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1.  Effect of the tip state during qPlus noncontact atomic force microscopy of Si(100) at 5 K: Probing the probe 
Summary
Background: Noncontact atomic force microscopy (NC-AFM) now regularly produces atomic-resolution images on a wide range of surfaces, and has demonstrated the capability for atomic manipulation solely using chemical forces. Nonetheless, the role of the tip apex in both imaging and manipulation remains poorly understood and is an active area of research both experimentally and theoretically. Recent work employing specially functionalised tips has provided additional impetus to elucidating the role of the tip apex in the observed contrast.
Results: We present an analysis of the influence of the tip apex during imaging of the Si(100) substrate in ultra-high vacuum (UHV) at 5 K using a qPlus sensor for noncontact atomic force microscopy (NC-AFM). Data demonstrating stable imaging with a range of tip apexes, each with a characteristic imaging signature, have been acquired. By imaging at close to zero applied bias we eliminate the influence of tunnel current on the force between tip and surface, and also the tunnel-current-induced excitation of silicon dimers, which is a key issue in scanning probe studies of Si(100).
Conclusion: A wide range of novel imaging mechanisms are demonstrated on the Si(100) surface, which can only be explained by variations in the precise structural configuration at the apex of the tip. Such images provide a valuable resource for theoreticians working on the development of realistic tip structures for NC-AFM simulations. Force spectroscopy measurements show that the tip termination critically affects both the short-range force and dissipated energy.
doi:10.3762/bjnano.3.3
PMCID: PMC3304327  PMID: 22428093
force spectroscopy; image contrast; noncontact AFM; qPlus; Si(001); Si(100); tip (apex) structure
2.  Atomic Force Microscopy Application in Biological Research: A Review Study 
Atomic force microscopy (AFM) is a three-dimensional topographic technique with a high atomic resolution to measure surface roughness. AFM is a kind of scanning probe microscope, and its near-field technique is based on the interaction between a sharp tip and the atoms of the sample surface. There are several methods and many ways to modify the tip of the AFM to investigate surface properties, including measuring friction, adhesion forces and viscoelastic properties as well as determining the Young modulus and imaging magnetic or electrostatic properties. The AFM technique can analyze any kind of samples such as polymers, adsorbed molecules, films or fibers, and powders in the air whether in a controlled atmosphere or in a liquid medium. In the past decade, the AFM has emerged as a powerful tool to obtain the nanostructural details and biomechanical properties of biological samples, including biomolecules and cells. The AFM applications, techniques, and -in particular- its ability to measure forces, are not still familiar to most clinicians. This paper reviews the literature on the main principles of the AFM modality and highlights the advantages of this technique in biology, medicine, and- especially- dentistry. This literature review was performed through E-resources, including Science Direct, PubMed, Blackwell Synergy, Embase, Elsevier, and Scholar Google for the references published between 1985 and 2010.
PMCID: PMC3700051  PMID: 23825885
Atomic force microscopy; Scanning tunneling microscopy; Scanning probe microscopy; Dental; Biological
3.  Boosting the local anodic oxidation of silicon through carbon nanofiber atomic force microscopy probes 
Summary
Many nanofabrication methods based on scanning probe microscopy have been developed during the last decades. Local anodic oxidation (LAO) is one of such methods: Upon application of an electric field between tip and surface under ambient conditions, oxide patterning with nanometer-scale resolution can be performed with good control of dimensions and placement. LAO through the non-contact mode of atomic force microscopy (AFM) has proven to yield a better resolution and tip preservation than the contact mode and it can be effectively performed in the dynamic mode of AFM. The tip plays a crucial role for the LAO-AFM, because it regulates the minimum feature size and the electric field. For instance, the feasibility of carbon nanotube (CNT)-functionalized tips showed great promise for LAO-AFM, yet, the fabrication of CNT tips presents difficulties. Here, we explore the use of a carbon nanofiber (CNF) as the tip apex of AFM probes for the application of LAO on silicon substrates in the AFM amplitude modulation dynamic mode of operation. We show the good performance of CNF-AFM probes in terms of resolution and reproducibility, as well as demonstration that the CNF apex provides enhanced conditions in terms of field-induced, chemical process efficiency.
doi:10.3762/bjnano.6.20
PMCID: PMC4311679
carbon nanofiber; dynamic mode; local anodic oxidation; nanopatterning
4.  The Intrinsic Resolution Limit in the Atomic Force Microscope: Implications for Heights of Nano-Scale Features 
PLoS ONE  2011;6(8):e23821.
