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- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- Studies of fate patterning during development typically emphasize cell-cell communication via diffusible chemical signals. Recent experiments on stem cell colonies (see Xue et al. Nature Materials 2018), however, suggest that in some cases mechanical stresses, rather than secreted chemicals, enable long-ranged cell-cell interactions that specify positional information and pattern cell fates. The authors of this earlier publication reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. As part of these experiments, they showed that the concentric width of the outer fate domain is approximately constant as the colony diameter is increased from 300 um to 800 um. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. The experimental images of cell colonies, both for varying cell colony diameter (from Xue et al. Nature Materials 2018) and for varying substrate stiffness (data generated for the publication linked to these data), are provided here. Each example has an image for PAX3 signal (marker for outer fate domain; Paired box gene 3) and an image for DAPI signal (staining nuclei; 4′,6-diamidino-2-phenylindole).
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Science and Engineering
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- Creator:
- Nunley, Hayden and Lubensky, David K
- Description:
- In a previous study (Xue et al. Nature Materials 2018), the authors showed that a key fate patterning event in vertebrate development can be reproduced in an in vitro stem cell culture. They further showed that this in vitro fate pattern seems to depend on mechanical signals rather than secreted chemical signals. In this follow-up study, a mathematical model of this process is proposed. The code in this deposit is for the simulation of this mathematical model in various cell layer geometries and substrate geometries. These geometries include a 1D cell layer, quasi-1D stripe geometry, disc geometry (all on a very thin substrate or a substrate composed of microposts) as well as a 1D cell layer on a finite-thickness substrate. Our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, and Force sensing
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205, Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9, Banerjee S, Marchetti MC. Substrate rigidity deforms and polarizes active gels. EPL (Europhysics Letters) 96, 28003 (2011). https://doi.org/10.1209/0295-5075/96/28003, Edwards CM, Schwarz US. Force Localization in Contracting Cell Layers, Physical Review Letters 107, 128101 (2011). https://doi.org/10.1103/PhysRevLett.107.128101, and Banerjee S, Marchetti MC. Contractile Stresses in Cohesive Cell Layers on Finite-Thickness Substrates, Physical Review Letters 109, 108101 (2012). https://doi.org/10.1103/PhysRevLett.109.108101
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells. In a follow-up study (linked to this dataset), we quantitatively analyzed these data to demonstrate even further that the NPB cells are mechanically different than the NP cells and that the post displacement profile is not explained by a model of a cell layer with uniform mechanical properties. This analysis motivated the mathematical model -- for this cell colony system -- that we proposed and analyzed.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Hayden Nunley, Xufeng Xue, Jianping Fu, David K. Lubensky bioRxiv 2021.04.30.442205; doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Fu, Jianping, and Lubensky, David K
- Description:
- In an earlier publication (Xue et al. Nature Materials 2018), the authors reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. One ingredient of this mathematical model is that the cells at the very edge of the colony (lacking adherens junctions on one side) are geometrically different than the rest (by occupying a larger area on the micropattern). These images of DAPI (staining nuclei) and ECad (at adherens junctions) for colonies during early cell differentiation demonstrate this difference. Corresponding code for analysis is included.
- Keyword:
- Biomechanics, Cell mechanics, and Developmental pattern formation
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
-
- Creator:
- Liao, Jiankan, De Kleine, Robert, Kim, Hyung Chul, Luckey, George, Forsmark, Joy, Lee, Ellen C., and Cooper, Daniel R.
- Description:
- Laser Additive Manufacturing Process (LAMP) Model Decision Support Tool constructed in excel sheet to predict the environmental impact, cost and lead time associated with various manufacturing processes
- Keyword:
- Laser powder bed fusion, Die casting, Injection molding, Machining, Cradle-to-gate, and Life cycle assessment
- Citation to related publication:
- Jiankan Liao, Robert De Kleine, Hyung Chul Kim, George Luckey, Joy Forsmark, Ellen C. Lee, Daniel R. Cooper, Assessing the sustainability of laser powder bed fusion and traditional manufacturing processes using a parametric environmental impact model, Resources, Conservation and Recycling, Volume 198, 2023, 107138, https://doi.org/10.1016/j.resconrec.2023.107138.
