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“Establishing uniform acceptance in force biased Monte Carlo simulations”. Neyts EC, Thijsse BJ, Mees MJ, Bal KM, Pourtois G, Journal of chemical theory and computation 8, 1865 (2012). http://doi.org/10.1021/ct2008268
Abstract: Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter lambda = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter lambda = 0 [Rao, M. et al. Mol. Phys. 1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
Times cited: 20
DOI: 10.1021/ct2008268
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“Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds”. Bal KM, Neyts EC, Journal of chemical theory and computation 11, 4545 (2015). http://doi.org/10.1021/acs.jctc.5b00597
Abstract: The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
Times cited: 41
DOI: 10.1021/acs.jctc.5b00597
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“SBH17 : benchmark database of barrier heights for dissociative chemisorption on transition metal surfaces”. Tchakoua T, Gerrits N, Smeets EWF, Kroes G-J, Journal of chemical theory and computation 19, 245 (2023). http://doi.org/10.1021/ACS.JCTC.2C00824
Abstract: Accurate barriers for rate controlling elementary reactions on metal surfaces are key to understanding, controlling, and predicting the rate of heterogeneously catalyzed processes. While barrier heights for gas phase reactions have been extensively benchmarked, dissociative chemisorption barriers for the reactions of molecules on metal surfaces have received much less attention. The first database called SBH10 and containing 10 entries was recently constructed based on the specific reaction parameter approach to density functional theory (SRP-DFT) and experimental results. We have now constructed a new and improved database (SBH17) containing 17 entries based on SRP-DFT and experiments. For this new SBH17 benchmark study, we have tested three algorithms (high, medium, and light) for calculating barrier heights for dissociative chemisorption on metals, which we have named for the amount of computational effort involved in their use. We test the performance of 14 density functionals at the GGA, GGA+vdW-DF, and meta-GGA rungs. Our results show that, in contrast with the previous SBH10 study where the BEEF-vdW-DF2 functional seemed to be most accurate, the workhorse functional PBE and the MS2 density functional are the most accurate of the GGA and meta-GGA functionals tested. Of the GGA+vdW functionals tested, the SRP32-vdW-DF1 functional is the most accurate. Additionally, we found that the medium algorithm is accurate enough for assessing the performance of the density functionals tested, while it avoids geometry optimizations of minimum barrier geometries for each density functional tested. The medium algorithm does require metal lattice constants and interlayer distances that are optimized separately for each functional. While these are avoided in the light algorithm, this algorithm is found not to give a reliable description of functional performance. The combination of relative ease of use and demonstrated reliability of the medium algorithm will likely pave the way for incorporation of the SBH17 database in larger databases used for testing new density functionals and electronic structure methods.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.5
DOI: 10.1021/ACS.JCTC.2C00824
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“Reweighted Jarzynski sampling : acceleration of rare events and free energy calculation with a bias potential learned from nonequilibrium work”. Bal KM, Journal Of Chemical Theory And Computation 17, 6766 (2021). http://doi.org/10.1021/ACS.JCTC.1C00574
Abstract: We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the reaction coordinate, and the Jarzynski equality is used to learn an approximate free energy surface from the nonequilibrium work distribution. This free energy estimate is represented in a compact form as an artificial neural network and used as an external bias potential to accelerate rare events in a subsequent molecular dynamics simulation. The final free energy estimate is then obtained by reweighting the equilibrium probability distribution of the reaction coordinate sampled under the influence of the external bias. We apply our reweighted Jarzynski sampling recipe to four processes of varying scales and complexities.spanning chemical reaction in the gas phase, pair association in solution, and droplet nucleation in supersaturated vapor. In all cases, we find reweighted Jarzynski sampling to be a very efficient strategy, resulting in rapid convergence of the free energy to high precision.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
DOI: 10.1021/ACS.JCTC.1C00574
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“Monitoring the laccase reaction of vanillin and poplar hydrolysate”. Sóti V, Jacquet N, Apers S, Richel A, Lenaerts S, Cornet I, Journal of chemical technology and biotechnology 91, 1914 (2016). http://doi.org/10.1002/JCTB.4789
