Fits are simultaneously performed on all con- sidered SRs and CRs of each analysis independently in order to constrain the normalisation of backgrounds and the nui- sance parameters (NPs) describing the systematic uncertain- ties. Each systematic variation enters the fit as an individual nuisance ...
The crucial computing support from all WLCG partners is acknowl- edged gratefully, in particular from CERN, the ATLAS Tier-1 facili- ties at TRIUMF (Canada), NDGF (Denmark, Norway, Sweden), CC- IN2P3 (France), KIT/GridKA (Germany), INFN-CNAF (Italy), NL- T1 (Netherlands), PIC (...
7 are used to compute the uncertain- ties of all the bins in the fit and are then mapped to the nui- sance parameters. The widths of the Gaussian distributions correspond to the magnitudes of these uncertainties. Poisson distributions are used for modelling MC simulation statistical uncertainties...
The AMBER ff14SB and CHARMM22/CMAP force field parameters were utilized for the disordered peptides in separate simulations. The Onufriev-Bashford-Case implicit model for water and the modified TIP5P model for water were used for modeling the solvent (see above) in separate simulations. The ...
AMBER-18 [55] was used throughout working with force fields, protein.ff14SB, DNA.bsc1, water.tip3p and ion- sjc_tip3. An initial correspondence between 6MCE nucleotides and target positions in the ds (AT/GC) hairpin oligonucleotides was established as follows, 5 -C19A20T21A22T26A27T28...
Figure 18. Infrared absorption spectra of the backbone C=O stretching vibration that forms the am- yloid fibril (black), α-helix (red), and random coil (green). The snapshot images were created using FFySPiglioyogucMiuirdeerOtefyL1i.b18[8r.1i.l7II1(nnb]ff.lrraRaacerrkeep)ddr,iα...
Aptamers are short single-stranded DNA or RNA oligonucleotides (usually from 20 to 80 nucleotides) that tether proteins with high affinity due to their unique three-dimensional conformation [30]. These molecules are specifically designed to recognize and bind to the molecular targets and induce a ...
lamblia MD simulations were carried out with the AMBER 16 software package [34] using the ff14SB forcefield [35]. NADP+ parameters were obtained from a previous work [36]. Four systems were studied: the Apo form of G6PD::6PGL (APO) with the NADP+ cofactor (cofactor), with the ...