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Advancements and applications of AMOEBA force fields for biomolecular simulations
Get PDFExploring biochemical processes in diverse biomolecular systems, including proteins, DNA, and RNA, is essential yet challenging. Molecular modeling serves as an indispensable tool for understanding biomolecular interactions, particularly in drug discovery and mechanism research. The Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, renowned for its explicit polarization and high-order electrostatic representation, outperforms classical force fields in studying complex biochemical systems. This dissertation introduces the physical intricacies of AMOEBA including the parametrization process. In application, AMOEBA demonstrates exceptional capability in elucidating the binding mechanisms and the thermodynamic properties of Fluorescent light-up aptamers (FLAPs) with their cognate fluorogens. FLAPs, as versatile biosensors for cellular imaging and target detection, can activate strong fluorescence of their cognate fluorogen upon binding. By utilizing AMOEBA, MD simulations of one kind of FLAP called Mango-II with TO1-Biotin and TO3-Biotin fluorogens yield binding free energies in excellent agreement with experimental values. Despite the successes of conventional molecular dynamics (MD), its sampling efficiency remains limited, particularly for long-timescale dynamics. To address this, a novel program (Tinker-Milestoning) integrating Milestoning, an enhanced sampling method, with AMOEBA via Tinker MD software is developed. Milestoning theory proves stable across diverse energy landscapes, providing accurate thermodynamic and kinetic properties. This program enables the exploration of conformational dynamics in systems such as alanine dipeptide, DNA, and RNA A-B form conversion, showcasing the power of combining polarizable force fields with enhanced sampling techniques for atomic-level characterization of biomolecules.Biomedical Engineerin
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Communities of misinformation : Japanese QAnon conspiracy theorists and their online "Watchers"
Get PDFPrevious research has investigated how the participatory dynamics of social media have been leveraged for a wide range of democratic social movements. In recent years, however, scholars have called attention to how such near-instantaneous participation of everyday social media users and methods used by activists can be co-opted to spread lethal misinformation that can have deadly consequences on people’s well-being, highlighting the need to understand the phenomenon in diverse contexts. At the same time, such participatory dynamics within grassroots communities can also be deployed to confront misinformation, representing an underexplored and promising site of counter-efforts.
This dissertation argues that misinformation spreads effectively by employing an activist logic, which highlights that misinformation is not only a matter concerning an epistemological question of facticity but also an issue of community and belonging. Seeing misinformation and counter-misinformation through the lens of activism illuminates more human-centered approaches to the problem. Meeting activist logic with activist logic, community-based interventions may offer an effective way to respond to the centrality of community and belonging in participatory misinformation.
The empirical portion of this dissertation examines the roles everyday social media users play in both disseminating and addressing misinformation, taking up two examples in the context of Japan. First, as an example of participatory lethal misinformation, I investigate YamatoQ (神真都Q), a conspiracy-informed, anti-vaccine movement in Japan, through qualitative thematic analysis of social media data. Second, as a case of community-based interventions to misinformation, I interview anonymous Japanese social media “Watchers” (ウォッチャー), who confronted misinformation propagated by YamatoQ. YamatoQ members drew on various online and offline strategies to propagate their anti-vaccine narratives (AVN), investing considerable efforts to build solidarity and a sense of togetherness by offering various opportunities for social interactions. In the case of the Watchers, analysis of in-depth interview data demonstrates that they used improvisational and humanizing approaches to address emotional aspects of YamatoQ’s multiplatform misinformation, with playfulness underpinning their overall strategies to confront the conspiracy group.
