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See detailModeling of non-covalent complexes of the cell-penetrating peptide CADY and its siRNA cargo.
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Deshayes, Sebastien et al

in Biochimica et Biophysica Acta (2012)

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D ... [more ▼]

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D models of CADY and of the non-covalent CADY-siRNA complexes in order to understand their formation and stabilization. Data from the ab initio calculations and molecular dynamics support that, in agreement with the experimental data, CADY is a polymorphic peptide partly helical. Taking into consideration the polymorphism of CADY, we calculated and compared several complexes with peptide/siRNA ratios of up to 40. Four complexes were run by using molecular dynamics. The initial binding of CADYs is essentially due to the electrostatic interactions of the arginines with siRNA phosphates. Due to a repetitive arginine motif (XLWR(K)) in CADY and to the numerous phosphate moieties in the siRNA, CADYs can adopt multiple positions at the siRNA surface leading to numerous possibilities of complexes. Nevertheless, several complex properties are common: an average of 14+/-1 CADYs is required to saturate a siRNA as compared to the 12+/-2 CADYs experimentally described. The 40 CADYs/siRNA that is the optimal ratio for vector stability always corresponds to two layers of CADYs per siRNA. When siRNA is covered by the first layer of CADYs, the peptides still bind despite the electrostatic repulsion. The peptide cage is stabilized by hydrophobic CADY-CADY contacts thanks to CADY polymorphism. The analysis demonstrates that the hydrophobicity, the presence of several positive charges and the disorder of CADY are mandatory to make stable the CADY-siRNA complexes. [less ▲]

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See detailModeling of Pulverized Coal Combustion in Cement Rotary Kiln
Wang, Shijie; Lu, Jidong; Li, Weijie et al

in Energy & Fuels (2006), 20

In this paper, based on analysis of the chemical and physical processes of clinker formation, a heat flux function was introduced to take account of the thermal effect of clinker formation. Combining the ... [more ▼]

In this paper, based on analysis of the chemical and physical processes of clinker formation, a heat flux function was introduced to take account of the thermal effect of clinker formation. Combining the models of gas-solid flow, heat and mass transfer, and pulverized coal combustion, a set of mathematical models for a full-scale cement rotary kiln were established. In terms of commercial CFD code (FLUENT), the distributions of gas velocity, gas temperature, and gas components in a cement rotary kiln were obtained by numerical simulation of a 3000 t/d rotary kiln with a four-channel burner. The predicted results indicated that the improved model accounts for the thermal enthalpy of the clinker formation process and can give more insight (such as fluid flow, temperature, etc,) from within the cement rotary kiln, which is a benefit to better understanding of combustion behavior and an improvement of burner and rotary kiln technology. [less ▲]

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See detailModeling of strain localization around the radioactive waste disposal galleries
Salehnia, Fatemeh ULg; Charlier, Robert ULg; Levasseur, Séverine ULg

in Coupled Phenomena in Environmental Geotechnics (2013)

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See detailModeling of Surrogate Fuels with Real Components
Mair-Zelenka, P; Wallek, T; Reiter, A M et al

Conference (2012)

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See detailModeling of the auroral thermal structure and morphology of Jupiter
Grodent, Denis ULg

Doctoral thesis (2000)

The general introduction of this work presents the main characteristics of the planet Jupiter and a detailed description of its magnetosphere. The latter reminds the basic motion of a charged particle in ... [more ▼]

