| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Lis, D. C., et al.
(författare)
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Herschel/HIFI discovery of interstellar chloronium (H2Cl+)
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 521:1
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Tidskriftsartikel (refereegranskat)abstract
- We report the first detection of chloronium, H_2Cl^+, in the interstellar medium, using the HIFI instrument aboard the Herschel Space Observatory. The 2_12-1_01 lines of ortho-H\_2^35Cl^+ and ortho-H\_2^37Cl^+ are detected in absorption towards NGC 6334I, and the 1_11-0_00 transition of para-H\_2^35Cl^+ is detected in absorption towards NGC 6334I and Sgr B2(S). The H_2Cl^+ column densities are compared to those of the chemically-related species HCl. The derived HCl/H_2Cl^+ column density ratios, ~1-10, are within the range predicted by models of diffuse and dense photon dominated regions (PDRs). However, the observed H_2Cl^+ column densities, in excess of 10^13 cm^-2, are significantly higher than the model predictions. Our observations demonstrate the outstanding spectroscopic capabilities of HIFI for detecting new interstellar molecules and providing key constraints for astrochemical models.
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| 3. |
- Wamers, F., et al.
(författare)
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Diverse mechanisms in proton knockout reactions from the Borromean nucleus Ne-17
- 2023
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Ingår i: European Physical Journal A. - : Springer. - 1434-6001 .- 1434-601X. ; 59
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Tidskriftsartikel (refereegranskat)abstract
- Nucleon knockout experiments using beryllium or carbon targets reveal a strong dependence of the quenching factors, i.e., the ratio (Rs) of theoretical to the experimental spectroscopic factors (C2S), on the proton-neutron asymmetry in the nucleus under study. However, this dependence is greatly reduced when a hydrogen target is used. To understand this phenomenon, exclusive H-1(Ne-17, 2p F-16) and inclusive C-12(Ne-17, 2p 1(6)F)X, 1(2)C(Ne-17, F-16)X as well as 1H(Ne-17,(16) F)X(X-denotes undetected reaction products) reactions with F-16 in the ground and excited states were anal- ysed. The longitudinal momentum distribution of F-16 and the correlations between the detached protons were studied. In the case of the carbon target, there is a significant deviation from the predictions of the eikonal model. The eikonal approximation was used to extract spectroscopic factor values (CS)-S-2. The experimental (CS)-S-2 value obtained with C target is markedly lower than that for H target. This is interpreted as rescattering due to simultaneous nucleon knockout from both reaction partners, Ne-17 and C-12.
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| 4. |
- Chen, Yu, 1990, et al.
(författare)
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Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0
- 2024
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Ingår i: Nature Protocols. - 1754-2189 .- 1750-2799. ; 19:3, s. 629-667
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Tidskriftsartikel (refereegranskat)abstract
- Genome-scale metabolic models (GEMs) are computational representations that enable mathematical exploration of metabolic behaviors within cellular and environmental constraints. Despite their wide usage in biotechnology, biomedicine and fundamental studies, there are many phenotypes that GEMs are unable to correctly predict. GECKO is a method to improve the predictive power of a GEM by incorporating enzymatic constraints using kinetic and omics data. GECKO has enabled reconstruction of enzyme-constrained metabolic models (ecModels) for diverse organisms, which show better predictive performance than conventional GEMs. In this protocol, we describe how to use the latest version GECKO 3.0; the procedure has five stages: (1) expansion from a starting metabolic model to an ecModel structure, (2) integration of enzyme turnover numbers into the ecModel structure, (3) model tuning, (4) integration of proteomics data into the ecModel and (5) simulation and analysis of ecModels. GECKO 3.0 incorporates deep learning-predicted enzyme kinetics, paving the way for improved metabolic models for virtually any organism and cell line in the absence of experimental data. The time of running the whole protocol is organism dependent, e.g., ~5 h for yeast.
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| 5. |
- Ding, Shaozhen, et al.
(författare)
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novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W477-W487
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Tidskriftsartikel (refereegranskat)abstract
- To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.
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| 6. |
- Gu, Irene Yu-Hua, 1953, et al.
(författare)
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Signal Processing and Classification Tools for Intelligent Distributed Monitoring and Analysis of the Smart Grid
- 2011
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Ingår i: IEEE PES Innovative Smart Grid Technologies Conference Europe. 2011 2nd IEEE PES International Conference and Exhibition on Innovative Smart Grid Technologies, ISGT Europe 2011, Manchester, 5 - 7 December 2011. - Piscataway, N.J : IEEE Communications Society. - 9781457714214
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Konferensbidrag (refereegranskat)abstract
- This paper proposes a novel framework for an intelligent monitoring system that supervises the performance of the future power system. The increased complexity of the power system could endanger the reliability, voltage quality, operational security or resilience of the power system. A distributed structure for such a monitoring system is described and some of the advanced signal processing techniques or tools that could be used in such a monitoring system are given. Several examples for seeking the spatial locations and finding the underlying causes of disturbances are included.
