Translocation of DNA oligonucleotide through carbon nanotube channels under induced pressure difference

This paper presents molecular dynamics (MD) simulations of DNA oligonucleotide and water molecules translocating through carbon nanotube (CNT) channels. Induced pressure difference is applied to the system by pushing a layer of water molecules towards the flow direction to drive the oligonucleotide and other molecules. This novel MD simulation investigates the flow behaviour of oligonucleotide and water molecules in nanochannel while controlling the temperature and volume of the system in canonical ensemble. The results show that the oligonucleotide is unable to translocate through the (8, 8)-(12, 12) CNT channel under the induced pressures applied. However, the oligonucleotide can transport through the (10, 10)-(14, 14) CNT channel easily under the same induced pressures. It is observed that less water molecules permeate through the center of the (8, 8)-(12, 12) CNT channel as the strength of the induced pressure is increased. In contrast, more water molecules flow through the (10, 10)-(14, 14) CNT channel at a higher induced pressure. The conformational energy of the oligonucleotide in the CNT channels has been shown to be affected by both the strength of the induced pressure and the size of the nanotube. Although the interactive force between oligonucleotide and CNT channel is dependent on their distance apart, the induced pressure within the (8, 8)-(12, 12) nanotube channel acts as an external factor that affects the distance between the oligonucleotide and the CNT junction. The insertion depth of the oligonucleotide in the (8, 8)-(12, 12) CNT channel relies on the magnitude of the induced pressure. Both the velocity of oligonucleotide and the interactive force between oligonucleotide and nanotube wall are shown to increase when the oligonucleotide is travelling through the narrower part of the (10, 10)-(14, 14) CNT channel.     

Generation of surface features in films deposited by matrix-assisted pulsed laser evaporation: the effects of the stress confinement and droplet landing velocity

Coarse-grained molecular dynamics simulations are applied to investigate the origins of the surface features observed in films deposited by the Matrix-Assisted Pulsed Laser Evaporation (MAPLE) technique. The formation of transient balloon-like structures with a polymer-rich surface layer enclosing matrix vapor, observed in earlier simulations of slow heating of polymer-matrix droplets, has been explored in this work at higher rates of thermal energy deposition. Tensile stresses generated in the regime of partial stress confinement are found to induce an internal boiling in the overheated droplets and associated generation of “molecular balloons” at thermal energy densities at which no homogeneous boiling takes place without the assistance of tensile stresses. Simulations of the dynamic processes occurring upon the collision of a polymer-matrix droplet with a substrate provide the molecular-level pictures of the droplet impact phenomenon and reveal the connections between the droplet landing velocity and the shapes of the polymer features observed in scanning electron microscopy images of films deposited in MAPLE experiments. The distinct types of surface features observed in MAPLE experiments, namely, wrinkled “deflated balloons,” localized arrangements of interconnected polymer filaments, and elongated “nanofibers,” are shown to emerge from different scenarios of droplet landing and/or disintegration observed in the simulations.     

Thresholds for front-side ablation and rear-side spallation of metal foil irradiated by femtosecond laser pulse

The mechanical action of laser exposure on a foil may result in the ablation of irradiated front layer and the rear-side spallation. The dynamics of an Al foil is studied by means of two-temperature (2T) hydrodynamics and molecular dynamics (MD). It is found that the rear-side spallation threshold F _s exceeds the front-side ablation threshold F _a. We propose to extend the common approach in laser-matter experiments by pump–probe measuring of the rear-side displacement.     

Ground-state energy of a classical artificial molecule

We study the ground-state energy of a classical artificial molecule formed by two-dimensional clusters (artificial atoms) of N/2 charged particles separated by a distance d. For the small molecules of N = 2 and 4, we obtain analytical expressions for this energy. For the larger ones, we calculate the ground-state energy using molecular dynamics simulation for N up to 128. From our numerical results, we are able to find out a function to approximate the ground-state energy of the molecules covering the range from atoms to molecules for any inter-atom distance d and for particle number from N = 8 to 128 within a difference less than one percent from the MD data.     

Development of a ReaxFF description for gold

Atomistic simulations of the chemistry of thiol-gold-systems have been restricted by the lack of interatomic interaction models for the involved elements. The ReaxFF framework already has potentials for hydrocarbons, making it an attractive basis for extending to the complete AuSCH-system. Here, an interatomic potential for gold, based on the ReaxFF framework, is presented and compared to existing gold potentials available in the literature. Electronic supplementary material  Supplementary Online Material     

Covalent-to-ionic transition in liquid zinc dichloride

We report molecular-dynamics simulations of self-diffusion and structure in a pseudoclassical model of liquid and crystalline ZnCl₂ over a wide region of the pressure-temperature plane. The model parameters are adjusted to reproduce a liquid structure of corner-sharing ZnCl₄ tetrahedra at the standard freezing point and the measured diffusion coefficients as functions of temperature on the sfp isobar. We find that compression first weakens the intermediate-range order of the melt near freezing into a fourfold-coordinated crystal structure, and then drives at higher temperatures a novel liquid-liquid transition consisting of two broad steps: (i) a transition in which the Zn atoms start to leave their tetrahedral cages, followed by (ii) a structural transition from a covalent network of Cl atoms to a dissociated ionic liquid which then freezes into a sixfold-coordinated crystal. Good agreement is found with data from X-ray diffraction experiments under pressure.     

Characterization of defects introduced in Sb doped Ge by 3 keV Ar sputtering using deep level transient spectroscopy (DLTS) and Laplace-DLTS (LDLTS)

We have used deep level transient spectroscopy (DLTS), and Laplace-DLTS to investigate the defects created in antimony doped germanium (Ge) by sputtering with 3 keV Ar ions. Hole traps at E_V+0.09 eV and E_V+0.31 eV and an electron trap at E_C−0.38 eV (E-center) were observed soon after the sputtering process. Room temperature annealing of the irradiated samples over a period of a month revealed a hole trap at E_V+0.26 eV. Above room temperature annealing studies revealed new hole traps at E_V+0.27 eV, E_V+0.30 eV and E_V+0.40 eV.     

Preparing a laser cooled plasma for stopping highly charged ions

We present a new cooling scheme for the preparation of highly charged ions for future in-trap precision experiments. A plasma of laser cooled ²⁴Mg⁺ ions trapped in a 3D harmonic confinement potential is used as a stopping medium for the highly charged ions. We focus on the dynamic evolution of the plasma, determining suitable cooling conditions for fast recooling of the ²⁴Mg⁺ ions. The results of a realistic parallel simulation of the complete stopping process presented here indicate that a small, constant detuning of the laser frequency is sufficient for subsequent recooling of the plasma, thus maintaining the stability of the plasma.     

Band bending and quasi‐2DEG in the metallized β‐SiC(001) surface

We study the mechanism leading to the metallization of the β‐SiC(001) Si‐rich surface induced by hydrogen adsorption. We analyze the effects of band bending and demonstrate the existence of a quasi‐2D electron gas, which originates from the donation of electrons from adsorbed hydrogen to bulk conduction states. We also provide a simple model that captures the main features of the results of first‐principles calculations, and uncovers the basic physics of the process. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)