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189 results for “thermodynamics”
Data Set Accompanying "Free Energy Decompositions Illuminate Synergistic Effects in Interfacial Binding Thermodynamics of Mixed Surfactant Systems"
<p>This data set accompanies "Free Energy Decompositions Illuminate Synergistic Effects in Interfacial Binding<br> Thermodynamics of Mixed Surfactant Systems" by Colin K. Egan and Ali Hassanali. It includes example GROMACS<br> input files for all simulations analyzed in the paper, as well as example data sets and analysis scripts. See<br> https://doi.org/10.26434/chemrxiv-2023-h11k5 for the preprint manuscript.</p>
Modeling the thermodynamic properties of saturated lactones in non-ideal mixtures with the SAFT-γ Mie approach. JCED 2023
<p>All computational data in the publication.</p>
Dataset for PNAS: Adiabatic computing for optimal thermodynamic efficiency of information processing
<p>Data set for the article to be published in PNAS "Adiabatic computing for optimal thermodynamic efficiency of information processing"</p> <p>This data set contains:</p> <ul> <li><strong>optimal_1ms.zip</strong> : raw data files of the response to an optimal erasure protocol of characteristic duration 1ms. This Matlab file includes all necessary quantitites to compute the average work and heat during the procedure ( ie position trajectory and driving parameters).</li> <li><strong>optimal_3ms_part1 & _part2.zip</strong>: same for optimal protocols of 3ms.</li> <li><strong>Analysis_code_optimal.m</strong>: Analysis Matlab code to be run on the mat files above. The code run the full analysis and output the work, heat, kinetic and potential energy and some calibration parameters. The processed data is saved in <strong>optimal_1 & 3ms_result.mat</strong>.</li> <li><strong>Fast_erasure_v1_0.3 & _0.12.zip</strong>: same for basic protocol at v<sub>1</sub>=0 & v<sub>1</sub>=0.12. The processed data is saved in <strong>Fast_erasure_v1_0.3 & _0.12.mat</strong>. This data corresponds tp the two speeds used to draw the heating kinetic energy curves of Fig.4</li> <li> <p><strong>BasicAndOptimalTranslations.mat:</strong> Mat file containing the data used to create Fig. 3:</p> <ul> <li> <p>tprotocol (ms), x1basprotocol and x1optprotocol (sigma) define the ramps of the well center for the basic and optimal protocols (time and value of x1 for each ramp).</p> </li> <li> <p>t (ms), xbas and xopt (sigma) are the recording from the experiment (time, and arrays corresponding to 2000 measurements with 10ms of data sampled at 2Mhz each). The data is post processed with a low pass filter at 8kHz (filtfilt function in Matlab, using a 4th order butterworth filter). Fig. 3 correspond to the average of those 2000 trajectories.</p> </li> <li> <p>f0 (Hz) is the resonance frequency of the cantilever.</p> </li> </ul> </li> <li><strong>FigX.fig: </strong>Matlab format figure source used to draw all of the plots of the article, embedding the all data.</li> </ul>
Quantum chemical investigation of the predominant conformation of the antibiotic azithromycin in water and DMSO solutions: an integrated thermodynamic and NMR analysis
<p><span>Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and treat serious infection</span><span>s (mycobacteria or MAC) that significantly inhibit bacterial growth. Knowledge of the predominant conformation in solution is of fundamental importance for advancing our understanding of the intermolecular interactions of AZM with biological targets. We report an extensive density functional theory (DFT) study of plausible AZM structures in solution considering implicit and explicit solvent effects. The best match between the experimental and theoretical nuclear magnetic resonance (NMR) profiles was used to assign the preferred conformer in solution, which was supported by the thermodynamic analysis. Among the 15 distinct AZM structures, conformer M14, having a short intramolecular C6-OH…N H-bond, is predicted to be dominant in water and DMSO solutions. The results indicated that the X-ray structure backbone is mostly conserved in solution, showing that large flexible molecules with several possible conformations may assume a preferential spatial orientation in solution, which is the molecular structure that ultimately interacts with biological targets.</span></p>
Data and code from: Thermodynamics underpinning the microbial community-level nitrogen networks
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Quantum chemical investigation of the predominant conformation of the antibiotic azithromycin in water and DMSO solutions: an integrated thermodynamic and NMR analysis
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Data from: Towards sustainable urea electrooxidation: A thermodynamic and green chemistry evaluation of alternative pathways
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Sample programs of an eco-redox model for the article: Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity
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Data for: Many-body thermodynamics on quantum computers via partition function zeros
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Supplementary Material for "Efficient biocatalytic synthesis of dihalogenated purine nucleoside analogues applying thermodynamic calculations"
<p>This is the supplementary material for our publication "Efficient biocatalytic synthesis of dihalogenated purine nucleoside analogues applying thermodynamic calculations". We wish to thank all authors for their contribution and have uploaded this dataset in their name.</p> <p>We apologize that these files are not publicly available. Please contact Dr. Anke Kurreck for access to raw and analyzed data.</p> <p>Naturally, this work builds on previous publications. Specifically, we have borrowed data from our recent work on the thermodynamic control of nucleoside phosphorolysis (10.1002/adsc.201901230; the full dataset can be found at 10.5281/zenodo.3568858) and employed equations and methodology described in our piece on yield optimization of nucleoside transgylcosylations (10.1002/cbic.201900740; the external supplementary information can be accessed at 10.5281/zenodo.3565561 and 10.5281/zenodo.3522588).</p>
