Polymerized LB films imaged with a combined atomic force microscope-fluorescence microscope

The first results obtained with a new stand-alone atomic force microscope (AFM) integrated with a standard Zeiss optical fluorescence microscope are presented. The optical microscope allows location and selection of objects to be imaged with the high-resolution AFM. Furthermore, the combined microscope enables a direct comparison between features observed in the fluorescence microscope and those observed in the images obtained with the AFM, in air or under liquid. The cracks in polymerized Langmuir-Blodgett films of lO,l2-pentacosadiynoic acid as observed in the fluorescence microscope run parallel to one of the lattice directions of the crystal as revealed by molecular resolution images obtained with the AFM. The orientation of these cracks also coincides with the polarization direction of the fluorescent light, indicating that the cracks run along the polymer backbone. Ripple-like corrugations on a submicrometer scale have been observed, which may be due to mechanical stress created during the polymerization process

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

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

Methods and instruments for materials testing

Methods and instruments for characterizing a material, such as the properties of bone in a living human subject, using a test probe constructed for insertion into the material and a reference probe aligned with the test probe in a housing. The housing is hand held or placed so that the reference probe contacts the surface of the material under pressure applied either by hand or by the weight of the housing. The test probe is inserted into the material to indent the material while maintaining the reference probe substantially under the hand pressure or weight of the housing allowing evaluation of a property of the material related to indentation of the material by the probe. Force can be generated by a voice coil in a magnet structure to the end of which the test probe is connected and supported in the magnet structure by a flexure, opposing flexures, a linear translation stage, or a linear bearing. Optionally, a measurement unit containing the test probe and reference probe is connected to a base unit with a wireless connection, allowing in the field material testing

The Stochastic Dynamics of an Array of Atomic Force Microscopes in a Viscous Fluid

We consider the stochastic dynamics of an array of two closely spaced atomic force microscope cantilevers in a viscous fluid for use as a possible biomolecule sensor. The cantilevers are not driven externally, as is common in applications of atomic force microscopy, and we explore the stochastic cantilever dynamics due to the constant buffeting of fluid particles by Brownian motion. The stochastic dynamics of two adjacent cantilevers are correlated due to long range effects of the viscous fluid. Using a recently proposed thermodynamic approach the hydrodynamic correlations are quantified for precise experimental conditions through deterministic numerical simulations. Results are presented for an array of two readily available atomic force microscope cantilevers. It is shown that the force on a cantilever due to the fluid correlations with an adjacent cantilever is more than 3 times smaller than the Brownian force on an individual cantilever. Our results indicate that measurements of the correlations in the displacement of an array of atomic force microscopes can detect piconewton forces with microsecond time resolution.Comment: 7 page article with 11 images submitted to the International Journal of Nonlinear Mechanic

Scalable Bayesian Functional Connectivity Inference for Multi-Electrode Array Recordings

Multi-electrode arrays (MEAs) can record extracellular action potentials (also known as 'spikes') from hundreds or thousands of neurons simultaneously. Inference of a functional network from a spike train is a fundamental and formidable computational task in neuroscience. With the advancement of MEA technology, it has become increasingly crucial to develop statistical tools for analyzing multiple neuronal activity as a network. In this paper, we propose a scalable Bayesian framework for inference of functional networks from MEA data. Our framework makes use of the hierarchical structure of networks of neurons. We split the large scale recordings into smaller local networks for network inference, which not only eases the computational burden from Bayesian sampling but also provides useful insights on regional connections in organoids and brains. We speed up the expensive Bayesian sampling process by using parallel computing. Experiments on both synthetic datasets and large-scale real-world MEA recordings show the effectiveness and efficiency of the scalable Bayesian framework. Inference of networks from controlled experiments exposing neural cultures to cadmium presents distinguishable results and further confirms the utility of our framework.Comment: in BIOKDD 202

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

Integrated stratigraphic correlation of Upper Devonian platform-to-basin carbonate sequences, Lennard Shelf, Canning Basin, Western Australia: advances in carbonate margin-to-slope sequence stratigraphy and stacking patterns

High-resolution, time-significant correlations are integral to meaningful stratigraphic frameworks in depositional systems, but may be difficult to achieve using traditional sequence stratigraphic or biostratigraphic approaches alone, particularly in geologically complex settings. In steep, reefal carbonate margin-to-slope systems, such correlations are essential to unravel shelf-to-basin transitions, characterize strike variability, and develop predictive sequence stratigraphic models – concepts which are currently poorly understood in these heterogeneous settings. The Canning Basin Chronostratigraphy Project (CBCP) integrates multiple independent datasets (including biostratigraphy, magnetostratigraphy, stable isotope chemostratigraphy, and sequence stratigraphy) extracted from Upper Devonian (Frasnian and Famennian) reefal platform exposures along the Lennard Shelf, Canning Basin, Western Australia. These were used to generate a well-constrained stratigraphic framework and shelf-to-basin composite reconstruction of the carbonate system. The resultant integrated framework allows for unprecedented analysis of carbonate margin-to-slope heterogeneity, depositional architecture, and sequence stratigraphy along the Lennard Shelf. Systems tract architecture, facies partitioning, and stacking patterns of margin to lower-slope environments were assessed for six composite-scale sequences that form part of a transgressive-to-regressive supersequence and span the Frasnian-Famennian (F-F) biotic crisis. Variations are apparent in margin styles, foreslope facies proportions, dominant resedimentation processes, downslope contributing sediment factories, and vertical rock successions, related to hierarchical accommodation signals and ecological changes associated with F-F boundary. We present these results in the form of carbonate margin-to-basin sequence stratigraphic models and associations that link seismic-scale architecture to fine-scale facies heterogeneity. These models provide a predictive foundation for characterization of steep-sided flanks of reefal carbonate platform systems that is useful for both industry and academia. This study emphasizes the utility of an integrated stratigraphic approach and the insights gained from better-constrained facies and stratal architecture analysis; insights that were not achievable with traditional sequence stratigraphic or biostratigraphic techniques alone

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution