Imaging Single-Stranded DNA, Antigen-Antibody Reaction and Polymerized Langmuir-Blodgett Films with an Atomic Force Microscope

The combination of an (AFM) atomic force microscope together with microfabricated cantilevers that have integrated tips opens many possibilities for imaging systems of great importance in biology. We have imaged single-stranded 25mer DNA that was adsorbed on treated mica or that was covalently bound with a crosslinker to a polymerized Langmuir-Blodgett (LB) film, the top monolayer of a bilayer system. At low magnification the AFM shows cracks between solid domains, like in an image taken with a fluorescence microscope. At higher magnification, however, the AFM reveals much finer cracks and at still higher magnification it reveals rows of individual molecules in the polymerized LB film with a spacing of 0.45 nm. We have also imaged a LB film consisting of lipids in which 4% of the lipids had hapten molecules chemically bound to the lipid headgroups. Specific antibodies can then bind to these hapten molecules and be imaged with the AFM. This points to the possibility of using the AFM to monitor selective antibody binding

Scanning Tunneling Microscopy and Fabrication of Nanometer Scale Structures at the Liquid-Gold Interface

The Scanning Tunneling Microscope (STM) can image gold surfaces covered with a variety of liquids. This paper reviews the results obtained using the STM to image gold surfaces covered with liquid. These results include the creation of 10 nm structures, images of the electrochemical process of electroplating, and the production of atomically flat Au (111) surfaces. We conclude that in the future STM will find further application in the area of nanostructure fabrication and electrochemistry. The trend in the field is toward greater control of the electrochemical environment

Theory of a Scanning Tunneling Microscope with a Two-Protrusion Tip

We consider a scanning tunneling microscope (STM) such that tunneling occurs through two atomically sharp protrusions on its tip. When the two protrusions are separated by at least several atomic spacings, the differential conductance of this STM depends on the electronic transport in the sample between the protrusions. Furthermore two-protrusion tips commonly occur during STM tip preparation. We explore possible applications to probing dynamical impurity potentials on a metallic surface and local transport in an anisotropic superconductor.Comment: revtex, 11 pages, 6 figures upon reques

Inelastic transport theory from first-principles: methodology and applications for nanoscale devices

We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TranSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green's function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in [Frederiksen et al., Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.Comment: 24 pages, 17 figure

Molecular mechanistic origin of the toughness of natural adhesives, fibres and composites

Natural materials are renowned for their strength and toughness(1-5). Spider dragline silk has a breakage energy per unit weight two orders of magnitude greater than high tensile steel(1,6), and is representative of many other strong natural fibres(3,7,8). The abalone shell, a composite of calcium carbonate plates sandwiched between organic material, is 3,000 times more fracture resistant than a single crystal of the pure mineral(4,5). The organic component, comprising just a few per cent of the composite by weight(9), is thought to hold the key to nacre's fracture toughness(10,11). Ceramics laminated with organic material are more fracture resistant than non-laminated ceramics(11,12), but synthetic materials made of interlocking ceramic tablets bound by a few weight per cent of ordinary adhesives do not have a toughness comparable to nacre(13). We believe that the key to nacre's fracture resistance resides in the polymer adhesive, and here we reveal the properties of this adhesive by using the atomic force microscope(14) to stretch the organic molecules exposed on the surface of freshly cleaved nacre. The adhesive fibres elongate in a stepwise manner as folded domains or loops are pulled open. The elongation events occur for forces of a few hundred piconewtons, which are smaller than the forces of over a nanonewton required to break the polymer backbone in the threads. We suggest that this 'modular' elongation mechanism might prove to be quite general for conveying toughness to natural fibres and adhesives, and we predict that it might be found also in dragline silk

Force-Extension Relations for Polymers with Sliding Links

Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable size. For a single loop in a phantom chain, we obtain exact expressions for the average end-to-end separation: The linear response to a small force is related to the properties of the unstressed chain, while for a large force the polymer backbone can be treated as a sequence of Pincus--de Gennes blobs, the constraint effecting only a single blob. Generalizing this picture, scaling arguments are used to include self-avoiding effects.Comment: 4 pages, 5 figures; accepted to Phys. Rev. E (Brief Report

Nanoscopic Tunneling Contacts on Mesoscopic Multiprobe Conductors

We derive Bardeen-like expressions for the transmission probabilities between two multi-probe mesoscopic conductors coupled by a weak tunneling contact. We emphasize especially the dual role of a weak coupling contact as a current source and sink and analyze the magnetic field symmetry. In the limit of a point-like tunneling contact the transmission probability becomes a product of local, partial density of states of the two mesoscopic conductors. We present expressions for the partial density of states in terms of functional derivatives of the scattering matrix with respect to the local potential and in terms of wave functions. We discuss voltage measurements and resistance measurements in the transport state of conductors. We illustrate the theory for the simple case of a scatterer in an otherwise perfect wire. In particular, we investigate the development of the Hall-resistance as measured with weak coupling probes.Comment: 10 pages, 5 figures, revte

Aggregate structure of hydroxyproline-rich glycoprotein (HRGP) and HRGP assisted dispersion of carbon nanotubes

Hydroxyproline-rich glycoproteins (HRGP) comprise a super-family of extracellular structural glycoproteins whose precise roles in plant cell wall assembly and functioning remain to be elucidated. However, their extended structure and repetitive block co-polymer character of HRGPs may mediate their self-assembly as wall scaffolds by like-with-like alignment of their hydrophobic peptide and hydrophilic glycopeptide modules. Intermolecular crosslinking further stabilizes the scaffold. Thus the design of HRGP-based scaffolds may have practical applications in bionanotechnology and medicine. As a first step, we have used single-molecule or single-aggregate atomic force microscopy (AFM) to visualize the structure of YK20, an amphiphilic HRGP comprised entirely of 20 tandem repeats of: Ser-Hyp4-Ser-Hyp-Ser-Hyp4-Tyr-Tyr-Tyr-Lys. YK20 formed tightly aggregated coils at low ionic strength, but networks of entangled chains with a porosity of ~0.5–3 μm at higher ionic strength. As a second step we have begun to design HRGP-carbon nanotube composites. Single-walled carbon nanotubes (SWNTs) can be considered as seamless cylinders rolled up from graphene sheets. These unique all-carbon structures have extraordinary aromatic and hydrophobic properties and form aggregated bundles due to strong inter-tube van der Waals interactions. Sonicating aggregated SWNT bundles with aqueous YK20 solubilized them presumably by interaction with the repetitive, hydrophobic, Tyr-rich peptide modules of YK20 with retention of the extended polyproline-II character. This may allow YK20 to form extended structures that could potentially be used as scaffolds for site-directed assembly of nanomaterials

Tuning the translational freedom of DNA for high speed AFM

Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy it is becoming possible to observe directly DNA protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bio-nanotechnology but also functional biologically inspired materials. Critically, sample preparation plays a central role in all microscopy studies and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions of DNA molecules with the surface such that an association strong enough to enable high resolution AFM imaging while providing sufficient translational freedom to allow the relevant protein DNA interactions to take place, can be maintained. Furthermore, we describe a quantitative method for measuring the DNA mobility, which also allows the dissection of the different contributions to the overall movement of the DNA molecules. We find that for weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy