Daems E (2021) Shaping up oligonucleotides : aptamer-target recognition investigated by native mass spectrometry. 235 p
Abstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“The shielding effect of the protective glazing of historical stained glass windows from an atmospheric chemistry perspective: case study Sainte Chapelle, Paris”. Godoi RHM, Kontozova V, Van Grieken R, Atmospheric environment : an international journal 40, 1255 (2006). http://doi.org/10.1016/J.ATMOSENV.2005.10.033
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/J.ATMOSENV.2005.10.033
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“Short and long term effect of decreasing temperature on anammox activity and enrichment in mainstream granular sludge process”. De Cocker P, Bessiere Y, Hernandez-Raquet G, Dubos S, Mercade M, Sun XY, Mozo I, Barillon B, Gaval G, Caligaris M, Martin Ruel S, Vlaeminck SE, Sperandio M, 4, 50 (2017). http://doi.org/10.1007/978-3-319-58421-8_8
Abstract: This study investigates the impact of lower temperature on short term and long term (down to 10 degrees C) on a completely anoxic anammox granular sludge process. This is the first time granular sludge Anammox is operated in pure anoxic condition in SBR and at low temperature. Conversion performance, kinetic parameters, sludge characteristics and microbial community were analyzed.
Keywords: P1 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1007/978-3-319-58421-8_8
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“Short and long term effect of decreasing temperature on anammox activity and enrichment in mainstream granular sludge process”. De Cocker P, Bessiere Y, Hernandez-Raquet G, Dubos S, Mercade M, Sun XY, Mozo I, Barillon B, Gaval G, Caligaris M, Ruel SM, Vlaeminck SE, Sperandio M, Frontiers In Wastewater Treatment And Modelling, Ficwtm 2017 4, 50 (2017). http://doi.org/10.1007/978-3-319-58421-8_8
Abstract: This study investigates the impact of lower temperature on short term and long term (down to 10 degrees C) on a completely anoxic anammox granular sludge process. This is the first time granular sludge Anammox is operated in pure anoxic condition in SBR and at low temperature. Conversion performance, kinetic parameters, sludge characteristics and microbial community were analyzed.
Keywords: P1 Proceeding; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1007/978-3-319-58421-8_8
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“Siberian Haze: complex study of aerosols in Siberia”. Koutsenogii PK, van Malderen H, Hoornaert S, Van Grieken R, Koutsenogii KP, Boufetov N, Makarov VI, Smoljakov BS, Nemirovski AM, Osipova LP, Krjukov JA, Ivakin EA, Posukh OL, Bronstein EL, Optics of the atmosphere and ocean 9, 712 (1996)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Sidestream deammonification on thermal hydrolysis process digestate : strategies to overcome nitritation inhibition”. Zhang Q, De Clippeleir H, Al-Omari A, Wett B, Vlaeminck SE, Murthy S, , 11 p.
T2 (2015)
Keywords: P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
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“Signatures of subband excitons in few-layer black phosphorus”. Chaves A, Sousa GO, Khaliji K, da Costa DR, Farias GA, Low T, Physical Review B 103, 165428 (2021). http://doi.org/10.1103/PHYSREVB.103.165428
Abstract: Recent experimental measurements of light absorption in few-layer black phosphorus (BP) revealed a series of high and sharp peaks, interspersed by pairs of lower and broader features. Here, we propose a theoretical model for these excitonic states in few-layer BP within a continuum approach for the in-plane degrees of freedom and a tight-binding approximation that accounts for interlayer couplings. This yields excitonic transitions between different combinations of the subbands created by the coupled BP layers, which leads to a series of high and low oscillator strength excitonic states, consistent with the experimentally observed bright and dark exciton peaks, respectively. The main characteristics of such subband exciton states, as well as the possibility to control their energies and oscillator strengths via applied electric and magnetic fields, are discussed, towards a full understanding of the excitonic spectrum of few-layer BP and its tunability.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.836
DOI: 10.1103/PHYSREVB.103.165428
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“A simple absorption correction for electron probe X-ray microanalysis of bulk samples”. Markowicz A, Storms H, Van Grieken R, X-ray spectrometry 15, 115 (1986). http://doi.org/10.1002/XRS.1300150209
