Abstract: The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273CT284R, R273HT284R, and R273HS240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273CT284R, R273HT284R and R273HS240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer.

Abstract: Ferropericlase (fPer) inclusions from kimberlitic lower-mantle diamonds recovered in the Juina area, Mato Grosso State, Brazil were analyzed with transmission electron microscopy, electron energy-loss spectroscopy and the flank method. The presence of exsolved non-stoichiometric Fe3+-enriched clusters, varying in size from 1-2 nm to 10-15 nm and comprising similar to 3.64 vol.% of fPer was established. The oxidation conditions necessary for fPer formation within the uppermost lower mantle (P = 25 GPa, T = 1960 K) vary over a wide range: Delta log f(o2) (IW) from 1.58 to 7.76 (Delta = 6.2), reaching the fayalite-magnetite-quartz (FMQ) oxygen buffer position. This agrees with the identification of carbonates and free silica among inclusions within lower-mantle Juina diamonds. On the other hand, at the base of the lower mantle Delta log f(o2) values may lie at and below the iron-wustite (IW) oxygen buffer. Hence, the variations of Delta log f(o2) values within the entire sequence of the lower mantle may reach ten logarithmic units, varying from the IW buffer to the FMQ buffer values. The similarity between lower- and upper-mantle redox conditions supports whole mantle convection, as already suggested on the basis of nitrogen and carbon isotopic compositions in lower- and upper-mantle diamonds. The mechanisms responsible for redox differentiation in the lower mantle may include subduction of oxidized crustal material, mechanical separation of metallic phase(s) and silicate-oxide mineral assemblages enriched in ferric iron, as well as transfer of fused silicate-oxide material presumably also enriched in ferric iron through the mantle. (C) 2015 Elsevier B.V. All rights reserved.

Abstract: Various theoretical and experimental methods are utilized to investigate the thermal conductivity of nanostructured materials; this is a critical parameter to increase performance of thermoelectric devices. Among these methods, equilibrium molecular dynamics (EMD) is an accurate technique to predict lattice thermal conductivity. In this study, by means of systematic EMD simulations, thermal conductivity of bulk Si-Ge structures (pristine, alloy and superlattice) and their nanostructured one dimensional forms with square and circular cross-section geometries (asymmetric and symmetric) are calculated for different crystallographic directions. A comprehensive temperature analysis is evaluated for selected structures as well. The results show that one-dimensional structures are superior candidates in terms of their low lattice thermal conductivity and thermal conductivity tunability by nanostructuring, such as by diameter modulation, interface roughness, periodicity and number of interfaces. We find that thermal conductivity decreases with smaller diameters or cross section areas. Furthermore, interface roughness decreases thermal conductivity with a profound impact. Moreover, we predicted that there is a specific periodicity that gives minimum thermal conductivity in symmetric superlattice structures. The decreasing thermal conductivity is due to the reducing phonon movement in the system due to the effect of the number of interfaces that determine regimes of ballistic and wave transport phenomena. In some nanostructures, such as nanowire superlattices, thermal conductivity of the Si/Ge system can be reduced to nearly twice that of an amorphous silicon thermal conductivity. Additionally, it is found that one crystal orientation, <100>, is better than the <111> crystal orientation in one-dimensional and bulk SiGe systems. Our results clearly point out the importance of lattice thermal conductivity engineering in bulk and nanostructures to produce high-performance thermoelectric materials.

Abstract: Nitrogenated holey graphene (NHG) is a recently synthesized two-dimensional material. In this paper the structural and electronic properties of heterostructures of graphene and NHG are investigated using first-principles and tight-binding calculations. Due to the lattice mismatch between NHG and graphene, the formation of a moire pattern is preferred in the graphene/NHG heterostructure, instead of a lattice-coherent structure. In moire-patterned graphene/NHG, the band gap opening at the K point is negligible, and the linear band dispersion of graphene survives. Applying an electric field modifies the coupling strength between the two atomic layers. The Fermi velocity upsilon(F) is reduced as compared to the one of pristine graphene, and its magnitude depends on the twist angle theta between graphene and NHG: For theta = 0 degrees, upsilon(F) is 30% of that of graphene, and it increases rapidly to a value of 80% with increasing theta. The heterostructure exhibits electron-hole asymmetry in upsilon(F), which is large for small theta. In NHG encapsulated between two graphene layers, a “Dirac ring” appears around the K point. Its presence is robust with respect to the relative stacking of the two graphene layers. These findings can be useful for future applications of graphene/NHG heterostructures.

