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Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria (open access)

Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria

Article describes how, since the discovery of the second chromosome in the Rhodobacter spaeroides 2.4.1 in 1989 and the revelation of gene sequences, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. In this study, the authors have attempted to leverage machine learning as a means to identify the genetic factors that underlie the differentiation of bacteria with multipartite and unipartite genomes.
Date: November 13, 2023
Creator: Almalki, Fatemah; Sunuwar, Janak & Azad, Rajeev K.
Object Type: Article
System: The UNT Digital Library
A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1 (open access)

A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1

Article describes how within the genome of a pathogen is the information regarding factors responsible for its pathogenicity. the authors of the article developed a novel pipeline that uses standard protocol in combination with gene co-expression network of a pathogen constructed using publicly available RNA-Seq data sets.
Date: November 3, 2023
Creator: De, Ronika; Whiteley, Marvin & Aza, Rajeev K.
Object Type: Article
System: The UNT Digital Library
Conference: Dynamical Systems and Fractal Geometry (open access)

Conference: Dynamical Systems and Fractal Geometry

Data management plan for the grant, "Conference: Dynamical Systems and Fractal Geometry."
Date: 2024-04-15/2025-03-31
Creator: Allaart, Pieter C.
Object Type: Text
System: The UNT Digital Library
Computational study of the gas-phase reactions of sulfuric acid with OH(ΠJ), O(3PJ), Cl(2P) and O(1D2) radicals (open access)

Computational study of the gas-phase reactions of sulfuric acid with OH(ΠJ), O(3PJ), Cl(2P) and O(1D2) radicals

This article is about how rate coefficients for reactions of H2SO4 with OH, O(3P) and Cl radicals over 160–298 K were estimated computationally. The authors propose kOH = 8.5 × 10-14 exp(-50 K/T), kO = 1.1 × 10-12 exp(-5012 K/T) and kCl = 3.1 × 10-9 exp(-3314 K/T) cm3 molecule-1 s−1.
Date: December 27, 2021
Creator: Marshall, Paul & Burkholder, James B. (James Bart), 1954-
Object Type: Article
System: The UNT Digital Library
Experimental and Modeling Study of Water Time Histories during H2S-N2O Combustion in a Shock Tube (open access)

Experimental and Modeling Study of Water Time Histories during H2S-N2O Combustion in a Shock Tube

Article describes how, in the present study, the water formation was followed by laser absorption with N2O as an oxidant, instead of O2. Three H2S/N2O mixtures diluted in 98% Ar were studied to cover the following range of equivalence ratios: 0.5, 1.0, and 2.0, over a wide range of temperatures (1580–1940 K) around atmospheric pressure.
Date: June 7, 2023
Creator: Cooper, Sean P.; Marshall, Paul; Mathieu, Olivier; Pinzón, Laura T.; Mulvihill, Clayton R. & Glarborg, Peter
Object Type: Article
System: The UNT Digital Library
Measurement of the Intramolecular Hydrogen-Shift Rate Coefficient for the CH3SCH2OO Radical Between 314 and 433 K (open access)

Measurement of the Intramolecular Hydrogen-Shift Rate Coefficient for the CH3SCH2OO Radical Between 314 and 433 K

Article describes how the intramolecular hydrogen-shift rate coefficient of the CH3SCH2O2 (methylthiomethylperoxy, MSP) radical, a product formed in the oxidation of dimethyl sulfide (DMS), was measured using a pulsed laser photolysis flow tube reactor coupled to a high-resolution time-of-flight chemical ionization mass spectrometer that measured the formation of the DMS degradation end product HOOCH2SCHO. Measurements performed over the temperature range of 314–433 K yielded a hydrogen-shift rate coefficient of k1(T) = (2.39 ± 0.7) × 109 exp(−(7278 ± 99)/T) s–1 Arrhenius expression and a value extrapolated to 298 K of 0.06 s–1.
Date: March 2, 2023
Creator: Assaf, Emmanuel; Finewax, Zachary; Marshall, Paul; Veres, Patrick R.; Neuman, Andrew & Burkholder, James B. (James Bart), 1954-
Object Type: Article
System: The UNT Digital Library
Re-evaluation of rate constants for the reaction N2H4 (+ M) ⇄ NH2 + NH2 (+ M) (open access)