- Discipline:
- Engineering
-
- Creator:
- Dong, Jiayuan, Liao, Jiankan, Huan, Xun, and Cooper, Daniel R.
- Description:
- We apply expert elicitation to assign informative prior to material flow analysis and conduct Bayesian inference for parameter and data noise learning.
- Keyword:
- Bayesian inference, Bayes factor, data noise, prior elicitation and aggregation, and uncertainty quantification
- Citation to related publication:
- Dong, Jiayuan, Jiankan Liao, Xun Huan, and Daniel Cooper. "Expert elicitation and data noise learning for material flow analysis using Bayesian inference." Journal of Industrial Ecology 27, no. 4 (2023): 1105-1122.
- Discipline:
- Engineering
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- Creator:
- Hawes, Jason K, Goldstein, Benjamin P. , Newell, Joshua P. , Dorr, Erica , Caputo, Silvio , Fox-Kämper, Runrid , Grard, Baptiste , Ilieva, Rositsa T. , Fargue-Lelièvre, Agnès , Poniży, Lidia , Schoen, Victoria , Specht, Kathrin , and Cohen, Nevin
- Description:
- Urban agriculture (UA) is a widely proposed strategy to make cities and urban food systems more sustainable. However, its carbon footprint remains understudied. In fact, the few existing studies suggest that UA may be worse for the climate than conventional agriculture. This is the first large-scale study to resolve this uncertainty across cities and types of UA, employing citizen science at 73 UA sites in Europe and the United States to compare UA products to food from conventional farms. The results reveal that food from UA is six times as carbon intensive as conventional agriculture (420g vs 70g CO2 equivalent per serving). Some UA crops (e.g., tomatoes) and sites (e.g., 25% of individually-managed gardens), however, outperform conventional agriculture. These exceptions suggest that UA practitioners can reduce their climate impacts by cultivating crops that are typically greenhouse grown or air-freighted, maintaining UA sites for many years, and leveraging waste as inputs.This database contains the necessary reference material to trace the path of our analysis from raw garden data to carbon footprint and nutrient results. It also contains the final results of the analyses in various extended forms not available in the publication. For more information, see manuscript at link below. (Introduction partially quoted from Hawes et al., 2023)
- Citation to related publication:
- Hawes, J. K., Goldstein, B. P., Newell, J. P., Dorr, E., Caputo, S., Fox-Kämper, R., Grard, B., Ilieva, R. T., Fargue-Lelièvre, A., Poniży, L., Schoen, V., Specht, K., & Cohen, N. (2024). Comparing the carbon footprints of urban and conventional agriculture. Nature Cities, 1–10. https://doi.org/10.1038/s44284-023-00023-3
- Discipline:
- Engineering
-
- Creator:
- Liao, Jiankan, Deng, Sidi, Huan, Xun, and Cooper, Daniel R.
- Description:
- We apply Bayesian inference to reduce network structure uncertainty on material flow analysis (MFA) and demonstrate the methodology through a case study on U.S. steel flow. In addition, we derive an input/output-based analysis to conduct decision-making based on the uncertainty results from MFA
- Keyword:
- Bayesian inference, Network structure uncertainty, Bayesian model selection, and Input/output analysis
- Citation to related publication:
- Liao, Jiankan, Deng, Sidi, Xun Huan, and Daniel Cooper. "Bayesian Model Selection for Network Discrimination and Risk-informed Decision Making in Material Flow Analysis." arXiv preprint arXiv:2501.05556 (2025).