Abstract: A simple procedure is proposed for the calculation of the absorption correction factor in electron-probe x-ray microanalysis. It is based on the concept of an effective depth of x-ray production, assuming a rectangular depth distribution function for x-ray generation. This effective x-ray production depth is expressed as a fraction of the x-ray excitation depth given by Whelan's expression. Adequate values for this fraction are presented. Two versions are considered. In the first the effective x-ray production is a function of both the characteristic x-ray energy and the atomic numbers of the matrix elements, whereas in the second one, which is indicated for routine use, the energy dependence is neglected. Calculations pointed to satisfactory results, even for low x-ray energies and high overvoltages.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1002/XRS.1300150209
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“Simulating highly activated sticking of H₂, on Al(110) : quantum versus quasi-classical dynamics”. Tchakoua T, Powell AD, Gerrits N, Somers MF, Doblhoff-Dier K, Busnengo HF, Kroes G-J, The journal of physical chemistry: C : nanomaterials and interfaces 127, 5395 (2023). http://doi.org/10.1021/ACS.JPCC.3C00426
Abstract: We evaluate the importance of quantum effects on the sticking of H2 on Al(110) for conditions that are close to those of molecular beam experiments that have been done on this system. Calculations with the quasi-classical trajectory (QCT) method and with quantum dynamics (QD) are performed using a model in which only motion in the six molecular degrees of freedom is allowed. The potential energy surface used has a minimum barrier height close to the value recently obtained with the quantum Monte Carlo method. Monte Carlo averaging over the initial rovibrational states allowed the QD calculations to be done with an order of magnitude smaller computational expense. The sticking probability curve computed with QD is shifted to lower energies relative to the QCT curve by 0.21 to 0.05 kcal/mol, with the highest shift obtained for the lowest incidence energy. Quantum effects are therefore expected to play a small role in calculations that would evaluate the accuracy of electronic structure methods for determining the minimum barrier height to dissociative chemisorption for H2 + Al(110) on the basis of the standard procedure for comparing results of theory with molecular beam experiments.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.7
DOI: 10.1021/ACS.JPCC.3C00426
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Piñ,era Herná,ndez I (2014) Simulation of atom displacements induced by photons and electrons in solids. 137 p
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Simultaneous determination of chromium and silicon in steel by 14-mev neutron activation analysis”. Vandecasteele C, Van Grieken R, Hoste J, Analytica chimica acta 72, 31 (1974). http://doi.org/10.1016/S0003-2670(01)82945-7
Abstract: Chromium and silicon are determined simultaneously in steel by 14-MeV neutron activation analysis. The activities of 52V(Eγ=1.43 MeV,TView the MathML source=3.76 min) from 52Cr(n,p)52V and 28Al (Eγ=1.78 MeV; TView the MathML source=2.24 min) from 28Si(n,p)28Al are evaluated by mixed γ-ray spectrometry. The influence of manganese and phosphorus, the main interfering elements, is negligible for most stainless steels. The count rate should be limited, to avoid 52V pulse pile-up effects interfering in the 28Al energy region. Precisions in the 2-10% range are reached, depending on the concentrations, for a 10-min analysis time. Results for a series of steel samples are compared with industrial analyses.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/S0003-2670(01)82945-7
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“Simultaneous determination of silicon and phosphorus in cast iron by 14 MeV neutron activation analysis”. Van Grieken R, Speecke A, Hoste J, Journal of radioanalytical chemistry 6, 385 (1970). http://doi.org/10.1007/BF02513966
Abstract: A fast (10 min), non-destructive simultaneous determination of silicon and phosphorus in cast iron and steel by 14 MeV neutron activation was developed. The 1.78 MeV28Al activity (T=2.24 min) induced by the reaction28Si(n, p)28Al is counted on a NaI(Tl) detector. Two measurements are made to correct for the 1.81 MeV56Mn activity (T=2.58 hr) from the iron matrix. However,28Al is also produced via31P(n, α)28Al. By (n, 2n) reaction, phosphorus yields also30P (T=2.6 min), the 0.511 MeV annihilation radiation of which is counted by two opposite NaI(Tl) detectors in coincidence. Again, two successive coincidence measurements are carried out in order to take into account the53Fe activity (β+; T=8.9 min) from54Fe(n, 2n)53Fe. The28Al measurement is appropriately corrected via the computed phosphorus content. An oxygen flux monitor was used to normalize to the same flux. Nuclear interferences have been examined. Special attention has been paid to the presence of copper. The standard deviation for phosphorus being as high as ca. 0.09% P for a single determination, this technique can only be practical as an independent phosphorus analysis for high phosphorus cast irons. The precision on the28Al measurement is 5% relative for 0.2% Si and 2.5% above 1% Si.
