Center for Theoretical Biological Physics

Rice University Research Repository
Not a member yet
    70302 research outputs found

    Ion Selective Electrochemical Process for Pollutant Removal and Resource Recovery

    No full text
    Water scarcity worldwide has prompted the complete utilization of every drop of water sources by removing pollutants and recovering resources from multiple water sources. Electrified water treatment technologies such as electrocatalysis and electrodialysis are promising technologies to achieve such targets by consuming renewable energy, causing no secondary pollution and requiring no harsh chemicals. However, the efficiency of electrified technology is not satisfied due to complicated water matrix and high salinity in some water sources, where competing ions may decrease the product purity and waste more energy during major process. High selectivity is a key parameter to improve electrified technology efficiency in a multi-solute water matrix via high energy efficiency, fast kinetics, and low by-product production or less by-process. The selectivity towards certain ions can be achieved by its size, electrostatic force, chemical affinity and even design of operation. In this work, We reported several approaches including process design, membrane development and material synthesizing to deliver a comprehensive strategy of achieving ion selectivity by multiple mechanisms. The removal efficiency of nitrate as a pollutant and the recovery of Lithium as a resource were evaluated and compared with commercial or conventional design

    Controlling the taxonomic composition of biological information storage in microbial communities

    No full text
    Horizontal gene transfer (HGT) is an important mechanism for adaptation in microbes, and the rapid dissemination of antimicrobial resistance is often associated with HGT. Existing technologies for monitoring horizontal gene transfer (HGT) are arduous, requiring reporters, processing of samples following gene transfer, and specialized instrumentation. I helped develop an autonomous barcoding device that can record information about who participates in HGT in a community. These devices record information about DNA uptake by producing a catalytic RNA (cat-RNA) that anneals to 16S ribosomal RNA (rRNA) and splices a synthetic barcode onto the rRNA. In initial studies, this cat-RNA was able to record community-level information about HGT host range. However, it was not clear how the location targeted within rRNA sequences impacts barcoding host range. To control which organisms are targeted by the cat-RNA, I created Ribodesigner, a program that generates cat-RNA designs optimized to target a user-defined set of microbes within a community. By designing cat-RNA guide sequences using different input sets of complete 16S rRNA sequences, Ribodesigner can generate designs that are: (i) universal for all organisms within each kingdom, or (ii) selective to specific taxonomic groups within a community while purposefully avoiding other community members. The performance of universal and selective cat-RNA designs was validated in-vivo in model bacteria. These experiments revealed that selective cat-RNA designed by Ribodesigner can target one of the most abundant orders in a wastewater microbial community, Pseudomonadales, while avoiding a second highly abundant order, Enterobacterales. Ribodesigner can be useful for designing cat-RNA devices that program environmental communities to autonomously record the host range of mobile DNA containing cat-RNA without the need for domestication of individual microbes. By targeting select taxonomic groups for information storage in a community, this approach can increase the sensitivity of cat-RNA for studying mobile DNA host range, particularly when studying HGT in rare community members. In this way, Ribodesigner is useful to researchers seeking to deepening our understanding of HGT in situ

    Integrated Modeling of Future Energy Systems to Enhance Grid Reliability and Sustainability

    No full text
    The shift to a sustainable, low-carbon energy economy requires advancements in technology, system design, and policy reform. Electric power systems face challenges such as rising demand, price volatility, geopolitical tensions, and extreme weather events. Recent major outages have exposed vulnerabilities across the current energy system, revealing risks from extreme weather, fuel supply disruptions, and grid instability. Electrifying sectors such as industrial heating and transportation offers a pathway to decarbonize energy and reduce pollution-related deaths, requiring a comprehensive investigation. This dissertation employs integrated modeling approaches to explore how technological, system design, and policy innovations can enhance the reliability and sustainability of U.S. energy systems. It tackles the computational complexity of linking energy system models with air quality assessments, forecasting future energy scenarios while factoring in air quality and health impacts. The study shows the value of integrated modeling in plotting a decarbonized, reliable energy future, addressing both environmental and human health dimensions while adapting to regional and sectoral needs in the United States

