Atomistic simulations of fluid structure and solvation forces in atomic force microscopy

We describe results of atomistic molecular dynamics simulations modelling an atomic force microscope (AFM) tip immersed in a fluid. Both the tip and the surface are modelled by rigid arrays of atoms. The tip is pyramidal and the surface is the (100) face of a fcc crystal. The focus is on the solvation forces acting on the tip and on the surface and their relation to the structural and dynamic properties of the fluid. Fluid particles in the neighborhood of the tip-surface junction are found to be highly ordered compared to the bulk, as shown by localized variations in the average fluid density. The atomistic nature of the model gives rise to several effects related to the discrete sizes of the fluid, tip, and surface particles which are not observed in continuum-based theories. A number of simulated force-distance curves are presented, along with an analysis of the effect of changing fluid particle size, tip (lateral) position, tip shape, and the lyocompatability of the tip and surface materials. The atomic-scale distribution of fluid-surface forces is examined for various positions of the tip, and the extent to which the fluid can act as a “cushion” by increasing the effective area of the tip-surface interaction is studied. The effect of a fluid on AFM imaging is investigated by generating “fluid images”, which are shown to be comparable in magnitude to the direct tip-surface interaction in the noncontact mode. We compare images generated by defective and defect-free surfaces, and analyse the fluid-tip forces acting in a lateral direction. An image formed from fluid forces acting in the direction of the surface normal does not show the presence of a vacancy, but an image formed from lateral fluid forces does.     

Lateral force microscopy in low normal force limit

We have studied frictional force between SiN tip and Si surface by using lateral force microscopy. The cantilever we have used has very low stiffness of 0.006 N/m, and the normal force acting on the surface was much lower than the attractive force such as van der Waals force. In this low normal force limit, it was found that the frictional force did not depend on the normal force. We suggest a calibration method to estimate the attractive force from the lateral force data in this limit. The estimated attractive force between Si sample and SiN tip with radius of 10 nm was 0.4 nN in flat region and 0.65 nN at the corner of a rectangular hole.     

Atomic force microscopy for the investigation of molecular and cellular behavior

The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.     

Condensed-phase properties of n-alkyl-amines from molecular dynamics simulations using charge equilibration force fields

Charge equilibration force fields are applied to molecular dynamics simulations of liquid straight-chain alkyl-amine systems—methylamine, ethylamine, and n-propylamine. The models used are based on the CHARMM charge equilibration force field developed for methylamine and applied here to simulations for larger n-alkyl amines. The effects of the parameter set used for extension to larger systems, and the importance of defining the extent of molecular charge transfer via judicious selection of charge normalization units are considered and evaluated. Condensed-phase properties including molecular volumes, enthalpy of vaporization, isothermal compressibility, isobaric heat capacity, dielectric constants, and self-diffusion constants are calculated for each system. Molecular volumes are predicted to within 2.3–18.0% of the experimental values, where the error increases with the size of the molecule. Enthalpy of vaporization is predicted to be within 2.5–24.4% of experiment. Dielectric constants are calculated within 0.5–17.3% of experimental values. Properties of ethylamine and n-propylamine (to which the original charge equilibration force field was not calibrated/fitted) calculated using parameters from an alkane model outperformed those from a lysine model in most cases by up to a 16% reduction in error from experiment. Compared to previous MD simulations [T. Kosztolanyi, I. Bako, and G. Palinkas, Hydrogen Bonding in Liquid Methanol, Methylamine, and Methanethiol Studied by Molecular-Dynamics Simulations. Journal of Chemical Physics, 2003. 118(10): 4546–4555.], the radial distribution functions (RDF) of methylamine showed reduced values of the first maximum and minimum position by up to 8.2% for N–N and 12.4% for N–H. The need for careful treatment of charge transfer schemes is suggested by the significant difference in condensed-phase and single-molecule properties when charge transfer was normalized in a partitioned n-propylamine molecule as opposed to normalization over the whole molecule. The partitioned normalization reduced the error from experiment nearly 15% for molecular volume and 10% for enthalpy of vaporization. The influence of various applied normalization schemes on condensed-phase and select gas-phase properties (gas-phase dipole moment) was greater than the effects of different parameterizations, indicating the importance of a proper selection of charge normalization unit in the application and parameterization of charge equilibration force fields for small molecules to larger biological assemblies.     