Abstract: BACKGROUND Laccase is an intensively researched enzyme for industrial use. Except for decolorisation measurements, HPLC analysis is the conventional method for monitoring the phenolic removal during laccase enzyme reaction. This paper reports an investigation of the continuous UV absorbance follow-up of the laccase reaction with steam pretreated poplar hydrolysate. RESULTS Vanillin was used as a model substrate and lignocellulose xylose rich fraction (XRF) as a biologically complex substrate for laccase detoxification. The reaction was followed by HPLC-UV as well as by UV spectrometric measurements. Results suggest that the reaction can be successfully monitored by measuring the change of UV absorbance at 280 nm, without previous compound separation. In case of XRF experiments the spectrophotometric follow-up is especially useful, as HPLC analysis takes a long time and provides less information than in case of single substrates. The method seems to be suitable for optimization and process control. CONCLUSION The obtained results can help to construct a fast, easy and straightforward monitoring system for laccase-phenolic substrate reactions.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL); Biochemical Wastewater Valorization & Engineering (BioWaVE)
Impact Factor: 3.135
Times cited: 3
DOI: 10.1002/JCTB.4789
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“Effects of salinity, pH and growth phase on the protein productivity by Dunaliella salina”. Sui Y, Vlaeminck SE, Journal of chemical technology and biotechnology 94, 1032 (2019). http://doi.org/10.1002/JCTB.5850
Abstract: BACKGROUND Microalgae have long been adopted for use as human food, animal feed and high‐value products. For carotenogenesis, Dunaliella salina is one of the most studied microalgae, yet its protein synthesis has been limitedly reported. In this study, D. salina was cultivated at different NaCl and pH levels to optimize its protein productivity. RESULTS The biomass protein content followed an increasedecrease pattern throughout the growth phases, with a maximum in the exponential phase (6080% over ash‐free dry weight). Adversely, the biomass pigment contents were at relatively stable levels (around 0.5% carotenoids, 1.3% chlorophyll a and 0.5% chlorophyll b over ash‐free dry weight). Among the tested conditions (13 mol L−1 salinity, pH 7.59.5), the highest protein productivity (43.5 mg L−1 day−1) was achieved at 2 mol L−1 salinity and pH 7.5 during the exponential phase, which surpassed others by 1697%. Additionally, table salts were tested to be equivalent and cost‐efficient salt sources for the growth medium. CONCLUSION This study highlighted the suitability of D. salina as a protein source, providing guidelines for 70% cheaper medium formulation in the lab and for maximum protein productivity at larger scale.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1002/JCTB.5850
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“Enhanced carbon and nitrogen removal performance of simultaneous anammox and denitrification (SAD) with mannitol addition treating saline wastewater”. Yang Z, Zhu W, Yu D, Bo Y, Li J, Journal of chemical technology and biotechnology 94, 377 (2019). http://doi.org/10.1002/JCTB.5781
Abstract: BACKGROUND Simultaneous anammox and denitrification (SAD) can remove carbon and nitrogen. However, its performance is suppressed under saline surroundings. In this work, mannitol was used to enhance a SAD process treating saline wastewater. RESULTS The optimum carbon and nitrogen removal was achieved at 0.2 mmol L-1 mannitol, during which ammonium removal efficiency (ARE), nitrite removal efficiency (NRE) and chemical oxygen demand (COD) removal efficiency were 96.95%, 93.70% and 90.05%, respectively. The maximum ammonium removal rate (ARR), nitrite removal rate (NRR) and the specific anammox activity (SAA) were increased by 25.49%, 55.84% and 33.83% with optimum addition (0.2 mmol L-1 mannitol) respectively. The diameter of sludge was enlarged with the addition of mannitol (<= 0.2 mmol L-1). The Tseng-Wayman model was more suitable to simulate the whole SAD process. The modified logistic model, the modified Boltzman model and the modified Gompertz model were all appropriate to describe nitrogen removal in a typical cycle with the addition of mannitol. CONCLUSION Mannitol was effective in enhancing a SAD process treating saline wastewater, and maximum nitrogen removal was achieved at mannitol = 0.2 mmol L-1. The Tseng-Wayman model satisfactorily predicted the whole SAD process treating saline wastewater with mannitol addition. (c) 2018 Society of Chemical Industry
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1002/JCTB.5781
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“Adsorption of potassium and oxygen on graphite: a theoretical study”. Lamoen D, Persson BNJ, Journal Of Chemical Physics 108, 3332 (1998). http://doi.org/10.1063/1.475732
Keywords: A1 Journal article; Electron Microscopy for Materials Science (EMAT);
Impact Factor: 2.965
Times cited: 91
DOI: 10.1063/1.475732
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“Thermodynamic consistency and integral equations for the liquid structure”. Leys FE, March NH, Lamoen D, Journal Of Chemical Physics 117, 10726 (2002). http://doi.org/10.1063/1.1522377
Keywords: A1 Journal article; Electron Microscopy for Materials Science (EMAT);
Impact Factor: 2.965
DOI: 10.1063/1.1522377
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“Free energy barriers from biased molecular dynamics simulations”. Bal KM, Fukuhara S, Shibuta Y, Neyts EC, Journal Of Chemical Physics 153, 114118 (2020). http://doi.org/10.1063/5.0020240
Abstract: Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.4
DOI: 10.1063/5.0020240
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“Stable single-layers of calcium halides (CaX₂, X = F, Cl, Br, I)”. Baskurt M, Yagmurcukardes M, Peeters FM, Sahin H, Journal Of Chemical Physics 152, 164116 (2020). http://doi.org/10.1063/5.0006011