Re-evaluation of rate constants for the reaction N2H4 (+ M) ⇄ NH2 + NH2 (+ M)

Article describes how rate constants for the dissociation/recombination reaction N2H4 (+ M) ⇄ NH2 + NH2 (+ M) are determined by a combination of quantum-chemical calculations and statistical unimolecular rate theory. Implications of the present re-evaluated rate constants for the modeling of high temperature ammonia oxidation kinetics are discussed, showing an only small influence of their precise values on the overall properties of the process.
Date: October 4, 2023
Creator: Cobos, Carlos J.; Glarborg, Peter; Marshall, Paul & Troe, Jürgen
Object Type: Article
System: The UNT Digital Library
Probing High-Temperature Amine Chemistry: Is the Reaction NH3 + NH2 ⇄ N2H3 + H2 Important? (open access)

Probing High-Temperature Amine Chemistry: Is the Reaction NH3 + NH2 ⇄ N2H3 + H2 Important?

Article describes how the reaction NH3 + NH2 ⇄ N2H3 + H2 (R1) has been identified as a key step to explain experimental results for pyrolysis and oxidation of ammonia. In the present work, the reaction was studied by ab initio theory and by reinterpretation of experimental data.
Date: March 14, 2023
Creator: Marshall, Paul & Glarborg, Peter
Object Type: Article
System: The UNT Digital Library
Reactions of hydrazine with the amidogen radical and atomic hydrogen (open access)

Reactions of hydrazine with the amidogen radical and atomic hydrogen

Article describes how the rate coefficient k1 for NH2 + N2H4 was measured to be (5.4 ± 0.4) × 10−14 cm3 molecule−1 s−1 at 296 K. The authors then describe how a combination of experiment and theory leads to a recommended rate coefficient for hydrogen abstraction of k1 = 6.3 × 10−23 T3.44 exp(+289 K/T) cm3 molecule−1 s−1.
Date: June 7, 2023
Creator: Gao, Yide; Alecu, I. M.; Hashemi, Hamid; Glarborg, Peter & Marshall, Paul
Object Type: Article
System: The UNT Digital Library
Re-examination of the N2O+O reaction (open access)

Re-examination of the N2O+O reaction

This article is about how the reaction of N20 with O is a key step in consumption of nitrous oxide in thermal processes. In the present work ,the authors re-examined a wide range of experiments relevant for the N2O+O reaction through kinetic modeling, paying attention to the impact of artifacts such as impurities and surface reactions.
Date: July 27, 2023
Creator: Glarborg, Peter; Allingham, Johanne S.; Skov, Alexander B.; Hashemi, Hamid & Marshall, Paul
Object Type: Article
System: The UNT Digital Library
An experimental and modeling study on auto-ignition kinetics of ammonia/methanol mixtures at intermediate temperature and high pressure (open access)

An experimental and modeling study on auto-ignition kinetics of ammonia/methanol mixtures at intermediate temperature and high pressure

Article describes how a rapid compression machine has been applied to measure the ignition delay times of NH3/CH3OH mixtures covering pressures of 20 and 40 bar, equivalence ratios of 0.5, 1.0 and 2.0, and temperatures between 845 and 1100 K. Analysis of the pressure profiles shows three distinct ignition modes for NH3/CH3OH mixtures, facilitated by the pre-ignition heat release from NH3 consumption. A detailed mechanism for ignition of NH3/CH3OH fuel blends has been developed, capable of reproducing the ignition behavior of mixtures with reasonable accuracy.
Date: April 29, 2022
Creator: Li, Mengdi; He, Xiaoyu; Hashemi, Hamid; Glarborg, Peter; Lowe, Vincent M.; Marshall, Paul et al.
Object Type: Article
System: The UNT Digital Library
Comment on ‘Extremely rapid self-reactions of hydrochlorofluoromethanes and hydrochlorofluoroethanes and implications in destruction of ozone’ (open access)

Comment on ‘Extremely rapid self-reactions of hydrochlorofluoromethanes and hydrochlorofluoroethanes and implications in destruction of ozone’

Article comments on the claims made by the authors of the original article. The authors of the commentary note flaws in the DFT-based methodology and the commentators describe differences between their application and the original article's described application.
Date: May 26, 2022
Creator: Marshall, Paul & Burkholder, James B. (James Bart), 1954-
Object Type: Article
System: The UNT Digital Library