Search

The search of DNA-binding proteins for their target sites positioned on DNA plays a very important role in many cellular processes, and this search process combines 3D excursions in the bulk solution with one-dimensional sliding along the DNA chain. In living cells, there exist roadblocks along DNA chain formed by other proteins; however, the role of the roadblock in search rate is poorly understood. Based on 3D Langevin dynamics simulations, we have investigated the effect of the blocker on the search dynamics. For a pair of symmetrically placed blockers with respect to the target, we find that, with increasing the distance between the blocker and the target, the search time, τ, rapidly decreases and then saturates. For randomly placed blockers with density φ, τ may initially increase to its maximum and then unexpectedly decreases with increasing φ, or always increase with φ, depending on the nonspecific interaction strength and the volume fraction of DNA in the system. The previous contradicted results on the role of the blocker in search time are reconciled by these findings. Particularly, the nonmonotonic behavior of τ with φ indicates that blockers may facilitate the search after a critical φ. [ABSTRACT FROM AUTHOR]

DNA-binding proteins locate and bind their target sequences positioned on DNA in crowded environments, but the molecular crowding effect on this search process is not clear. Using analytical techniques and Langevin dynamics simulations in two dimensions (2D), we find that the essential physics for facilitated diffusion in 2D search and 3D search is the same. We observe that the average search times have minima at the same optimal nonspecific binding energy for the cases with and without the crowding particle. Moreover, the molecular crowding increases the search time by increasing the average search rounds and the one-dimensional (1D) sliding time of a round, but almost not changing the average 2D diffusion time of a round. In addition, the fraction of 1D sliding time out of the total search time increases with increasing the concentration of crowders. For 2D diffusion, the molecular crowding decreases the jumping length and narrows its distribution due to the cage effect from crowders. These results shed light on the role of facilitated diffusion in DNA targeting kinetics in living cells. [ABSTRACT FROM AUTHOR]

Spectroscopic ellipsometry was used to characterize the complex refractive index of chemical-vapor-deposited monolayer transition metal dichalcogenides (TMDs). The extraordinary large value of the refractive index in the visible frequency range is obtained. The absorption response shows a strong correlation between the magnitude of the exciton binding energy and band gap energy. Together with the observed giant spin-orbit splitting, these findings advance the fundamental understanding of their novel electronic structures and the development of monolayer TMDs-based optoelectronic and spintronic devices. [ABSTRACT FROM AUTHOR]

An experimental method for measuring thermal boundary resistances of thermoelectrics/metal interfaces using two specially designed multilayer structures is presented. The thermal boundary resistances of Bi0.4Sb1.6Te3 thin films in contact with respective Ni and Ti metal layers are experimentally determined to be 2.65±0.98×10-8 and 2.85±1.06×10-8 m²K/W. The results agree reasonably well with the predictions from the diffusive mismatch model for Bi0.4Sb1.6Te3/metal interfaces. The effect of phonon transport property of metals on thermal boundary resistance at thermoelectrics/metal interfaces is investigated. [ABSTRACT FROM AUTHOR]

Flow induced structural evolution in a supercooled metallic liquid Vit106a (Zr58.5Cu15.6Al10.3 Ni12.8Nb2.8, at. %) was investigated via uni-axial compression combined with differential scanning calorimeter (DSC). Compression tests at strain rates covering the transition from Newtonian flow to non-Newtonian flow and at the same strain rate 2×10–1 s–1 to different strains were performed at the end of glass transition (Tg-end=703 K). The relaxation enthalpies measured by DSC indicate that the samples underwent non-Newtonian flow contain more free volume than the thermally annealed sample (703 K, 4min), while the samples underwent Newtonian flow contain less, namely, the free volume of supercooled metallic liquids increases in non-Newtonian flow, while decreases in Newtonian flow. The oscillated variation of the relaxation enthalpies of the samples deformed at the same strain rate 2×10–1 s–1 to different strains confirms that the decrease of free volume was caused by flow stress, i.e., "mechanical annealing." Micro-hardness tests were also performed to show a similar structural evolution tendency. Based on the obtained results, the stress-temperature scaling in the glass transition of metallic glasses are supported experimentally, as stress plays a role similar to temperature in the creation and annihilation of free volume. In addition, a widening perspective angle on the glass transition of metallic glasses by exploring the 3-dimensional stress-temperature-enthalpy phase diagram is presented. The implications of the observed mechanical annealing effect on the amorphous structure and the work-hardening mechanism of metallic glasses are elucidated based on atomic level stress model. [ABSTRACT FROM AUTHOR]