This dissertation contributes a useful lens for understanding how activist logics both propagate and challenge misinformation, and provides empirical evidence that grassroots dynamics may offer a complementary approach alongside formal solutions for remedying misinformation.Journalism and Medi
A political history of Chinese elite sport during the Great Proletariat Cultural Revolution, 1966-1976
Get PDFThis dissertation probes the political history of Chinese elite sport during the Great Proletarian Cultural Revolution, a nationwide radical leftist sociopolitical movement launched by Chairman Mao Zedong in the spring of 1966. The Cultural Revolution, one of the most catastrophic political movements in human history, severely damaged the elite sport system both structurally and viscerally, which was under direct oversight of the central government of the Communist Party-state and thus suffered immensely from the power struggles within the party and state leadership. From 1966 to 1969, elite sport was suspended in extreme upheaval, with many sportspersons and sport officials interned, interrogated, and persecuted, despite their enthusiastic display of allegiance to Mao and his revolutionary cause at the onset of the Cultural Revolution. The State Sports Commission, China’s central sport authority, was twice transferred to the administration of the People’s Liberation Army in order to be revolutionized. However, after 1970, Chinese leaders’ revival of the strategy of sport diplomacy enabled the rehabilitation of most elite sportspersons and officials and contributed to both China’s diplomatic breakthroughs and Chinese sport’s partial reintegration in Asian and global sport, despite the fact that the austere domestic political climate often played a hindering role. In examining this nonlinear history and the nuances and complexities to it in depth, this dissertation analyzes the factors at the individual, national and international levels behind the course of events in the development or lack thereof of Chinese elite sport from mid-1960s to 1976 in three aspects: domestic sport governance, the fate of elite sportspersons, and participation in international sporting exchange and sport governance. It particularly probes the contrast in the party-state leadership’s treatment of elite sport before and after 1970. It is argued that in fulfilling its obligations to China’s national interests as defined by party and state leaders, Chinese elite sport and sportspersons recovered from the pre-1970 atrocities and contributed tremendously to China’s rise in world politics, but the political breakthroughs failed to carry Chinese sport to full reintegration into global sport.Kinesiology and Health Educatio
Texas National Security Review: The Changing Face of War Vol. 9, Issue 1, 2026
Get PDFTABLE OF CONTENTS
FOUNDATION
2 The Changing Face of War—And of Our Work
Adam Klein and Joseph Maguire
SCHOLAR
8 Wars of the Greater Middle East, 1945–92
Carter Malkasian
28 Threading the Needle: The Logic of Conventional Coercion
in Nuclear Crises
Tyler Bowen
52 Bombs, Bots, and the Principle of Distinction: The Law of Armed
Conflict and Contemporary Warfare
Nathan G. Wood
STRATEGIST
72 A New World Order? Careful What You Wish For
Shivshankar Menon
82 How a US “Suez Moment” Could Hollow the US Alliance System
Bence Nemeth
98 The Arsenal of Democracy: Keeping China Deterred in an
Age of Hard Choices
Eyck Freymann and Harry Halem
ROUNDTABLE
114 Shaping National Security Decisions: An Insider’s View
of The Insiders’ Game
Mara Karlin
119 Would a China War Scenario Break the Insiders’ Hold?
Mathew BurrowsLBJ School of Public Affair
Defying distance : remembrance, narration, and the gender imaginary in Assia Djebar’s Loin de Médine
Get PDFThis dissertation explores Algerian author Assia Djebar’s Loin de Médine (1991) (Far from Madina), a novel that re-imagines the early Islamic past through women’s perspectives. Djebar framed the work as an inspired re-reading of the earliest Sunni historiography compendiums: Ibn Hishām’s (d. 828-835) prophetic biography, the biographical dictionary of Ibn Saʿd (d. 845), and the historical chronicles of al-Ṭabarī (d. 923). This study approaches the novel through its intertextuality with classical Islamic tradition, attending to how it reconfigures historical narratives, identifying unnamed sources, and taking up new readings through lenses from Arabo-Islamic religio-scholarly and literary traditions. Djebar models a practice of transmission that centers women’s subjectivities, re/claims the literary voice of compendium text tradition, and embraces a collective, performative practice in constructing a relationship to the past. I argue that Djebar’s project is compelled not only by an ethical imperative to respond to gendered silences in the archive but also by a desire to recall beloved figures of Muslim memory and make them speak to her contemporary moment. I attend to the models of narration imagined in the novel and works including La Nouba des femmes du Mont Chenoua (1979) and L’Amour, la fantasia (1985) to suggest that Djebar’s reflexive practice of transmission not only inscribes counter-discourse in tradition but also recovers the dynamism and collective voice of oral literary culture. Djebar re-enters the scene of history and invites the reader to dwell on events through women’s perspectives, unsettling narratives that have naturalized gender discourses in the received canon and challenging gender ideologies of her own time. By asserting the ethical dimensions of representational practice, including the obligation to expand the horizons of the imaginary, and by calling the reader to participate in re-evaluating tradition and making meaning out of the past as a mode of moral-ethical witness, the novel revives the classical definition of the concept of adab. Djebar’s imaginative treatment makes visible a range of women’s experiences that prompt ethical deliberation over gender codes propagated by tradition, law, and the state and opens a space for Muslims to envision avenues for overcoming gendered patterns of injustice and alienation.Comparative Literatur
