Collision site effect on the radiation dynamics of cytosine induced by proton

By combing the time-dependent density functional calculations for electrons with molecular dynamics simulations for ions (TDDFT-MD) nonadiabatically in real time, we investigate the microscopic mechanism of collisions between cytosine and low-energy protons with incident energy ranging from 150 eV to 1000 eV. To explore the effects of the collision site and the proton incident energy on irradiation processes of cytosine, two collision sites are specially considered, which are N and O both acting as the proton receptors when forming hydrogen bonds with guanine. Not only the energy loss and the scattering angle of the projectile, but also the electronic and ionic degrees of freedom of the target are identified. It is found that the energy loss of proton increases linearly with the increase of the incident energy in both situations, which are 14.2% and 21.1% of the incident energy respectively. However, the scattering angles show different behaviors in these two situations when the incident kinetic energy increases. When proton collides with O, the scattering angle of proton is larger and the energy lost is more, while proton captures less electrons from O. The calculated fragment mass distribution shows the high counts of the fragment mass of 1, implying the production of H+ fragment ion from cytosine even for proton with the incident energy lower than keV. Furthermore, the calculated results show that N on cytosine is easier to be combined with low-energy protons to form NH bonds than O.

Monte Carlo simulation of the measurement by the 2E technique of the average prompt neutron multiplicity as a function of the mass of fragments from thermal neutron-induced fission of 239Pu

Using a Monte Carlo method, we simulate the measurement, by the 2E technique, of the average prompt neutron multiplicity as a function of the mass of fragments from the thermal neutron-induced fission of 239Pu. The input data for the simulation, associated with the primary fragment mass (A), consist of the yield (Y), the distribution of the total kinetic energy characterized by its average ((TKE) ̅) and its standard deviation (σ_TKE), the average prompt neutron multiplicity (ν ̅_s, a sawtooth approach of experimental data), and the slope of neutron multiplicity against total kinetic energy (dν_s/d<TKE>). The output data, associated with the simulated as the fragment mass measured by the 2E technique (µ), consist of the yield (y), the distribution of the total kinetic energy characterized by its average ((tke) ̅) and its standard deviation (σ_tke), and the average prompt neutron multiplicity (ν ̅_µ). In the mass regions A≈115 and A>150, ν ̅_µ is higher than ν ̅_s. This result suggests that, in those mass regions, the 2E experimental values associated with the average neutron multiplicity are overestimated, referred to the corresponding to the primary fragments.

On the Mass Distribution of Fragments of an Asteroid Disrupted in the Earth’s Atmosphere

To model the interaction with the atmosphere of fragments of a disrupted asteroid, which move independently of each other, it is necessary to know their mass distribution. In this regard, an analogy is drawn with fragmentation in high-speed impact experiments performed to simulate the disruption of asteroids at their collisions in outer space. Based on the results of impact experiments and assuming a power law for the mass distribution in a differential form, we obtained the cumulative number of fragments as a function of the fragment mass m normalized to the total mass of fragments, the mass fraction of the largest fragment(s), the number of the largest fragments, and the power index. The formula for the cumulative number of fragments of a disrupted body is used to describe the results of impact experiments for different fragmentation types. The proposed fragment mass distribution is also tested by comparison with the mass distributions of recovered meteorites in the cases of Mbale, Bassikounou, Almahata Sitta, Košice, and Chelyabinsk meteorite falls.

A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventional settings, such as fully specific enzymatic constraints. Here we evaluated the impact of the fragment mass tolerance in combination with the enzymatic constraints on the performance of three search engines. Three open-source search engines (Myrimatch, X! Tandem, and MSGF+) were evaluated concerning the suitability in semi- and unspecific searches as well as the importance of accurate fragment mass spectra in non-specific peptide searches. We then performed a semispecific reanalysis of the published NCI-60 deep proteome data applying the most suited parameters. Semi- and unspecific LC-MS/MS data analyses particularly benefit from accurate fragment mass spectra while this effect is less pronounced for conventional, fully specific peptide-spectrum matching. Search speed differed notably between the three search engines for semi- and non-specific peptide-spectrum matching. Semispecific reanalysis of NCI-60 proteome data revealed hundreds of previously undescribed N-terminal peptides, including cases of proteolytic processing or likely alternative translation start sites, some of which were ubiquitously present in all cell lines of the reanalyzed panel. Highly accurate MS2 fragment data in combination with modern open-source search algorithms enable the confident identification of semispecific peptides from large proteomic datasets. The identification of previously undescribed N-terminal peptides in published studies highlights the potential of future reanalysis and data mining in proteomic datasets.