Measurements of ionization cross sections by molecular beam experiments: information content on the imaginary part of the optical potential

In this work, we present and analyze in detail new and recent ionization cross section and mass spectrum determinations, collected in the case of He*, Ne*-H2O, -H2S, and -NH3 ionizing collisions. These sets of data, obtained under the same experimental conditions, are relevant to identify differences in the autoionization stereodynamics of the three hydrogenated molecules and on the selective role of the imaginary part of the optical potential. We demonstrate that in these autoionization processes hydrogen and halogen bonds are competing because they are controlling both real and imaginary components of the optical potential that drives the complete reaction dynamics. In particular, we found that both components critically depend on the angular and radial approach between the reagent partners in determining the collision dynamics

Investigating Rare Events by Transition Interface Sampling

We briefly review simulation schemes for the investigation of rare transitions and we resume the recently introduced Transition Interface Sampling, a method in which the computation of rate constants is recast into the computation of fluxes through interfaces dividing the reactant and product state.Comment: 12 pages, 1 figure, contributed paper to the proceedings of NEXT 2003, Second Sardinian International Conference on News and Expectations in Thermostatistics, 21-28 Sep 2003, Cagliari (Italy

Protein folding on the ribosome studied using NMR spectroscopy

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity

CO2 packing polymorphism under pressure: mechanism and thermodynamics of the I-III polymorphic transition

In this work we describe the thermodynamics and mechanism of CO$_2$ polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics and committor analysis. We find that the phase transformation takes place through a concerted rearrangement of CO$_2$ molecules, which unfolds via an anisotropic expansion of the CO$_2$ supercell. Furthermore, at high pressures we find that defected form I configurations are thermodynamically more stable with respect to form I without structural defects. Our computational approach shows the capability of simultaneously providing an extensive sampling of the configurational space, estimates of the thermodynamic stability and a suitable description of a complex, collective polymorphic transition mechanism