Effect of substitution of Al2O3 and B2O3 for SiO2 on the structural and thermodynamic properties of cover glass for liquid crystal display
By the substitution of Al2O3 and B2O3 for SiO2 of the glass network former, the structural and thermodynamic properties of aluminosilicate glass were investigated. Judged by Raman spectra, the bridging vibration Si-Ob increased with the Al2O3/SiO2 substitute. And the total non-bridging vibration Si-Onb decreased, indicating the enhancement of the structure compactness. While for B2O3/SiO2 substitute, the vibration at around 1010cm-1 and the bridging vibration Si-Ob in Q4 unit both decreased and the structure got loosened. Based on the study of the structure of glass, the thermodynamic properties such as viscosity, coefficient of the linear thermal expansion, high-temperature resistance, strain point, annealing point and softening point, as well as density and elastic modulus were investigated. With the enhancement of thermodynamic properties requirements, the difficulty in industrialized manufacturing was increased. In this paper, glass composition of sample 4 was suitable for floating process production.
Breaking Free from Thermodynamic Constraints: Thermal Acclimation and Metabolic Compensation in a freshwater zooplankton species
<p>Ectothermic organisms' respiration rates are largely controlled by environment temperatures and the ability to meet metabolic demands at high temperatures sometimes sets their upper thermal limit. Organisms are hypothesized to exhibit acclimatory effects, adjusting their metabolism and physiology by deceleration of metabolic processes including respiration below Arrhenius expectations based in temperature alone. Such deceleration is termed metabolic compensation. We test the hypothesis that either heritable (among genotypes) or plastic (between acclimation regimes) heat tolerance differences can be explained by metabolic compensation in the eurythermal freshwater zooplankton crustacean Daphnia magna. We measured oxygen consumption rates over a range of assay temperatures (5°C - 37°C) in 8 genotypes of Daphnia representing a range of previously reported genotype-specific acute heat tolerance values and, in a narrower range of temperatures (10°C - 35°C) in Daphnia with different acclimation history (either 10°C or 25°C). In a ramp-up experiment we discovered no difference in temperature-specific respiration rates between heat tolerant and heat-sensitive genotypes. In contrast, we observed compensatory differences in respiration rates at both extremes of the temperature range studied. Notably, there was a deceleration of oxygen consumption at higher temperature in the 25°C-acclimated Daphnia relative to their 10°C-acclimated counterparts, observed in active, but not anaesthetized animals, a pattern corroborated by similar changes in filtering rate and, partly, by changes in mitochondrial membrane potential. Daphnia exposed to a sublethal temperature (35°C) with a 24-hour recovery period at a 25°C-acclimation temperature showed no difference in respiration compared to unexposed 25°C-acclimated Daphnia, indicating that the reduction of respiration is not caused by irreversible damage. Response time necessary to acquire the respiratory adjustment to high temperature was much lower than to low temperature, indicating that metabolic compensation at the lower temperatures require slower structural changes.</p>
The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"
<p>The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"</p>
Modeled Atmospheric Optical and Thermodynamic Responses to an Exceptional Trans-Atlantic Dust Outbreak
<p>Nine WRF-Chem 3.8.0 hindcasts, each utilizing a different dust emission configuration, from 1 March – 31 May 2015, coinciding with a Saharan air layer (SAL) dust outbreak during the 2015 Caribbean drought. WRF-Chem modeled aerosol optical depth (AOD) and Gálvez-Davison Index (GDI), a convective forecasting parameter, are provided in the files. These data correspond to the results published in "Modeled Atmospheric Optical and Thermodynamic Responses to an Exceptional Trans-Atlantic Dust Outbreak" by Paul Miller, Marcus Williams, and Thomas Mote, published the <em>Journal of Geophysical Research: Atmospheres</em>.</p>
Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints
To better predict how populations and communities respond to climatic temperature variation, it is necessary to understand how the shape of the response of fitness-related rates to temperature evolves (the thermal performance curve). Currently, there is disagreement about the extent to which the evolution of thermal performance curves is constrained. One school of thought has argued for the prevalence of thermodynamic constraints through enzyme kinetics, whereas another argues that adaptation can—at least partly—overcome such constraints. To shed further light on this debate, we perform a phylogenetic meta-analysis of the thermal performance curves of growth rate of phytoplankton—a globally important functional group—, controlling for environmental effects (habitat type and thermal regime). We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of maximum performance with the temperature at which the curve peaks, suggesting a weak "hotter-is-better" constraint. Also, instead of a constant thermal sensitivity of growth across species, as might be expected from strong constraints, we find that all aspects of the thermal performance curve evolve along the phylogeny. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.
