Structure of Carbon Nanotube-dendrimer composite

Using all atomistic molecular dynamics (MD) simulations we report the microscopic picture of the nanotube-dendrimer complex for PAMAM dendrimer of generation 2 to 4 and carbon nanotube of chirality (6,5). We find compact wrapping conformations of dendrimer onto the nanotube surface for all the three generations of PAMAM dendrimer. The degree of wrapping is more for non-protonated dendrimer compared to the protonated dendrimer. For comparison we also study the interaction of another dendrimer, poly(propyl ether imine) (PETIM), with nanotube and show that PAMAM dendrimer interacts strongly as compared to PETIM dendrimer as is evident from the distance of closest approach as well as the number of close contacts between the nanotube and dendrimer. We also calculate the binding energy between the nanotube and the dendrimer using MM/PBSA methods and attribute the strong binding to the charge transfer between them. Dendrimer wrapping on CNT will make it soluble and can act as an efficient dispersing agent for nanotube

Coarse-grained simulation of polymer translocation through an artificial nanopore

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation.Comment: 37 pages Revtex, 11 postscript figure

Collapse of Double-Walled Carbon Nanotube Bundles under Hydrostatic Pressure

We use classical molecular dynamics simulations to study the collapse of single (SWNT) and double-walled (DWNT) carbon nanotube bundles under hydrostatic pressure. The collapse pressure (pc) varies as 1/R^3, where R is the SWNT radius or the DWNT effective radius. The bundles show ~ 30% hysteresis and the hexagonally close packed lattice is completely restored on decompression. The pc of DWNT is found to be close to the sum of its values for the inner and the outer tubes considered separately as SWNT, demonstrating that the inner tube supports the outer tube and that the effective bending stiffness of DWNT, D(DWNT) ~ 2D(SWNT) . We use an elastica formulation to derive the scaling and the collapse behavior of DWNT and multi-walled carbon nanotubes.Comment: This paper has been accepted for publication in Physical Review B. After publication, it will be available at http://prb.aps.org

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor−liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations

Understanding DNA based Nanostructures

We use molecular dynamics (MD) simulations to understand the structure, and stability of various Paranemic crossover (PX) DNA molecules and their topoisomer JX molecules, synthesized recently by Seeman and coworkers at New York University (NYU). Our studies include all atoms (4432 to 6215) of the PX structures with an explicit description of solvent and ions (for a total of up to 42,000 atoms) with periodic boundary conditions. We report the effect of divalent counterions Mg(+2) on the structural and thermodynamic properties of these molecules and compare them to our previously reported results in presence of monovalent Na+ ions. The dynamic structures averaged over the 3-nanosecond simulations preserves the Watson-Crick hydrogen bonding as well as the helical structure. We find that PX65 is the most stable structure both in Na+ and Mg(+2) in accordance with the experimental results. PX65 has helical twist and other helical structural parameters close to the values for normal B-DNA of similar length and sequence. Our strain energy calculations demonstrate that stability of the crossover structure increases with the increase in crossover points

Monitoring the Reaction of the Body State to Antibiotic Treatment against Helicobacter pylori via Infrared Spectroscopy: A Case Study

The current understanding of deviations of human microbiota caused by antibiotic treatment is poor. In an attempt to improve it, a proof-of-principle spectroscopic study of the breath of one volunteer affected by a course of antibiotics for Helicobacter pylori eradication was performed. Fourier transform spectroscopy enabled searching for the absorption spectral structures sensitive to the treatment in the entire mid-infrared region. Two spectral ranges were found where the corresponding structures strongly correlated with the beginning and end of the treatment. The structures were identified as methyl ester of butyric acid and ethyl ester of pyruvic acid. Both acids generated by bacteria in the gut are involved in fundamental processes of human metabolism. Being confirmed by other studies, measurement of the methyl butyrate deviation could be a promising way for monitoring acute gastritis and anti-Helicobacter pylori antibiotic treatment

Magnetic Response in a Zigzag Carbon Nanotube

Magnetic response of interacting electrons in a zigzag carbon nanotube threaded by a magnetic flux is investigated within a Hartree-Fock mean field approach. Following the description of energy spectra for both non-interacting and interacting cases we analyze the behavior of persistent current in individual branches of a nanotube. Our present investigation leads to a possibility of getting a filling-dependent metal-insulator transition in a zigzag carbon nanotube.Comment: 9 pages, 14 figure

Spin Hall effect in a Kagome lattice driven by Rashba spin-orbit interaction

Using four-terminal Landauer-B\"{u}ttiker formalism and Green's function technique, in this present paper, we calculate numerically spin Hall conductance (SHC) and longitudinal conductance of a finite size kagome lattice with Rashba spin-orbit (SO) interaction both in presence and absence of external magnetic flux in clean limit. In the absence of magnetic flux, we observe that depending on the Fermi surface topology of the system SHC changes its sign at different values of Fermi energy, along with the band center. Unlike the infinite system (where SHC is a universal constant $\pm \frac{e}{8 \pi}$), here SHC depends on the external parameters like SO coupling strength, Fermi energy, etc. We show that in the presence of any arbitrary magnetic flux, periodicity of the system is lost and the features of SHC tends to get reduced because of elastic scattering. But again at some typical values of flux ($\phi=1/2, 1/4, 3/4..., etc.) the system retains its periodicity depending on its size and the features of spin Hall effect (SHE) reappears. Our predicted results may be useful in providing a deeper insight into the experimental realization of SHE in such geometries.Comment: 10 pages, 10 figure