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Peer Reviewed
See detailModeling of the cyclic lipodepsipeptide Pseudodesmin A self-assembly through molecular dynamic simulations
Crowet, Jean-Marc ULg; Sinnaeve, Davy; Fehér, Krisztina et al

Poster (2014, August 21)

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. Pseudodesmine A is a ... [more ▼]

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. Pseudodesmine A is a cyclic lipodepsipeptide of nine residues which presents a moderate antibacterial activity and whose structure has been resolved by X-ray and NMR. In acetonitrile, Pseudodesmine A is monomeric while in chloroform, it has the same structure but assembles in a supramolecular complex. This structure could associate with membranes and be responsible for the biological activity of the peptide. Comparison of NMR data in the two solvents has given indications on the intermolecular contacts that arise in chloroform and a model for the self-association was proposed. To study in more details this assembly, molecular dynamics simulations have been carried on. The resultswere compared with detailed information given by NMR, regarding the dimensions of the assembly and the orientation of the individual peptide building blocks inside the supramolecular assembly. In acetonitrile, the simulations show that the peptide has transient interactions while in chloroform, interactions between monomers are always observed. In agreement with NMR, these interactions arise mainly between the backbone protons of the LEU1 and the GLN2, the GLN2 sidechain and the loop located on the opposite end of the monomer structure. From 10 simulations of dimerization, hydrogen bonds were followed and specific interaction patterns were identified regarding the hydrogen bonds formed. Peptide interactions are mainly described by 13 interaction patterns characterized by 2 to 4 hydrogen bonds. In dimers, the peptides can have a linear, a perpendicular or a side by side configuration. From the linear dimer, it is possible to reconstruct filaments and, by combining a linear and a lateral dimer, it is possible to build fibrils with multifilaments, as found in the NMR-derived model. Two self-consistent supramolecular models can be built from dimers and they present a very good correlation with NMR data regarding the supramolecular organization. Besides, the perpendicular dimer can gives peptide rings that can also explain the potential ability of this peptide to form ion pores in membranes. [less ▲]

Detailed reference viewed: 5 (1 ULg)
Peer Reviewed
See detailModeling of the cyclic lipodepsipeptide Pseudodesmin A self-assembly through molecular dynamic simulations
Crowet, Jean-Marc ULg; Sinnaeve, Davy; Fehér, Krisztina et al

Conference (2014, August 20)

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. Pseudodesmine A is a ... [more ▼]

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. Pseudodesmine A is a cyclic lipodepsipeptide of nine residues which presents a moderate antibacterial activity and whose structure has been resolved by X-ray and NMR. In acetonitrile, Pseudodesmine A is monomeric while in chloroform, it has the same structure but assembles in a supramolecular complex. This structure could associate with membranes and be responsible for the biological activity of the peptide. Comparison of NMR data in the two solvents has given indications on the intermolecular contacts that arise in chloroform and a model for the self-association was proposed. To study in more details this assembly, molecular dynamics simulations have been carried on. The resultswere compared with detailed information given by NMR, regarding the dimensions of the assembly and the orientation of the individual peptide building blocks inside the supramolecular assembly. In acetonitrile, the simulations show that the peptide has transient interactions while in chloroform, interactions between monomers are always observed. In agreement with NMR, these interactions arise mainly between the backbone protons of the LEU1 and the GLN2, the GLN2 sidechain and the loop located on the opposite end of the monomer structure. From 10 simulations of dimerization, hydrogen bonds were followed and specific interaction patterns were identified regarding the hydrogen bonds formed. Peptide interactions are mainly described by 13 interaction patterns characterized by 2 to 4 hydrogen bonds. In dimers, the peptides can have a linear, a perpendicular or a side by side configuration. From the linear dimer, it is possible to reconstruct filaments and, by combining a linear and a lateral dimer, it is possible to build fibrils with multifilaments, as found in the NMR-derived model. Two self-consistent supramolecular models can be built from dimers and they present a very good correlation with NMR data regarding the supramolecular organization. Besides, the perpendicular dimer can gives peptide rings that can also explain the potential ability of this peptide to form ion pores in membranes. [less ▲]

Detailed reference viewed: 9 (2 ULg)
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Peer Reviewed
See detailModeling of the Diffusion of VOCs Emitted by Barley Roots
Hirtt, Laura ULg; Destain, Marie-France ULg; Lognay, Georges ULg et al

Poster (2012, July 02)