Background
Accurate mechanical characterization by the atomic force microscope at the highest spatial resolution requires that topography is deconvoluted from indentation. The measured height of nanoscale features in the atomic force microscope (AFM) is almost always smaller than the true value, which is often explained away as sample deformation, the formation of salt deposits and/or dehydration. We show that the real height of nano-objects cannot be obtained directly: a result arising as a consequence of the local probe-sample geometry.
Methods and Findings
We have modeled the tip-surface-sample interaction as the sum of the interaction between the tip and the surface and the tip and the sample. We find that the dynamics of the AFM cannot differentiate between differences in force resulting from 1) the chemical and/or mechanical characteristics of the surface or 2) a step in topography due to the size of the sample; once the size of a feature becomes smaller than the effective area of interaction between the AFM tip and sample, the measured height is compromised. This general result is a major contributor to loss of height and can amount to up to ∼90% for nanoscale features. In particular, these very large values in height loss may occur even when there is no sample deformation, and, more generally, height loss does not correlate with sample deformation. DNA and IgG antibodies have been used as model samples where experimental height measurements are shown to closely match the predicted phenomena.
Conclusions
Being able to measure the true height of single nanoscale features is paramount in many nanotechnology applications since phenomena and properties in the nanoscale critically depend on dimensions. Our approach allows accurate predictions for the true height of nanoscale objects and will lead to reliable mechanical characterization at the highest spatial resolution.
doi:10.1371/journal.pone.0023821
PMCID: PMC3166059  PMID: 21912608
5.  Linking of Sensor Molecules with Amino Groups to Amino-Functionalized AFM Tips 
Bioconjugate Chemistry  2011;22(6):1239-1248.
The measuring tip of an atomic force microscope (AFM) can be upgraded to a specific biosensor by attaching one or a few biomolecules to the apex of the tip. The biofunctionalized tip is then used to map cognate target molecules on a sample surface or to study biophysical parameters of interaction with the target molecules. The functionality of tip-bound sensor molecules is greatly enhanced if they are linked via a thin, flexible polymer chain. In a typical scheme of tip functionalization, reactive groups are first generated on the tip surface, a bifunctional cross-linker is then attached with one of its two reactive ends, and finally the probe molecule of interest is coupled to the free end of the cross-linker. Unfortunately, the most popular functional group generated on the tip surface is the amino group, while at the same time, the only useful coupling functions of many biomolecules (such as antibodies) are also NH2 groups. In the past, various tricks or detours were applied to minimize the undesired bivalent reaction of bifunctional linkers with adjacent NH2 groups on the tip surface. In the present study, an uncompromising solution to this problem was found with the help of a new cross-linker (“acetal-PEG-NHS”) which possesses one activated carboxyl group and one acetal-protected benzaldehyde function. The activated carboxyl ensures rapid unilateral attachment to the amino-functionalized tip, and only then is the terminal acetal group converted into the amino-reactive benzaldehyde function by mild treatment (1% citric acid, 1–10 min) which does not harm the AFM tip. As an exception, AFM tips with magnetic coating become demagnetized in 1% citric acid. This problem was solved by deprotecting the acetal group before coupling the PEG linker to the AFM tip. Bivalent binding of the corresponding linker (“aldehyde-PEG-NHS”) to adjacent NH2 groups on the tip was largely suppressed by high linker concentrations. In this way, magnetic AFM tips could be functionalized with an ethylene diamine derivative of ATP which showed specific interaction with mitochondrial uncoupling protein 1 (UCP1) that had been purified and reconstituted in a mica-supported planar lipid bilayer.
