Exact solution of the ion‐laser interaction in all regimes

We show that in the trapped ion‐laser interaction all the regimes may be considered analytically. We may solve not only for different laser intensities, but also away from resonance and from the Lamb‐Dicke regime. It is found a dispersive Hamiltonian for the high intensity regime, that, being diagonal, its evolution operator may be easily calculated.     

HPLC with inductively coupled plasma optical emission spectrometric detection for the analysis of inositol phosphates

The use of inductively coupled plasma optimal emission spectroscopy as a detector for the high-performance liquid chromatographic analysis of inositol phosphates is studied. It is found that separation of different inositol phosphates with a mobile phase consisting of tetraethylammonium (0.14%, w/v), methanol (5%, v/v), and formic acid (0.18%, w/v) may be obtained on a PRP-1 column with an analysis time of 18 min. In addition, high specificity and sensitivity of the detection system used permits detection of the inositol phosphates from bi- to hexaphosphate free from interference of other chromatographic peaks, which could be from the sample or mobile phase. Additionally, it is possible to use less sample because of the high sensitivity of the detection system.     

Influence of hydrogen gas over the interference of acids in inductively coupled plasma atomic emission spectrometry

The effect of hydrogen gas on the plasma and its influence on acid interferences in plasma atomic emission spectrometry was studied. The study was performed with HCl and HNO₃ in the concentration range of 0–2 mol l⁻¹. Vanadium and magnesium were used as test elements, the study was extended to other several elements. The effects of hydrogen gas on the plasma were studied by measuring excitation temperature, electron number density and the ionic-to-atomic line intensity ratio. The net effect of hydrogen was an increase in electron density and ionic to atomic line intensity ratio. A small increase in the excitation temperature was observed. The signal suppression for ionic lines causes by mineral acid was reduced when small amounts of hydrogen was introduced into the plasma as sheathing gas. This effect was attributed to the increase in plasma electron density.     

Superscaling in charged current neutrino quasielastic scattering in the relativistic impulse approximation

Superscaling of the quasielastic cross section in charged-current neutrino-nucleus reactions at energies of a few GeV is investigated within the framework of the relativistic impulse approximation. Several approaches are used to describe final-state interactions and comparisons are made with the plane-wave approximation. Superscaling is very successful in all cases. The scaling function obtained using a relativistic mean field for the final states shows an asymmetric shape with a long tail extending towards positive values of the scaling variable, in excellent agreement with the behavior presented by the experimental scaling function.     

D3R Grand Challenge 2: blind prediction of protein–ligand poses,affinity rankings,and relative binding free energies

The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank (http://www.pdb.org), and in affinity ranking and scoring of bound ligands.     

Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2

The causative agent of African sleeping sickness, Trypanosoma brucei , undergoes an unusual mitochondrial RNA editing process that is essential for its survival. RNA editing terminal uridylyl transferase 2 of T. brucei (TbRET2) is an indispensable component of the editosome machinery that performs this editing. TbRET2 is required to maintain the vitality of both the insect and bloodstream forms of the parasite, and with its high-resolution crystal structure, it poses as a promising pharmaceutical target. Neither the exclusive requirement of uridine 5'-triphosphate (UTP) for catalysis, nor the RNA primer preference of TbRET2 is well-understood. Using all-atom explicitly solvated molecular dynamics (MD) simulations, we investigated the effect of UTP binding on TbRET2 structure and dynamics, as well as the determinants governing TbRET2's exclusive UTP preference. Through our investigations of various nucleoside triphosphate substrates (NTPs), we show that UTP preorganizes the binding site through an extensive water-mediated H-bonding network, bringing Glu424 and Arg144 side chains to an optimum position for RNA primer binding. In contrast, cytosine 5'-triphosphate (CTP) and adenosine 5'-triphosphate (ATP) cannot achieve this preorganization and thus preclude productive RNA primer binding. Additionally, we have located ligand-binding "hot spots" of TbRET2 based on the MD conformational ensembles and computational fragment mapping. TbRET2 reveals different binding pockets in the apo and UTP-bound MD simulations, which could be targeted for inhibitor design.