Detailed reference viewed: 49 (20 ULg)
See detailModeling of the fabrication and operation of 3-D self-assembled SOI MEMS
Mendez, Carlos; Louis, Christophe; Paquay, Stéphane et al

(2006)

Detailed reference viewed: 9 (0 ULg)
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Peer Reviewed
See detailModeling of the fatigue cracks in welded beam-to-column connection of steel moment frame buildings submitted to earthquake
Lequesne, Cédric ULg; Gerday, Anne-Françoise ULg; Plumier, André ULg et al

in Aliabadi, M. H.; Planas, J.; Buchholz, F.-G. (Eds.) et al Proceedings of the 4th International Conference on Fracture and Damage Mechanics (2005)

Fatigue cracks in welded connections of steel moment frame buildings submitted to earthquakes are studied. The connections of beams with thick flanges designed to resist to seismic phenomena by plastic ... [more ▼]

Fatigue cracks in welded connections of steel moment frame buildings submitted to earthquakes are studied. The connections of beams with thick flanges designed to resist to seismic phenomena by plastic dissipation are presented. The structural components, the materials and the crack mechanics are described. To predict the crack initiation, the knowledge of residual internal stresses, generated by the welding process, is required. So these stresses are assessed by a FEM thermo-mechanical analysis. The potential sites of crack locations are detected by using an FEM model of the connection with the continuum damage model of Lemaître and Chaboche. After these FEM analyses, new meshes with specific elements located at the potential crack locations are defined. A cohesive zone law is used to model the crack propagation. This model describes the crack growth by analyzing the energy released by the generation of the new surfaces and damage micro-phenomena behind the crack tip. A constitutive tension-separation law computes this energy. In these cases of low cycle fatigue, the damage and the cyclic loading conditions are taken into account. [less ▲]

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See detailModeling of the influence of electric forces on mechanical structures
Rochus, Véronique ULg; Duysinx, Pierre ULg; Golinval, Jean-Claude ULg

Conference (2003)

This paper is a summary concerning the modeling of the strong electro-mechanical coupling appearing in micro-electro-mechanical systems (MEMS). These systems are very small devices (typical size of a few ... [more ▼]

This paper is a summary concerning the modeling of the strong electro-mechanical coupling appearing in micro-electro-mechanical systems (MEMS). These systems are very small devices (typical size of a few microns), in which electric phenomena as well as mechanical and dynamical phenomena exist. The finite element method is used to discretize simultaneously the electrostatic and mechanical fields. The formulation is consistently derived from variational principles based on the electro-mechanical free energy. In classical weakly coupled formulations staggered iteration is used between the electrostatic and the mechanical domain. Therefore, in those approaches, linear stiffness is evaluated by finite differences and equilibrium is reached typically by relaxation techniques. The strong coupling formulation presented here allows to derive exact tangent matrices of the electro-mechanical system. Thus it allows to compute non-linear equilibrium positions using Newton- Raphson type iterations combined with adaptive meshing in case of large displacements. Furthermore, the tangent matrix obtained in the method considered in this paper greatly simplifies the computation of vibration modes and frequencies of the coupled system around equilibrium configurations. The non-linear variation of frequencies with respect to voltage and stiffness can then be investigated until pull-in appears. In order to illustrate the effectiveness of the proposed formulation numerical results are shown first for the reference problem of a simple flexible cap acitor, then for the model of a micro-bridge. [less ▲]

Detailed reference viewed: 27 (3 ULg)
Peer Reviewed
See detailModeling of the Iturinic Antimicrobial Lipopeptide Mycosubtilin at Interfaces
Loison, Claire; Nasir, Mehmet Nail ULg; Benichou, Emmanuel et al

Conference (2014, June)

Detailed reference viewed: 12 (2 ULg)
See detailModeling of the longitudinal modulation of the Io interaction
Hess, S.; Bonfond, Bertrand ULg; Delamere, P. A. et al

Poster (2010)

The Io interaction with the Jovian magnetosphere is the best known case of moon-magnetosphere interaction. It leads to bright emissions from radio to UV, which are mostly due to the acceleration of ... [more ▼]

