Molecular Modeling and Simulation: Force Field Development, Evaporation Processes and Thermophysical Properties of Mixtures

To gain physical insight into the behavior of fluids on a microscopic level as well as to broaden the data base for thermophysical properties especially for mixtures, molecular modeling and simulation is utilized in this work. Various methods and applications are discussed, including a procedure for the development of new force field models. The evaporation of liquid nitrogen into a supercritical hydrogen atmosphere is presented as an example for large scale molecular dynamics simulation. System-size dependence and scaling behavior are discussed in the context of Kirkwood-Buff integration. Further, results for thermophysical mixture properties are presented, i.e. the Henry’s law constant of aqueous systems and diffusion coefficients of a ternary mixture

ms2: A molecular simulation tool for thermodynamic properties, release 3.0

A new version release (3.0) of the molecular simulation tool ms2 (Deublein et al., 2011; Glass et al.. 2014) is presented. Version 3.0 of ms2 features two additional ensembles, i.e. microcanonical (NVE) and isobaric–isoenthalpic (NpH), various Helmholtz energy derivatives in the NVE ensemble, thermodynamic integration as a method for calculating the chemical potential, the osmotic pressure for calculating the activity of solvents, the six Maxwell-Stefan diffusion coefficients of quaternary mixtures, statistics for sampling hydrogen bonds, smooth-particle mesh Ewald summation as well as the ability to carry out molecular dynamics runs for an arbitrary number of state points in a single program execution. Previous versions of this program (AEJF_v1_0 and AEJF_v2_0) may be found at http://dx.doi.org/10.1016/j.cpc.2011.04.026 and http://dx.doi.org/10.1016/j.cpc.2014.07.012, respectively

Etude de proprietes asymptotiques en classification

SIGLEINIST T 72954 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

eIF3a cooperates with sequences 5′ of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA

Yeast initiation factor eIF3 (eukaryotic initiation factor 3) has been implicated in multiple steps of translation initiation. Previously, we showed that the N-terminal domain (NTD) of eIF3a interacts with the small ribosomal protein RPS0A located near the mRNA exit channel, where eIF3 is proposed to reside. Here, we demonstrate that a partial deletion of the RPS0A-binding domain of eIF3a impairs translation initiation and reduces binding of eIF3 and associated eIFs to native preinitiation complexes in vivo. Strikingly, it also severely blocks the induction of GCN4 translation that occurs via reinitiation. Detailed examination unveiled a novel reinitiation defect resulting from an inability of 40S ribosomes to resume scanning after terminating at the first upstream ORF (uORF1). Genetic analysis reveals a functional interaction between the eIF3a-NTD and sequences 5′ of uORF1 that is critically required to enhance reinitiation. We further demonstrate that these stimulatory sequences must be positioned precisely relative to the uORF1 stop codon and that reinitiation efficiency after uORF1 declines with its increasing length. Together, our results suggest that eIF3 is retained on ribosomes throughout uORF1 translation and, upon termination, interacts with its 5′ enhancer at the mRNA exit channel to stabilize mRNA association with post-termination 40S subunits and enable resumption of scanning for reinitiation downstream