Abstract: By means of density functional theory based first-principles calculations, the structural, vibrational, and electronic properties of 1H- and 1T-phases of single-layer CaX2 (X = F, Cl, Br, or I) structures are investigated. Our results reveal that both the 1H- and 1T-phases are dynamically stable in terms of their phonon band dispersions with the latter being the energetically favorable phase for all single-layers. In both phases of single-layer CaX2 structures, significant phonon softening occurs as the atomic radius increases. In addition, each structural phase exhibits distinctive Raman active modes that enable one to characterize either the phase or the structure via Raman spectroscopy. The electronic band dispersions of single-layer CaX2 structures reveal that all structures are indirect bandgap insulators with a decrease in bandgaps from fluorite to iodide crystals. Furthermore, the calculated linear elastic constants, in-plane stiffness, and Poisson ratio indicate the ultra-soft nature of CaX2 single-layers, which is quite important for their nanoelastic applications. Overall, our study reveals that with their dynamically stable 1T- and 1H-phases, single-layers of CaX2 crystals can be alternative ultra-thin insulators.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 4.4
Times cited: 14
DOI: 10.1063/5.0006011
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“Quantitative morphometric analysis of single gold nanoparticles by optical extinction microscopy: Material permittivity and surface damping effects”. Payne LM, Masia F, Zilli A, Albrecht W, Borri P, Langbein W, Journal Of Chemical Physics 154, 044702 (2021). http://doi.org/10.1063/5.0031012
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.965
DOI: 10.1063/5.0031012
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“Abnormal in-plane permittivity and ferroelectricity of confined water : from sub-nanometer channels to bulk”. Hamid I, Jalali H, Peeters FM, Neek-Amal M, Journal Of Chemical Physics 154, 114503 (2021). http://doi.org/10.1063/5.0038359
Abstract: Dielectric properties of nano-confined water are important in several areas of science, i.e., it is relevant in the dielectric double layer that exists in practically all heterogeneous fluid-based systems. Molecular dynamics simulations are used to predict the in-plane dielectric properties of confined water in planar channels of width ranging from sub-nanometer to bulk. Because of suppressed rotational degrees of freedom near the confining walls, the dipole of the water molecules tends to be aligned parallel to the walls, which results in a strongly enhanced in-plane dielectric constant (epsilon (parallel to)) reaching values of about 120 for channels with height 8 angstrom < h < 10 angstrom. With the increase in the width of the channel, we predict that epsilon (parallel to) decreases nonlinearly and reaches the bulk value for h > 70 angstrom. A stratified continuum model is proposed that reproduces the h > 10 angstrom dependence of epsilon (parallel to). For sub-nanometer height channels, abnormal behavior of epsilon (parallel to) is found with two orders of magnitude reduction of epsilon (parallel to) around h similar to 7.5 angstrom, which is attributed to the formation of a particular ice phase that exhibits long-time (similar to mu s) stable ferroelectricity. This is of particular importance for the understanding of the influence of confined water on the functioning of biological systems.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.965
Times cited: 13
DOI: 10.1063/5.0038359
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“Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory”. Bal KM, Neyts EC, Journal Of Chemical Physics 157, 184113 (2022). http://doi.org/10.1063/5.0120136
Abstract: We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.4
DOI: 10.1063/5.0120136
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“Nucleation rates from small scale atomistic simulations and transition state theory”. Bal KM, Journal Of Chemical Physics 155, 144111 (2021). http://doi.org/10.1063/5.0063398
Abstract: The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion relying only on the free energy barrier, transition state theory, and a simple dynamical correction for diffusive recrossing. In this setup, the time scale problem is overcome by using enhanced sampling methods, in casu metadynamics, whereas the impact of finite size effects can be naturally circumvented by reconstructing the free energy surface from an appropriate ensemble. Approximations from classical nucleation theory are avoided. We demonstrate the accuracy of the approach by calculating macroscopic rates of droplet nucleation from argon vapor, spanning 16 orders of magnitude and in excellent agreement with literature results, all from simulations of very small (512 atom) systems.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.965
DOI: 10.1063/5.0063398
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“Conformational analysis of TMC114, a novel HIV-1 protease inhibitor”. Nivesanond K, Peeters A, Lamoen D, van Alsenoy C, Journal of Chemical Information and Modeling 48, 99 (2008). http://doi.org/10.1021/ci7001318
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.76
Times cited: 13
DOI: 10.1021/ci7001318
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“Lipid Oxidation: Role of Membrane Phase-Separated Domains”. Oliveira MC, Yusupov M, Bogaerts A, Cordeiro RM, Journal Of Chemical Information And Modeling 61, 2857 (2021). http://doi.org/10.1021/acs.jcim.1c00104
Abstract: Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy.
