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Physical and biogeochemical variables from the NOAA-GFDL Earth System Model 2M experiments (pre-processed), previously published observation-based datasets, and code to reproduce figures from these datasets, used for the study 'Hydrological cycle amplification reshapes warming-driven oxygen loss in Atlantic Ocean'.
Microscopy images are part of a paper entitled "Structured foraging of soil predators unveils functional responses to bacterial defenses" by Fernando Rossine, Gabriel Vercelli, Corina Tarnita, and Thomas Gregor. For detailed acquisition methods see the paper. Experiments were performed between 2019 and 2020 at Princeton University. Two types of images are provided, macroscopic and microscopic widefiled Images. Macroscopic images all show Petri dishes covered in fluorescent bacteria being consumed by amoebae. Images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum. Images used for the creation of a profile were all taken within 30 minutes of each other. Within each directory numbered images are independent replicates. The raw video directory contains time series for dishes under drug treatments. Each numbered folder is a sequence of photos (taken 30 minutes apart of each other) of a single dish. Microscopic images all show amoebae consuming bacteria on a petri dish. The 45 minute videos show either edge cells (located at the edge of amoebae colonies), or inner cells (located 2.5 millimeters towards the center of the colony, from the edge). Videos are confocal stacks, with bacteria showing in green and amoebae appearing as black holes within the bacterial lawn. As was for the macroscopic images, images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum.
Khanna, Jaya; Medvigy, David; Fueglistaler, Stephan; Walko, Robert
Abstract:
More than 20% Amazon rainforest has been cleared in the past three decades triggering important hydroclimatic changes. Small-scale (~few kilometers) deforestation in the 1980s has caused thermally-triggered atmospheric circulations that increase regional cloudiness and precipitation frequency. However, these circulations are predicted to diminish as deforestation increases. Here we use multi-decadal satellite records and numerical model simulations to show a regime shift in the regional hydroclimate accompanying increasing deforestation in Rondônia, Brazil. Compared to the 1980s, present-day deforested areas in downwind western Rondônia are found to be wetter than upwind eastern deforested areas during the local dry season. The resultant precipitation change in the two regions is approximately ±25% of the deforested area mean. Meso-resolution simulations robustly reproduce this transition when forced with increasing deforestation alone, showing a negligible role of large-scale climate variability. Furthermore, deforestation-induced surface roughness reduction is found to play an essential role in the present-day dry season hydroclimate. Our study illustrates the strong scale-sensitivity of the climatic response to Amazonian deforestation and suggests that deforestation is sufficiently advanced to have caused a shift from a thermally- to a dynamically-driven hydroclimatic regime.
In this publication we provide the LAMMPS example files to reproduce simulations for the manuscript "A Deep Potential model for liquid-vapor equilibrium and cavitation rates of water"
Petsev, Nikolai D.; Nikoubashman, Arash; Latinwo, Folarin
Abstract:
Source code for our genetic algorithm optimization investigation of conglomerate and racemic chiral crystals. In this work, we address challenges in determining the stable structures formed by chiral molecules by applying the framework of genetic algorithms to predict the ground state crystal lattices formed by a chiral tetramer model. Using this code, we explore the relative stability and structures of the model’s conglomerate and racemic crystals, and extract a structural phase diagram for the stable Bravais crystal types in the zero-temperature limit.
The materials include codes and example input / output files for Monte Carlo simulations of lattice chains in the grand canonical ensemble, for determining phase behavior, critical points, and formation of aggregates.
This item contains two files. A multi-layer perceptron (MLP) neural network is built using the MATLAB Deep Network Designer (.m file). It imports a quantum cascade laser (QCL) dataset and splits it into 70% training, 15% validation, and 15% testing subsets. The network consists of an input layer, three hidden layers (each having a normalization and activation layer), and a regression output layer. All of the layers are fully connected, and the root-mean-square error (RMSE) is used to evaluate the accuracy of the network. An algorithm is trained on the [-2, +3] QCL dataset using 50 neurons, ReLU activation function, solver Adam, 0.001 learning rate, over 150 epochs, and is saved to be used in the prediction of figure of merit values for QCL designs (.mat file).
This item contains two files. A multi-layer perceptron (MLP) neural network is built using the MATLAB Deep Network Designer (.m file). It imports a quantum cascade laser (QCL) dataset and splits it into 70% training, 15% validation, and 15% testing subsets. The network consists of an input layer, three hidden layers (each having a normalization and activation layer), and a regression output layer. All of the layers are fully connected, and the root-mean-square error (RMSE) is used to evaluate the accuracy of the network. An algorithm is trained on the [-5, +20] QCL dataset using 50 neurons, ReLU activation function, solver Adam, 0.001 learning rate, over 50 epochs, and is saved to be used in the prediction of figure of merit values for QCL designs (.mat file).
A code to identify the laser transition for a quantum cascade laser design based on the figure of merit. Variables such as the number of layers, and layer thicknesses, as well the applied electric field, materials composition, number of period repetitions, and layer tolerance ranges to generate random designs are specified. A folder containing a .csv file with all electronic state-pair transitions collected, a .png file of the bandstructure and the laser transition chosen (in red), for all electric field iterations, and a summary .csv file of all these laser transitions for a structure at each electric field is generated by the code. To use, first install ErwinJr2 on your computer. Then locate the "ErwinJr2" folder and copy these 6 files into that directory, overwriting the previous five files (Material.py, QCLayers.py, QCPlotter.py, QuantumTab.py, rFittings.py). Lastly, run the "acej-qcl-layer_10-lwrandom-v23.py" script using Python.
The "summary-fomstar-3lu-eVmiddle-19.csv" file is generated after running the laser transition code, with all of the data collected for one structure at many electric fields. Running the script various times will generate random structures with the same electric field range. Joining these "summary" .csv files makes a QCL dataset.
This is the raw experimental dataset and the corresponding code to reproduce plots from the paper "Shear-induced migration of confined flexible fibers".