Abstract: To determine and control the spatial confinement of charge carriers is of importance for nanoscale optoelectronic device applications. Using first-principles calculations, we investigate the tunability of band alignment and Charge localization in lateral and combined lateral vertical heterostructures of MoS2 and WS2. First, we Show that a type-II to type-I band alignment transition takes place when tensile strain is applied on the WS2 region. This band alignment transition is a result of the different response of the band edge states with strain and is caused by their different wave function characters. Then we show that the presence of the grain boundary introduces localized in-gap states. The boundary at the armchair interface significantly modifies the charge distribution of the valence band maximum (VBM) state, whereas in a heterostructure with tilt grain domains both conducation band maximum (CBM) and VBM are found to be localized around the grain boundary. We also found that the thickness of the constituents in a lateral heterostructure also determines how the electrons and holes are confined. Creating combined lateral vertical heterostructures of MOS2/WS2 provides another way cif tuning the charge confinement. These results provide possible ways to tune the carrier confinement in MoS2/WS2 heterostructures, which are interesting for its practical: applications in the future.

Abstract: Despite numerous attempts to use human mesenchymal stem cells (hMSCs) in the field of tissue engineering, the control of their differentiation remains challenging. Here, we investigated possible applications of a non-thermal atmospheric pressure plasma jet (NTAPPJ) to control the differentiation of hMSCs. An air- or nitrogen-based NTAPPJ was applied to hMSCs in culture media, either directly or by media treatment in which the cells were plated after the medium was exposed to the NTAPPJ. The durations of exposure were 1, 2, and 4 min, and the control was not exposed to the NTAPPJ. The initial attachment of the cells was assessed by a water-soluble tetrazolium assay, and the gene expression in the cells was assessed through reverse-transcription polymerase chain reaction and immunofluorescence staining. The results showed that the gene expression in the hMSCs was generally increased by the NTAPPJ exposure, but the enhancement was dependent on the conditions of the exposure, such as the source of the gas and the treatment method used. These results were attributed to the chemicals in the extracellular environment and the reactive oxygen species generated by the plasma. Hence, it was concluded that by applying the best conditions for the NTAPPJ exposure of hMSCs, the control of hMSC differentiation was possible, and therefore, exposure to an NTAPPJ is a promising method for tissue engineering.

Abstract: Group IV based tunnel field-effect transistors generally show lower on-current than III-V based devices because of the weaker phonon-assisted tunneling transitions in the group IV indirect bandgap materials. Direct tunneling in Ge, however, can be enhanced by strain engineering. In this work, we use a 30-band k.p method to calculate the band structure of biaxial tensile strained Ge and then extract the bandgaps and effective masses at Gamma and L symmetry points in k-space, from which the parameters for the direct and indirect band-to-band tunneling (BTBT) models are determined. While transitions from the heavy and light hole valence bands to the conduction band edge at the L point are always bridged by phonon scattering, we highlight a new finding that only the light-holelike valence band is strongly coupling to the conduction band at the Gamma point even in the presence of strain based on the 30-band k.p analysis. By utilizing a Technology Computer Aided Design simulator equipped with the calculated band-to-band tunneling BTBT models, the electrical characteristics of tensile strained Ge point and line tunneling devices are self-consistently computed considering multiple dynamic nonlocal tunnel paths. The influence of field-induced quantum confinement on the tunneling onset is included. Our simulation predicts that an on-current up to 160 (260) mu A/mu m can be achieved along with on/off ratio > 10(6) for V-DD = 0.5V by the n-type (p-type) line tunneling device made of 2.5% biaxial tensile strained Ge. (C) 2014 AIP Publishing LLC.