The Io interaction with the Jovian magnetosphere is the best known case of moon-magnetosphere interaction. It leads to bright emissions from radio to UV, which are mostly due to the acceleration of electrons by Alfvén waves along the magnetic field lines passing Io. We previously presented a model of the electron acceleration by the Iogenic Alfvén waves, which explains the average brightness of the emissions. We now present a study of the modulation of the Io-magnetosphere interaction with longitude, and compare our results with the observed brightness modulation of the auroral emissions. This study highlights how the satellite-magnetosphere interactions depend on the variation of the magnetic field, the equatorial plasma density,... A new model of the Jovian internal magnetic field, giving an accurate description of the longitudinal modulations of the Jovian magnetic field has been computed for this study, and is also presented. [less ▲]

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See detailModeling of the surface mass balance in Svalbard with the regional climate model MAR over 1958-2010
Lang, Charlotte ULg

Master's dissertation (2011)

It is well known that high latitude zones are very sensitive to climate change. As a result of global warming, ice sheet melting has increased which in turn has an influence on climate through ... [more ▼]

It is well known that high latitude zones are very sensitive to climate change. As a result of global warming, ice sheet melting has increased which in turn has an influence on climate through modifications of the thermohaline circulation, feedback of ice albedo, sea level rise,. . . Svalbard is an archipelago located between 74 and 81 ◦lat N and 60 percent of its area (62 248 km2 ) is covered with glaciers and ice sheets. The impact of global warming on the Svalbard cryosphere can be estimated with climate models. However, we need to use regional climate models as they offer the possibility of a higher resolution than general circulation models. We have carried out a simulation of the Svalbard climate over the last 50 years (from 1958 to 2010) with the regional climate MAR model (tuned for the Greenland ice sheet) at a 10 km resolution forced with the ECMWF reanalysis. As validation, the modeled climate has been compared to near surface measurements at several weather stations through the archipelago. The results show a large interannual variability of the surface mass balance over Svalbard along with an increasing melting. The increase in temperature is responsible for the melting rate and the interannual variability is due to the variations of the mean summer temperature. [less ▲]

Detailed reference viewed: 19 (3 ULg)
Peer Reviewed
See detailModeling of Thin Insulating Layers in Dual Magnetodynamic Formulations
Dular, Patrick ULg; Geuzaine, Christophe ULg

in Proceedings of the 10th IEEE Conference on Electromagnetic Field Computation (CEFC'2002) (2002)

Detailed reference viewed: 6 (1 ULg)
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Peer Reviewed
See detailModeling of Thin Insulating Layers with Dual 3-D Magnetodynamic Formulations
Dular, Patrick ULg; Geuzaine, Christophe ULg

in IEEE Transactions on Magnetics (2003), 39(3), 1139--1142

Detailed reference viewed: 12 (2 ULg)
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Peer Reviewed
See detailModeling of Transformer Core Joints via a Subproblem FEM and a Homogenization Technique
Ferreira da Luz, Mauricio Valencia; Dular, Patrick ULg; Vianei Leite, Jean et al

in IEEE Transactions on Magnetics (2014), 50(2),

A subproblem finite element method is developed for modeling the transformer core joints. It applies magnetostatic and magnetodynamic models on progressive geometries and different components of the ... [more ▼]

A subproblem finite element method is developed for modeling the transformer core joints. It applies magnetostatic and magnetodynamic models on progressive geometries and different components of the solution, supported by different meshes. It allows an efficient and robust analysis of magnetic circuits in any frequency range, with an accurate calculation of flux density, losses, reluctance, and impedance in transformer core joint zone. The models of the study properly account for the effects of core design parameters such as length of air gaps and overlap length in stacked-lamination cores. The proposed models, which include saturation, are applied to grain-oriented silicon steel and two types of step-lap joints are considered: single-step-lap (SSL) joints and multistep-lap (MSL) joints. The values of magnetic reluctance, impedance, and Joule losses obtained with SSL joint are bigger than with MSL joint. [less ▲]

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Peer Reviewed
See detailModeling of tumor growth in dendritic cell-based immunotherapy using artificial neural networks.
Mehrian, Mohammad ULg; Asemani, Davud; Arabameri, Abazar et al

in Computational biology and chemistry (2014), 48

Exposure-response modeling and simulation is especially useful in oncology as it permits to predict and design un-experimented clinical trials as well as dose selection. Dendritic cells (DC) are the most ... [more ▼]