    [ ] In Progress - An Incremental Degrowth System

    No full text
    The prolonged vacancy problem in post industrial cities of the rust belt has been uprooted by numerous factors including deindustrialization, white flight, and suburbanization. Surmounting in communal, societal, and legislative pressure, the city of Detroit saw decline in population since the mid 20th century, which continues to disproportionately affect historically marginalized communities within the city limits. Since the beginning of industrialization, growth has become an expectation. This thesis explores how the community can maintain, retain, and repair some essence of the existing condition by prioritizing a system to manage a shrinking city. By reinforcing the local, contesting urban growth, and redefining ownership, the plethora of city owned parcels are incrementally collected and consolidated across multiple residential blocks to restructure areas of growth and provide a public space that gives back to the community. In the vicinity of the consolidated block, underutilized infrastructure and homes are deconstructed with the help of permanent and temporal built interventions. A series of lightweight modular buildings stretch across the central residential block, promoting communal activity and incentives for degrowth while alleviating maintenance efforts and costs to benefit nearby residents

    A Career Stage Perspective on the Impact of Fully Remote and Hybrid Work: Pathways to Engagement and Exhaustion

    No full text
    Fully remote and hybrid work have increased in recent years; however, the extent to which these work arrangements impact employees based on their career stage remains relatively unexplored. The majority of research has examined hybrid employees, leaving much to be understood about the experience of fully remote workers. Drawing on job demands-resources theory (Demerouti et al., 2001) and career stage theory (Super, 1957; Super et al., 1988), this study assessed the extent to which fully remote employees, compared to hybrid employees, perceived role ambiguity and learning opportunities. Additionally, this study examined the extent to which role ambiguity and perceived learning opportunities related to exhaustion and engagement directly, in addition to examining the moderating effect of a person’s career stage (operationalized via occupational tenure). A survey-based study of 520 working adults with an average age of 39 years (SD = 10.2) recruited from Prolific (258 hybrid workers, 262 fully remote workers) was conducted to test the hypotheses. The results failed to show a significant relationship between a person’s work arrangement and perceived learning opportunities, and while a significant relationship was found between work arrangement and role ambiguity, the result was in the opposite direction than expected. Both perceived learning opportunities and role ambiguity were positively related to engagement and exhaustion, respectively, as hypothesized. Moreover, although work arrangement was not indirectly related to engagement via perceived learning opportunities, it was related to exhaustion via role ambiguity such that fully remote workers tended to be less exhausted as a result of experiencing less role ambiguity. Additionally, no evidence was found for a moderating effect of career stage when operationalized as occupational tenure. However, exploratory analyses revealed a significant interaction between age and role ambiguity. Finally, in addition to examining the psychometric properties of the Adult Career Concerns Inventory – Short Form (Perrone et al., 2003), exploratory analyses suggested that fully remote workers may experience less role ambiguity due to lower levels of job complexity. This study contributes to the literature by providing insight into the differences between fully remote and hybrid workers and examining the reliability and validity of an alternative to time-based proxies of career stage

    Towards Trapped-Ion Quantum Simulation with Ground-State and Optical qubits

    No full text
    Trapped ions offer a controlled and versatile platform for the simulation of spin and spin-boson quantum systems. The Coulomb interaction between ions trapped in a harmonic potential can be used to mediate interactions between effective spins in the ion chain. Generally, coherent operations on ions are performed on ground-state qubits encoded in magnetically insensitive hyperfine sublevels. In this thesis, we extend this toolbox with the aim of simultaneously manipulating both ground-state and optical qubits, with the latter encoded in metastable optically excited states. The optical qubit provides another set of coherent and dissipative operations that can be performed on the ions, opening new avenues for quantum computing and simulation. In our experiment, we use 171Yb+ and 172Yb+ ions to encode ground-state and optical qubits. We discuss the laser setup needed to address the narrow quadrupole transition from 2S1/2 →2 D3/2 of 3.02 Hz linewidth, and we describe spectroscopy techniques to study this transition in both the isotopes. We describe how the low linewidth allows resolved sideband cooling on the shared motional modes in an ion chain, enabling sympathetic cooling with one ion, 172Yb+ , while simultaneously performing coherent operations on the 171Yb+ ion. Finally, we discuss the prospects of using this tool for light-shift entangling gates, showing the flexibility of this trapped-ion system for simulating coherent as well as dissipative quantum systems

