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Molecular Design of Polymer Combs and Living Gels
No full textThermosetting resins are materials that undergo crosslinking by forming interchain linkages to create robust 3D networks that impart creep, thermomechanical, and solvent resistance. These materials are critical for a number of high-performance applications, such as aerospace and automotives, and biomedical crosslinked hydrogels. Thermosetting materials can be cured chemically or thermally, or by using ultraviolet (UV) light or electron beams. However, these methods are not always possible, accessible, and they can be harsh to embedded cells. Taking inspiration from natural materials such as fibronectin, a protein that contains hidden or cryptic sites that become exposed under tension, this dissertation first presents a new class of synthetic force-responsive materials that exhibit force-responsive behavior by exposing cryptic sites and forming new crosslinks. Long pendant poly(ethylene glycol) (PEG) chains along the polymer backbone create a significant steric barrier and prevent reactive moieties from spontaneously crosslinking, which is overcome by mechanical force. In this dissertation, I extended this approach to densely grafted comb polymers with reactive side chains, which resulted in highly crosslinked comb copolymers with minimal intramolecular crosslinking. Finally, I harnessed xanthogen disulfides to produce telechelic acrylic polymers and hydrogels responsive to visible light. Overall, I successfully designed and produced methods of easily implementing mechanosensitivity in synthetic polymers, strategies for producing high molecular weight crosslinkable resins, and fast techniques for synthesizing biocompatible gels. Importantly, the design principles laid out in this work provide a blueprint for developing next-generation stimuli responsive materials.Doctor of Philosophy (Ph.D.
STUDYING FUNCTIONAL AND REGULATORY MECHANISMS OF BIOMOLECULES USING SIMULATIONS
No full textElucidating molecular mechanisms of biomolecule functions is crucial for advancing understanding of biological processes, pathology of many hereditary and acquired diseases, as well as developing novel therapeutic strategies or targeting drugs. Recent years have witnessed a huge pike on high resolution structures of biologically critical membrane proteins shedding lights on atomistic level details, meanwhile functional studies have provided us with abundant macroscopic functional measurements upon
perturbations, such as mutations and change of experimental conditions. Rationalizing those functional data in the molecular level based on resolved structures has been an
important but challenging knowledge gap, which can be bridged by dynamics studies through computational simulations achieving high spatial and temporal resolutions.
In Chapter two to four, we focused on studying gating and regulation mechanisms of two membrane channel protein: the TMEM16F lipid scramblase and the TRPV4 ion
channel. We performed all-atom simulations on the inner gate charged TMEM16F mutants and observed spontaneous the pore opening and hydration process. The sampled closed-to-open transition detailed in pore-forming helices movements on different specific directions in the atomistic level. The resulting open state was found to be functionally active since a direct lipid scrambling event was sampled. Our study predicted a possible biologically relevant open state eluded from previous cryo-EM studies and revealed the activation transition process as well as the ion and lipid translocation pathways. In the TRPV4 gating study, we aimed at resolving free energy barrier contributions from the classic bundle-crossing gating mechanism and the hydrophobic gating mechanism. We first demonstrated the dewetting transition can readily happen in the bundle-crossing and highly hydrophobic pore. Through thorough free energy calculations, we showed that disruption of the hydrophobicity of the pore can significantly reduce the ion permeation barrier through lowering down the hydration free energies of the lower pore region. In Chapter four, we presented a story of PI(4,5)P2 regulation of the TRPV4 ion channel. We first disapproved previously proposed PI(4,5)P2 binding sites and identified two more plausible binding sites in the inner leaflet-protomer interface. Relative free energy calculations between the two sites showed they almost have similar binding affinities, indicating the possibility of dynamic binding of multiple PI(4,5)P2 for regulation. Careful dynamic coupling network analysis further resolved dynamics implications of binding in those two sites, suggesting PI(4,5)P2 can prime the channel for temperature activation. In Chapter five, we used extensive coarse-grained simulations to examine important domain-domain interaction modes in the chemotaxis protein CheA, the
autokinase initiating phosphorylation cascade to regulate downstream flagellar rotation for motile bacteria to swim towards favorable environment. Important P1-P4 trans- productive contacting modes and P1/P1’ dimerization modes were predicted, generating testable measurements and hypotheses for experimental validations. All Chapters together showed how powerful it is to combine functional studies, structural biology and computational simulations for investigating functional and regulatory mechanisms of biomolecules in the biologically relevant environment.NIH (R35 GM144045)
