Molecular Dynamics Simulation Study of Single DNA Nucleotides Transport Through Nanoslits

There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with 2 or more detectors. Molecular dynamics simulation of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits was performed. Electric field strength (E) varied from 0.0 to 0.6 V/nm. Slit walls were smooth or had a roughness similar to nucleotide size. Multiple nucleotide-wall adsorptions occurred. The electric field did not influence the nucleotide adsorption and desorption mechanism for E ¡Ü 0.1 V/nm, but influenced nucleotide orientation relative to the field direction. The nucleotide-wall interactions differed due to nucleotide hydrophobicities and wall roughness, and determined duration and frequency of nucleotide adsorptions and their velocities while adsorbed. Transient association of nucleotides with 1 to 3 sodium ions occurred but the mean association numbers (AN) were weak functions of nucleotide type. ANs for pyrimidine nucleotides were slightly lower than for purine nucleotides. Nucleotide-wall interactions contributed more to separation of nucleotide flight time distributions than ion association. A PMMA slab was built and a CHARMM force field file modified from the force field for a PMMA trimer was verified and then utilized to study the transport of dNMPs through PMMA nanoslits. The simulation studies show that, while moving along the PMMA nanoslit the mononucleotides are adsorbed and desorbed from the walls multiple times. Due to their strong interaction with the PMMA walls the mononucleotides can be trapped in adsorbed state for hundreds of nanoseconds. When dNMPs are in the desorbed state, their traveling velocity along the axis of the nanochannel is mainly affected by the association between Na+ and the phosphate group. The Brownian MD simulation studies show that, the main characteristics of the mononucleotides through a nanochannel can be obtained by performing simulations of the dNMPs-PMMA wall system using a coarse-grained representation of the system. The accuracy of this method depends on the accuracy of the potential of mean force used to describe the interaction between dNMP and the PMMA wall

Shot noise in magnetic tunnel junctions from first principles

We compute the shot noise in ballistic and disordered Fe/MgO/Fe tunnel junctions by a wave function-matching method. For tunnel barriers with no more than 5 atomic layers we find a suppression of the Fano factor as a function of the magnetic configuration. For thicker MgO barriers the shot noise is suppressed up to a threshold bias indicating the onset of resonant tunneling. We find excellent agreement with recent experiments when interface disorder is taken into accountComment: 5 pages,5 figure

Enhanced visibility of graphene: effect of one-dimensional photonic crystal

We investigate theoretically the light reflectance of a graphene layer prepared on the top of one-dimensional Si/SiO2 photonic crystal (1DPC). It is shown that the visibility of the graphene layers is enhanced greatly when 1DPC is added, and the visibility can be tuned by changing the incident angle and light wavelengths. This phenomenon is caused by the absorption of the graphene layer and the enhanced reflectance of the 1DPC.Comment: 4 pages, 4 figures. published, ApplPhysLett_91_18190

On Uniqueness of Participation Factors

In modal analysis and control of a nonlinear dynamical system, participation factors of state variables with respect to a mode of interest serve as pivotal tools for stability studies. Linear participation factors are uniquely determined by the mode's shape and composition, which are defined by the right and left eigenvectors of the linearized model. For nonlinear participation factors as well as five other variants of participation factors, this paper finds the sufficient conditions for them to be unique against scaling factors on the shape and composition of a mode. Besides, the similarity between the scaling factor and perturbation amplitude is also discussed

Effect of Prandtl number on heat transport enhancement in Rayleigh-B\'enard convection under geometrical confinement

We study, using direct numerical simulations, the effect of geometrical confinement on heat transport and flow structure in Rayleigh-B\'enard convection in fluids with different Prandtl numbers. Our simulations span over two decades of Prandtl number $Pr$, $0.1 \leq Pr \leq 40$, with the Rayleigh number $Ra$ fixed at $10^8$. The width-to-height aspect ratio $\Gamma$ spans between $0.025$ and $0.25$ while the length-to-height aspect ratio is fixed at one. We first find that for $Pr \geq 0.5$, geometrical confinement can lead to a significant enhancement in heat transport as characterized by the Nusselt number $Nu$. For those cases, $Nu$ is maximal at a certain $\Gamma = \Gamma_{opt}$. It is found that $\Gamma_{opt}$ exhibits a power-law relation with $Pr$ as $\Gamma_{opt}=0.11Pr^{-0.06}$, and the maximal relative enhancement generally increases with $Pr$ over the explored parameter range. As opposed to the situation of $Pr \geq 0.5$, confinement-induced enhancement in $Nu$ is not realized for smaller values of $Pr$, such as $0.1$ and $0.2$. The $Pr$ dependence of the heat transport enhancement can be understood in its relation to the coverage area of the thermal plumes over the thermal boundary layer (BL) where larger coverage is observed for larger $Pr$ due to a smaller thermal diffusivity. We further show that $\Gamma_{opt}$ is closely related to the crossing of thermal and momentum BLs, and find that $Nu$ declines sharply when the thickness ratio of the thermal and momentum BLs exceeds a certain value of about one. In addition, through examining the temporally averaged flow fields and 2D mode decomposition, it is found that for smaller $Pr$ the large-scale circulation is robust against the geometrical confinement of the convection cell.Comment: 25 pages, 11 figures, and 1 table in main tex