Nanoscale Structure and Elasticity of Pillared DNA Nanotubes

We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically by two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. We calculate the persistence length of these nanotubes from their equilibrium bend angle distributions. The values of persistence length are ~10 {\mu}m, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes we carried out nonequilibrium Steered Molecular Dynamics (SMD). The linear part of the force extension plot gives stretch modulus in the range of 6500 pN for 6HB without pillars which increases to 11,000 pN for tubes with three pillars. The values of the stretch modulus calculated from contour length distributions obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.Comment: Published in ACS Nan

Micellar Aggregates of Gemini Surfactants: Monte Carlo Simulation of a Microscopic Model

We propose a "microscopic" model of gemini surfactants in aqueous solution. Carrying out extensive Monte Carlo simulations, we study the variation of the critical micellar concentration (CMC) of these model gemini surfactants with the variation of the (a) length of the spacer connecting the two hydrophilic heads, (b) length of the hydrophobic tail and (c) the bending rigidity of the hydrocarbon chains forming the spacer and the tail; some of the trends of variation are counter-intuitive but are in excellent agreement with the available experimental results. Our simulations also elucidate the dependence of the shapes of the micellar aggregates and the magnitude of the CMC on the geometrical shape and size of the surfactant molecules and the electrical charge on the hydrophilic heads

PTEN negatively regulates mTORC2 formation and signaling in grade IV glioma via Rictor hyperphosphorylation at Thr1135 and direct the mode of action of an mTORC1/2 inhibitor

To investigate the role of PTEN (phosphatase and tensin homolog) in mammalian target of rapamycin complex 2 (mTORC2) signaling in glioblastoma multiforme (GBM), we found higher activation of mTORC2 in PTENmu cells, as evidenced by enhanced phosphorylation of mTOR (Ser2481), AKT (Ser473) and glycogen synthase kinase 3 beta (GSK3β) (Ser9) as compared with PTENwt cells. In addition, PTENwt cells upon PTEN depletion showed mTORC2 activation. The reduced mTORC2 signaling in PTENwt cells was related to higher Rictor phosphorylation at Thr1135 residue. Phosphorylation of Rictor at Thr1135 inhibited its association with mTORC and thus there was a reduction in mTORC2 complex formation. In addition, PTENwt cells expressing mutated Rictor in which Thr1135 was substituted with alanine, showed enhanced mTORC2 formation and signaling. This enhanced mTORC2 signaling promoted inactivation of GSK3β. Thus, we established the reciprocal activation of mTORC2 and GSK3β in GBM. To the best of our knowledge, this is the first report describing role of PTEN in mTORC2 formation by promoting Rictor phosphorylation (Thr1135) in GBM. Furthermore, the drug sensitivity of mTORC2 was evaluated. A newly identified carbazole alkaloid, mahanine, showed cytotoxicity in both PTENmu and PTENwt cells. It inhibited both mTORC1/2 and AKT completely in PTENmu cells, whereas it inhibited only mTORC1 in PTENwt cells. Cytotoxity and AKT-inhibitory activity of the mTORC1/2 inhibitor was increased either by depleting PTEN or in combination with phosphatidylinositol 3 kinase inhibitors in PTENwt cells. In contrast, depletion of Rictor decreased the cytotoxicity of the mTORC1/2 inhibitor in PTENmu cells. Thus, PTEN has an important role in mTORC2 formation and also influences the effectiveness of an mTORC1/2 inhibitor in GBM

Magneto-transport in a quantum network: Evidence of a mesoscopic switch

We investigate magneto-transport properties of a $\theta$ shaped three-arm mesoscopic ring where the upper and lower sub-rings are threaded by Aharonov-Bohm fluxes $\phi_1$ and $\phi_2$, respectively, within a non-interacting electron picture. A discrete lattice model is used to describe the quantum network in which two outer arms are subjected to binary alloy lattices while the middle arm contains identical atomic sites. It is observed that the presence of the middle arm provides localized states within the band of extended regions and lead to the possibility of switching action from a high conducting state to a low conducting one and vice versa. This behavior is justified by studying persistent current in the network. Both the total current and individual currents in three separate branches are computed by using second-quantized formalism and our idea can be utilized to study magnetic response in any complicated quantum network. The nature of localized eigenstates are also investigated from probability amplitudes at different sites of the quantum device.Comment: 7 pages, 9 figure

Finite temperature magnetism in Gd: evidence against a Stoner behavior

The temperature dependence of the rare-earth valence bands has been regarded as a realization of the Stoner behavior. The exchange splitting of the electronic states appears to scale as the magnetic order parameter for T<TC and to vanish at T = TC. We report here a spin-resolved photoemission study on the evolution of Gd bulk bands for 0.5≤ T/TC≤ 1. The spin-polarized spectral line shapes display a complex temperature dependence, which clearly contrasts with the interpretation of previous experimental results. The spin-resolved photoemission data demonstrate the inadequacy of the Stoner model to the description of magnetism in rare earths

Stoner vs. spin-mixing behavior in the bulk magnetism of Gd: a spin-resolved photoemission study

The temperature dependence of the rare-earth Δ2-bulk band has been regarded as an exemplary case which realizes the simple Stoner behavior. We examined the evolution of GdΔ2 bulk bands with temperature in the range 0.5≤ T/TC≤ 1 with spin-resolved, photoemission spectroscopy. The direct observation of the spin-dependent spectral line shapes reveals a complex temperature dependence and manifests a clear inadequacy of the Stoner model to the description of the magnetism in rare earths

Structure of poly(propyl ether imine) (PETIM) dendrimer from fully atomistic molecular Dynamics Simulation and by Small Angle X-ray scattering

We study the structure of carboxylic acid terminated neutral poly (propyl ether imine) (PETIM) dendrimer from generation 1 through 6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation such structural properties as: radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by Small Angle X-Ray Scattering (SAXS) experiment on dendrimer of generation 2 to 4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as ~ N^x with the number of monomers. We find two distinct exponents depending on the generations: x = 0.47 for G1-G3 and x = 0.28 for G3-G6 which reveals their non-space filling nature. In comparison with the amine terminated PAMAM dendrimer, we find Rg of G-th generation PETIM dendrimer is nearly equal to that of (G+1)-th generation of PAMAM dendrimer as observed by Maiti et. al. [Macromolecules,38, 979 2005]. We find substantial back folding of the outer sub generations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules suggesting using PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.Comment: 33 page