Pushing the frontiers of first-principles based computer simulations of chemical and biological systems

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these methods to larger systems, longer time scales and increased accuracies. Their versatility is illustrated with a diverse range of applications, ranging from the determination of the gas phase structure of the cyclic decapeptide gramicidin S, to the study of G protein coupled receptors, the interaction of transition metal based anti-cancer agents with protein targets, the mechanism of action of DNA repair enzymes, the role of metal ions in neurodegenerative diseases and the computational design of dye-sensitized solar cells. Many of these projects are done in collaboration with experimental groups from the Institute of Chemical Sciences and Engineering (ISIC) at the EPFL.     

Engineering of Facets,Band Structure,and Gas‐Sensing Properties of Hierarchical Sn2+‐Doped SnO2 Nanostructures

Hierarchical SnO₂ nanoflowers, assembled from single‐crystalline SnO₂ nanosheets with high‐index (11$ \bar 3 $ ) and (10$ \bar 2 $ ) facets exposed, are prepared via a hydrothermal method using sodium fluoride as the morphology controlling agent. Formation of the 3D hierarchical architecture comprising of SnO₂ nanosheets takes place via Ostwald ripening mechanism, with the growth orientation regulated by the adsorbate fluorine species. The use of Sn(II) precursor results in simultaneous Sn²⁺ self‐doping of SnO₂ nanoflowers with tunable oxygen vacancy bandgap states. The latter further results in the shifting of semiconductor Fermi levels and extended absorption in the visible spectral range. With increased density of states of Sn²⁺‐doped SnO₂ selective facets, this gives rise to enhanced interfacial charge transfer, that is, high sensing response, and selectivity towards oxidizing NO₂ gas. The better gas sensing performance over (10$ \bar 2 $ ) compared to (11$ \bar 3 $ ) faceted SnO₂ nanostructures is elucidated by surface energetic calculations and Bader analyses. This work highlights the possibility of simultaneous engineering of surface energetics and electronic properties of SnO₂ based materials.     

Adaptive packet scheduling for the uplink traffic in IEEE 802.16e networks

IEEE 802.16e is a telecommunication standard technology designed to support a wide variety of multimedia applications. It defines five service classes, each one with its respective QoS requirements, but does not define the scheduling algorithm for these service classes. In this paper, an adaptive packet scheduling algorithm for the uplink traffic in IEEE 802.16e networks is proposed. This algorithm is designed to be completely dynamic, mainly in networks that use various modulation and coding schemes (MCSs). The algorithm is applied directly to the bandwidth request queues in the base station (BS) and aims at supporting the real‐time and non‐real‐time applications. Using a cross‐layer approach and the states of the bandwidth request queues in the BS, a new deadlines based scheme was defined, aiming at limiting the maximum delay to the real‐time applications. Moreover, this algorithm interacts with the polling management mechanisms of the BS and controls the periodicity of sending unicast polling to the real‐time and non‐real‐time service connections, in accordance with the QoS requirements of the applications. The proposed algorithm was evaluated by means of modeling and simulation in environments where various MCSs were used and also in environments where only one type of modulation was used. The simulations showed satisfactory results in both environments. Copyright © 2012 John Wiley & Sons, Ltd.     

Increasing flow efficiency of high-pressure and low-pressure steam turbine stages from numerical optimization of 3D blading

3D blading of a high-pressure and low-pressure steam turbine stage is optimized using Nelder–Mead method of deformed polyhedron. Values of the minimized objective function, i.e. stage losses with the exit energy are found from 3D viscous compressible flow computations, including turbulence effects. Among the optimized parameters are stator and rotor blade numbers and stagger angles, rotor blade twist angle, stator blade sweep and lean, both straight and compound. The blade sections (profiles) are assumed not to change during the optimization. There are constraints imposed on the design parameters, including the mass flow rate and stage reaction. Optimization gives designs with new 3D blade stacking lines, and with increased efficiencies, compared with the original design.     

Synthesis and properties of a new crosslinkable polymer containing benzoxazine moiety in the main chain

Using difunctional phenolic and amine compounds, a new polymer with benzoxazine groups in the main chain has been synthesized through the Mannich reaction of a phenol, formaldehyde, and an amine. ¹H and ¹³C nuclear magnetic resonance spectroscopies, Fourier transform infrared spectroscopy, size exclusion chromatography, and elemental analysis are used to characterize the resulting polymer. Polymer with molecular weight of approximately 10,000 Da is obtained. The resultant polymer has a moderately broad polydispersity index. The thermal properties of the polymer have also been studied by differential scanning calorimetry and thermogravimetric analysis.     

Vanadium peroxocomplexes as oxidation catalysts of sulfur organic compounds by hydrogen peroxide in bi-phase systems

New vanadium oxodiperoxocomplexes Bu₄N⁺[VO(O2)₂ L₂]⁻ were synthesized, where L=pyridine (1), 2-methylpyridine (2), 4-methylpyridine (3), 2-oxymethylpyridine (4). All complexes were characterized by NMR (¹H, ⁵¹V) and IR spectroscopy. The oxidation of sulfur organic compounds and diesel fuel desulfurization catalyzed by vanadium peroxocomplexes in bi-phase system was investigated in various solvents. The complexes manifested high catalytic activity and selectivity in oxidation of sulfides.     

Non-oxidative dehydrogenation of ethane to ethylene over chromium catalysts prepared from layered double hydroxide precursors

Non-oxidative dehydrogenation of ethane into ethylene at 700 °C over reductively pretreated Cr–Mg–Al and Cr–Mg mixed oxide catalysts has been studied. The catalysts were prepared from layered double hydroxide (LDH) precursors that contained various species of chromium (i.e., cationic Cr(III), complex of Cr(III) with an anionic chelating agent, and chromate anion). Synthesized materials were characterized with powder X-ray diffraction, X-ray photoelectron spectroscopy and Raman spectroscopy techniques. It was shown that the surface area of the LDH-derived mixed oxides, their catalytic performance, coking ability, and susceptibility to sintering were highly dependent on the method used for introducing chromium into the LDH precursors of the catalysts.     

Effects of Hydro‐Impulse Forming of Blanks

This work presents the outcomes of investigations on dynamic effects and parameters of Hydro‐Impulse Forming (HIF) and their influence on the shaping process. Parameters for the blanks exposed to hydro‐impulse forming are defined by FE‐simulations, which use AUTODYN 2D‐3D software. These simulations enable a clear visualization of the processes that occur in the material and the working media. Results are presented for the simulated deep drawing of a semi‐sphere for the aluminium alloy A2024 and the steel QStE340. A larger influence of dynamic forces on the forming process was detected by numerical simulations on the “transmission medium ‐ die ‐ blank” scheme. These outcomes were confirmed by experimental investigations and a classification of the typical malformations during HIF (unusual in conventional forming processes). As shown by the performed experiments and numerical simulations, HIF offers great advantages in comparison with common forming processes, e.g. with regard to the creation of deeper reliefs and low residual springing.     

The influence of artificial-thunderstorm cell polarity on discharge initiation by model hydrometeor arrays

The initiation of discharge by model hydrometeors between an artificial-thunderstorm cell (aerosol cloud) of negative or positive polarity and ground has been experimentally studied. It is established for the first time that the conditions of cloud–ground spark discharge initiation by hydrometeors, as well as the characteristics of discharge significantly depend on the polarity of charged cloud. The effect of hydrometeor arrays can be manifested by the cloud–ground lightning initiated in a thundercloud and used for developing scientific principles of artificial lightning discharge.