentralised Transactive Energy Market Considering Physical System Constraints
(Institute of Electrical and Electronics Engineers (IEEE), 2024-05) Pankhurst, Colton; Cañizares, Claudio A.; Bhattacharya, Kankar
Local energy markets leveraging direct Peer-to-Peer (P2P) trading have been proposed as a solution, which can increase prosumer participation in lower cost and more reliable supply of energy to consumers. Many approaches have been proposed to determine the optimal dispatch of distributed resources; however, existing approaches either provide inadequate representation of the physical layer or insufficient handling of infeasibilities for a continuous pricing mechanism. Hence, a gap remains in the research to date on efficiently allowing for prosumer decision autonomy while ensuring that the physical layer of the power system is considered. This paper addresses these issues with a proposed decentralised transactive solution that retains prosumer negotiation and decision autonomy, while using market determined prices to allocate limited system resources for a feasible system state. This is achieved through a transaction fee mechanism for prosumer interactions that considers the network characteristics such as topology and line congestion, and a congestion-clearing process to ensure efficient allocation of network resources. Previously reported distribution networks are used to compare the economic performance and transaction decisions of the proposed solution with existing approaches.
A DNA Aptamer for Theophylline with Ultrahigh Selectivity Reminiscent of the Classic RNA Aptamer
(American Chemical Society, 2022-08-09) Huang, Po-Jung Jimmy; Liu, Juewen
Since the report of the RNA aptamer for theophylline, theophylline has become a key molecule in chemical biology for designing RNA switches and riboswitches. In addition, theophylline is an important drug for treating airway diseases including asthma. The classic RNA aptamer with excellent selectivity for theophylline has been used to design biosensors, although DNA aptamers are more desirable for stability and cost considerations. In this work, we selected DNA aptamers for theophylline, and all the top sequences shared the same binding motifs. Binding was confirmed using isothermal titration calorimetry and a nuclease digestion assay, showing a dissociation constant (Kd) around 0.5 μM theophylline. The Theo2201 aptamer can be truncated down to 23-mer while still has a Kd of 9.8 μM. The selectivity for theophylline over caffeine is around 250,000-fold based on a strand-displacement assay, which was more than 20-fold higher compared to the classic RNA aptamer. For other tested analogs, the DNA aptamer also showed better selectivity. Using the structure-switching aptamer sensor design method, a detection limit of 17 nM theophylline was achieved in the selection buffer, and a detection limit of 31 nM was obtained in 10% serum.
A Knowledge-Based Framework for Power Flow and Optimal Power Flow Analyses
(Institute of Electrical and Electronics Engineers (IEEE), 2016-04-07) Vaccaro, Alfredo; Canizares, Claudio A.
This paper proposes the application of formal methods for knowledge discovery from large quantity of data to reduce the complexity of power flow (PF) and optimal power flow (OPF) problems. In particular, a knowledge-based paradigm for PF and OPF analyses is used to extract complex features, hidden relationships, and useful hypotheses potentially describing regularities in the problem solutions from operation data-sets. This is realized by designing a knowledge-extraction process based on principal components analysis. The structural knowledge extracted by this process is then used to project the problem equations into a domain in which these equations can be solved more effectively. In this new domain, the cardinality of the PF and OPF problem is sensibly reduced and, consequently, the problem solutions can be obtained more efficiently. The effectiveness of the proposed framework is demonstrated with numerical results obtained for realistic power networks for several operating conditions.
