Size-dependent trajectories of DNA macromolecules due to insulative dielectrophoresis in submicrometer-deep fluidic channels.

In this paper, we demonstrate for the first time that insulative dielectrophoresis can induce size-dependent trajectories of DNA macromolecules. We experimentally use lambda (48.5 kbp) and T4GT7 (165.6 kbp) DNA molecules flowing continuously around a sharp corner inside fluidic channels with a depth of 0.4 mum. Numerical simulation of the electrokinetic force distribution inside the channels is in qualitative agreement with our experimentally observed trajectories. We discuss a possible physical mechanism for the DNA polarization and dielectrophoresis inside confining channels, based on the observed dielectrophoresis responses due to different DNA sizes and various electric fields applied between the inlet and the outlet. The proposed physical mechanism indicates that further extensive investigations, both theoretically and experimentally, would be very useful to better elucidate the forces involved at DNA dielectrophoresis. When applied for size-based sorting of DNA molecules, our sorting method offers two major advantages compared to earlier attempts with insulative dielectrophoresis: Its continuous operation allows for high-throughput analysis, and it only requires electric field strengths as low as approximately 10 Vcm.

The effect of carbon encapsulation on the magnetic properties of Ni nanoparticles produced by arc discharge in de-ionized water

Despite intensive research on optimizing the methods for depositing carbon encapsulated ferromagnetic nanoparticles, the effect of the carbon cages remains unclear. In the present work, the effect of the graphitic cages on the magnetization of the ferromagnetic core has been studied by comparing the magnetic properties of pure and carbon encapsulated Ni particles of the same size. The carbon encapsulated Ni particles were formed using an electric arc discharge in de-ionized water between a solid graphite cathode and an anode consisting of Ni and C in a mass ratio of Ni:C = 7:3. This method is shown to have potential for low cost production of carbon encapsulated Ni nanoparticle samples with narrow particle size distributions. X-ray diffraction (XRD) and high resolution transmission electron microscopy (HRTEM) analysis were used to study the crystallography, morphology, and size distribution of the encapsulated and pure Ni nanoparticle samples. The availability of encapsulated particles with various sizes allowed us to elucidate the role of carbon cages in size-dependent properties. Our data suggest that even though encapsulation is beneficial for protection against hostile chemical environments and for avoiding low proximity phenomena, it suppresses the saturation magnetization of the Ni cores.

Flux closure vortexlike domain structures in ferroelectric thin films

Enhanced piezoresponse force microscopy was used to study flux closure vortexlike structures of 90° ferroelastic domains at the nanoscale in thin ferroelectric lead zirconium titanate (PZT) films. Using an external electric field, a vortexlike structure was induced far away from a grain boundary, indicating that physical edges are not necessary for nucleation contrary to previous suggestions. We demonstrate two different configurations of vortexlike structures, one of which has not been observed before. The stability of these structures is found to be size dependent, supporting previous predictions. © 2010 The American Physical Society.

Tunable electronic transport characteristics of surface-architecture-controlled ZnO nanowire field effect transistors.

Surface-architecture-controlled ZnO nanowires were grown using a vapor transport method on various ZnO buffer film coated c-plane sapphire substrates with or without Au catalysts. The ZnO nanowires that were grown showed two different types of geometric properties: corrugated ZnO nanowires having a relatively smaller diameter and a strong deep-level emission photoluminescence (PL) peak and smooth ZnO nanowires having a relatively larger diameter and a weak deep-level emission PL peak. The surface morphology and size-dependent tunable electronic transport properties of the ZnO nanowires were characterized using a nanowire field effect transistor (FET) device structure. The FETs made from smooth ZnO nanowires with a larger diameter exhibited negative threshold voltages, indicating n-channel depletion-mode behavior, whereas those made from corrugated ZnO nanowires with a smaller diameter had positive threshold voltages, indicating n-channel enhancement-mode behavior.

