Dataset Information

Molecular-scale modeling of light emission by combustion: An ab initio study.

ABSTRACT: Despite the advanced understanding of combustion, the mechanisms of subsequent light emission have not attracted much attention. In this work, we model the light emission as electronic excitation throughout the oxidation reaction. We examined the simple dynamics of the collision of an oxygen molecule (O2) with a kinetic energy of 4, 6, or 10?eV with a stationary target molecule (Mg2, SiH4 or CH4). Time-dependent density functional theory was used to monitor electronic excitation. For a collision between O2 and Mg2, the electronic excitation energy increased with the incident kinetic energy. In contrast, for a collision between O2 and SiH4 molecules, a substantial electronic excitation occurred only at an incident kinetic energy of 10?eV. The electronic excitation was qualitatively reproduced by analysis using complete active space self-consistent field method. On the other hand, collision between O2 and CH4 molecules shows reflection of these molecules indicating that small-mass molecules could show neither oxidation nor subsequent electronic excitation upon collision with an O2 molecule. We believe that this work provides a first step toward understanding the light-emission process during combustion.

SUBMITTER: Miyamoto Y

PROVIDER: S-EPMC6722116 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Molecular-scale modeling of light emission by combustion: An ab initio study.

Miyamoto Yoshiyuki Y Komatsu Tokutaro T

Scientific reports 20190903 1

Despite the advanced understanding of combustion, the mechanisms of subsequent light emission have not attracted much attention. In this work, we model the light emission as electronic excitation throughout the oxidation reaction. We examined the simple dynamics of the collision of an oxygen molecule (O2) with a kinetic energy of 4, 6, or 10 eV with a stationary target molecule (Mg2, SiH4 or CH4). Time-dependent density functional theory was used to mo ...[more]

PMID: 31481746

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Project description:BackgroundPredicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB) library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins.ResultsWe developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (< 90 residues) were used to generate I-TASSER models, which had an average Calpha-root mean square deviation (RMSD) of 3.8A, with 6 of them having a Calpha-RMSD < 2.5A. The overall result was comparable with the all-atomic ROSETTA simulation, but the central processing unit (CPU) time by I-TASSER was much shorter (150 CPU days vs. 5 CPU hours). Second, data on 20 small proteins (< 120 residues) were used. I-TASSER folded four of them with a Calpha-RMSD < 2.5A. The average Calpha-RMSD of the I-TASSER models was 3.9A, whereas it was 5.9A using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (< 120 residues) were taken from the PDB library. An average Calpha-RMSD of 3.9A was obtained for the third benchmark, with seven cases having a Calpha-RMSD < 2.5A.ConclusionOur simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server) in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP)7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.

Dataset Information

Molecular-scale modeling of light emission by combustion: An ab initio study.

Publications

Molecular-scale modeling of light emission by combustion: An ab initio study.

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