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Fabrication of Macroscopic Nanofibrous Multidomain Peptide Hydrogels to Engineer Biological Tissues
No full textEMBARGO NOTE: This item is embargoed until 2025-05-01Fibrous extracellular matrix (ECM) proteins mechanically support cells and are hierarchically organized within macroscopic biological tissues. A longstanding goal of tissue engineering has been to fabricate scaffolds that mimic this organization, but it has been difficult to simultaneously mirror both micro and macroscale tissue complexity. Biomaterial design innovations have fostered the creation of synthetic ECM-mimetic hydrogels that recapitulate the mechanical and chemical properties of soft tissues. Still, the creation of large scaffolds at high fidelity has remained a bottleneck and is especially challenging when using soft biomaterials. Three- dimensional (3D) printing has emerged as a fabrication technology able to meet this goal due to its layer-by-layer working principal, but the number of hydrogels that have been adopted for 3D printing has remained limited. For over a decade, the Hartgerink lab has developed a synthetic class of biomaterials called multidomain peptides (MDPs), which form nanofibrous hydrogels that are useful for a variety of biomedical applications. My thesis presents the optimization of MDPs for 3D printing and the development of methods to create macroscopic MDP hydrogels with hierarchical order. In addition, I explore how biomaterial charge and fibrous alignment cues can be used to direct cellular spreading and engineer tissues from the bottom up. In the first chapter, I contextualize my work by reviewing the extracellular matrix, hydrogels, 3D printing of hydrogels, and MDPs. In the second chapter, I optimize MDPs for extrusion 3D printing and fabricate complex hydrogel structures and multi-material prints. In addition, I show how MDP charge can be used to control cell growth, which allows chemical functionality to provide an additional dimension to printing complexity. In the third chapter, I develop an extrusion-based fabrication strategy using MDPs to generate nanofibrous hydrogels that possess a spectrum of fibrillar alignments. In addition, I show how anisotropic MDP hydrogels can be used to directionally guide cellular growth, while differences in cell-matrix interactions determine a cell’s ability to understand nanofibrous alignment cues. In the fourth chapter, I present progress towards fabricating macroscopic MDP scaffolds with local anisotropy by optimizing support bath assisted 3D printing
Insights into glacial processes from micromorphology of silt-sized sediment
No full textSilt-rich meltwater plume deposits (MPDs) analyzed from marine sediment cores have elucidated relationships that are clearly connected, yet difficult to constrain, between subglacial hydrology, ice-marginal landforms, and grounding-zone retreat patterns for several glacial catchments. Few attempts have been made to infer details of subglacial hydrology, such as flow regime, geometry of drainage pathways, and mode(s) of sediment transport through time, from grain-scale characteristics of MPDs. Using sediment samples from MPD, till, and grounding-zone proximal diamicton collected offshore of six modern and relict glacial catchments in both hemispheres, we examine grain shape distributions and microtextures (collectively, grain micromorphology) of the silt fraction to explore whether grains are measurably altered from their subglacial sources via meltwater action. We find that 75 % of all imaged grains (n = 9400) can be described by 25 % of the full range of measured shape morphometrics, indicating grain shape homogenization through widespread and efficient abrasive processes in subglacial environments. Although silt grains from MPDs exhibit edge rounding more often than silt grains from tills, grain surface textures indicative of fluvial transport (e.g., v-shaped percussions) occur in only a modest number of grains. Furthermore, MPD grain surfaces retain several textures consistent with transport beneath glacial ice (e.g., straight or arcuate steps, (sub)linear fractures) in comparable abundances to till grains. Significant grain shape alteration in MPDs compared to their till sources is observed in sediments from glacial regions where (1) high-magnitude, potentially catastrophic meltwater drainage events are inferred from marine sediment records and (2) submarine landforms suggest supraglacial melt contributed to the subglacial hydrological budget. This implies that quantifiable grain shape alteration in MPDs could reflect a combination of high-energy flow of subglacial meltwater, persistent sediment entrainment, and/or long sediment transport distances through subglacial drainage pathways. Integrating grain micromorphology into analysis of MPDs in site-specific studies could therefore aid in distinguishing periods of persistent, well-connected subglacial discharge from periods of sluggish or disorganized drainage. In the wider context of deglacial marine sedimentary and bathymetric records, a grain micromorphological approach may bolster our ability to characterize ice response to subglacial meltwater transmission through time. This work additionally demonstrates that glacial and fluvial surface textures are retained on silt-sized quartz grains in adequate amounts for microtexture analysis, which has heretofore been conducted exclusively on the sand fraction. Therefore, grain microtextures can be examined on silt-rich glaciogenic deposits that contain little to no sand as a means to evaluate sediment transport processes