Electrochemical and thermodynamic properties of 1-phenyl-3-(phenylamino)propan -1-one with Na2WO4 on N80 Steel
<p>The corrosion inhibition effect and adsorption behavior of 1-phenyl-3-(phenylamino)propan-1-one(PPAPO) on N80 steel in hydrochloric solution have been investigated by Fourier transform infrared (FTIR), electrochemical method and scanning electron microscopy (SEM). The corrosion inhibition mechanism of PPAPO with Na<sub>2</sub>WO<sub>4</sub> was interpreted from the point of view of the thermodynamic. The results indicated that PPAPO with Na<sub>2</sub>WO<sub>4</sub> acted as a mixed type inhibitor. The inhibition film formed on N80 steel surface can increase the charge transfer resistance and prevent the occurrence of corrosion reaction, thereby reducing the corrosion rate of metal surface. The inhibition efficiency was up to 99.65%; and the inhibitor PPAPO with Na<sub>2</sub>WO<sub>4</sub> showed good synergistic effect on N80 corrosion behavior in HCl solution. The adsorption behavior of inhibitors on N80 steel surface was in accordance with the Langmuir adsorption model, and mainly belonged to chemisorption. The adsorption process of PPAPO on N80 surface was spontaneous and irreversible endothermic reaction.</p>
Predicting p53-Dependent Cell Transitions From Thermodynamic Models
<p>Matlab codes containing Grand Canonical Monte Carlo (GCMC) simulation codes and theoretical codes to study the first-order phase transition behavior of a malignant cell to a normal healthy cell. In this work, we develop thermodynamic models to determine the fate of a malignant cell as governed by the tumor suppressor p53 signaling network.</p>
Long-term effects of intercropping on multi-trophic structure and bio-thermodynamic health of mixed Eucalyptus-native tree plantations
<p><span>1. </span><span>The intercropping approach of <em>Eucalyptus</em> and native trees has been widely recommended, as an ideal replacement for monoculture <em>Eucalyptus</em> plantations (EUs), to ameliorate global biodiversity loss and mitigate environmental change. However, both suitable native tree species and the best intercropping ratio between <em>Eucalyptus</em> and native trees have not been determined. </span></p> <p><span>2. </span><span>To fill this gap, a four-level intercropping gradient of <em>Eucalyptus urophylla</em> planted with eight native tree species was set up (i.e., 20%NS, 30%NS, 40%NS, 50%NS), monitored and compared to a monoculture <em>E. urophylla</em> plantation (EU) and a randomly mixed plantation of nine native tree species (NS) in southern China. </span></p> <p><span>3. </span><span>The results showed that the intercropping ratio of <em>Eucalyptus</em> and native trees had a long-term effect on tree layer structure and health status and a cascading effect on the thermodynamic health state of soil microbes. Shade-tolerant woody species are more suitable for intercropping with <em>Eucalyptus</em>. Intercropping plantations with not less than 30% native trees were more favorable for long-term survival and growth of both planted <em>Eucalyptus</em> and native trees and provided much more favorable conditions for the natural immigration of other native trees, which leads to a healthy plant community with significantly higher eco-exergy compared to EU. The initial mixing ratio between <em>Eucalyptus</em> and high diversity native trees affected soil fertility through its long-term effects on the biodiversity and bio-thermodynamic state of trees and soil microbes.</span></p> <p><span>4. </span><span><em>Synthesis and applications</em>.</span><span> Our results highlight the long-term positive effect of the intercropping ratio of <em>Eucalyptus</em> and high diversity native trees on multi-trophic biodiversity conservation, bio-thermodynamic health development, and soil fertility conservation. In the conversion of monoculture <em>Eucalyptus</em> plantations (EU) to multi-species plantations, it is recommended to mix more than 30% native tree species that have different ecological niches with <em>Eucalyptus</em>.</span></p>
Equation of State of Liquid Fe7C3 and Thermodynamic Modeling of the Liquidus Phase Relations in the Fe-C System
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Computing solubility and thermodynamic properties of H2O2 in water
<p>The input files used for GROMACS and BRICK software in this work has been uploaded. The dataset contains .itp files for the H2O2 forcefields used and the .mdp file used for a NPT run on aqueous H2O2 solution. GROMACS was used to determine the densities, viscosities and diffusion coefficients of H2O2 in water. Also, BRICK input files (forcefield.in, settings.in, topology.in, H2O2, water, restart.in and weightfunction.in) has been uploaded. BRICK was used to calculate the solubility (Henry coefficient) of H2O2 in water. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.