The distribution of degree of coherence of a partially coherent vortex beam reveals rich information about the vortex phase, and it is known that one can determine the topological charge (or orbital angular moment) of a partially coherent vortex beam from its degree of coherence distribution in the focal plane (or in the far field). In this letter, we demonstrate both numerically and experimentally that the degree of coherence distribution of a partially coherent vortex beam that is blocked by an opaque obstacle can self-reconstruct in the focal plane. Thus, one still can determine the topological charge of an obstructed partially coherent vortex beam from its degree of coherence distribution in the focal plane. Our results can find application in information transmission and recovery. [ABSTRACT FROM AUTHOR]

Past research has revealed the propagation of dense, asymmetric ionization zones in both high and low current magnetron discharges. Here, we report about the direction reversal of ionization zone propagation as observed with fast cameras. At high currents, zones move in the E × B direction with velocities of 103-104 m/s. However, at lower currents, ionization zones are observed to move in the opposite, the -E × B direction, with velocities ~103 m/s. It is proposed that the direction reversal is associated with the local balance of ionization and supply of neutrals in the ionization zone. [ABSTRACT FROM AUTHOR]

Numerical thermalization in collisional one-dimensional (1D) electrostatic (ES) particle-in-cell (PIC) simulations was investigated. Two collision models, the pitch-angle scattering of electrons by the stationary ion background and large-angle collisions between the electrons and the neutral background, were included in the PIC simulation using Monte-Carlo methods. The numerical results show that the thermalization times in both models were considerably reduced by the additional Monte-Carlo collisions as demonstrated by comparisons with Turner's previous simulation results based on a head-on collision model [M. M. Turner, Phys. Plasmas 13, 033506 (2006)]. However, the breakdown of Dawson's scaling law in the collisional 1D ES PIC simulation is more complicated than that was observed by Turner, and the revised scaling law of the numerical thermalization time with numerical parameters are derived on the basis of the simulation results obtained in this study. [ABSTRACT FROM AUTHOR]

Dysprosium(Dy)-doped zinc oxide (Dy:ZnO) thin films were fabricated on c-oriented sapphire substrate by pulsed-laser deposition with doping concentration ranging from 1 to 10 at. %. X-ray diffraction (XRD), Raman-scattering, optical transmission spectroscopy, and spectroscopic ellipsometry revealed incorporation of Dy into ZnO host matrix without secondary phase. Solubility limit of Dy in ZnO under our deposition condition was between 5 and 10 at.% according to XRD and Raman-scattering characteristics. Optical transmission spectroscopy and spectroscopic ellipsometry also showed increase in both transmittance in ultraviolet regime and band gap of Dy:ZnO with increasing Dy density. Zinc vacancies and zinc interstitials were identified by photoluminescence spectroscopy as the defects accompanied with Dy incorporation. Magnetic investigations with a superconducting quantum interference device showed paramagnetism without long-range order for all Dy:ZnO thin films, and a hint of antiferromagnetic alignment of Dy impurities was observed at highest doping concentration—indicating the overall contribution of zinc vacancies and zinc interstitials to magnetic interaction was either neutral or toward antiferromagnetic. From our investigations, Dy:ZnO thin films could be useful for spin alignment and magneto-optical applications. [ABSTRACT FROM AUTHOR]

Samarium ions of 200 keV in energy were implanted into highly-resistive molecular-beam-epitaxy grown GaN thin films with a focused-ion-beam implanter at room temperature. The implantation doses range from 1×1014 to 1×1016cm-2. Structural properties studied by x-ray diffraction and Raman-scattering spectroscopy revealed Sm incorporation into GaN matrix without secondary phase. The optical measurements showed that the band gap and optical constants changed very slightly by the implantation. Photoluminescence measurements showed emission spectra similar to p-type GaN for all samples. Magnetic investigations with a superconducting quantum interference device identified magnetic ordering for Sm dose of and above 1×1015cm-2 before thermal annealing, while ferromagnetism was only observed after thermal annealing from the sample with highest Sm dose. The long-range magnetic ordering can be attributed to interaction of Sm ions through the implantation-induced Ga vacancy. [ABSTRACT FROM AUTHOR]

Dynamic strain measurement is rather important for the characterization of mechanical behaviors in electromagnetic forming process, but it has been hindered by high strain rate and serious electromagnetic interference for years. In this work, a simple and effective strain measuring technique for physical and mechanical behavior studies in the electromagnetic forming process has been developed. High resolution (~5 ppm) of strain curves of a budging aluminum tube in pulsed electromagnetic field has been successfully measured using this technique. The measured strain rate is about 105 s-1, which depends on the discharging conditions, nearly one order of magnitude of higher than that under conventional split Hopkins pressure bar loading conditions (~104 s-1). It has been found that the dynamic fracture toughness of an aluminum alloy is significantly enhanced during the electromagnetic forming, which explains why the formability is much larger under electromagnetic forging conditions in comparison with conventional forging processes. [ABSTRACT FROM AUTHOR]