Exposure-response modeling and simulation is especially useful in oncology as it permits to predict and design un-experimented clinical trials as well as dose selection. Dendritic cells (DC) are the most effective immune cells in the regulation of immune system. To activate immune system, DCs may be matured by many factors like bacterial CpG-DNA, Lipopolysaccharaide (LPS) and other microbial products. In this paper, a model based on artificial neural network (ANN) is presented for analyzing the dynamics of antitumor vaccines using empirical data obtained from the experimentations of different groups of mice treated with DCs matured by bacterial CpG-DNA, LPS and whole lysate of a Gram-positive bacteria Listeria monocytogenes. Also, tumor lysate was added to DCs followed by addition of maturation factors. Simulations show that the proposed model can interpret the important features of empirical data. Owing to the nonlinearity properties, the proposed ANN model has been able not only to describe the contradictory empirical results, but also to predict new vaccination patterns for controlling the tumor growth. For example, the proposed model predicts an exponentially increasing pattern of CpG-matured DC to be effective in suppressing the tumor growth. [less ▲]

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Peer Reviewed
See detailModeling of Wastewater Sludge Drying with Determination of Diffusivity Moisture
Bennamoun, Lyes ULg; Fraikin, Laurent ULg; Salmon, Thierry ULg et al

in Journal of Residuals Science and Technology [=JRST] (2013), 10(4), 165

Detailed reference viewed: 41 (3 ULg)
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Peer Reviewed
See detailModeling of Weakly Conducting Thin Sheets in the Discontinuous Galerkin Method for Shielding Effectiveness Evaluation
Boubekeur, Mohamed; Kameni, Abelin; Modave, Axel ULg et al

in ACES Journal (2013), 28(10), 931

This paper presents a modeling of weakly conducting thin sheets in the time domain discontinuous Galerkin method. This interface condition is used to avoid the mesh of resistive sheets in order to ... [more ▼]

This paper presents a modeling of weakly conducting thin sheets in the time domain discontinuous Galerkin method. This interface condition is used to avoid the mesh of resistive sheets in order to evaluate the shielding effectiveness in high frequency electromagnetic compatibility problems. This condition is valid when the thickness of the sheet is smaller than the skin depth. This approach is validated by a comparison with an analytical solution. A 1D two sheets example, 2D and 3D cavities are treated to illustrate the efficiency of the condition. [less ▲]

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See detailModeling Operational Risk Based on Multiple Experts’ Opinion
Peters, Jean-Philippe; Hübner, Georges ULg

in Gregoriou, Greg (Ed.) Operational Risk Towards Basel III (2009)

While the Basel II accord has now gone live in most parts of the world, many discrepancies still remain on advanced modeling techniques for operational risk among large international banks. The two major ... [more ▼]

While the Basel II accord has now gone live in most parts of the world, many discrepancies still remain on advanced modeling techniques for operational risk among large international banks. The two major families of models include the loss distribution approaches (LDAs) that focus on observed past internal and external loss events and the scenario-based techniques that use subjective opinions from experts as the starting point to determine the regulatory capital charge to cover operational risk. A major methodological challenge is the combination of both techniques so as to fulfill Basel II requirements. In this chapter we discuss and investigate the use of various alternatives to model expert opinion in a sound statistical way so as to allow for subsequent integration with loss distributions fitted on internal and/or external data. A numerical example supports the analysis and shows that solutions exist to merge information arising from both sources. [less ▲]

Detailed reference viewed: 87 (8 ULg)
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Peer Reviewed
See detailModeling p-18FMPPF pet kinetics for the detremination of local 5-HT1A receptor concentration.
Costes, N.; Le Bars, D.; Merlet, I. et al

in Journal of Nuclear Medicine : Official Publication, Society of Nuclear Medicine (2001), 42(S1), 209

Detailed reference viewed: 7 (0 ULg)
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Peer Reviewed
See detailModeling post-combustion CO2 capture with amine solvents
Léonard, Grégoire ULg; Heyen, Georges ULg

in Computer Aided Chemical Engineering (2011), 29

Carbon capture and storage is a technology that can contribute to face the challenge of rising energy demand combined with a growing environmental awareness. In the present work, the CO2 capture process ... [more ▼]

Carbon capture and storage is a technology that can contribute to face the challenge of rising energy demand combined with a growing environmental awareness. In the present work, the CO2 capture process with monoethanolamine (MEA) is modeled using the simulation tool Aspen Plus. Two different modeling approaches are studied and compared: the equilibrium and the rate-based approaches. An optimization of key process parameters is performed and process modifications are studied with the objective of improving the global process energy efficiency. [less ▲]

Detailed reference viewed: 125 (30 ULg)