Temperature dependence of circular DNA topological states

Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo simulation, we predict the temperature dependence of the linking number distribution of small circular DNAs. Our predictions are based on flexible defect excitations resulted from local melting or unstacking of DNA base pairs. We found that the reduced bending rigidity alone can lead to measurable changes of the variance of linking number distribution of short circular DNAs. If the defect is accompanied by local unwinding, the effect becomes much more prominent. The predictions can be easily investigated in experiments, providing a new method to study the micromechanics of sharply bent DNAs and the thermal stability of specific DNA sequences. Furthermore, the predictions are directly applicable to the studies of binding of DNA distorting proteins that can locally reduce DNA rigidity, form DNA kinks, or introduce local unwinding.Comment: 15 pages in preprint format, 4 figure

Can Electric Field Induced Energy Gaps In Metallic Carbon Nanotubes?

The low-energy electronic structure of metallic single-walled carbon nanotube (SWNT) in an external electric field perpendicular to the tube axis is investigated. Based on tight-binding approximation, a field-induced energy gap is found in all (n, n) SWNTs, and the gap shows strong dependence on the electric field and the size of the tubes. We numerically find a universal scaling that the gap is a function of the electric field and the radius of SWNTs, and the results are testified by the second-order perturbation theory in weak field limit. Our calculation shows the field required to induce a 0.1 ${\rm eV}$ gap in metallic SWNTs can be easily reached under the current experimental conditions. It indicates a kind of possibility to apply nanotubes to electric signal-controlled nanoscale switching devices

Magnetoelectrically driven catalytic degradation of organics

Here, we report the catalytic degradation of organic compounds by exploiting the magnetoelectric (ME) nature of cobalt ferrite-bismuth ferrite (CFO-BFO) core-shell nanoparticles. The combination of magnetostrictive CFO with the multiferroic BFO gives rise to a magnetoelectric engine that purifies water under wireless magnetic fields via advanced oxidation processes, without involvement of any sacrificial molecules or co-catalysts. Magnetostrictive CoFe2O4 nanoparticles are fabricated using hydrothermal synthesis, followed by sol-gel synthesis to create the multiferroic BiFeO3 shell. We perform theoretical modeling to study the magnetic field induced polarization on the surface of magnetoelectric nanoparticles. The results obtained from these simulations are consistent with the experimental findings of the piezo-force microscopy analysis, where we observe changes in the piezoresponse of the nanoparticles under magnetic fields. Next, we investigate the magnetoelectric effect induced catalytic degradation of organic pollutants under AC magnetic fields and obtained 97% removal efficiency for synthetic dyes and over 85% removal efficiency for routinely used pharmaceuticals. Additionally, we perform trapping experiments to elucidate the mechanism behind the magnetic field induced catalytic degradation of organic pollutants by using scavengers for each of the reactive species. Our results indicate that hydroxyl and superoxide radicals are the main reactive species in the magnetoelectrically induced catalytic degradation of organic compounds

Dynamic disorder in receptor-ligand forced dissociation experiments

Recently experiments showed that some biological noncovalent bonds increase their lifetimes when they are stretched by an external force, and their lifetimes will decrease when the force increases further. Several specific quantitative models have been proposed to explain the intriguing transitions from the "catch-bond" to the "slip-bond". Different from the previous efforts, in this work we propose that the dynamic disorder of the force-dependent dissociation rate can account for the counterintuitive behaviors of the bonds. A Gaussian stochastic rate model is used to quantitatively describe the transitions observed recently in the single bond P-selctin glycoprotein ligand 1(PSGL-1)$-$P-selectin force rupture experiment [Marshall, {\it et al.}, (2003) Nature {\bf 423}, 190-193]. Our model agrees well to the experimental data. We conclude that the catch bonds could arise from the stronger positive correlation between the height of the intrinsic energy barrier and the distance from the bound state to the barrier; classical pathway scenario or {\it a priori} catch bond assumption is not essential.Comment: 4 pages, 2 figure

The structure relaxation of carbon nanotube

A simple macroscopic continuum elasticity theory (CET) is used to calculate the structure relaxation of single-wall carbon nanotube (SWNT), an analytic formula is obtained. We also expand an atomic scale three-parameter empirical model [ T. Lenosky {\emph et al.} Nature 355, 333(1992)] in order to correctly describe the bond-length change effects. The structure relaxation of SWNT expected by the model is good in agreement with our CET results, and very well consistent with the previous calculation from a first principles local density function approximation. Using the expanded Lenosky model, we calculate the strain energy of bending tube. The obtained results are good in agreement with the previous theoretical expectation. It shows the model may be a good simple replacement of some more sophisticated methods on determining carbon networks deformations.Comment: 9 pages, 4 eps figure

Nematic Films and Radially Anisotropic Delaunay Surfaces

We develop a theory of axisymmetric surfaces minimizing a combination of surface tension and nematic elastic energies which may be suitable for describing simple film and bubble shapes. As a function of the elastic constant and the applied tension on the bubbles, we find the analogues of the unduloid, sphere, and nodoid in addition to other new surfaces.Comment: 15 pages, 18 figure

Coiling Instabilities in Multilamellar Tubes

Myelin figures are densely packed stacks of coaxial cylindrical bilayers that are unstable to the formation of coils or double helices. These myelin figures appear to have no intrinsic chirality. We show that such cylindrical membrane stacks can develop an instability when they acquire a spontaneous curvature or when the equilibrium distance between membranes is decreased. This instability breaks the chiral symmetry of the stack and may result in coiling. A unilamellar cylindrical vesicle, on the other hand, will develop an axisymmetric instability, possibly related to the pearling instability.Comment: 6 pages, 2 figure

Influence of packing density and surface roughness of vertically-aligned carbon nanotubes on adhesive properties of gecko-inspired mimetics.

We have systematically studied the macroscopic adhesive properties of vertically aligned nanotube arrays with various packing density and roughness. Using a tensile setup in shear and normal adhesion, we find that there exists a maximum packing density for nanotube arrays to have adhesive properties. Too highly packed tubes do not offer intertube space for tube bending and side-wall contact to surfaces, thus exhibiting no adhesive properties. Likewise, we also show that the surface roughness of the arrays strongly influences the adhesion properties and the reusability of the tubes. Increasing the surface roughness of the array strengthens the adhesion in the normal direction, but weakens it in the shear direction. Altogether, these results allow progress toward mimicking the gecko's vertical mobility.The authors acknowledge funding from the EC project Technotubes.This is the accepted manuscript. The final version is available at http://pubs.acs.org/doi/abs/10.1021/am507822b