    Graph-based Learning for Efficient Resource Allocation and Management in Wireless Networks

    No full text
    Wireless network optimization faces challenges in several aspects. System-level objective functions are typically non-convex due to multiuser interference, rendering NP-hard problems. Moreover, real-world factors like delay and energy requirements could translate into non-convex constraints. As a result, traditional practices tend to be suboptimal and often rely on computationally expensive iterations or simulations. This inefficiency limits the design and management of scalable wireless networks. To improve efficiency, this thesis leverages deep learning techniques, with a focus on the permutation-equivariant graph neural networks (GNNs), across various wireless applications. The first part of this thesis presents a graph-based trainable framework for power allocation, namely the unfolded successive concave approximation (USCA), to maximize weighted-sum energy efficiency (WSEE) in wireless interference networks. The second part revisits power allocation and, by devising a primal-dual (PD) learning framework, handles non-convex constraints specific to the context of wireless federated learning (FL). Finally, the third part creates a learnable digital twin (DT) for efficient network evaluation, a thousandfold more efficient tool than simulators for network design and management. These three bodies of work demonstrate comprehensive theoretical and experimental results highlighting the superior performance of the proposed architectures over existing approaches. Overall, this work seeks to integrate deep learning into wireless applications by innovating specialized architectures that retain the core structure of original regimes. Key advantages include better interpretability than non-specialized end-to-end learning, enhanced generalizability across varying network configurations, and faster inference speed compared to optimization-based methods and simulators. The methodologies presented herein have substantial potential for diverse wireless applications, including network design, resource allocation, and network management

    Convergence Results and a New Preconditioner for Spectral Collocation in Time

    No full text
    Spectral collocation methods provide a systematic construction for the approximate solution of ordinary differential equations (ODEs) of arbitrarily high order. These methods approximate the solution with a piecewise polynomial, which is determined by requiring the residual of the ODE to vanish at collocation points. This thesis presents three algebraically equivalent forms of the collocation method corresponding to different choices of polynomial bases. The convergence of global collocation for linear problems is analyzed from the viewpoint of projection methods, in which the projection operator represents interpolation by polynomials. This analysis is extended to nonlinear problems using the Kantorovich Theorem. Finally, a new preconditioner is presented that facilitates the efficient implementation of Chebyshev collocation methods. Numerical experiments demonstrate that the solution time of preconditioned spectral collocation behaves like O(K log K), where K is the number of collocation points, allowing for solves with over a million points

    Understanding and Leveraging the Temperature-Dependent Curing of Silicone Elastomers

    No full text
    Silicone elastomers offer a wide range of mechanical properties, and their inherent compliance renders them suitable for use in applications including medical devices, shock absorbers, water-repellant surfaces, and cookware. Moreover, in the past decade, silicone elastomers have facilitated significant progress in the field of soft robotics. However, knowledge of the curing duration at a given temperature for thermally polymerizable elastomers often relies on empirical trends, and furthermore, the curing parameters—typically determined through trial and error—are limited to specific geometries and elastomers. Additionally, over-curing elastomeric parts at elevated temperatures consumes excess energy and contributes to device failure due to subsequent weak adhesion between components. The lack of understanding of the curing behavior limits the accessible design space of elastomers. Building on a framework introduced in my prior research quantifying the inactivation reaction of viruses, in this thesis, I present a modeling framework based on thermo-rheological experiments and the Arrhenius equation to provide a new understanding of the temperature-dependent curing of platinum catalyzed elastomers. The experimental results reveal that the curing behavior exhibits self-similarity upon normalizing with the gelation time, and the reaction is characterized by a dimensionless reaction coordinate that represents the extent of curing. Next, I leverage this understanding of the curing kinetics to study the adhesion between elastomer layers only as a function of the extent of curing, which accounts for both duration and temperature, and demonstrate the utility of the reaction coordinate to pinpoint failure regimes. Adhesion between elastomeric components represents a longstanding problem in the field of soft robotics and soft lithography. New insight into improving adhesion will enable new fabrication methodologies. Finally, I investigate the effects of curing silicone elastomers at temperatures beyond room temperature on the mechanical properties. The corresponding experimental results highlight the feasibility of using temperature to control the speed of curing while maintaining the desired mechanical behavior. Overall, my thesis aims to understand and leverage the curing behavior of elastomers as a function of time and temperature, informed by reaction kinetics, to broaden elastomer processing beyond traditional casting, and expand the accessible design space for the manufacturing of elastomeric devices