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1007/BF02513966
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“Single-particle analysis of aerosols at Cheju Island, Korea, using low-Z electron probe X-ray microanalysis: a direct proof of nitrate formation from sea salts”. Ro C-U, Oh K-Y, Kim H, Kim YP, Lee CB, Kim K-H, Kang CH, Osán J, de Hoog J, Worobiec A, Van Grieken R, Environmental science and technology 35, 4487 (2001). http://doi.org/10.1021/ES0155231
Keywords: A1 Journal article; Laboratory Experimental Medicine and Pediatrics (LEMP); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1021/ES0155231
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“Single particle analysis of aerosols from Siberia”. van Malderen H, Van Grieken R, Khodzher TV, Grachev M, Bufetov NS, Koutsenogii KP, Proceedings of the Russian-Ukrainian-Austrian-German Analytical Symposium (1994)
Keywords: P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Single particle analysis of aerosols, observed in the marine boundary layer during the Monterey Area Ship Tracks Experiment (MAST), with respect to cloud droplet formation”. de Bock LA, Joos PE, Noone KJ, Pockalny RA, Van Grieken RE, Journal of atmospheric chemistry 37, 299 (2000). http://doi.org/10.1023/A:1006416600722
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1023/A:1006416600722
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“Single particle analysis of Hungarian background aerosol”. Török S, Sandor S, Xhoffer C, Van Grieken R, Meszaros E, Molnar A, Idojaras: quarterly journal of the Hungarian Meteorological Service 96, 223 (1992)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Single particle analysis of suspended matter in the Makasar Strait and Flores Sea with particular reference to tin-bearing particles”. Dekov VM, van Put A, Eisma D, Van Grieken R, Journal of sea research 41, 35 (1999). http://doi.org/10.1016/S1385-1101(98)00035-5
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/S1385-1101(98)00035-5
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“Single particle analysis techniques”. de Bock LA, Van Grieken RE page 243 (1999).
Keywords: H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Single particle and inorganic characterization of rainwater collected above the North Sea”. Jambers W, Dekov V, Van Grieken R, The science of the total environment 256, 133 (2000). http://doi.org/10.1016/S0048-9697(00)00477-0
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/S0048-9697(00)00477-0
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“Single particle characterisation of inorganic and organic North Sea suspension”. Jambers W, Dekov V, Van Grieken R, Marine chemistry 67, 17 (1999). http://doi.org/10.1016/S0304-4203(99)00046-8
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/S0304-4203(99)00046-8
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“Single particle characterisation of inorganic North Sea suspensions”. Jambers W, Van Grieken R, (1996)
Keywords: P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Single particle characterisation of inorganic suspension in Lake Baikal”. Jambers W, Van Grieken R, Environmental science and technology 31, 1525 (1997)
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Single particle characterisation of the aerosol in the marine boundary layer and free troposphere over Tenerife, NE Atlantic, during ACE-2”. Hoornaert S, Godoi RHM, Van Grieken R, Journal of atmospheric chemistry 46, 271 (2003). http://doi.org/10.1023/A:1026383403878
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1023/A:1026383403878
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“Single-particle characterization of four “Asian Dust&rdquo, samples collected in Korea, using low-Z particle electron probe X-ray microanalysis”. Ro C-U, Hwang H, Kim HK, Chun Y, Van Grieken R, Environmental science and technology 39, 1409 (2005). http://doi.org/10.1021/ES049772B
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1021/ES049772B
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“Single-particle characterization of urban aerosol particles collected in three Korean cities using low-Z electron probe x-ray microanalysis”. Ro C-U, Kim H, Oh K-Y, Yea SK, Lee CB, Jang M, Van Grieken R, Environmental science and technology 36, 4770 (2002). http://doi.org/10.1021/ES025697Y
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1021/ES025697Y
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“Single-run ion chromatographic separation of inorganic and low-molecular-mass organic anions under isocratic elution: application to environmental samples”. Krata A, Kontozova-Deutsch V, Bencs L, Deutsch F, Van Grieken R, Talanta : the international journal of pure and applied analytical chemistry 79, 16 (2009). http://doi.org/10.1016/J.TALANTA.2009.02.044
