Tip-sample interactions in atomic force microscopy: I. Modulating adhesion between silicon nitride and glass

An adhesive interaction between a silicon nitride AFM tip and glass substrate in water is described. This adhesion is in the range 5-40 nN, of which a large component is likely to be due to hydrogen bonding between the silanol groups on both surfaces. The interaction can be modulated by a variety of buffers commonly used in biochemical and biological research, including sodium phosphate, tris(hydroxymethyl)aminomethane, glycine, and N-2-hydroxyethyl-piperazine N'-2-ethanesulfonic acid. Using these buffers it appears that there are effects of ion concentration, ion type and pH on the measured adhesion. Of the conditions examined, phosphate was most effective at reducing adhesion and could be used at concentrations as low as 10 mM at neutral pH. The results demonstrate that the chemical interactions between tip and sample can be modulated, and provide a basis for designing conditions for imaging and manipulating biological molecules and structures

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

Membrane-membrane and membrane-substrate adhesion during dissection of gap junctions with the atomic-force microscope

The gap junction is a specialized region of the plasma membrane that consists of an array of cell-to-cell ion channels. These channels form where the membranes from two cells come together, and the gap junction is therefore composed of two lipid bilayers. The atomic force microscope (AFM) can be used to dissect the gap junction, removing one membrane and exposing the extracellular domains of the second. The force required to dissect the membrane, near 10^(-8) N vertical force for gap junctions adsorbed to mica, provides a measure of the strength of the interaction between the two membranes. Since a single membrane is left in contact with the mica, this interaction must be stronger than the membrane-membrane interaction. Non-junctional membrane attached to the gap junctions is easily removed with the AFM tip while the gap junction membrane remains attached to the mica, providing evidence that the interaction with the mica is mainly mediated by protein-mica interactions. Consistent with this hypothesis is the observation that material trapped under the membrane sometimes results in pieces of membrane above the material being pulled out during dissection. These results lay the foundation for examining the molecular details of the basis for membrane- membrane and membrane-substrate adhesion

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

Membrane-membrane and membrane-substrate adhesion during dissection of gap junctions with the atomic-force microscope

The gap junction is a specialized region of the plasma membrane that consists of an array of cell-to-cell ion channels. These channels form where the membranes from two cells come together, and the gap junction is therefore composed of two lipid bilayers. The atomic force microscope (AFM) can be used to dissect the gap junction, removing one membrane and exposing the extracellular domains of the second. The force required to dissect the membrane, near 10^(-8) N vertical force for gap junctions adsorbed to mica, provides a measure of the strength of the interaction between the two membranes. Since a single membrane is left in contact with the mica, this interaction must be stronger than the membrane-membrane interaction. Non-junctional membrane attached to the gap junctions is easily removed with the AFM tip while the gap junction membrane remains attached to the mica, providing evidence that the interaction with the mica is mainly mediated by protein-mica interactions. Consistent with this hypothesis is the observation that material trapped under the membrane sometimes results in pieces of membrane above the material being pulled out during dissection. These results lay the foundation for examining the molecular details of the basis for membrane- membrane and membrane-substrate adhesion

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

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

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