We study through time-dependent density-functional theory (TDDFT) method the electronic stopping power of low-energy protons and helium ions moving through CdTe under the condition of channeling. The agreement between our calculated results and SRIM data roughly up to the stopping maximum for the proton along the 〈1 0 0〉 and 〈1 1 1〉 crystalline axes and for helium ions along 〈1 0 0〉 crystalline axis is satisfactory, which can be explained by the energy transfer mechanism that electron–hole excitation caused by ions in the solid. However, in the channel of 〈1 1 1〉 for helium ions, a transition between two velocities regimes is observed at about v = 0.4 a.u. This may be an indication of extra energy loss channel beyond the electron–hole excitation. To analyze it, we calculate the amount of electrons captured by the moving projectiles in real time. It is found that the soft transition between two velocities regimes can be attributed to the charge transfer and charge resonance between helium ion and host atoms of CdTe crystal, which are considered as additional energy loss channels.

•A single bounce ellipsoidal glass monocapillary was designed and fabricated.•The slope error of monocapillary measured by optical equipment was small.•The focal spot size and ring obtained by X-ray test showed that the quality of monocapillary was high.A single bounce ellipsoidal glass monocapillary was designed and fabricated and its performance was measured by both an optical measurement and an X-ray test. This monocapillary had a slope error of 17 μrad. The images of the focal spot and the far-field pattern recorded by a CCD detector showed that this fabricated monocapillary had high quality and satisfied the requirement of the designed data for X-ray nano-imaging.

The three-dimensional structure of a protein defines not only its size and shape, but also its physiological function. It is known that changing the surrounding environment, such as adding an osmolyte or increasing the temperature, could significantly affect the structural and thermodynamic properties of proteins. Therefore, keeping a conserved protein conformation in a specific state is fundamental and very useful for correctly executing the necessary functions. In our present work, the structure change of a single alanine-based ACE-AEAAAKEAAAKA-NH2 peptide in modified polarised water solvents has been investigated by using intensive molecular dynamics simulations. A surprising structural conservation, which is polarity dependent, has been found. When the parameter of polarity S is 0.7 (lower polarity) or 1.2 (higher polarity), the peptide is consistently kept in a folded α-helix state, suggesting the pivotal role of the solvent effect on conformational conservation. In other cases, the peptide mostly exhibits a ringlike structure. The effects of the side chain and salt on the conservation of the peptide’s conformation were explored further and little change was found.

Excited-states ab initio   molecular dynamics model is employed to study the electronic stopping power of cubic silicon carbide nanocrystal when low-energy protons and helium ions are hyperchanneling in the 〈〈1 0 0〉,〈〉,〈1 1 0〉〉 and 〈〈1 1 1〉〉 major crystal axes. The energy transfer processes between the ions and the electronic subsystem of the cubic silicon carbide nanocrystalline are studied. The channeling effect in the electronic stopping power is determined by the unique electronic structure of these channels. The velocity-proportional stopping power is predicted for both protons and helium ions in the low-energy region. The calculated stopping power is in a quantitative agreement with the experimental data up to the stopping power maximum. The deviations of the stopping power of helium ions from the linear proportionality are attributed to the electron transfer at higher velocities.

•We study the collision dynamics of carbon ions with single-walled carbon nanotubes.•Using a SCC-DFTB MD instead of an empirical potential one.•Adsorption, reflection, substitution, penetration and damage processes are observed.•The charge transfer between the incident carbon ion and the nanotube is quantitatively studied.•Stone–Wales, 7-4-5-9-5 and 5-7-7-6-5 defects are observed.The collision process of a low-energy carbon ion impinging single-walled carbon nanotubes is studied by using a self-consistent-charge density-functional tight-binding molecular dynamics method. The simulation shows that the outcome of the collision highly depends on the incident kinetic energy and the impact location in the nanotube. There are five types of processes observed: adsorption, reflection, substitution, penetration and damage. The adsorption process becomes dominant at energies lower than 20 eV. Defect formation events are observed at energies larger than 20 eV. For this process, 5-1DB, 5-8-5, Stone–Wales, 7-4-5-9-5 and 5-7-7-6-5 defects are obtained. The formation processes of the typical defects are described in detail. Moreover, the energy exchange and the charge transfer between the incident carbon ion and the nanotube have also been quantitatively studied.

