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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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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- ...