doi:10.1021/bc200099t
PMCID: PMC3115690  PMID: 21542606
6.  Apertureless scanning near-field optical microscopy of sparsely labeled tobacco mosaic viruses and the intermediate filament desmin 
Summary
Both fluorescence imaging and atomic force microscopy (AFM) are highly versatile and extensively used in applications ranging from nanotechnology to life sciences. In fluorescence microscopy luminescent dyes serve as position markers. Moreover, they can be used as active reporters of their local vicinity. The dipolar coupling of the tip with the incident light and the fluorophore give rise to a local field and fluorescence enhancement. AFM topographic imaging allows for resolutions down to the atomic scale. It can be operated in vacuum, under ambient conditions and in liquids. This makes it ideal for the investigation of a wide range of different samples. Furthermore an illuminated AFM cantilever tip apex exposes strongly confined non-propagating electromagnetic fields that can serve as a coupling agent for single dye molecules. Thus, combining both techniques by means of apertureless scanning near-field optical microscopy (aSNOM) enables concurrent high resolution topography and fluorescence imaging. Commonly, among the various (apertureless) SNOM approaches metallic or metallized probes are used. Here, we report on our custom-built aSNOM setup, which uses commercially available monolithic silicon AFM cantilevers. The field enhancement confined to the tip apex facilitates an optical resolution down to 20 nm. Furthermore, the use of standard mass-produced AFM cantilevers spares elaborate probe production or modification processes. We investigated tobacco mosaic viruses and the intermediate filament protein desmin. Both are mixed complexes of building blocks, which are fluorescently labeled to a low degree. The simultaneous recording of topography and fluorescence data allows for the exact localization of distinct building blocks within the superordinate structures.
doi:10.3762/bjnano.4.60
PMCID: PMC3778390  PMID: 24062977
apertureless scanning near-field optical microscope; atomic force microscopy; fluorescence microscopy
7.  Interpreting motion and force for narrow-band intermodulation atomic force microscopy 
Summary
Intermodulation atomic force microscopy (ImAFM) is a mode of dynamic atomic force microscopy that probes the nonlinear tip–surface force by measurement of the mixing of multiple modes in a frequency comb. A high-quality factor cantilever resonance and a suitable drive comb will result in tip motion described by a narrow-band frequency comb. We show, by a separation of time scales, that such motion is equivalent to rapid oscillations at the cantilever resonance with a slow amplitude and phase or frequency modulation. With this time-domain perspective, we analyze single oscillation cycles in ImAFM to extract the Fourier components of the tip–surface force that are in-phase with the tip motion (F I) and quadrature to the motion (F Q). Traditionally, these force components have been considered as a function of the static-probe height only. Here we show that F I and F Q actually depend on both static-probe height and oscillation amplitude. We demonstrate on simulated data how to reconstruct the amplitude dependence of F I and F Q from a single ImAFM measurement. Furthermore, we introduce ImAFM approach measurements with which we reconstruct the full amplitude and probe-height dependence of the force components F I and F Q, providing deeper insight into the tip–surface interaction. We demonstrate the capabilities of ImAFM approach measurements on a polystyrene polymer surface.
doi:10.3762/bjnano.4.5
PMCID: PMC3566785  PMID: 23400552
atomic force microscopy; AFM; frequency combs; force spectroscopy; high-quality-factor resonators; intermodulation; multifrequency
8.  A measurement of the hysteresis loop in force-spectroscopy curves using a tuning-fork atomic force microscope 
Summary
Measurements of the frequency shift versus distance in noncontact atomic force microscopy (NC-AFM) allow measurements of the force gradient between the oscillating tip and a surface (force-spectroscopy measurements). When nonconservative forces act between the tip apex and the surface the oscillation amplitude is damped. The dissipation is caused by bistabilities in the potential energy surface of the tip–sample system, and the process can be understood as a hysteresis of forces between approach and retraction of the tip. In this paper, we present the direct measurement of the whole hysteresis loop in force-spectroscopy curves at 77 K on the PTCDA/Ag/Si(111) √3 × √3 surface by means of a tuning-fork-based NC-AFM with an oscillation amplitude smaller than the distance range of the hysteresis loop. The hysteresis effect is caused by the making and breaking of a bond between PTCDA molecules on the surface and a PTCDA molecule at the tip. The corresponding energy loss was determined to be 0.57 eV by evaluation of the force–distance curves upon approach and retraction. Furthermore, a second dissipation process was identified through the damping of the oscillation while the molecule on the tip is in contact with the surface. This dissipation process occurs mainly during the retraction of the tip. It reaches a maximum value of about 0.22 eV/cycle.