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| 7. |
- Han, Mengying, et al.
(författare)
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ChemHub: a knowledgebase of functional chemicals for synthetic biology studies
- 2021
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:22, s. 4275-4276
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Tidskriftsartikel (refereegranskat)abstract
- The field of synthetic biology lacks a comprehensive knowledgebase for selecting synthetic target molecules according to their functions, economic applications and known biosynthetic pathways. We implemented ChemHub, a knowledgebase containing >90 000 chemicals and their functions, along with related biosynthesis information for these chemicals that was manually extracted from >600 000 published studies by more than 100 people over the past 10 years.
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| 8. |
- Jiang, Jinyang, et al.
(författare)
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The manner and extent to which the hydration shell impacts interactions between hydrated species
- 2021
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 23:36, s. 20496-20508
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Tidskriftsartikel (refereegranskat)abstract
- The hydration shell (HS) has a critical impact on every contact between hydrated species, which is a prerequisite for a great many physical and chemical processes, such as ion adsorption at the solution-solid interface. This paper reveals the extent and manner to which the HS interferes with ion adsorption utilizing molecular dynamics. The single-layer HS is the smallest unit that maintains the ionic hydration structure and the force on it. The energy penalty incurred by partial dehydration upon adsorption is one of the approaches through which HS influences ion adsorption, yet the collision of water molecules in HS may be the critical one. The repulsive force during dehydration is, to great extent, neutralized by HS collision. The index for estimating the extent of the influence of the HS is not the hydration energy, but the quantification of the contest between HS' collision and the binding of adsorption sites. The hydration energy is larger for charged functional groups, but the HS' impact is much smaller, as compared with electroneutral group cases. As a result, the order of the adsorption capacity for different ionic species may be quite different between charged and electroneutral cases.
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| 9. |
- Le, Cuong, 1982, et al.
(författare)
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A method to evaluate harmonic model-based estimations under non-white measured noise
- 2011
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Ingår i: 2011 IEEE PES Trondheim PowerTech. - Piscataway, NJ : IEEE Communications Society. - 9781424484195 - 9781424484171
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Konferensbidrag (refereegranskat)abstract
- Automatic extracting information from power-system event recordings requires applications of signal-processing estimation techniques whose performance has been verified under white noise. This paper proposes a method to test these techniques under real power-system noise, which is very different from white noise, to evaluate their application feasibility. The first part of the paper describes the evaluation method used to evaluate the techniques in a statistical sense and a method to extract noise from measured power-system recordings. The second part of the paper focuses on the evaluation of a number of harmonic model-based techniques under non-white noise, including: Kalman filter, MUSIC, ESPRIT, and segmentation algorithms. The paper shows that for the Kalman filter, a very high order with high computational burden is necessary only if high frequency components are of interest. The application of MUSIC, ESPRIT, and the segmentation algorithms under natural power-system noise is shown to be feasible.
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| 10. |
- Le, Cuong, 1982, et al.
(författare)
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Analysis of Power Disturbances from Monitoring Multiple Levels and Locations in a Power System
- 2010
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Ingår i: The 14th IEEE Int'l Conf. on Harmonics and Quality of Power, 26-29 Sep. 2010, Bergamo, Italy. - : IEEE Communications Society. - 9781424472444 - 9781424472451
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Konferensbidrag (refereegranskat)abstract
- This paper proposes a new methodology for diagnosing the original source and underlying causes of power system disturbances, where voltage and current recordings from different locations of a power system are collected. In the proposed method, disturbances are first pre-classified based on the number of transition segments. The spatial zone of the source of disturbances is coarsely determined from voltage recordings only. Disturbances are then further analyzed and characterized by extracting information from both voltages and currents. Finally more accurate information about the location of the source of disturbances is obtained by different techniques depending on the type of disturbances. Several underlying causes are analyzed and classified by using the proposed features extracted from both voltage and current waveforms. Finally, the location of the source of disturbances is refined once the underlying causes are found. Case studies were performed on a large grid-connected wind farm with disturbances from several underlying causes, including: fault, unit tripping, transformer, capacitor, and cable energizing generated by PSCAD/EMTDC.
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