A quantitative analysis of surface deformation by stick/slip atomic force microscopy

This article presents a quantitative determination of static deformation at a nanometer scale of a surface caused by the tip of an atomic force microscope. An analysis of cantilever displacements while in contact with the surface leads to a directly measurable dimensionless parameter which is well sensitive to surface deformation. The method is specifically aimed at stick/slip friction measurements like on layered compounds, like TiS2 or on a relatively rigid surface of an ionic crystal, in this study NaCl [100]. Stick/slip friction images offer a possibility to investigate details of strain-dependent deformation. The observed deformation in TiS2 could play an important role in the occurrence of strong stick/slip friction in this and other layered materials

High-quality epitaxial iron nitride films grown by gas-assisted molecular-beam epitaxy

Thin films of γ’-Fe4N were grown on polished (001) MgO substrates by molecular-beam epitaxy of iron in the presence of a gas flow from a rf atomic source. By means of x-ray diffraction, Mössbauer Spectroscopy, Rutherford backscattering/channeling, and scanning probe microscopy, it is shown that, with this method, single-phase, high-quality epitaxial thin films can be grown with a very smooth surface (root-mean-square roughness ∼0.4 nm). Magnetic measurements reveal square hysteresis loops, moderate coercivities (45 Oe for a 33 nm thick film) and complete in-plane orientation of the magnetization. These properties make the films interesting candidates for device applications

Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids

The double-stranded nature of DNA links its replication, transcription and repair to rotational motion and torsional strain. Magnetic tweezers (MT) are a powerful single-molecule technique to apply both forces and torques to individual DNA or RNA molecules. However, conventional MT do not track rotational motion directly and constrain the free rotation of the nucleic acid tether. Here we present freely orbiting MT (FOMT) that allow the measurement of equilibrium fluctuations and changes in the twist of tethered nucleic acid molecules. Using a precisely aligned vertically oriented magnetic field, FOMT enable tracking of the rotation angle from straight forward (x,y)-position tracking and permits the application of calibrated stretching forces, without biasing the tether's free rotation. We utilize FOMT to measure the force-dependent torsional stiffness of DNA from equilibrium rotational fluctuations and to follow the assembly of recombination protein A filaments on DNA

Atomic force microscopy imaging of transition metal layered compounds:A two‐dimensional stick–slip system

Various layered transition metal dichalcogenides were scanned with an optical-lever atomic force microscope (AFM). The microscopic images indicate the occurrence of strong lateral stick-slip effects. In this letter, two models are presented to describe the observations due to stick-slip, i.e., either as a static or as a dynamic phenomenon. Although both models describe correctly the observed shapes of the unit cell, details in the observed and simulated images point at dynamic nonequilibrium effects. This exact shape of the unit cell depends on cantilever stiffness, scan direction, and detector direction. (C) 1995 American Institute of Physics

Direct Imaging of the circular chromosome of a live bacterium

Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower-density origin of replication and an ultrathin flexible string of DNA at the terminus of replication. At the single-cell level, the torus is strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. Our data show a domain organization underlying the chromosome structure of E. coli, where MatP proteins induce site-specific persistent domain boundaries at Ori/Ter, while transcription regulators HU and Fis induce weaker transient domain boundaries throughout the genome. These findings provide an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells

Analysis of a microscopic stochastic model of microtubule dynamic instability

A novel theoretical model of dynamic instability of a system of linear (1D) microtubules (MTs) in a bounded domain is introduced for studying the role of a cell edge in vivo and analyzing the effect of competition for a limited amount of tubulin. The model differs from earlier models in that the evolution of MTs is based on the rates of single unit (e.g., a heterodimer per protofilament) transformations, in contrast to postulating effective rates/frequencies of larger-scale changes, extracted, e.g., from the length history plots of MTs. Spontaneous GTP hydrolysis with finite rate after polymerization is assumed, and theoretical estimates of an effective catastrophe frequency as well as other parameters characterizing MT length distributions and cap size are derived. We implement a simple cap model which does not include vectorial hydrolysis. We demonstrate that our theoretical predictions, such as steady state concentration of free tubulin, and parameters of MT length distributions, are in agreement with the numerical simulations. The present model establishes a quantitative link between microscopic parameters governing the dynamics of MTs and macroscopic characteristics of MTs in a closed system. Lastly, we use a computational Monte Carlo model to provide an explanation for non-exponential MT length distributions observed in experiments. In particular, we show that appearance of such non-exponential distributions in the experiments can occur because the true steady state has not been reached, and/or due to the presence of a cell edge.Comment: 14 pages, 7 figure