doi:10.3762/bjnano.3.23
PMCID: PMC3323909  PMID: 22496993
atomic force microscopy; energy dissipation; force spectroscopy; hysteresis loop; PTCDA/Ag/Si(111) √3 × √3
9.  Surface morphology of leukemic cells from chronic myeloid leukemia under atomic force microscopy 
Atomic force microscopy (AFM) represents an important instrument for measuring mechanical properties of biological materials ranging from single molecules to normal or malignant cells. AFM provides a 3D profile of the surface on a nanoscale, by measuring forces between a sharp probe (<10 nm), supported on a flexible cantilever, and surface at very short distance (0.2-10 nm probe-sample separation). The AFM tip “gently” touches the surface and records the small force between the probe and the surface. The patients were three normal human subjects and nine patients with chronic myeloid leukemia in different phases of disease. With atomic force microscope, numerous spicules were observed on the surface of leukemic cells, especially in blastic phase of CML
PMCID: PMC3945254  PMID: 24778854
atomic force microscopy; 3D profile; leukemic cells
10.  Nanomechanical properties of α-synuclein amyloid fibrils: a comparative study by nanoindentation, harmonic force microscopy, and Peakforce QNM 
Nanoscale Research Letters  2011;6(1):270.
We report on the use of three different atomic force spectroscopy modalities to determine the nanomechanical properties of amyloid fibrils of the human α-synuclein protein. α-Synuclein forms fibrillar nanostructures of approximately 10 nm diameter and lengths ranging from 100 nm to several microns, which have been associated with Parkinson's disease. Atomic force microscopy (AFM) has been used to image the morphology of these protein fibrils deposited on a flat surface. For nanomechanical measurements, we used single-point nanoindentation, in which the AFM tip as the indenter is moved vertically to the fibril surface and back while the force is being recorded. We also used two recently developed AFM surface property mapping techniques: Harmonic force microscopy (HarmoniX) and Peakforce QNM. These modalities allow extraction of mechanical parameters of the surface with a lateral resolution and speed comparable to tapping-mode AFM imaging. Based on this phenomenological study, the elastic moduli of the α-synuclein fibrils determined using these three different modalities are within the range 1.3-2.1 GPa. We discuss the relative merits of these three methods for the determination of the elastic properties of protein fibrils, particularly considering the differences and difficulties of each method.
doi:10.1186/1556-276X-6-270
PMCID: PMC3211334  PMID: 21711775
11.  Noncontact microrheology at acoustic frequencies, using frequency-modulated atomic force microscopy 
Nature methods  2010;7(8):650-654.
We report an atomic force microscopy (AFM) method for assessing elastic and viscous properties of soft samples at acoustic frequencies under non-contact conditions. The method can be used to measure material properties via frequency modulation and is based on hydrodynamics theory of thin gaps we developed here. A cantilever with an attached microsphere is forced to oscillate tens of nanometers above a sample. The elastic modulus and viscosity of the sample are estimated by measuring the frequency-dependence of the phase lag between the oscillating microsphere and the driving piezo at various heights above the sample. This method features an effective area of pyramidal tips used in contact AFM but with only piconewton applied forces. Using this method, we analyzed polyacrylamide gels of different stiffness and assessed graded mechanical properties of guinea pig tectorial membrane. The technique enables the study of microrheology of biological tissues that produce or detect sound.
doi:10.1038/nmeth.1474
PMCID: PMC3508509  PMID: 20562866
12.  Research on Double-Probe, Double- and Triple-Tip Effects during Atomic Force Microscopy Scanning 
Scanning  2004;26(4):155-161.
Summary
Information obtained by atomic force microscopy (AFM) depends strongly on the kind of probe or tip used; therefore, probe and tip effects have to be taken into account when verifying or interpreting the data acquired. In many papers, double-tip effects have been mentioned while other research was done; however, there are only a few special reports on double- or triple-tip effects, especially double-probe effects. In our paper, metaphase chromosomes of Chinese hamster ovary (CHO) cells, aggregates of pectin molecules, membrane surface of mouse embryonic stem cells, and R-phycoerythrin-conjugated immunoglobulin G complexes were imaged by AFM with high-quality probes, double-probe cantilever, and double-tip and triple-tip probes, respectively, in order to determine double-probe, double-tip, and triple-tip effects during AFM scanning. We found that the double-probe, double-tip, and triple-tip effects share the same principle, and that these effects correlate with distance and height differences between probes of double-probe cantilever or tips of double-tip or multiple-tip probes. Since many other factors influence double-probe or double-tip effects, more in-depth studies must be undertaken. However, this initial research will make all users of AFM techniques aware of double-probe and double-tip or triple-tip effects during AFM scanning and aid in verifying or interpreting the data acquired.