Abstract: We develop an analytical model for a tunnel field-effect transistor (TFET) with a tilted source junction angle. The tunnel current is derived by using circular tunnel paths along the electric field. The analytical model predicts that a smaller junction angle improves the TFET performance, which is supported by device simulations. An analysis is also made based on straight tunnel paths and tunnel paths corresponding to the trajectory of a classical particle. In all the aforementioned cases, the same conclusions are obtained. A TFET configuration with an encroaching polygon source junction is studied to analyze the junction angle dependence at the smallest junction angles. The improvement of the subthreshold swing (SS) with decreasing junction angle can be achieved by using thinner effective oxide thickness, smaller band gap material and longer encroaching length of the encroaching junction. A TFET with a smaller junction angle on the source side also has an innate immunity against the degradation of the fringing field from the gate electrode via a high-k spacer. A large junction angle on the drain side can suppress the unwanted ambipolar current of TFETs. (c) 2011 Elsevier Ltd. All rights reserved.

Abstract: Recent advances in manufacturing arrays of artificial pinning sites, i.e., antidots, blind holes and magnetic dots, allowed an effective control of magnetic flux in superconductors. An array of magnetic bars deposited on top of a superconducting film was shown to display different pinning regimes depending on the direction of the in-plane magnetization of the bars. Changing the sign of their magnetization results in changes in the induced magnetic pinning potentials. By numerically solving the time-dependent Ginzburg-Landau equations in a superconducting film with periodic arrays of zigzag-arranged magnetic bars, we revealed various flux dynamics regimes. In particular, we demonstrate flux pinning and flux flow, depending on the direction of the magnetization of the magnetic bars. Remarkably, the revealed different flux-motion regimes are associated with different mechanisms of vortex-antivortex dynamics. For example, we found that for an 'antiparallel' configuration of magnetic bars this dynamics involves a repeating vortex-antivortex generation and annihilation. We show that the depinning transition and the onset of flux flow can be manipulated by the magnetization of the bars and the geometry of the array. This provides an effective control of the depinning critical current that can be useful for possible fluxonics applications.

Abstract: By numerically solving the time-dependent Ginzburg-Landau equations in a type-II superconductor, characterized by a critical temperature T-c1, and the coherence length xi(1), with a channel formed by overlapping rhombuses (diamond-like channel) made of another type-II superconductor, characterized, in general, by different T-c2 and xi(2), we investigate the dynamics of driven vortex matter for varying parameters of the channel: the width of the neck connecting the diamond cells, the cell geometry, and the ratio between the coherence lengths in the bank and the channel. We analyzed samples with periodic boundary conditions (which we call 'infinite' samples) and finite-size samples (with boundaries for vortex entry/exit), and we found that by tuning the channel parameters, one can manipulate the vortex dynamics, e.g., change the transition from flux-pinned to flux-flow regime and tune the slope of the IV-curves. In addition, we analyzed the effect of interstitial vortices on these characteristics. The critical current of this device was studied as a function of the applied magnetic field, j(c)(H). The function j(c)(H) reveals a striking commensurability peak, in agreement with recent experimental observations. The obtained results suggest that the diamond channel, which combines the properties of pinning arrays and flux-guiding channels, can be a promising candidate for potential use in devices controlling magnetic flux motion.

Abstract: Efficient thermal transport control is a fundamental issue for electronic device applications such as information, communication, and energy storage technologies in modern electronics in order to achieve desired thermal conditions. Structural defects in materials provide a mechanism to adjust the thermal transport properties of these materials on demand. In this context, the effect of structural defects on lattice thermal conductivities of two-dimensional hexagonal binary group-III nitride (XN, X = B, Al, and Ga) semiconductors is systematically investigated by means of classical molecular dynamics simulations performed with recently developed transferable inter-atomic potentials accurately describing defect energies. Here, two different Green-Kubo based approaches and another approach based on non-equilibrium molecular dynamics are compared in order to get an overall understanding. Our investigation clearly shows that defect concentrations of 3% decrease the thermal conductivity of systems containing these nitrites up to 95%. Results hint that structural defects can be used as effective adjustment parameters in controlling thermal transport properties in device applications associated with these materials. Published under an exclusive license by AIP Publishing.

Abstract: Determination of count losses and pile-up pulse effects in quantitative and qualitative analysis became a vital step in various analyses. Therefore, compensating for counting losses is of importance. These counting losses are due to the pulse pile-up, paralyzable and non-paralyzable system dead time or a combination of these mechanisms. In this work, a new method is suggested for the correction of dead time losses resulting from the above mechanisms. For this purpose, a source code was developed. It was found that the peaking time was an important parameter over system dead time. The method suggested seems to be more effective even at high count rate. (C) 2009 Elsevier B.V. All rights reserved.