To investigate the collision processes of proton with formic acid at 5 eV, time-dependent density functional theory coupled with molecular dynamics is used. Eight specific collision configurations with various impact parameters are taken into account, which results in scattering, replacement, and protonation. The protonation happens when the incoming proton is parallel to the molecular plane. The 1,3-intramolecular H transfer is found in the formation of protonated formic acid. During the evolution, the protonated formic acid tends to be the carbonyl protonated formic acid.Graphical abstractHighlights► We study the collision dynamics of proton with formic acid. ► The formation and evolution of protonated formic acid is investigated. ► At 5 eV, protonation more likely occurs for the in-plane collision. ► The 1,3-hydrogen shift plays an important role in the formation of protonated HCOOH. ► The carbonyl protonated HCOOH is the dominant structure.

•We studied the dynamics of radioactive ions around DNA.•Radioactive ions influence the distribution of Na+ and K+ and competitions of them.•I− ions affect original distributions of K+ and Na+ the most while Sr2+ the least.•The structure of DNA can be changed by radioactive ions.•The structure of the A tract is completely affected by Cs+.Molecular dynamics simulations of B-DNA in aqueous solution containing Na+ and K+ ions, or Na+, K+ and one kind of 90Sr2+,137Cs+90Sr2+,137Cs+ or 131I-131I- are investigated at 298 K. For the ions in the minor groove, K+ ions are dispersed as Sr2+ or Cs+ added, but Na+ ions dominate the minor groove when I− ions are added. For the ions in the major groove, the interaction of K+ and DNA becomes stronger as I− added. As for the DNA conformation, Cs+ ions affect most while Sr2+ ions the least.

The collision processes, H+ + C2Hm (m = 2, 4, 6), are studied at 30 eV by using time-dependent density functional theory combined with molecular dynamics approach. The reaction channel, electronic density evolution, scattering pattern, total ionization cross sections are presented based on three projectile incident orientations. We find that the primary mechanism of target ionization at 30 eV is electron capture, and the bond dilution effect is prevalent in present collisions. The structure of the scattering angle is different in distinct orientations, which is investigated by means of the force which proton is subjected to. The rainbow angle is in reasonable agreement with experimental and other theoretical results. Calculated ionization cross sections increase with increasing C–C bond length except for the orientation parallel to the C–C bond, and the reason is explained by the C–C bond effect.Graphical abstractHighlights► We study the collision dynamics of proton with C2Hm (m = 2, 4, 6). ► The nature of target ionization at 30 eV is electron capture. ► The proton exchange and the collision-induced dissociation process are studied in details. ► The complex structure of the scattering angle results from the force which the projectile is subjected to. ► The fact that calculated ionization cross sections increase with C–C bond length arises from the C–C bond effect.

We explore from a theoretical perspective the steric effect in the collision dynamics of proton to formic acid at 2 eV by a time-dependent local-density approximation for valence electrons, coupled to molecular dynamics for the ionic cores. Eight specific collision configurations are taken into consider. We find that at this low impact energy, protonation is the dominant reaction channel. There are two forms of protonation–formation induced by steric effect: 1,3-intramolecular H shift and out-of-plane oscillation.

The process of proton impinging upon CH4 molecule has been theoretically studied at 30 eV. The study is based on time-dependent local density approximation coupled with molecular dynamics model. The electronic density evolution, ionic motion, and the scattering angle are presented. We found that the mechanism of target ionization in present simulation is electron capture. The predicted rainbow angle is in good agreement with experiments and previous calculations. By comparing the scattering angle from present calculation with that from classical collision, we found that the nuclear stopping is dominant in small impact parameters, and the discrepancy in large impact parameters may be due to the neglect of electronic stopping in classical collision.

The nucleus–nucleus interaction potentials for the fusion reactions 16O + 208Pb, 64Ni + 64Ni, 58Ni + 58Ni and 16O + 154Sm are extracted from the improved isospin-dependent quantum molecular dynamics model. The shell correction effects are discussed. The negative shell correction energies lower potential barriers of a certain reaction. The incident energy dependence of the potential barrier is investigated for each system. A complex phenomenon of energy dependence is observed. It is also found that incident energy dependence of the barrier radius and barrier height shows opposite behaviors. The Coulomb potential shows weak energy dependence when distance of two colliding nuclei is lower than the touching distance. The isospin effects of the potential barrier are investigated. The orientation effects of the potential barrier is also discussed for the system 16O + 154Sm. The fusion cross sections that correspond to the equatorial orientation of 154Sm are very low in sub-barrier region because of the high fusion barriers and the shallow potential pockets.