The general introduction of this work presents the main characteristics of the planet Jupiter and a detailed description of its magnetosphere. The latter reminds the basic motion of a charged particle in a magnetic field. It describes the interplanetary magnetic field and its reconnection with the planetary magnetosphere. The notions of corotating field and magnetospheric convection are used to differentiate the Earth and Jovian magnetospheres. Among these differences the interaction with the satellite Io is stressed out as Io provides most of the magnetospheric plasma material. These notions allow to discuss the potential origin of the particles responsible for the Earth aurorae and, by extension, the Jovian aurorae. It is postulated that the auroral particles are related to the presence of field-aligned currents and fields. The main characteristics of the Hubble Space Telescope and of the WFPC2 and GHRS instruments, which were used for this work, are briefly described at the end of the introduction. The first part describes a model simulating Earth views of UV auroral arcs and diffuse emissions in the Jovian north polar region. Simple geometric cases are described to illustrate the dependence of the altitude, atmospheric scale height and central meridian longitude of an idealized auroral morphology seen from Earth orbit. As an application of the simulation model, four images obtained with the WFPC2 camera on board the Hubble Space Telescope are used to determine the characteristics of their auroral (discrete and diffuse) structures. A composite average auroral distribution is built by mapping 10 WFPC2 images from the same dataset. It illustrates the dichotomy frequently observed between a narrow single structure confined to the morning sector, and the multiple arc and broad diffuse emission in the afternoon sector. Location of these structures are given and constrained in a reference frame linked to the GSFC-O6 magnetic field model. This model is then applied to assess the role of the viewing geometry on the auroral far UV color ratio. This value gives the ratio between the intensity measured in an unabsorbed spectral band and the intensity in a methane-absorbed band. The simulated color ratios, obtained from a geometry deduced from images taken with HST, are compared to the color ratio measurements obtained with the IUE spectrograph. We attempt to reproduce the IUE observations by imposing an intrinsic longitudinal dependence of the column of methane above the level of the auroral emission. The second part is devoted to the energy degradation model of the auroral electrons in the jovian atmosphere. It then describes the coupling of this model with a thermal conduction model. The theoretical section includes an introduction on the jovian atmosphere and its confinement in regions characterized by different dynamical and thermal regimes. The notion of hydrostatic equilibrium is reminded and used to establish a pressure-altitude relationship. We describe the electron transport model of Banks and Nagy and the numerical resolution method that we applied to it. The set of cross sections used to quantify the energy loss processes is described along with the numerical treatment of the energy "reapportionment" of the auroral electrons. The vertical thermal profile is calculated from the heat conduction equation. Among the different heat sources we consider H2 dissociation, thermal electron heating, and chemical heating. Other sources, such as the breaking gravity waves, are indirectly accounted for. The heat sinks account for the IR radiative cooling from H3+, CH4 and C2H2. A correction regarding the departure from local thermodynamic equilibrium is applied for these species. In order to calculate the response of the atmospheric structure to the auroral precipitation, the model iteratively solves the diffusion equation for the major constituents. The vertical profiles of the eddy and molecular diffusion coefficients and their connection are addressed. The adopted method for the approximation of the H3+ density in the ionosphere as a function of the auroral activity is presented. The thermostatic role of H3+ in the thermosphere is then discussed. The heat conduction equation, the diffusion equation and the electron transport equations are tightly coupled. The resolution of this set of equations therefore requires an iterative approch for which we describe a strategy meant to limit the convergence speed. The energy degradation model is then applied with different energy distributions to assess the importance of the energy spectrum of the incident electrons for the thermal balance of Jupiter's auroral thermosphere. The values of observable quantities such as the altitude of the H2 emission peak, the IR and UV emissions, the FUV color ratio and temperatures associated with various optical signatures are used to constrain the parameters of these energy distributions. A series of sensitivity tests are carried out to analyse the role of critical parameters such as the value of the eddy diffusion coefficient at the homopause. The third part describes the H2 UV high-resolution spectral generator and the global coupling of the different models. We begin with an overview of H2 far-UV spectroscopy notions that are used in the spectral generator, especially regarding the Lyman and Werner band systems. For the Werner bands, the cascade effect from the E,F state is considered. The coupling of the energy degradation model with the spectral generator is described. In a first stage an unconverged thermal profile is adopted. Three examples are used to illustrate the effect of the electron energy distribution on the spectra. The temperature effect is also highlighted. The H2 temperature is determined from two GHRS spectra. It gives a best fit temperature of 600 K, in disagreement with the temperature predicted by the energy degradation model. The latter predicts an average temperature, weighted by the H2 UV emission profile, of the order of 200 K. It is shown that the use of converged thermal profiles, obtained with the heat conduction equation, does not remove the contradiction. The coupling of the three models (energy degradation, spectral generator, and morphology) is performed in the last section. This coupling reveals a wavelength and a viewing geometry effect on the temperature deduced from the observed spectra. It is shown how these effects impinge on the thermal, density and emission vertical profiles to produce an effective H2 temperature of 600 K in agreement with the temperature deduced from the observed spectra. We finally discuss a possible application of the coupled models that would allow a spectroscopic probing of the jovian thermal profile. [less ▲]

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See detailModeling of the cardio-pulmonary system assisted by ECMO
Habran, Simon ULg; Dauby, Pierre ULg; Desaive, Thomas ULg et al

in National Day on Biomedical Engineering 2014 (2014, October)

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Peer Reviewed
See detailModeling of the chemical processes in a longwall face underground gasifier at great depth
COEME, Antoinette; Pirard, Jean-Paul ULg; MOSTADE, Marc

in In Situ (1993), 17(1), 83-104

In order to simulate the cavity growth of an underground gasifier in thin seams, at great depth, Wilks1,2 has developed an original model based on the distribution of fluid flows around an injection well ... [more ▼]

In order to simulate the cavity growth of an underground gasifier in thin seams, at great depth, Wilks1,2 has developed an original model based on the distribution of fluid flows around an injection well. In this paper, we aim to introduce within this model a description of chemical processes on the wall and within the fluid phase, in order to determine the temperature and concentration profiles along the coal wall. These profiles are dependent only on two factors: the transfer coefficients and the energy balance of the gas generator. A study of the sensitivity of the operating variables has been carried out. [less ▲]

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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, September 30)

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 ▲]

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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 ▲]

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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

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 ▲]

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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)

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See detailModeling of the fabrication and operation of 3-D self-assembled SOI MEMS
Mendez, Carlos; Louis, Christophe; Paquay, Stéphane et al

(2006)

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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 ▲]

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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: 14 (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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