PMCID: PMC2863299  PMID: 15473266
double-probe effects; double-tip effects; triple-tip effects; atomic force microscopy; tip artifacts; chromosome; pectin; phycoerythrin conjugated immunoglobulin G
13.  The Emergence of AFM Applications to Cell Biology: How new technologies are facilitating investigation of human cells in health and disease at the nanoscale 
Journal of nanoscience letters  2011;1`(2):87-101.
Atomic Force Microscopy (AFM) based nanorobotics has been used for building nano devices in semiconductors for almost a decade. Leveraging the unparallel precision localization capabilities of this technology, high resolution imaging and mechanical property characterization is now increasingly being performed in biological settings. AFM also offers the prospect for handling and manipulating biological materials at nanometer scale. It has unique advantages over other methods, permitting experiments in the liquid phase where physiological conditions can be maintained. Taking advantage of these properties, our group has visualized membrane and cytoskeletal structures of live cells by controlling the interaction force of the AFM tip with cellular components at the nN or sub-nN range. Cell stiffness changes were observed by statistically analyzing the Young’s modulus values of human keratinocytes before and after specific antibody treatment. Furthermore, we used the AFM cantilever as a robotic arm for mechanical pushing, pulling and cutting to perform nanoscale manipulations of cell-associated structures. AFM guided nano-dissection, or nanosurgery was enacted on the cell in order to sever intermediate filaments connecting neighboring keratinocytes via sub 100 nm resolution cuts. Finally, we have used a functionalized AFM tip to probe cell surface receptors to obtain binding force measurements. This technique formed the basis for Single Molecule Force Spectroscopy (SMFS). In addition to enhancing our basic understanding of dynamic signaling events in cell biology, these advancements in AFM based biomedical investigations can be expected to facilitate the search for biomarkers related to disease diagnosis progress and treatment.
PMCID: PMC3886279  PMID: 24416719
14.  The Influence of Physical and Physiological Cues on Atomic Force Microscopy-Based Cell Stiffness Assessment 
PLoS ONE  2013;8(10):e77384.
Atomic force microscopy provides a novel technique for differentiating the mechanical properties of various cell types. Cell elasticity is abundantly used to represent the structural strength of cells in different conditions. In this study, we are interested in whether physical or physiological cues affect cell elasticity in Atomic force microscopy (AFM)-based assessments. The physical cues include the geometry of the AFM tips, the indenting force and the operating temperature of the AFM. All of these cues show a significant influence on the cell elasticity assessment. Sharp AFM tips create a two-fold increase in the value of the effective Young’s modulus (Eeff) relative to that of the blunt tips. Higher indenting force at the same loading rate generates higher estimated cell elasticity. Increasing the operation temperature of the AFM leads to decreases in the cell stiffness because the structure of actin filaments becomes disorganized. The physiological cues include the presence of fetal bovine serum or extracellular matrix-coated surfaces, the culture passage number, and the culture density. Both fetal bovine serum and the extracellular matrix are critical for cells to maintain the integrity of actin filaments and consequently exhibit higher elasticity. Unlike primary cells, mouse kidney progenitor cells can be passaged and maintain their morphology and elasticity for a very long period without a senescence phenotype. Finally, cell elasticity increases with increasing culture density only in MDCK epithelial cells. In summary, for researchers who use AFM to assess cell elasticity, our results provide basic and significant information about the suitable selection of physical and physiological cues.
doi:10.1371/journal.pone.0077384
PMCID: PMC3806741  PMID: 24194882
15.  Atomic force microscopy measurements of lens elasticity in monkey eyes 
Molecular Vision  2007;13:504-510.
Purpose
To demonstrate the feasibility of measuring the elasticity of intact crystalline lenses using atomic force microscopy (AFM).
Methods
AFM elasticity measurements were performed on intact lenses from 18 fresh cynomolgus monkey cadaver eyes (4-10 years old, <1 day postmortem) that had been left attached to their zonule-ciliary body-sclera framework. The eyes were prepared by bonding a plastic ring on the sclera after removal of the conjunctival, adipose, and muscle tissues. The posterior pole was sectioned, with the excess vitreous removed, and the eye's anterior section was placed on a Teflon slide to protect the posterior pole of the lens. The cornea and iris were then sectioned. The lens-zonule-ciliary body-sclera section was then placed in a Petri dish filled with balanced salt solution in an AFM system designed for force measurements. Next, the central pole of the anterior surface of the intact lens was probed with the AFM cantilever tip. The recorded AFM cantilever deflection-indentation curves were used to derive force-indentation curves for the lens after factoring out the deflection of the cantilever on a hard surface. Young's modulus of the lens was calculated from the force-indentation relation using the Hertz model.
