Simulations of the synthesis of boron-nitride nanostructures in a hot, high pressure gas volume.

We performed nanosecond timescale computer simulations of clusterization and agglomeration processes of boron nitride (BN) nanostructures in hot, high pressure gas, starting from eleven different atomic and molecular precursor systems containing boron, nitrogen and hydrogen at various temperatures from 1500 to 6000 K. The synthesized BN nanostructures self-assemble in the form of cages, flakes, and tubes as well as amorphous structures. The simulations facilitate the analysis of chemical dynamics and we are able to predict the optimal conditions concerning temperature and chemical precursor composition for controlling the synthesis process in a high temperature gas volume, at high pressure. We identify the optimal precursor/temperature choices that lead to the nanostructures of highest quality with the highest rate of synthesis, using a novel parameter of the quality of the synthesis (PQS). Two distinct mechanisms of BN nanotube growth were found, neither of them based on the root-growth process. The simulations were performed using quantum-classical molecular dynamics (QCMD) based on the density-functional tight-binding (DFTB) quantum mechanics in conjunction with a divide-and-conquer (DC) linear scaling algorithm, as implemented in the DC-DFTB-K code, enabling the study of systems as large as 1300 atoms in canonical NVT ensembles for 1 ns time.

DNA translocating through a carbon nanotube can increase ionic current.

Translocation of DNA through a narrow, single-walled carbon nanotube can be accompanied by large increases in ion current, recently observed in contrast to the ion current blockade. We use molecular dynamics simulations to show that large electro-osmotic flow can be turned into a large net current via ion-selective filtering by a DNA molecule inside the carbon nanotube.

Stability of an aqueous quadrupole micro-trap.

The recently demonstrated functionality of an aqueous quadrupole micro- or nano-trap opens a new avenue for applications of Paul traps, like confinement of a charged biomolecule which requires a water environment for its chemical stability. Besides the strong viscosity forces, the motion of a charged particle in the aqueous trap is subject to dielectrophoretic and electrophoretic forces. In this study, we describe the general conditions for stability of a charged particle in an aqueous quadrupole trap. We find that for typical micro-trap parameters, the effects of both dielectrophoresis and electrophoresis significantly influence the trap stability. In particular, an aqueous quadrupole trap could play the role of a synthetic virtual nanopore for the third generation of DNA sequencing technology.

Detection of hydrogen using graphene.

Irradiation dynamics of a single graphene sheet bombarded by hydrogen atoms is studied in the incident energy range of 0.1 to 200 eV. Results for reflection, transmission, and adsorption probabilities, as well as effects of a single adsorbed atom to the electronic properties of graphene, are obtained by the quantum-classical Monte Carlo molecular dynamics within a self-consistent-charge-density functional tight binding formalism We compare these results with those, distinctly different, obtained by the classical molecular dynamics.PACS: 61.80.Az, 61.48.Gh, 61.80.Jh, 34.50.Dy.

Thermal noise in aqueous quadrupole micro- and nano-traps.

Recent simulations and experiments with aqueous quadrupole micro-traps have confirmed a possibility for control and localization of motion of a charged particle in a water environment, also predicting a possibility of further reduction of the trap size to tens of nano-meters for trapping charged bio-molecules and DNA segments. We study the random thermal noise due to Brownian motion in water which significantly influences the trapping of particles in an aqueous environment. We derive the exact, closed-form expressions for the thermal fluctuations of position and velocity of a trapped particle and thoroughly examine the properties of the rms for the fluctuations as functions of the system parameters and time. The instantaneous signal transferring mechanism between the velocity and position fluctuations could not be achieved in the previous phase-average approaches.

Tunable aqueous virtual micropore.

A charged microparticle can be trapped in an aqueous environment by forming a narrow virtual pore--a cylindrical space region in which the particle motion in the radial direction is limited by forces emerging from dynamical interactions of the particle charge and dipole moment with an external radiofrequency quadrupole electric field. If the particle satisfies the trap stability criteria, its mean motion is reduced exponentially with time due to the viscosity of the aqueous environment; thereafter the long-time motion of particle is subject only to random, Brownian fluctuations, whose magnitude, influenced by the electrophoretic and dielectrophoretic effects and added to the particle size, determines the radius of the virtual pore, which is demonstrated by comparison of computer simulations and experiment. The measured size of the virtual nanopore could be utilized to estimate the charge of a trapped micro-object.

Origin of giant ionic currents in carbon nanotube channels.

Fluid flow inside carbon nanotubes is remarkable: transport of water and gases is nearly frictionless, and the small channel size results in selective transport of ions. Very recently, devices have been fabricated in which one narrow single-walled carbon nanotube spans a barrier separating electrolyte reservoirs. Ion current through these devices is about 2 orders of magnitude larger than predicted from the bulk resistivity of the electrolyte. Electroosmosis can drive these large excess currents if the tube both is charged and transports anions or cations preferentially. By building a nanofluidic field-effect transistor with a gate electrode embedded in the fluid barrier, we show that the tube carries a negative charge and the excess current is carried by cations. The magnitude of the excess current and its control by a gate electrode are correctly predicted by the Poisson-Nernst-Planck-Stokes equations.

Paul trapping of charged particles in aqueous solution.