Magnetization process of a single chain of nanomagnets

We have investigated the magnetization reversal process of a single chain of identical nanomagnetic dots fabricated from 30 nm thick Ni 80Fe20. The structures consist of two 5 μm wide support wires bridged with a single chain of identical dots of diameter δ in the range 100-250 nm. For fields applied perpendicular to the single chain, we observed an unusual size dependent hysteretic behavior in the magnetoresistance curve at high field. This is due to the magnetostatic interaction arising from the proximity of the magnetic charges. We are able to deduce from a simple micromagnetic simulation that the reversal process in the chain of dots with δ=100nm is mediated by a collective process of nearly coherent spin rotation. The magnetotransport measurements along the chain reveal a complex magnetization reversal process in the chain of nanomagnets. © 2002 American Institute of Physics.

Optimal inference of sameness.

Deciding whether a set of objects are the same or different is a cornerstone of perception and cognition. Surprisingly, no principled quantitative model of sameness judgment exists. We tested whether human sameness judgment under sensory noise can be modeled as a form of probabilistically optimal inference. An optimal observer would compare the reliability-weighted variance of the sensory measurements with a set size-dependent criterion. We conducted two experiments, in which we varied set size and individual stimulus reliabilities. We found that the optimal-observer model accurately describes human behavior, outperforms plausible alternatives in a rigorous model comparison, and accounts for three key findings in the animal cognition literature. Our results provide a normative footing for the study of sameness judgment and indicate that the notion of perception as near-optimal inference extends to abstract relations.

Evaluating boundary dependent errors in QM/MM simulations.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant.

The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-Dependent RNA Polymerase 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth. Nearly all known miRNAs were enriched in this mutant and we identified 13 new miRNAs, all of which were relatively low abundance and constitute new families. Trans-acting siRNAs (ta-siRNAs) were even more highly enriched. Computational and gel blot analyses suggested that the minimal number of miRNAs in Arabidopsis is approximately 155. The size profile of small RNAs in rdr2 reflected enrichment of 21-nt miRNAs and other classes of siRNAs like ta-siRNAs, and a significant reduction in 24-nt heterochromatic siRNAs. Other classes of small RNAs were found to be RDR2-independent, particularly those derived from long inverted repeats and a subset of tandem repeats. The small RNA populations in other Arabidopsis small RNA biogenesis mutants were also examined; a dcl2/3/4 triple mutant showed a similar pattern to rdr2, whereas dcl1-7 and rdr6 showed reductions in miRNAs and ta-siRNAs consistent with their activities in the biogenesis of these types of small RNAs. Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs.

Size effects in indentation of hydrated biological tissues

Fluid flow in biological tissues is important in both mechanical and biological contexts. Given the hierarchical nature of tissues, there are varying length scales at which time-dependent mechanical behavior due to fluid flow may be exhibited. Here, spherical nanoindentation and microindentation testings are used for the characterization of length scale effects in the mechanical response of hydrated tissues. Although elastic properties were consistent across length scales, there was a substantial difference between the time-dependent mechanical responses for large and small contact radii in the same tissue specimens. This difference was far more obvious when poroelastic analysis was used instead of viscoelastic analysis. Overall, indentation testing is a fast and robust technique for characterizing the hierarchical structure of biological materials from nanometer to micrometer length scales and is capable of making quantitative material property measurements to do with fluid flow. © 2011 Materials Research Society.

Size effects in the conical indentation of an elasto-plastic solid

The size effect in conical indentation of an elasto-plastic solid is predicted via the Fleck and Willis formulation of strain gradient plasticity (Fleck, N.A. and Willis, J.R., 2009, A mathematical basis for strain gradient plasticity theory. Part II: tensorial plastic multiplier, J. Mech. Phys. Solids, 57, 1045-1057). The rate-dependent formulation is implemented numerically and the full-field indentation problem is analyzed via finite element calculations, for both ideally plastic behavior and dissipative hardening. The isotropic strain-gradient theory involves three material length scales, and the relative significance of these length scales upon the degree of size effect is assessed. Indentation maps are generated to summarize the sensitivity of indentation hardness to indent size, indenter geometry and material properties (such as yield strain and strain hardening index). The finite element model is also used to evaluate the pertinence of the Johnson cavity expansion model and of the Nix-Gao model, which have been extensively used to predict size effects in indentation hardness. © 2012 Elsevier Ltd.