Results
Young's modulus was 1,720±880 Pa (range: 409-3,210 Pa) in the 18 cynomolgus monkey lenses.
Conclusions
AFM can be used to provide measurements of the elasticity of the whole lens including the capsule. Values obtained using AFM on cynomolgus monkey lenses are similar to published values obtained using dynamic mechanical analysis on young human lenses.
PMCID: PMC2649306  PMID: 17417612
16.  Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface 
We discuss a new classical water force field that explicitly accounts for differences in polarizability between liquid and vapor phases. The TIP4P-QDP (4-point transferable intermolecular potential with charge dependent-polarizability) force field is a modification of the original TIP4P-FQ fluctuating charge water force field of Rick et al.1 that self-consistently adjusts its atomic hardness parameters via a scaling function dependent on the M-site charge. The electronegativity (χ) parameters are also scaled in order to reproduce condensed-phase dipole moments of comparable magnitude to TIP4P-FQ. TIP4P-QDP is parameterized to reproduce experimental gas-phase and select condensed-phase properties. The TIP4P-QDP water model possesses a gas phase polarizability of 1.40 Å3 and gas-phase dipole moment of 1.85 Debye, in excellent agreement with experiment and high-level ab initio predictions. The liquid density of TIP4P-QDP is 0.9954(±0.0002) g/cm3 at 298 K and 1 atmosphere, and the enthalpy of vaporization is 10.55(±0.12) kcal/mol. Other condensed-phase properties such as the isobaric heat capacity, isothermal compressibility, and diffusion constant are also calculated within reasonable accuracy of experiment and consistent with predictions of other current state-of-the-art water force fields. The average molecular dipole moment of TIP4P-QDP in the condensed phase is 2.641(±0.001) Debye, approximately 0.02 Debye higher than TIP4P-FQ and within the range of values currently surmised for the bulk liquid. The dielectric constant, ε = 85.8 ± 1.0, is 10% higher than experiment. This is reasoned to be due to the increase in the condensed phase dipole moment over TIP4P-FQ, which estimates ε remarkably well. Radial distribution functions for TIP4P-QDP and TIP4P-FQ show similar features, with TIP4P-QDP showing slightly reduced peak heights and subtle shifts towards larger distance interactions. Since the greatest effects of the phase-dependent polarizability are anticipated in regions with both liquid and vapor character, interfacial simulations of TIP4P-QDP were performed and compared to TIP4P-FQ, a static polarizability analog. Despite similar features in density profiles such as the position of the GDS and interfacial width, enhanced dipole moments are observed for the TIP4P-QDP interface and onset of the vapor phase. Water orientational profiles show an increased preference (over TIP4P-FQ) in the orientation of the permanent dipole vector of the molecule within the interface; an enhanced z-induced dipole moment directly results from this preference. Hydrogen bond formation is lower, on average, in the bulk for TIP4P-QDP than TIP4P-FQ. However, the average number of hydrogen bonds formed by TIP4P-QDP in the interface exceeds that of TIP4P-FQ, and observed hydrogen bond networks extend further into the gaseous region. The TIP4P-QDP interfacial potential, calculated to be -11.98(±0.08) kcal/mol, is less favorable than that for TIP4P-FQ by approximately 2% as a result of a diminished quadrupole contribution. Surface tension is calculated within a 1.3% reduction from the experimental value. Results reported demonstrate TIP4P-QDP as a model comparable to the popular TIP4P-FQ while accounting for a physical effect previously neglected by other water models. Further refinements to this model, as well as future applications are discussed.