- Discipline:
- Engineering
-
- Creator:
- Dorman, Cole J
- Description:
- CHIME provides accurate measurements while enabling inter-spacecraft calibration in constellation missions, offering a significantly more affordable alternative to traditional magnetometers without compromising measurement quality. The development of CHIME is motivated by the high number of magnetometers needed in spacecraft constellations that require a cost-effective commercial solution, as traditional, precise magnetometers are expensive and require complex ground and on-orbit calibration methods that depend on geomagnetic models or special conditions. CHIME Accuracy Calibration: - Various PNI RM3100s were used for data collection, each specified when used and how - Ground CHIME was used for experiments (50 turns per axis, hand wound) - Bartington HC1 500 mm Helmholtz coil was used for calibration baseline experiments. - Python 3.7+ Coil Homogeneity Simulations: - Python 3.7+ Optimal Calibration Pulse Parameters: - Python 3.7+ - ESA Swarm Simulation Data 50 Hz: Level 1B MAGx_HR ( https://swarm-diss.eo.esa.int). - ESA Swarm Simulation Data 1 Hz: Level 1B MAGx_LR. CHIME Calibration Accuracy Across Orbital Environments: - Python 3.7+ - ESA Swarm Simulation Data 50 Hz: Level 1B MAGx_HR ( https://swarm-diss.eo.esa.int). Comparison Simulations of Single Sensor Attitude Indepedent Calibration Methods: - Python 3.7+ - ESA Swarm Simulation Data 50 Hz: Level 1B MAGx_HR ( https://swarm-diss.eo.esa.int). Definitions: CHIME- protagonist of the dataset and accompanying manuscript, the self-calibrating magnetometer Scale Factor (SF), Non-Orthogonality (NO)- forms of magnetic sensor error PNI RM3100- internal magnetic sensor in CHIME Bartington HC1 Coil- calibration tool for the RM3100 and CHIME, a Helmholtz coil itself. ESA - European Space Agency and Updates: - March 2025: Changes to simulated calibration methodology, completed before publication initial submission or peer-review
- Keyword:
- magnetometer, calibration, Helmholtz, spacecraft, and remote sensing
- Citation to related publication:
- Dorman, C.J., Vata, J., Ojeda, L. V., Moldwin, M.B., The CHIME Magnetometer: A Self-Calibrating Approach for Enhanced Accuracy in Spaceborne Applications, Forthcoming.
- Discipline:
- Engineering
-
- Creator:
- Wan, Zhiwen, Pannala, Sravan, Solbrig, Charles, Stefanopoulou, Anna G. , Siegel, Jason B. , and Lee, Junseo
- Description:
- Lithium-ion batteries with silicon/graphite (Si/Gr) anodes achieve higher energy densities but face challenges such as rapid capacity fade, resistance growth, and complex expansion behavior under various cycling conditions. This study systematically addresses these challenges through a comprehensive test matrix to investigate the effects of pressure, temperature, state-of-charge (SoC) windows, and charge rates (C-rates) on the evolution of expansion, resistance, and capacity behavior over the lifetime of the battery. Increasing the applied pressure between 34 and 172 kPa reduced both reversible and irreversible expansion per cycle, as well as resistance growth over time, without significantly impacting capacity fade. Electrochemical Impedance Spectroscopy (EIS) confirmed that increased pressure lowered initial solution resistance and mitigated the growth of the solution and solid electrolyte interphase (SEI) resistance. Elevated temperature (45°C) extended battery cycle life despite an initial increase in resistance. Under these conditions, the lifetime impedance increase was dominated by SEI resistance. Consistent with prior studies, operating in a narrow SoC window at high SoC minimized capacity loss. Additionally, charge rates up to 2C had a limited effect on the overall degradation trends. Incremental capacity analysis (ICA) and differential voltage analysis (DVA) identified lithium inventory loss (LLI) as the primary driver of pre-knee degradation, whereas post-knee degradation resulted from a combination of LLI and anode-active material loss, particularly silicon. The deeper understanding of degradation mechanisms in batteries with Si/Gr anodes provided by this work enables the optimal packaging design and selection of operating conditions for the battery management system to extend battery cycle life.
- Keyword:
- Lithium-ion Batteries, Si/Gr Anodes, Battery Expansion, Incremental Capacity Analysis, Differential Voltage Analysis, Electrochemical Impedance Spectroscopy, and Lifetime Degradation Metrics
- Citation to related publication:
- Z. Wan et al. Degradation and Expansion of Lithium-Ion Batteries with Silicon/Graphite Anodes: Impact of Pretension, Temperature, C-rate and State-of-Charge Window
- Discipline:
- Engineering