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5 results for “Thermodynamic Integration”
Dataset - Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
<p><strong>Simulation data needed to reproduce the results from the manuscript “Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models”</strong><br> by V. Pandey, N. Hadadi and V. Hatzimanikatis</p> <p>"REMI manuscript - simData" folder contains all simulation data which can be used to generate results of the paper: <br> • Expression_data: This folder contains Transcriptomics data from both studies: Ishii et al (see test_expr.mat) and Holm et al.<br> • Fluxdata: Fluxomics data can be found form the studies Ishii et al and Holm et al.<br> • Metabolomics: This contains metabolomics data of aforementioned both studies.<br> • ModelsSolutions: We generated different models using with thermodynamics (TGex, TGexM, TM) and without thermodynamics models (Gex, GexM, M). Gex indicates integration with only gene expression, GexM indicates gene expression and metabolite, and M indicates only metabolites. ‘T’ is used for thermodynamic models. Models for different mutants and conditions (e.g. pgm, pgi) can be found in the corresponding folders (TGex, TGexM, TM, Gex, GexM, and M). Variables with the ‘store’ tag comprises flux solutions, correlation values and percentage error between simulation and experiment fluxes.<br> • AlternativeMCS: We generated alternative states for MCS and saved results.<br> • FVAMM: This is the result flux variability analysis can be found in this folder.<br> • Scatter_plot: Scatter plots indicates correlation between measured and model predicted fluxes.</p> <p> </p>
Data for: Thermodynamics of a dilute Bose gas: a path-integral Monte-Carlo study
<p>Path-integral Monte-Carlo results of the thermodynamics of a homogeneous dilute Bose gas. Data used to plot the figures for internal energy, pressure, isothermal compressibility and contact parameter.</p>
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>
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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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>
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