Huxley at Rice
No full textCreated under archivist Rebecca Russell and historian Dr. Luis Campos's mentorship as part of the Fondren Fellows program, this poster exhibits Sir Julian Sorell Huxley's time at the Rice Institute. As a founding member of the Rice biology program, Huxley pioneered the curriculum to tackle the ever-emerging field of evolutionary biology and genetics. While at the newly inaugurated Institute, Huxley befriended other professors, taught students who would nostalgically recount his antics, and adventured through Texas and beyond in search of wildlife and experiences. To learn more about this project, visit Fondren Library's Online Exhibit titled "Julian Huxley At Rice": https://digitalcollections.rice.edu/online-exhibits/julian-huxley-at-ric
Scaling Deep Learning through Optimizing Data- and Management-Plane Communications
No full textThe recording-breaking performance of deep neural networks (DNNs) has brought remarkable success to many domains, such as computer vision, natural language processing, and recommendation systems. However, the powerful DNNs come with significant computational complexity due to the increased training data and model
sizes. Because the network bandwidth upgrade in GPU clouds has not kept pace with the improvements in the computation capacity of GPUs as well as the fast growth in dataset and model sizes, deep learning practitioners have struggled to efficiently scale up training DNNs. This thesis identifies and addresses research challenges in
scaling distributed deep learning (DDL) by optimizing communications in both the data plane and the management plane.
The first half of the thesis focuses on data-plane communications that support
gradient synchronization in DDL. We introduce Zen, a system that fully leverages the sparsity in gradient tensors to scale deep learning with a provable optimal scheme for sparse tensor synchronization. We then propose Espresso and Cupcake to optimize
the scalability of compression-enabled DDL that applies gradient compression
algorithms to reduce traffic volume in communications for DNNs with low sparsity.
The second half of the thesis focuses on management-plane communications that
provide fault tolerance to DDL. We introduce Gemini, a scalable distributed training system that checkpoints the model states at the optimal frequency to minimize failure recovery overhead in DDL, especially for large DNNs towards trillions of parameters
Emergency of per- and polyfluoroalkyl substances in drinking water: Status, regulation, and mitigation strategies in developing countries
No full textThe detection of per- and polyfluoroalkyl substances (PFAS) in water presents a significant challenge for developing countries, requiring urgent attention. This review focuses on understanding the emergence of PFAS in drinking water, health concerns, and removal strategies for PFAS in water systems in developing countries. This review indicates the need for more studies to be conducted in many developing nations due to limited information on the environmental status and fate of PFAS. The health consequences of PFAS in water are enormous and cannot be overemphasized. Efforts are ongoing to legislate a national standard for PFAS in drinking water. Currently, there are few known mitigation efforts from African countries, in contrast to several developing nations in Asia. Therefore, there is an urgent need to develop economically viable techniques that could be integrated into large-scale operations to remove PFAS from water systems in the region. However, despite the success achieved with removing long-chain PFAS from water, more studies are required on strategies for eliminating short-chain moieties in water
Annealed Langevin Dynamics for MIMO Communications
No full textSolving the optimal data detection problem in multiple-input multiple-output (MIMO) systems is known to
be NP-hard. Moreover, the difficulty is exacerbated when the channel state information is unavailable. In this work we propose a MIMO detector for the two scenarios, namely when the CSI is known and when it is unknown. First, for the case of perfect CSI, we proposed a MIMO detector based on an annealed version of Langevin dynamics. More precisely, we define a stochastic dynamical process whose stationary distribution coincides with the posterior distribution of the data given our observations. This allows us to approximate the maximum a posteriori estimator of the transmitted symbols by sampling from the proposed Langevin dynamic.