Atomic force microscopy probing of cell elasticity

Atomic force microscopy (AFM) has recently provided the great progress in the study of micro- and nanostructures including living cells and cell organelles. Modern AFM techniques allow solving a number of problems of cell biomechanics due to simultaneous evaluation of the local mechanical properties and the topography of the living cells at a high spatial resolution and force sensitivity. Particularly, force spectroscopy is used for mapping mechanical properties of a single cell that provides information on cellular structures including cytoskeleton structure.

This entry is aimed to review the recent AFM applications for the study of dynamics and mechanical properties of intact cells associated with different cell events such as locomotion, differentiation and aging, physiological activation and electromotility, as well as cell pathology. Local mechanical characteristics of different cell types including muscle cells, endothelial and epithelial cells, neurons and glial cells, fibroblasts and osteoblasts, blood cells and sensory cells are analyzed in this paper.     

25 nm resolution single molecular fluorescence imaging by scanning near-field optical/atomic force microscopy

High-resolution single molecular near-field fluorescence images were observed by scanning near-field optical/atomic force microscopy (SNOM/AFM). We modified the SNOM/AFM for both high-resolution fluorescence imaging and high-resolution topographic imaging. The imaged fluorophore, Alexa 532, is prepared with a poly-methyl-methacrylate (PMMA) film coating. A fluorescence resolution of 25 nm was obtained with a simultaneous topographic image of a flat surface. A sample prepared with a lower PMMA concentration exhibited a rough surface in the micro area. The results for the flat surface indicated that the fluorescence resolution is worst in the rough surface sample, that the maximum fluorescence intensities for the individual fluorophore are similar, and that the decay rate is faster. Thus, we concluded that the morphological effect is an important factor in fluorescence image resolution and the apparent lifetimes of the fluorescence molecules.     

Interpretation of scanning tunneling microscopy and atomic force microscopy images of 1T-TiS2

The surface of 1T-TiS₂ was examined by scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The STM and AFM images of this compound were interpreted on the basis of the partial electron density ρ(r,E_F) and total electron density ρ(r) of a slab which consists of six (001) 1T-TiS₂ layers. Electronic structure calculations were performed using the ab-initio Hartree–Fock program crystal. It was found that the bright spots in experimental STM images correspond to sulfur atoms at both positive and negative bias voltages. The AFM image showed a periodicity which can be explained by the atomic corrugation at the surface. Structural defects on the surface were also investigated, and their interpretation constitutes experimental proof that only sulfur atoms were detected by scanning probe microscopies.     

Possibility of measuring exchange force through force microscopy

This article describes the possibility of measuring exchange force through atomic force microscopy (AFM), based on the results of first-principles calculations for the exchange force between two magnetic Fe(001) films. We observed strong variation of the exchange force relative to the surface site. The magnitude of the force variation was larger than the force sensitivity of conventional AFM. These results suggest that a surface magnetic image with atomic resolution can be achieved by measuring the exchange force.     

Numerical study of the hydrodynamic drag force in atomic force microscopy measurements undertaken in fluids

When atomic force microscopy (AFM) is employed for in vivo study of immersed biological samples, the fluid medium presents additional complexities, not least of which is the hydrodynamic drag force due to viscous friction of the cantilever with the liquid. This force should be considered when interpreting experimental results and any calculated material properties. In this paper, a numerical model is presented to study the influence of the drag force on experimental data obtained from AFM measurements using computational fluid dynamics (CFD) simulation. The model provides quantification of the drag force in AFM measurements of soft specimens in fluids.The numerical predictions were compared with experimental data obtained using AFM with a V-shaped cantilever fitted with a pyramidal tip. Tip velocities ranging from 1.05 to 105 μm/s were employed in water, polyethylene glycol and glycerol with the platform approaching from a distance of 6000 nm. The model was also compared with an existing analytical model. Good agreement was observed between numerical results, experiments and analytical predictions. Accurate predictions were obtained without the need for extrapolation of experimental data. In addition, the model can be employed over the range of tip geometries and velocities typically utilized in AFM measurements.     