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 3.76
DOI: 10.1021/acs.jcim.1c00104
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“Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations”. Ghasemitarei M, Privat-Maldonado A, Yusupov M, Rahnama S, Bogaerts A, Ejtehadi MR, Journal Of Chemical Information And Modeling 62, 129 (2022). http://doi.org/10.1021/acs.jcim.1c00853
Abstract: Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.
Keywords: A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.6
DOI: 10.1021/acs.jcim.1c00853
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“Viscosity measurement and correlation of unloaded and CO₂-loaded aqueous solutions of N-methyldiethanolamine + 2-amino-2-methyl-1-propanol”. Kummamuru NB, Eimer DA, Idris Z, Journal Of Chemical And Engineering Data 65, 3072 (2020). http://doi.org/10.1021/ACS.JCED.0C00088
Abstract: This work contributes to new and complementary experimental viscosity data for blended amine mixtures of aqueous N-methyldiethanolamine + 2-amino-2-methyl-1-propanol (MDEA + AMP) solutions with and without CO2 at different temperatures and mass fractions. For the unloaded MDEA + AMP solutions, measurements were conducted with total amine mass fractions ranging from 0.30 to 0.60. In the case of CO2-loaded aqueous MDEA + AMP solutions, experiments were performed at CO2 loadings ranging from 0.11 to 0.80. Proposed correlations were used to represent viscosity at the unloaded and CO2-loaded solutions within experimental uncertainty.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 2.6
DOI: 10.1021/ACS.JCED.0C00088
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“Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)A Molecular Dynamics Approach”. Kamaraj B, Purohit R, Journal of cellular biochemistry 117, 2608 (2016). http://doi.org/10.1002/JCB.25555
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.085
Times cited: 28
DOI: 10.1002/JCB.25555
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“Electrochemical evidence for neuroglobin activity on NO at physiological concentrations”. Trashin S, De Jong M, Luyckx E, Dewilde S, De Wael K, Journal of biological chemistry 291, 18959 (2016). http://doi.org/10.1074/JBC.M116.730176
Abstract: The true function of neuroglobin (Ngb) and, particularly, human Ngb (NGB) has been under debate since its discovery 15 years ago. It has been expected to play a role in oxygen binding/supply, but a variety of other functions have been put forward, including NO dioxygenase activity. However, in vitro studies that could unravel these potential roles have been hampered by the lack of an Ngb-specific reductase. In this work, we used electrochemical measurements to investigate the role of an intermittent internal disulfide bridge in determining NO oxidation kinetics at physiological NO concentrations. The use of a polarized electrode to efficiently interconvert the ferric (Fe3+) and ferrous (Fe2+) forms of an immobilized NGB showed that the disulfide bridge both defines the kinetics of NO dioxygenase activity and regulates appearance of the free ferrous deoxy-NGB, which is the redox active form of the protein in contrast to oxy-NGB. Our studies further identified a role for the distal histidine, interacting with the hexacoordinated iron atom of the heme, in oxidation kinetics. These findings may be relevant in vivo, for example in blocking apoptosis by reduction of ferric cytochrome c, and gentle tuning of NO concentration in the tissues.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 4.125
Times cited: 11
DOI: 10.1074/JBC.M116.730176
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“Toxicity of iron oxide nanoparticles : size and coating effects”. Abakumov MA, Semkina AS, Skorikov AS, Vishnevskiy DA, Ivanova AV, Mironova E, Davydova GA, Majouga AG, Chekhonin VP, Journal of biochemical and molecular toxicology 32, e22225 (2018). http://doi.org/10.1002/JBT.22225
Abstract: Toxicological research of novel nanomaterials is a major developmental step of their clinical approval. Since iron oxide magnetic nanoparticles have a great potential in cancer treatment and diagnostics, the investigation of their toxic properties is very topical. In this paper we synthesized bovine serum albumin-coated iron oxide nanoparticles with different sizes and their polyethylene glycol derivative. To prove high biocompatibility of obtained nanoparticles the number of in vitro toxicological tests on human fibroblasts and U251 glioblastoma cells was performed. It was shown that albumin nanoparticles' coating provides a stable and biocompatible shell and prevents cytotoxicity of magnetite core. On long exposure times (48 hours), cytotoxicity of iron oxide nanoparticles takes place due to free radical production, but this toxic effect may be neutralized by using polyethylene glycol modification.