We carefully craft this stochastic dynamic by gradually adding a sequence of noise with decreasing variance to the trajectories, which ensures that the estimated symbols belong to a pre-specified discrete constellation. Second, for the case of unknown CSI, we propose a joint data detection and channel estimation solution, where we define an annealed Langevin diffusion whose stationary distribution is the joint posterior of the channels and data given noisy observations
Estimate of background baseline and upper limit on the chiral magnetic effect in isobar collisions at GeV at the BNL Relativistic Heavy Ion Collider
No full textFor the search of the chiral magnetic effect (CME), STAR previously presented the results from isobar collisions (9644Ru+9644Ru, 9640Zr+9640Zr) obtained through a blind analysis. The ratio of results in Ru+Ru to Zr+Zr collisions for the CME-sensitive charge-dependent azimuthal correlator (Δ), normalized by elliptic anisotropy (2), was observed to be close to but systematically larger than the inverse multiplicity ratio. The background baseline for the isobar ratio, =(Δ/2)Ru(Δ/2)Zr, is naively expected to be (1/)Ru(1/)Zr; however, genuine two- and three-particle correlations are expected to alter it. We estimate the contributions to from those correlations, utilizing both the isobar data and hijing simulations. After including those contributions, we arrive at a final background baseline for , which is consistent with the isobar data. We extract an upper limit for the CME fraction in the Δ measurement of approximately 10% at a 95% confidence level on in isobar collisions at √=200GeV, with an expected 15% difference in their squared magnetic fields
Breaking Cycles, Building Connections: Rethinking Market Edges in Abidjan for Sustainable Urban Transformation
No full textMy thesis focuses on markets in Abidjan, Côte d'Ivoire, specifically the reworking of the edges of the Marché de Marcory to better serve the market, its people, and the city as a whole. The different elements comprising this new edge can be implemented in other markets throughout the city to reconfigure their edges as well. The ground floor of this new edge is dedicated to the market, incorporating infrastructure such as storage, sinks, and refrigeration spaces to support the day-to-day activities of the market. The first floor is dedicated to the women of the market and their children. Since the markets are predominantly run by women, and unfortunately, many of them lack formal education, they often enter a cycle from a young age. Initially brought to the market by their mothers, who are working there, they gradually assume more responsibilities and eventually take over their mothers’ stalls. This perpetuates a challenging cycle, making it difficult for them to break free as they, too, end up having their own children
Coffee & Quality Case Study #1: Angel Reach
No full textThe Kinder Institute for Urban Research and United Way of Greater Houston created a program called Coffee & Quality Case Study that works with designated United Way organizations to 1) identify ways to build and bolster the organization's current data-collecting practices and 2) use data to understand and improve program outcomes. The first Coffee & Quality Case Study focused on Angel Reach (https://angelreach.org/), a nonprofit working with young people aging out of the foster care system and/or at risk of homelessness
Non-local optical response of a multi-phased quantum material
No full textLight–matter interaction in quantum materials presents a new paradigm as light can tip the balance between many competing quantum many-body phases to result in new phenomena. Describing the optical response of such materials requires complex models. Here, we develop a non-local model to describe the optical response of a quantum material, 1T- TaS 2. 1T- TaS 2 is a charge density wave material that supports competing stacking configurations of its charge domains. The presence of various stacking domains results in an inhomogeneity that necessitates a non-local dielectric function. We experimentally measure the non-local optical response of 1T- TaS 2 films under various illumination intensities and validate our model. The non-local parameter extracted from our measurements sheds light on the competition between the two stacking configurations of 1T- TaS 2. Our technique of measuring non-local optical response serves as a quick, simple, and non-invasive method to probe the energy landscape of strong correlations in many such quantum materials