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Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptiv ...
We have studied the influence of implicit solvent models, inclusion of explicit water molecules, inclusion of vibrational effects, and density functionals on the quality of the predicted pK a of small amino acid side chain models. We found that the inclusi ...
We introduce an improvement to the Hubbard U augmented density functional approach known as DFT+U that incorporates variations in the value of self-consistently calculated, linear-response U with changes in geometry. This approach overcomes the one major s ...
The mechanism of reaction between NO and two models of carbonaceous materials with active sites was investigated at the UB3LYP/6-31 + G(d) and UM06-2X theory levels. The small model is the anthracene radical and the large one is also a monoradical built wi ...
Cyclopentadienyl–ruthenium half-sandwich complexes with η2-bound alkyne ligands have been suggested as catalytic intermediates in the early stages of Ru-catalyzed reactions with alkynes. We show that electronically unsaturated complexes of the formula [RuC ...
A phase-field model for the solid-solid alpha -> gamma transition of Ti-Al binary alloys is presented based on analytical Gibbs free energies and couplings to the thermodynamical database ThermoCalc. The equilibrium values recover the alpha + gamma phase b ...
Intrachain loop formation allows unfolded polypeptide chains to search for favorable interactions during protein folding. We applied triplet-triplet energy transfer between a xanthone moiety and naphthylalanine to directly measure loop formation in various ...
We derived an orbital dependent Kohn-Sham based scheme for the correction of the self-interaction error in DFT, which is particularly suited for the study of open shell molecular systems. Our approach is based on a weighted form of the Perdew and Zunger (P ...
The reaction mechanisms of ZrCl4 adsorption and dissociation on Ge/Si(100)-(2 x 1) surface as the initial stage of ZrO2 atomic layer deposition process are investigated with density functional theory (DFT). The Si-Si, Si-Ge and Ge-Ge one-dimer cluster mode ...
The authors present a QM/MM ab initio mol. dynamics study of the peptide hydrolysis reaction catalyzed by HIV-1 protease. The QM/MM calcns. are based on previous extensive classical MD simulations on the protein in complex with a model substrate. Gradient- ...