the Chemistry-Biology Interface (CBI) training program from the UMass (National Research Service Award T32 GM139789)Doctor of Philosophy (Ph.D.)2026-03-0
Module 1
No full textThis unit contains materials on introductory concepts and practice, and an ArcGIS Pro installation guide
Reflecting on urban greening at an historic inflection point with Theodore Eisenman
No full textFor a transdisciplinary perspective on urban greening at this particular juncture in history, we spoke with landscape architect and urban planner Theodore S. Eisenman about the contemporary upswell of interest in urban tree planting and related greening initiatives
Lightning Talks: It Could Be Wonderful: OER Collaboration with Students
No full textOER textbooks already offer many advantages for our moral emotions. By removing cost and offering greater accessibility, they alleviate anxiety. By encouraging authors to create open resources for students in need, they foster empathy and sympathy, while reducing fear and anger over stolen intellectual property. This talk will address another step that can further promote the moral emotions of care and wonder: collaboration with students. These emotions are essential for keeping students engaged in their own learning, but often OER textbooks fall short in these areas. Care can be fostered by inviting students into the process of creating content for textbooks, such as student artists who could offer their works to liven up otherwise monotonous pages. Wonder is likewise fostered by challenging students to act as knowledge makers and content creators, while simultaneously offering perspectives that more directly inspire their generational peers
“If this initiative is truly aimed to make a difference”: Evaluating the University of Ottawa Library OER Grant Program
No full textSince 2020 the University of Ottawa Library has awarded over $215,000 to support the adaptation or creation of open educational resources. What started as a modest grant evolved into a program that especially encourage the production of French-language OER to address the persistent lack of pedagogical materials adapted to Francophone minority contexts in Canada and to promote linguistic equity for uOttawa students, 30% of whom study in French at this bilingual institution.
In its final year, the grant initiative is being assessed using a program evaluation framework to establish its relevance, effectiveness, and efficiency. After a brief overview of the University of Ottawa’s context, the presentation will focus on the workings of the grant program, the methods and data used to complete the assessment, and the challenges of conducting such an evaluation. It will conclude with the results indicating to which extent the program has reached its objectives
Ready for take-off? How emerging technologies are fueling new approaches around OER in the UK & the US
No full textToday we are faced with emerging technologies such as (Gen)AI, which have incredible potential - yet also significant risks and challenges. During this panel session, we will hear from two forward-looking universities in the UK and the US about their views and experiences with (Gen)AI and OER. While both are unique in terms of their local context, challenges and levels of experience with OER, they are unified by their ambition to locally grow OER success and by their high expectations for its future.
From this session, expect to learn more about practical and real-world examples of (Gen)AI use at these two universities and their library today: how it is used to identify OER gaps, how to understand local OER potential as well as convincing senior leadership to get behind this. Moreover, expect to walk away with concrete ideas for how we can fuel a scaleable OER future at any institution and why now is the time really for this to take off.
During this panel session, we will hear from two different institutions in the UK and the US about their views and experiences with (Gen)AI and OER. While both are unique in terms of their local context, challenges and levels of experience with OER, they are unified by their ambition to locally grow OER success and by their high expectations for its future. You’ll hear practical and real-world examples of (Gen)AI use, such as how it is used to identify OER gaps and to understand the potential of OER.
We’ll hear from each of the panelists about where they are with OER today and why they feel now is the time for OER to take off
Module 13
No full textThis module contains materials summarizing concepts reviewed in this course and other interesting GIS applications across fields
An Old Song: Analyzing Hadestown
No full textThere is little doubt that adaptations of ancient myths have become more mainstream in recent years–providing unique, accessible ways for people to learn more about stories from antiquity. One such adaptation takes the form of a Broadway show: Hadestown, written by Anaïs Mitchell. This paper explores some of the significant ways in which Hadestown has taken its ancient Greek source material–the myths of two mortals named Orpheus and Eurydice, as well as the two divinities Hades and Persephone–and modernized it for a contemporary audience in a way that retains the heart and meaning of both stories. The paper deems Hadestown to be a successful adaptation through analyzing the musical’s key plot points, the four primary characters along with their relationships, and the ways that Mitchell has thematically altered her iteration of the tale