71 research outputs found
Simulations of composite carbon films with nanotube inclusions
We study the interfacial structure, stability, and elastic properties of
composite carbon films containing nanotubes. Our Monte Carlo simulations show
that Van der Waals forces play a vital role in shaping up the interfacial
geometry, producing a curved graphitic wall surrounding the tubes. The most
stable structures are predicted to have intermediate densities, high
anisotropies, and increased elastic moduli compared to pure amorphous carbon
films.Comment: 3 pages, 3 figures, to appear in Appl. Phys. Let
Critical evaluation of the computational methods used in the forced polymer translocation
In forced polymer translocation, the average translocation time, ,
scales with respect to pore force, , and polymer length, , as . We demonstrate that an artifact in Metropolis Monte Carlo
method resulting in breakage of the force scaling with large may be
responsible for some of the controversies between different computationally
obtained results and also between computational and experimental results. Using
Langevin dynamics simulations we show that the scaling exponent is not universal, but depends on . Moreover, we show that forced
translocation can be described by a relatively simple force balance argument
and to arise solely from the initial polymer configuration
Stress variations near surfaces in diamond-like amorphous carbon
Using Monte Carlo simulations within the empirical potential approach, we
examine the effect produced by the surface environment on the atomic level
stresses in tetrahedral amorphous carbon. Both the distribution of stresses and
the distributions of sp^2 and sp^3 atoms as a function of depth from the
surface are highly inhomogeneous. They show the same close relationship between
local stress and bonding hybridization found previously in the bulk of the
material. Compressive local stress favors the formation of sp^3 sites, while
tensile stress favors the formation of sp^2 sites.Comment: 7pages, 4 figure
Multiscale model of electronic behavior and localization in stretched dry DNA
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on electronic properties at the atomic scale and on electrical transport along DNA. Accordingly, a multiscale approach is necessary to capture the electronic behavior of the stretched DNA helix. To construct such a model, we begin with accurate density-functional-theory calculations for electronic states in DNA bases and base pairs in various relative configurations encountered in the equilibrium and stretched forms. These results are complemented by semi-empirical quantum mechanical calculations for the states of a small size [18 base pair poly(CG)–poly(CG)] dry, neutral DNA sequence, using previously published models for stretched DNA. The calculated electronic states are then used to parametrize an effective tight-binding model that can describe electron hopping in the presence of environmental effects, such as the presence of stray water molecules on the backbone or structural features of the substrate. These effects introduce disorder in the model hamiltonian which leads to electron localization. The localization length is smaller by several orders of magnitude in stretched DNA relative to that in the unstretched structure
Insights into the fracture mechanisms and strength of amorphous and nanocomposite carbon
Tight-binding molecular dynamics simulations shed light into the fracture
mechanisms and the ideal strength of tetrahedral amorphous carbon and of
nanocomposite carbon containing diamond crystallites, two of the hardest
materials. It is found that fracture in the nanocomposites, under tensile or
shear load, occurs inter-grain and so their ideal strength is similar to the
pure amorphous phase. The onset of fracture takes place at weakly bonded sp^3
sites in the amorphous matrix. On the other hand, the nanodiamond inclusions
significantly enhance the elastic moduli, which approach those of diamond.Comment: 6 pages, 4 figure
Dynamics of forced biopolymer translocation
We present results from our simulations of biopolymer translocation in a
solvent which explain the main experimental findings. The forced translocation
can be described by simple force balance arguments for the relevant range of
pore potentials in experiments and biological systems. Scaling of translocation
time with polymer length varies with pore force and friction. Hydrodynamics
affects this scaling and significantly reduces translocation times.Comment: Published in:
http://www.iop.org/EJ/article/0295-5075/85/5/58006/epl_85_5_58006.htm
Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations
We investigate the process of biopolymer translocation through a narrow pore
using a multiscale approach which explicitly accounts for the hydrodynamic
interactions of the molecule with the surrounding solvent. The simulations
confirm that the coupling of the correlated molecular motion to hydrodynamics
results in significant acceleration of the translocation process. Based on
these results, we construct a phenomenological model which incorporates the
statistical and dynamical features of the translocation process and predicts a
power law dependence of the translocation time on the polymer length with an
exponent . The actual value of the exponent from the
simulations is , which is in excellent agreement with
experimental measurements of DNA translocation through a nanopore, and is not
sensitive to the choice of parameters in the simulation. The mechanism behind
the emergence of such a robust exponent is related to the interplay between the
longitudinal and transversal dynamics of both translocated and untranslocated
segments. The connection to the macroscopic picture involves separating the
contributions from the blob shrinking and shifting processes, which are both
essential to the translocation dynamics.Comment: 7 pages, 5 figures. to appear in Phys. Rev.
Energetics and stability of nanostructured amorphous carbon
Monte Carlo simulations, supplemented by ab initio calculations, shed light
into the energetics and thermodynamic stability of nanostructured amorphous
carbon. The interaction of the embedded nanocrystals with the host amorphous
matrix is shown to determine in a large degree the stability and the relative
energy differences among carbon phases. Diamonds are stable structures in
matrices with sp^3 fraction over 60%. Schwarzites are stable in low-coordinated
networks. Other sp^2-bonded structures are metastable.Comment: 11 pages, 7 figure
DNA nucleotide-specific modulation of \mu A transverse edge currents through a metallic graphene nanoribbon with a nanopore
We propose two-terminal devices for DNA sequencing which consist of a
metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its
interior through which the DNA molecule is translocated. Using the
nonequilibrium Green functions combined with density functional theory, we
demonstrate that each of the four DNA nucleotides inserted into the nanopore,
whose edge carbon atoms are passivated by either hydrogen or nitrogen, will
lead to a unique change in the device conductance. Unlike other recent
biosensors based on transverse electronic transport through DNA nucleotides,
which utilize small (of the order of pA) tunneling current across a nanogap or
a nanopore yielding a poor signal-to-noise ratio, our device concept relies on
the fact that in ZGNRs local current density is peaked around the edges so that
drilling a nanopore away from the edges will not diminish the conductance.
Inserting a DNA nucleotide into the nanopore affects the charge density in the
surrounding area, thereby modulating edge conduction currents whose magnitude
is of the order of \mu A at bias voltage ~ 0.1 V. The proposed biosensor is not
limited to ZGNRs and it could be realized with other nanowires supporting
transverse edge currents, such as chiral GNRs or wires made of two-dimensional
topological insulators.Comment: 6 pages, 6 figures, PDFLaTe
Transverse Electronic Transport through DNA Nucleotides with Functionalized Graphene Electrodes
Graphene nanogaps and nanopores show potential for the purpose of electrical
DNA sequencing, in particular because single-base resolution appears to be
readily achievable. Here, we evaluated from first principles the advantages of
a nanogap setup with functionalized graphene edges. To this end, we employed
density functional theory and the non-equilibrium Green's function method to
investigate the transverse conductance properties of the four nucleotides
occurring in DNA when located between the opposing functionalized graphene
electrodes. In particular, we determined the electrical tunneling current
variation as a function of the applied bias and the associated differential
conductance at a voltage which appears suitable to distinguish between the four
nucleotides. Intriguingly, we observe for one of the nucleotides a negative
differential resistance effect.Comment: 19 pages, 7 figure
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