We experimentally demonstrate the feasibility of an aqueous Paul trap using a proof-of-principle planar device. Radio frequency voltages are used to generate an alternating focusing/defocusing potential well in two orthogonal directions. Individual charged particles are dynamically confined into nanometer scale in space. Compared with conventional Paul traps working in frictionless vacuum, the aqueous environment associated with damping forces and thermally induced fluctuations (Brownian noise) exerts a fundamental influence on the underlying physics. We investigate the impact of these two effects on the confining dynamics, with the aim to reduce the rms value of the positional fluctuations. We find that the rms fluctuations can be modulated by adjusting the voltages and frequencies. This technique provides an alternative for the localization and control of charged particles in an aqueous environment.

Non-vanishing ponderomotive AC electrophoretic effect for particle trapping.

We present here a study on overlooked aspects of alternating current (AC) electrokinetics-AC electrophoretic (ACEP) phenomena. The dynamics of a particle with both polarizability and net charges in a non-uniform AC electric trapping field is investigated. It is found that either electrophoretic (EP) or dielectrophoretic (DEP) effects can dominate the trapping dynamics, depending on experimental conditions. A dimensionless parameter γ is developed to predict the relative strength of EP and DEP effects in a quadrupole AC field. An ACEP trap is feasible for charged particles in 'salt-free' or low salt concentration solutions. In contrast to DEP traps, an ACEP trap favors the downscaling of the particle size.

A long DNA segment in a linear nanoscale Paul trap.

We study the dynamics of a linearly distributed line charge such as single stranded DNA (ssDNA) in a nanoscale, linear 2D Paul trap in vacuum. Using molecular dynamics simulations we show that a line charge can be trapped effectively in the trap for a well defined range of stability parameters. We investigated (i) a flexible bonded string of charged beads and (ii) a ssDNA polymer of variable length, for various trap parameters. A line charge undergoes oscillations or rotations as it moves, depending on its initial angle, the position of the center of mass and the velocity. The stability region for a strongly bonded line of charged beads is similar to that of a single ion with the same charge to mass ratio. Single stranded DNA as long as 40 nm does not fold or curl in the Paul trap, but could undergo rotations about the center of mass. However, we show that a stretching field in the axial direction can effectively prevent the rotations and increase the confinement stability.

The potential and challenges of nanopore sequencing.

A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for approximately $1,000 in approximately 24 h.

Enhancement of the transverse conductance in DNA nucleotides.

We theoretically study the electron transport properties of DNA nucleotides placed in the gap between two single-wall carbon nanotubes capped or terminated with H or N. We show that in the case of C-cap and H-termination the current at low electric bias is dominated by nonresonant tunneling, similarly to the cases of gold electrodes. In nitrogen-terminated nanotube electrodes, the nature of current is primarily quasiresonant tunneling and is increased by several orders of magnitude. We discuss the consequence of our result on the possibility of recognition at the level of single molecule.

A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap.

We found by molecular dynamics simulations that a low energy ion can be trapped effectively in a nanoscale Paul trap in both vacuum and aqueous environments when appropriate AC/DC electric fields are applied to the system. Using the negatively charged chlorine ion as an example, we show that the trapped ion oscillates around the center of the nanotrap with an amplitude dependent on the parameters of the system and applied voltages. Successful trapping of the ion within nanoseconds requires an electric bias of GHz frequency, in the range of hundreds of mV. The oscillations are damped in the aqueous environment, but polarization of water molecules requires the application of a higher voltage bias to reach improved stability of the trapping. Application of a supplemental DC driving field along the trap axis can effectively drive the ion off the trap center and out of the trap, opening up the possibility of studying DNA and other charged molecules using embedded probes while achieving a full control of their translocation and localization in the trap.

Reply to "Comment on 'Characterization of the tunneling conductance across DNA bases' ".

Lagerqvist 's Comment regarding the calculation of the transverse conductance of a single-strand DNA heteropolymer translocated through a nanogap between two metal electrodes fully confirms the main conclusions of our study [Phys. Rev. E 74, 011919 (2006)]. In the absence of resonant tunneling, the sensitivity to geometrical factors and the uncertainty in the density functional theory model, which is used in our study and is the basis for the parametrization of the model used by Lagerqvist , raises doubt about the utility of static-bias measurements for DNA sequencing. A possible scheme discussed by Lagerqvist , the stabilization of geometry by an applied strong transverse voltage (1V) , is outside the applicability range of the near-equilibrium theory they (and we) used. More advanced theories and precise gap measurements are needed to resolve these issues.

Characterization of the tunneling conductance across DNA bases.

Characterization of the electrical properties of the DNA bases (adenine, cytosine, guanine, and thymine), in addition to building the basic knowledge on these fundamental constituents of a DNA, is a crucial step in developing a DNA sequencing technology. We present a first-principles study of the current-voltage characteristics of nucleotidelike molecules of the DNA bases, placed in a 1.5 nm gap formed between gold nanoelectrodes. The quantum transport calculations in the tunneling regime are shown to vary strongly with the electrode-molecule geometry and the choice of the density-functional theory exchange-correlation functionals. Analysis of the results in the zero-bias limit indicates that distinguishable current-voltage characteristics of different DNA bases are dominated by the geometrical conformations of the bases and nanoelectrodes.

First-principles transversal DNA conductance deconstructed.

First-principles calculation of the transverse conductance across DNA fragments placed between gold nanoelectrodes reveals that such conductance describes electron tunneling that depends critically on geometrical rather than electronic-structure properties. By factoring the first-principles result into two simple and approximately independent tunneling factors, we show that the conductances of the A, C, G, and T fragments differ only because of their sizes: the larger is the DNA base, the smaller its distance to the electrode, and the larger its conductance. Because the geometrical factors are difficult to control in an experiment, the direct-current measurements across DNA with gold contact electrodes may not be a convenient approach to DNA sequencing.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.