An effective force field for molecular dynamics simulations of dimethyl sulfone

A rigid five-site united atom model for dimethyl sulfone (DMSO₂) compatible with the GROMOS force field is parametrized and tested. The parameters were optimized with respect to experimental quantities such as liquid density, heat of vaporization, shear viscosity and excess free energy. Good agreement with pure component properties is achieved except for the static dielectric permittivity which is calculated too low. Together with the SPC model for water the new DMSO₂ model was used to study aqueous mixtures at low concentrations and compared to aqueous mixtures of DMSO. It is concluded that interaction parameters for sulfoxide oxygen are not directly transferable to sulfonyl oxygen.     

Observation of multicellular spinning behavior of Proteus mirabilis by atomic force microscopy and multifunctional microscopy

This study aimed to observe the multicellular spinning behavior of Proteus mirabilis by atomic force microscopy (AFM) and multifunctional microscopy in order to understand the mechanism underlying this spinning movement and its biological significance. Multifunctional microscopy with charge-coupled device (CCD) and real-time AFM showed changes in cell structure and shape of P. mirabilis during multicellular spinning movement. Specifically, the morphological characteristics of P. mirabilis, multicellular spinning dynamics, and unique movement were observed. Our findings indicate that the multicellular spinning behavior of P. mirabilis may be used to collect nutrients, perform colonization, and squeeze out competitors. The movement characteristics of P. mirabilis are vital to the organism's biological adaptability to the surrounding environment.     

Atomic force microscopy and transmission electron microscopy of biocompatible magnetic fluids: A comparative analysis

The present study provides a comparative analysis of the size dispersity of magnetic nanoparticles (MNPs) within magnetic fluids as obtained from atomic force microscopy (AFM) and transmission electron microscopy (TEM). Whereas the mean particle diameter obtained from the AFM data presented a reduction of about 34% as compared to the value obtained from the TEM data, the standard deviation obtained from the AFM data is twice the value found from the TEM data. Similarities and differences in the size dispersity parameters are discussed in terms of sample preparation and tip characteristics. A two-dimensional mode for the deposition of the MNPs on top of the mica substrate is discussed as well.     

Calculation of the frequency shift in dynamic force microscopy

A theoretical study of the quality and the range of validity of different numerical and analytical methods to calculate the frequency shift in dynamic force microscopy is presented. By comparison with exact results obtained by the numerical solution of the equation of motion, it is demonstrated that the commonly used interpretation of the frequency shift as a measure for the force gradient of the tip–sample interaction force is only valid for very small oscillation amplitudes and leads to misinterpretations in most practical cases. Perturbation theory, however, allows the derivation of useful analytic approximations.     

Noncontact atomic force microscopy: Bond imaging and beyond

It was a long-cherished dream for chemists to take a direct look at chemical bonding, a fundamental component of chemistry. This dream was finally accomplished by the state-of-the-art noncontact atomic force microscopy (NC-AFM) equipped with qPlus force sensors and carbon monoxide (CO) functionalized tips. The resolved interconnectivity between atoms and molecules in NC-AFM frequency shift images is interpreted as chemical bonding, providing essential knowledge of the bond length, bond angle and even bond order. The featured contrast of different chemical bonds can serve as fingerprints for further interpretation of chemical structures toward unknown species synthesized on surfaces. This breakthrough enriches characterization tools for surface science and brings our understanding of on-surface reactions to a new level. Beyond bond imaging, the application of NC-AFM has been extended to quantifying interatomic interactions, identifying three-dimensional nanostructures, manipulating molecules and reactions, as well as determining molecular electronic characteristics. Moreover, some recent efforts address the improvement of the usability and versatility of the bond-resolved NC-AFM technique, including high-resolution molecular investigation on bulk insulators, application-specific tip modification, stable bond imaging above liquid helium temperature and autonomous experimentation implemented by artificial intelligence.     

How to measure energy dissipation in dynamic mode atomic force microscopy

When studying a mechanical system like an atomic force microscope (AFM) in dynamic mode it is intuitive and instructive to analyse the forces involved in tip–sample interaction. A different but complementary approach is based on analysing the energy that is dissipated when the tip periodically interacts with the sample surface. This method does not require solving the differential equation of motion for the oscillating cantilever, but is based entirely on the analysis of the energy flow in and out of the dynamic system. Therefore the problem of finding a realistic model to describe the tip–sample interaction in terms of non-linear force–distance dependencies and damping effects is omitted. Instead, it is possible to determine the energy dissipated by the tip–sample interaction directly by measuring such quantities as oscillation amplitude, frequency, phase shift and drive amplitude. The method proved to be important when interpreting phase data obtained in tapping mode, but is also applicable to a variety of scanning probe microscopes operating in different dynamic modes. Additional electronics were designed to allow a direct mapping of local energy dissipation while scanning a sample surface. By applying this technique to the cross-section of a polymer blend a material specific contrast was observed.     

