Molecular dynamics study of accelerated ion-induced shock waves in biological media

We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which is not possible with the analytical model

Channeling of ultra-relativistic positrons in bent diamond crystals

Results of numerical simulations of channeling of ultra-relativistic positrons are reported for straight and uniformly bent diamond crystals. The projectile trajectories in a crystal are computed using a newly developed module of the MBN Explorer package which simulates classical trajectories in a crystalline medium by integrating the relativistic equations of motion with account for the interaction between the projectile and the crystal atoms. The Monte Carlo method is employed to sample the incoming positrons and to account for thermal vibrations of the crystal atoms. The channeling parameters and emission spectra of incident positrons with a projecti le energy of 855 MeV along C(110) crystallographic planes are calculated for different bending radii of the crystal. Two features of the emission spectrum associated with positron oscillations in a channel and synchrotron radiation are studied as a function of crystal curvature

Toward the exploration of the NiTi phase diagram with a classical force field

10 pags., 7 figs., 3 tabs.Classical force fields, used for atomistic modeling of metal materials, are typically constructed to match low-temperature properties obtained in experiments or from quantum-level calculations. However, force fields can systematically fail to reproduce further fundamental parameters, such as the melting point. In this work, we present a modified force field for modeling metallic compounds, which has been implemented in the MBN Explorer software package. It is employed to simulate different regions of the composition-temperature-size phase diagram of nickel-titanium nanoalloys with particular focus on the evaluation of the melting point of NiTi (x = 0.45-0.55) systems. A near-equiatomic NiTi alloy is of paramount interest for biomedical and nanotechnology applications due to its shape memory behavior, but experiments and theory are inconsistent regarding its structural ground-state properties. The presented force field is used to predict the ground-state structure of an equiatomic NiTi nanoalloy. We observe that this compound does not possess the shape memory capacity because it stabilizes in the austenite instead of the required martensite crystalline phase. All results of our atomistic approach utilizing molecular dynamics and Monte Carlo techniques are in agreement with respective ab initio calculations and the available experimental findings. (Figure Presented). Copyright © 2016 American Chemical SocietyA.V.V. acknowledges the support by the European Commission through the FP7 Initial Training Network “ARGENT” (grant agreement no. 608163), and A.V.K. acknowledges the support from Alexander von Humboldt-Foundation. We thank the Center for Scientific Computing Frankfurt for providing the opportunity to perform calculations on the clusters FUCHS and LOEWE-CSC.Peer Reviewe