Can communities save Bengaluru's lakes? Models for participatory restoration in Benniganahalli and B. Channasandra Keres
Get PDFThis professional report examines modes of community participation and co-management for lake restoration in two neighboring lakes, Benniganahalli and B. Channasandra (Kasturi Nagar), in urban Bengaluru East Taluk. Although they were part of a historical network of constructed keres (lakes), both lakes in this study suffered from various acts of omission and commission in city development priorities, and they received excessive pollution and waste dumping. To address these challenges and take ownership of their neighborhood lakes, residents organized central community groups to catalyze restoration efforts and advocate for government resources and intervention. To execute lake restoration, the Benniganahalli Kere Trust and Kasturinagar Welfare Association managed networks of hundreds of volunteers, navigated complex regulatory frameworks, and expanded upon existing local knowledge of the kere ecosystem. This study presents new archival findings about the historical development of these lakes and evaluates the role of community participation in restoration efforts through qualitative focus groups with lake volunteers and trustees. To assess the governance models used at these lakes, focus group findings are compared with the International Union for Conservation of Nature (IUCN) Global Standard for Nature-based Solutions Criteria. Inputs from focus group participants were also used to create a stakeholder network and UCINET centrality analysis for each lake. For both lakes, focus group participants viewed community groups as the most central stakeholders for lake restoration communications. The results of this study demonstrate the high potential of community groups to serve as bridging-actors between other stakeholders, such as government agencies. By evaluating these network analyses and qualifying their results with insights from the focus groups, we can gain a deeper understanding of the opportunities and challenges community members face in co-managing nature-based solutions within an urban neoliberal context. The outcome of this work expands the literature on participatory models for natural resource management in the Global South and provides a case study on the positive impact communities can have when provided the opportunity to help govern their local ecosystems.Community and Regional Plannin
Essays on strategic interactions in vertical supply chains and multi-sided markets
Get PDFFirms in vertical supply chains and multisided market often make decisions strategically, in anticipation of the reaction of the other firm(s) in the supply chain. This dissertation investigates two such strategic interactions that affect the operations and supply chain management decisions of the firms. The first strategic interaction studied in this dissertation involves the use of strategic inventory held by a downstream retailer in a supply chain, as a leverage to obtain favorable future wholesale prices from an upstream manufacturer, who offers a dynamic contract instead of a long-term commitment contract. We study two supply chain scenarios that differ from the existing literature on strategic inventory, which involves a single manufacturer and a single retailer, where the manufacturer can fully observe, and benefits from, the retailer holding inventory, while the retailer benefits only when the holding cost is sufficiently low. In the first scenario, the manufacturer cannot observe the retailer's inventory, and in the absence of supply chain uncertainties, prefers the dynamic contract, and not observing the inventory. When inventory is not observable to the manufacturer, the retailer benefits from the dynamic contract only when the holding cost is high. In the second scenario, while the manufacturer can observe the inventory, he faces competition from another partially substitutable product sold through the same retailer. When the degree of substitution is sufficiently high, the retailer benefits from the dynamic contract for all holding costs, while the manufacturer is worse-off. Instead, the manufacturer prefers a contract that involves two-way commitment from both the manufacturer and the retailer. The second strategic interaction involves the platform interface product line decisions, made by the sponsor of a multi-sided marketplace, or platform. The network effects and decentralization intrinsic in a multi-sided market, which help bring more consumers to the firm while creating more fragmentation on the supplier side, alter the firm's product line decisions when compared to a traditional supply chain. The findings of this dissertation provide valuable theoretical and managerial insights into the strategic decision-making process of the firm when it interacts with other strategic firms in different supply chain contexts.Information, Risk, and Operations Management (IROM