Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise

Solvated interaction energy (SIE) is an end-point physics-based scoring function for predicting binding affinities from force-field nonbonded interaction terms, continuum solvation, and configurational entropy linear compensation. We tested the SIE function in the Community Structure-Activity Resource (CSAR) scoring challenge consisting of high-resolution cocrystal structures for 343 protein-ligand complexes with high-quality binding affinity data and high diversity with respect to protein targets. Particular emphasis was placed on the sensitivity of SIE predictions to the assignment of protonation and tautomeric states in the complex and the treatment of metal ions near the protein-ligand interface. These were manually curated from an originally distributed CSAR-HiQ data set version, leading to the currently distributed CSAR-NRC-HiQ version. We found that this manual curation was a critical step for accurately testing the performance of the SIE function. The standard SIE parametrization, previously calibrated on an independent data set, predicted absolute binding affinities with a mean-unsigned-error (MUE) of 2.41 kcal/mol for the CSAR-HiQ version, which improved to 1.98 kcal/mol for the upgraded CSAR-NRC-HiQ version. Half-half retraining-testing of SIE parameters on two predefined subsets of CSAR-NRC-HiQ led to only marginal further improvements to an MUE of 1.83 kcal/mol. Hence, we do not recommend altering the current default parameters of SIE at this time. For a sample of SIE outliers, additional calculations by molecular dynamics-based SIE averaging with or without incorporation of ligand strain, by MM-PB(GB)/SA methods with or without entropic estimates, or even by the linear interaction energy (LIE) formalism with an explicit solvent model, did not further improve predictions.     

Y(P,V)O4:Dy phosphors for white light generation: Emission dynamics and host effect

The structural characteristics and optical spectra of Y(P,V)O₄:Dy³⁺phosphors obtained by solid state reaction, sol-gel and hydrothermal routes have been investigated and compared. The luminescence features of these materials show a complicate dependence on the composition, synthetic method and excitation conditions. The emission performance depends on different effects: host luminescence, energy transfer to the doping ions and host dependence of the Dy³⁺ emission properties. These effects have been rationalized in order to provide useful information for the development of a suitable material for the white light emitting phosphors technology.     

Comparison of mass transfer models for the numerical prediction of sheet cavitation around a hydrofoil

Cavitating flows, which can occur in a variety of practical cases, can be modelled with a wide range of methods. One strategy consists of using the RANS (Reynolds Averaged Navier Stokes) equations and an additional transport equation for the liquid volume fraction, where mass transfer rate due to cavitation is modelled by a mass transfer model. In this study, we compare three widespread mass transfer models available in literature for the prediction of sheet cavitation around a hydrofoil. These models share the common feature of employing empirical coefficients, to tune the models of condensation and evaporation processes, that can influence the accuracy and stability of the numerical predictions. In order to compare the different mass transfer models fairly and congruently, the empirical coefficients of the different models are first well tuned using an optimization strategy. The resulting well tuned mass transfer models are then compared considering the flow around the NACA66(MOD) and NACA009 hydrofoils. The numerical predictions based on the three different tuned mass transfer models are very close to each other and in agreement with the experimental data. Moreover, the optimization strategy seems to be stable and accurate, and could be extended to additional mass transfer models and further flow problems.     

Guest-controlled aggregation of cavitand gold nanoparticles and N-methyl pyridinium-terminated PEG

The introduction of a disulfide functionalized tetraphosphonate cavitand on Au nanoparticles promotes the reversible self-assembly of a hybrid network upon addition of a polymeric ditopic guest.     

Supramolecular assemblies tailored by dipyridyl-1,2-4-thiadiazoles: influence of the building blocks in the predictability of the final network

ABSTRACT

Coordinatively unsaturated dithiophosphato complex [Cd((MeO)₂PS₂)₂] (1) was reacted with the bifunctional ligands 3,5-di-(4-pyridyl)-1,2,4-thiadiazole (L1) and 3,5-di-(3-pyridyl)-1,2,4-thiadiazole (L2) to give the helicoidal coordination polymer (1·L1)_∞ and the paddle-wheel dimer (1·L2)₂, both characterised by single-crystal X-ray diffraction. A comparison of the structures with the different supramolecular constructs obtained by reacting L1 and L2 with differently P-substituted dithiophosphoric Ni^II complexes allowed to evaluate the role of the metal ion for the predictable assembly of this class of coordination polymers.     

Dye-Doped Silica Nanoparticles for Enhanced ECL-Based Immunoassay Analytical Performance

The combination of highly sensitive techniques such as electrochemiluminescence (ECL) with nanotechnology sparked new analytical applications, in particular for immunoassay-based detection systems. In this context, nanomaterials, particularly dye-doped silica nanoparticles (DDSNPs) are of high interest, since they can offer several advantages in terms of sensitivity and performance. In this work we synthesized two sets of monodispersed and biotinylated [Ru(bpy)₃]²⁺-doped silica nanoparticles, named bio-Triton@RuNP and bio-Igepal@RuNP, obtained following the reverse microemulsion method using two different types of nonionic surfactants. Controlling the synthetic procedures, we were able to obtain nanoparticles (NPs) offering highly intense signal, using tri-n-propylamine (TPrA) as coreactant, with bio-Triton@RuNps being more efficient than bio-Igepal@RuNP.     

Real-time manipulation of gold nanoparticles inside a scanning electron microscope

The forces needed to overcome static friction and move 150 nm diameter Au nanoparticles on an oxidized Si substrate were measured in Normal and Shear oscillation modes inside a scanning electron microscope (SEM) in real time. The experimental setup consisted of a quartz tuning fork (QTF) mounted onto a high-precision 3D nanomanipulator used with a glued silicon or tungsten tip as a force sensor. Static friction was found to range from tens of nN to several hundred nN. Large variations in static friction values were related to differences in particle shape. Kinetic friction tended to be close to the detection limit and in most cases did not exceed several nN. The influence of thermal treatment in reducing the static friction of nanoparticles was considered.     

An exact approach for the Vertex Coloring Problem

Given an undirected graph $G=(V,E)$, the Vertex Coloring Problem (VCP) requires to assign a color to each vertex in such a way that colors on adjacent vertices are different and the number of colors used is minimized. In this paper, we present an exact algorithm for the solution of VCP based on the well-known Set Covering formulation of the problem. We propose a Branch-and-Price algorithm embedding an effective heuristic from the literature and some methods for the solution of the slave problem, as well as two alternative branching schemes. Computational experiments on instances from the literature show the effectiveness of the algorithm, which is able to solve, for the first time to proven optimality, five of the benchmark instances in the literature, and reduce the optimality gap of many others.