Calculation of the optimal imaging parameters for frequency modulation atomic force microscopy

True atomic resolution of conductors and insulators is now routinely obtained in vacuum by frequency modulation atomic force microscopy. So far, the imaging parameters (i.e., eigenfrequency, stiffness and oscillation amplitude of the cantilever, frequency shift) which result in optimal spatial resolution for a given cantilever and sample have been found empirically. Here, we calculate the optimal set of parameters from first principles as a function of the tip–sample system. The result shows that the either the acquisition rate or the signal-to-noise ratio could be increased by up to two orders of magnitude by using stiffer cantilevers and smaller amplitudes than are in use today.     

Characterization of tip size and geometry of the pipettes used in scanning ion conductance microscopy

Scanning ion-conductance microscopy (SICM) belongs to the family of scanning-probe microscopies. The spatial resolution of these techniques is limited by the size of the probe. In SICM the probe is a pipette, obtained by heating and pulling a glass capillary tubing. The size of the pipette tip is therefore an important parameter in SICM experiments. However, the characterization of the tip is not a consolidated routine in SICM experimental practice. In addition, potential and limitations of the different methods available for this characterization may not be known to all users. We present an overview of different methods for characterizing size and geometry of the pipette tip, with the aim of collecting and facilitating the use of several pieces of information appeared in the literature in a wide interval of time under different disciplines. In fact, several methods that have been developed for pipettes used in cell physiology can be also fruitfully employed in the characterization of the SICM probes. The overview includes imaging techniques, such as scanning electron microscopy and atomic Force microscopy, and indirect methods, which measure some physical parameter related to the size of the pipette. Examples of these parameters are the electrical resistance of the pipette filled with a saline solution and the surface tension at the pipette tip. We discuss advantages and drawbacks of the methods, which may be helpful in answering a wide range of experimental questions.     

Atomic force microscopy evidence for K domains on freshly cleaved mica

The unit cell height in the c-direction of muscovite mica is well established at 10 Å. However, we have observed steps much lower than this whilst imaging freshly cleaved mica surfaces in an atomic force microscope. The steps, 1.0±0.05 Å high, are unstable and disappear in a period of minutes after cleavage. We propose that they are due to the presence of domains of residual K⁺ ions that form two matching patchworks on the cleaved faces. Upon cleavage, they relax inwards from the bulk equilibrium position 1.6 Å above the oxygen atoms of the tetrahedral silicate. Possible mechanisms for the disappearance of the steps are discussed.     

扫描力显微术在高聚物薄膜玻璃化转变研究中的应用

简述了高聚物薄膜玻璃化转变的复杂性，并结合文章作者的的一些研究结果介绍了扫描力显微术(SFM)在研究高聚物玻璃化转变中的一些方法，包括观察高聚物薄膜形貌的变化，测量其摩擦力、粘附力和弹性模量等物理量的变化，最后指出SFM是研究高聚物薄膜玻璃化转变的有力工具。     

Effect of tensor force on dissipation dynamics in time-dependent Hartree-Fock theory

The role of tensor force on the collision dynamics of ¹⁶O+¹⁶O is investigated in the framework of a fully three-dimensional time-dependent Hartree-Fock theory. The calculations are performed with modern Skyrme energy functional plus tensor terms. Particular attention is given on the analysis of dissipation dynamics in heavy-ion collisions. The energy dissipation is found to decrease as an initial bombarding energy increases in deep-inelastic collisions for all the Skyrme parameter sets studied here because of the competition between the collective motion and the single-particle degrees of freedom. We reveal that the tensor forces may either enhance or reduce the energy dissipation depending on the different parameter sets. The fusion cross section without tensor force overestimates the experimental value by about 25%, while the calculation with tensor force T11 has good agreement with experimental cross section.