Abstract: For the isocratic ion chromatography (IC) separation of low-molecular-mass organic acids and inorganic anions three different anion-exchange columns were studied: IonPac AS14 (9 ìm particle size), Allsep A-2 (7 ìm particle size), and IC SI-50 4E (5 ìm particle size). A complete baseline separation for all analyzed anions (i.e., F−, acetate, formate, Cl−, NO2−, Br−, NO3−, HPO42− and SO42−) in one analytical cycle of shorter than 17 min was achieved on the IC SI-50 4E column, using an eluent mixture of 3.2 mM Na2CO3 and 1.0 mM NaHCO3 with a flow rate of 1.0 mL min−1. On the IonPac AS14 column, it was possible to separate acetate from inorganic anions in one run (i.e., less than 9 min), but not formate, under the following conditions: 3.5 mM Na2CO3 plus 1.0 mM NaHCO3 with a flow rate of 1.2 mL min−1. Therefore, it was necessary to adapt a second run with a 2.0 mM Na2B4O7 solution as an eluent under a flow rate of 0.8 mL min−1 for the separation of organic ions, which considerably enlarged the analysis time. For the Allsep A-2 column, using an eluent mixture of 1.2 mM Na2CO3 plus 1.5 mM NaHCO3 with a flow rate of 1.6 mL min−1, it was possible to separate almost all anions in one run within 25 min, except the fluoride-acetate critical pair. A Certified Multianion Standard Solution PRIMUS for IC was used for the validation of the analytical methods. The lowest RSDs (less than 1%) and the best LODs (0.02, 0.2, 0.16, 0.11, 0.06, 0.05, 0.04, 0.14 and 0.09 mg L−1 for F−, Ac−, For−, Cl−, NO2−, Br−, NO3−, HPO42− and SO42−, respectively) were achieved using the IC SI-50 4E column. This column was applied for the separation of concerned ions in environmental precipitation samples such as snow, hail and rainwater.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/J.TALANTA.2009.02.044
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“Size-differentiated composition of aerosols in Khartoum, Sudan”. Eltayeb MAH, van Espen PJ, Cafmeyer J, Van Grieken RE, Maenhaut W, The science of the total environment 120, 281 (1992). http://doi.org/10.1016/0048-9697(92)90062-W
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Chemometrics (Mitac 3)
DOI: 10.1016/0048-9697(92)90062-W
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“Size distribution and chemical properties of welding fumes of inhalable particles”. Oprya M, Kiro S, Worobiec A, Horemans B, Darchuk L, Novakovic V, Ennan A, Van Grieken R, Journal of aerosol science 45, 50 (2012). http://doi.org/10.1016/J.JAEROSCI.2011.10.004
Abstract: The goal of the present study was to analyze the relationship between the fume formation rate, welding conditions, chemical composition of welding fume particles and their size. In the range from 0.25 to 16 μm aerodynamic diameter, three distinct types of welding fume particles were identified in the welder's breathing zone. The elemental composition of each type depended completely on the used welding materials, and reflects their mechanism of formation. Their relative abundance in the welding fume appeared to be dependent on the electrode coating, as well as the heat input during welding.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1016/J.JAEROSCI.2011.10.004
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“The size distribution and surface area of soot emitted by different sources”. Smekens A, Berghmans P, Van Grieken R, Journal of aerosol science 31, 706 (2000)
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Size resolved ultrafine particles emission model : a continues size distribution approach”. Nikolova I, Janssen S, Vrancken K, Vos P, Mishra V, Berghmans P, The science of the total environment 409, 3492 (2011). http://doi.org/10.1016/J.SCITOTENV.2011.05.015
Abstract: A new parameterization for size resolved ultrafine particles (UFP) traffic emissions is proposed based on the results of PARTICULATES project (Samaras et al., 2005). It includes the emission factors from the Emission Inventory Guidebook (2006) (total number of particles, #/km/veh), the shape of the corresponding particle size distribution given in PARTICULATES and data for the traffic activity. The output of the model UFPEM (UltraFine Particle Emission Model) is a sum of continuous distributions of ultrafine particles emissions per vehicle type (passenger cars and heavy duty vehicles), fuel (petrol and diesel) and average speed representative for urban, rural and highway driving. The results from the parameterization are compared with measured total number of ultrafine particles and size distributions in a tunnel in Antwerp (Belgium). The measured UFP concentration over the entire campaign shows a close relation to the traffic activity. The modelled concentration is found to be lower than the measured in the campaign. The average emission factor from the measurement is 4.29E + 14 #/km/veh whereas the calculated is around 30% lower. A comparison of emission factors with literature is done as well and in overall a good agreement is found. For the size distributions it is found that the measured distributions consist of three modes Nucleation, Aitken and accumulation and most of the ultrafine particles belong to the Nucleation and the Aitken modes. The modelled Aitken mode (peak around 0.040.05 μm) is found in a good agreement both as amplitude of the peak and the number of particles whereas the modelled Nucleation mode is shifted to smaller diameters and the peak is much lower that the observed. Time scale analysis shows that at 300 m in the tunnel coagulation and deposition are slow and therefore neglected. The UFPEM emission model can be used as a source term in dispersion models.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1016/J.SCITOTENV.2011.05.015
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