Keywords: A1 Journal article; Pharmacology. Therapy; Electron microscopy for materials research (EMAT)
DOI: 10.1002/JBT.22225
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“Atmospheric concentrations and deposition of heavy metals over the North Sea: a literature review”. Injuk J, Van Grieken R, Journal of atmospheric chemistry 20, 179 (1995). http://doi.org/10.1007/BF00696557
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1007/BF00696557
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“Characterisation of soot emitted by domestic heating, aircraft and cars using diesel or biodiesel”. Smekens A, Godoi RHM, Berghmans P, Van Grieken R, Journal of atmospheric chemistry 52, 45 (2005). http://doi.org/10.1007/S10874-005-6903-7
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1007/S10874-005-6903-7
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“Characterization of individual soot aggregates from different sources using image analysis”. Smekens A, Godoi RHM, Vervoort M, van Espen P, Potgieter-Vermaak SS, Van Grieken R, Journal of atmospheric chemistry 56, 211 (2007). http://doi.org/10.1007/S10874-006-9050-X
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Chemometrics (Mitac 3)
DOI: 10.1007/S10874-006-9050-X
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“Chemical characterization and multivariate analysis of atmospheric PM2.5 particles”. Ravindra K, Stranger M, Van Grieken R, Journal of atmospheric chemistry 59, 199 (2008). http://doi.org/10.1007/S10874-008-9102-5
Abstract: The new European Council Directive (PE-CONS 3696/07) frames the inhalable (PM10) and fine particles (PM2.5) on priority to chemically characterize these fractions in order to understand their possible relation with health effects. Considering this, PM2.5 was collected during four different seasons to evaluate the relative abundance of bulk elements (Cl, S, Si, Al, Br, Cu, Fe, Ti, Ca, K, Pb, Zn, Ni, Mn, Cr and V) and water soluble ions (F−, Cl−, NO2 −, NO3 −, SO4 2−, Na+, NH4 +, Ca2+ and Mg2+) over Menen, a Belgian city near the French border. The air quality over Menen is influenced by industrialized regions on both sides of the border. The most abundant ionic species were NO3 −, SO4 2− and NH4 +, and they showed distinct seasonal variation. The elevated levels of NO3 − during spring and summer were found to be related to the larger availability of the NOx precursor. The various elemental species analyzed were distinguished into crustal and anthropogenic source categories. The dominating elements were S and Cl in the PM2.5 particles. The anthropogenic fraction (e.g. Zn, Pb, and Cu) shows a more scattered abundance. Furthermore, the ions and elemental data were also processed using principal component analysis and cluster analysis to identify their sources and chemistry. These approach identifies anthropogenic (traffic and industrial) emissions as a major source for fine particles. The variations in the natural/anthropogenic fractions of PM2.5 were also found to be a function of meteorological conditions as well as of long-range transport of air masses from the industrialized regions of the continent.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1007/S10874-008-9102-5
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“Elemental and single particle aerosol characterisation at a background station in Kazakhstan”. Hoornaert S, Godoi RHM, Van Grieken R, Journal of atmospheric chemistry 48, 301 (2004). http://doi.org/10.1023/B:JOCH.0000044432.74476.B0
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1023/B:JOCH.0000044432.74476.B0
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“Elemental composition of mineral aerosol generated from Sudan Sahara sand”. Eltayeb MAH, Injuk J, Maenhaut W, Van Grieken RE, Journal of atmospheric chemistry 40, 247 (2001). http://doi.org/10.1023/A:1012272208129
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1023/A:1012272208129
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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 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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