    Evolution of Holiness Camp Kwali, Abuja: Gnosis and History Exemplifying a shift from Church-Centric to Community-Centric Christianity

    No full text
    Abstract Historically, the Evangelical Revival and the Great Awakenings of the eighteenth century primarily resulted in the establishment of church institutions through rituals. This work is going to demonstrate that while the early history of revivalism is well documented in Nigeria, the contrast today is that the current revival leaders have also expanded the scope of their vision to create Nigerian Pentecostal camp meeting revivals beyond church institutions into creating Christian neighborhoods governed according to the teachings and doctrines of specific movements. This research focuses on the Holiness Camp, Abuja. Ruth Marshall's observation that "In Nigeria, the line between the city and the church is rapidly vanishing" underscores the transformation of the Redemption Camp into the Redemption City of the Redeemed Christian Church of God, highlighting significant real estate investments that have turned the camp into a residential area. Despite the extensive literature on Nigerian Pentecostalism, a significant gap remains in understanding the connection between Pentecostalism and neighborhood development through the tradition of Pentecostal revival camps and their evolution into exclusive Christian enclaves. This dissertation addresses how daily spiritual devotions transform a camp space into a new and settled community by examining the Holiness Camp in Abuja, Nigeria, as a case study of a diastolic camp. It categorizes Pentecostal revival camps in Nigeria into three types: systolic, equilibrium, and diastolic (residential) camps. The research posits the perspective that the frequency and constancy of spiritual devotion, large expanse of land, and founder’s residence in the camp, are crucial for an equilibrium or seasonal camp to transition into a Holiness Revival Movement Worldwide’s camp into a diastolic or residential camp. Key activities for neighborhood development shift from seasonal to daily or weekly devotions, with four quarterly conferences hosted at the camp. I demonstrate that the presence of the founder's residence, internal security system, large expanses of land available for sale or gift to members, the administrative headquarters being located within the camp, and the emergence of socio-economic activities such as commercial laundry, printing press, mechanic workshops, restaurants, medical clinics, schools, and factories for block and water production, all guided by the doctrines of the movement, endow the camp with the features of a neighborhood with a religious worldview. This research employs descriptive analysis methods and Anthony Wallace’s event-analysis methodological principle to examine the spiritual and doctrinal systems addressing everyday needs in the Holiness Camp. The study is grounded in comprehensive fieldwork, utilizing diverse data sources, including field notes, diaries, devotional tracts, oral and telephone interviews, participant observation, and an extensive collection of over fifty books authored by Paul Rika, the founder of HOREMOW. Additionally, it incorporates the analysis of multimedia sources such as photographs, YouTube and Facebook videos, audio and video disks, websites, maps, Zoom meetings, and academic journal articles. This dissertation contributes to the understanding of the evolving nature of Pentecostal revival camps in Nigeria, providing insights into the complex interplay between Pentecostalism and neighborhood development

    1

    full texts

    70,302

    metadata records
    Updated in last 30 days.
    Rice University Research Repository is based in United States
    Access Repository Dashboard
    Do you manage Open Research Online? Become a CORE Member to access insider analytics, issue reports and manage access to outputs from your repository in the CORE Repository Dashboard! 👇