Deriving force fields with a multiscale approach: From ab initio calculations to molecular-based equations of state.

Using theoretical and computational tools for predicting thermophysical properties of fluid systems and the soft matter has always been of interest to the physical, chemical, and engineering sciences. Certainly, the ultimate goal is to be able to compute these macroscopic properties from first-principles calculations beginning with the very atomic constitution of matter. In this work, Mie potential parameters were obtained through dimer interaction energy curves derived from ab initio calculations to represent methane and substituted-methane molecules in a spherical one-site coarse-grained model.

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition.

Motivation: Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in the sample.

RawVegetable - A data assessment tool for proteomics and cross-linking mass spectrometry experiments.

We present RawVegetable, a software for mass spectrometry data assessment and quality control tailored toward shotgun proteomics and cross-linking experiments. RawVegetable provides four main modules with distinct features: (A) The charge state chromatogram that independently displays the ion current for each charge state; useful for optimizing the chromatography for highly charged ions and with lower XIC values such as those typically found in cross-linking experiments. (B) The XL-Artefact determination, which flags possible noncovalently associated peptides.

Mixed-Data Acquisition: Next-Generation Quantitative Proteomics Data Acquisition.

We present the Mixed-Data Acquisition (MDA) strategy for mass spectrometry data acquisition. MDA combines Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) in the same run, thus doing away with the requirements for separate DDA spectral libraries. MDA is a natural result from advances in mass spectrometry, such as high scan rates and multiple analyzers, and is tailored toward exploiting these features.

Caffeine exposure ameliorates acute ischemic cell death in avian developing retina.

In infants, the main cause of blindness is retinopathy of prematurity that stems in a hypoxic-ischemic condition. Caffeine is a psychoactive compound that at low to moderate concentrations, selectively inhibits adenosine A and A receptors. Caffeine exerts beneficial effects in central nervous system of adult animal models and humans, whereas it seems to have malefic effect on the developing tissue.