A multi-resolution approach to point cloud registration without control points
(MDPI, 2023-02-20) Bash, Eleanor A.; Wecker, Lakin; Rahman, Mir Mustafizur; Dow, Christine F.; McDermid, Greg; Samavati, Faramarz F.; Whitehead, Ken; Moorman, Brian J.; Medrzycka, Dorota; Copland, Luke
Terrestrial photographic imagery combined with structure-from-motion (SfM) provides a relatively easy-to-implement method for monitoring environmental systems, even in remote and rough terrain. However, the collection of in-situ positioning data and the identification of control points required for georeferencing in SfM processing is the primary roadblock to using SfM in difficult-to-access locations; it is also the primary bottleneck for using SfM in a time series. We describe a novel, computationally efficient, and semi-automated approach for georeferencing unreferenced point clouds (UPC) derived from terrestrial overlapping photos to a reference dataset (e.g., DEM or aerial point cloud; hereafter RPC) in order to address this problem. The approach utilizes a Discrete Global Grid System (DGGS), which allows us to capitalize on easily collected rough information about camera deployment to coarsely register the UPC using the RPC. The DGGS also provides a hierarchical set of grids which supports a hierarchical modified iterative closest point algorithm with natural correspondence between the UPC and RPC. The approach requires minimal interaction in a user-friendly interface, while allowing for user adjustment of parameters and inspection of results. We illustrate the approach with two case studies: a close-range (<1 km) vertical glacier calving front reconstructed from two cameras at Fountain Glacier, Nunavut and a long-range (>3 km) scene of relatively flat glacier ice reconstructed from four cameras overlooking Nàłùdäy (Lowell Glacier), Yukon, Canada. We assessed the accuracy of the georeferencing by comparing the UPC to the RPC, as well as surveyed control points; the consistency of the registration was assessed using the difference between successive registered surfaces in the time series. The accuracy of the registration is roughly equal to the ground sampling distance and is consistent across time steps. These results demonstrate the promise of the approach for easy-to-implement georeferencing of point clouds from terrestrial imagery with acceptable accuracy, opening the door for new possibilities in remote monitoring for change-detection, such as monitoring calving rates, glacier surges, or other seasonal changes at remote field locations.
A Novel Affine Arithmetic Method to Solve Optimal Power Flow Problems With Uncertainties
(Institute of Electrical and Electronics Engineers (IEEE), 2014-05-02) Pirnia, Mehrdad; Canizares, Claudio A.; Bhattacharya, Kankar; Vaccaro, Alfredo
An affine arithmetic (AA) method is proposed in this paper to solve the optimal power flow (OPF) problem with uncertain generation sources. In the AA-based OPF problem, all the state and control variables are treated in affine form, comprising a center value and the corresponding noise magnitudes, to represent forecast, model error, and other sources of uncertainty without the need to assume a probability density function (pdf). The proposed AA-based OPF problem is used to determine the operating margins of the thermal generators in systems with uncertain wind and solar generation dispatch. The AA-based approach is benchmarked against Monte Carlo simulation (MCS) intervals in order to determine its effectiveness. The proposed technique is tested and demonstrated on the IEEE 30-bus system and also a real 1211-bus European system.
A Procurement Market Model for Reactive Power Services Considering System Security
(Institute of Electrical and Electronics Engineers (IEEE), 2008-01-21) El-Samahy, Ismael; Bhattacharya, Kankar; Canizares, Claudio; Anjos, Miguel F.; Pan, Jiuping
This paper proposes a two-level framework for the operation of a competitive market for reactive power ancillary services. It is argued that the first-level, i.e., reactive power procurement, be on a seasonal basis while the second-level, i.e., reactive power dispatch, be close to real-time operation. To this effect, a reactive power procurement market model is proposed here taking into consideration system security aspects. This procurement procedure is based on a two-step optimization model. First, the marginal benefits of reactive power supply from each provider with respect to system security are obtained by solving an optimal power flow (OPF) that maximizes system loadability subject to transmission security constraints imposed by voltage limits, thermal limits, and stability limits. Second, the selected set of generators is then determined by solving an OPF-based auction to maximize a societal advantage function comprising generators' offers and their corresponding marginal benefits with respect to system security, considering all transmission system constraints. The proposed procedure yields the selected set of generators and zonal price components, which would form the basis for seasonal contracts between the system operator and the selected reactive power service providers.
A Range Arithmetic-Based Optimization Model for Power Flow Analysis Under Interval Uncertainty
(Institute of Electrical and Electronics Engineers (IEEE), 2012-09-18) Vaccaro, Alfredo; Canizares, Claudio A.; Bhattacharya, Kankar
This paper presents a novel framework based on range arithmetic for solving power flow problems whose input data are specified within real compact intervals. Reliable interval bounds are computed for the power flow problem, which is represented as an optimization model with complementary constraints to properly represent generator bus voltage controls, including reactive power limits and voltage recovery processes. It is demonstrated that the lower and upper bounds of the power flow solutions can be obtained by solving two determinate optimization problems. Several numerical results are presented and discussed, demonstrating the effectiveness of the proposed methodology and comparing it to a previously proposed affine arithmetic based solution approach.

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