doi:10.1021/ct800320f
PMCID: PMC3488353  PMID: 23133341
Phase Dependent Polarizability; Molecular Dynamics; Charge Equilibration; Polarizable Force Field; Liquid-Vapor Interface; TIP4P-QDP
17.  The role of surface corrugation and tip oscillation in single-molecule manipulation with a non-contact atomic force microscope 
Summary
Scanning probe microscopy (SPM) plays an important role in the investigation of molecular adsorption. The possibility to probe the molecule–surface interaction while tuning its strength through SPM tip-induced single-molecule manipulation has particularly promising potential to yield new insights. We recently reported experiments, in which 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules were lifted with a qPlus-sensor and analyzed these experiments by using force-field simulations. Irrespective of the good agreement between the experiment and those simulations, systematic inconsistencies remained that we attribute to effects omitted from the initial model. Here we develop a more realistic simulation of single-molecule manipulation by non-contact AFM that includes the atomic surface corrugation, the tip elasticity, and the tip oscillation amplitude. In short, we simulate a full tip oscillation cycle at each step of the manipulation process and calculate the frequency shift by solving the equation of motion of the tip. The new model correctly reproduces previously unexplained key features of the experiment, and facilitates a better understanding of the mechanics of single-molecular junctions. Our simulations reveal that the surface corrugation adds a positive frequency shift to the measurement that generates an apparent repulsive force. Furthermore, we demonstrate that the scatter observed in the experimental data points is related to the sliding of the molecule across the surface.
doi:10.3762/bjnano.5.22
PMCID: PMC3943512  PMID: 24605287
atomic force microscopy (AFM); force-field model; 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA); qPlus; single-molecule manipulation
18.  Microscopic study of electrical properties of CrSi2 nanocrystals in silicon 
Nanoscale Research Letters  2011;6(1):209.
Semiconducting CrSi2 nanocrystallites (NCs) were grown by reactive deposition epitaxy of Cr onto n-type silicon and covered with a 50-nm epitaxial silicon cap. Two types of samples were investigated: in one of them, the NCs were localized near the deposition depth, and in the other they migrated near the surface. The electrical characteristics were investigated in Schottky junctions by current-voltage and capacitance-voltage measurements. Atomic force microscopy (AFM), conductive AFM and scanning probe capacitance microscopy (SCM) were applied to reveal morphology and local electrical properties. The scanning probe methods yielded specific information, and tapping-mode AFM has shown up to 13-nm-high large-area protrusions not seen in the contact-mode AFM. The electrical interaction of the vibrating scanning tip results in virtual deformation of the surface. SCM has revealed NCs deep below the surface not seen by AFM. The electrically active probe yielded significantly better spatial resolution than AFM. The conductive AFM measurements have shown that the Cr-related point defects near the surface are responsible for the leakage of the macroscopic Schottky junctions, and also that NCs near the surface are sensitive to the mechanical and electrical stress induced by the scanning probe.
doi:10.1186/1556-276X-6-209
PMCID: PMC3211265  PMID: 21711727
19.  Ultrastable Atomic Force Microscopy: Atomic-Scale Stability and Registration in Ambient Conditions 
Nano letters  2009;9(4):1451-1456.
Instrumental drift in atomic force microscopy (AFM) remains a critical, largely unaddressed issue that limits tip–sample stability, registration, and the signal-to-noise ratio during imaging. By scattering a laser off the apex of a commercial AFM tip, we locally measured and thereby actively controlled its three-dimensional position above a sample surface to <40 pm (Δf = 0.01–10 Hz) in air at room temperature. With this enhanced stability, we overcame the traditional need to scan rapidly while imaging and achieved a 5-fold increase in the image signal-to-noise ratio. Finally, we demonstrated atomic-scale (~100 pm) tip–sample stability and registration over tens of minutes with a series of AFM images on transparent substrates. The stabilization technique requires low laser power (<1 mW), imparts a minimal perturbation upon the cantilever, and is independent of the tip–sample interaction. This work extends atomic-scale tip–sample control, previously restricted to cryogenic temperatures and ultrahigh vacuum, to a wide range of perturbative operating environments.
doi:10.1021/nl803298q
PMCID: PMC2953871  PMID: 19351191
20.  Using a Sharp Metal Tip to Control the Polarization and Direction of Emission from a Quantum Dot 
Scientific Reports  2014;4:6456.
Optical antennas can be used to manipulate the direction and polarization of radiation from an emitter. Usually, these metallic nanostructures utilize localized plasmon resonances to generate highly directional and strongly polarized emission, which is determined predominantly by the antenna geometry alone, and is thus not easily tuned. Here we show experimentally that the emission polarization can be manipulated using a simple, nonresonant scanning probe consisting of the sharp metallic tip of an atomic force microscope; finite element simulations reveal that the emission simultaneously becomes highly directional. Together, the measurements and simulations demonstrate that interference between light emitted directly into the far field with that elastically scattered from the tip apex in the near field is responsible for this control over polarization and directionality. Due to the relatively weak emitter-tip coupling, the tip must be positioned very precisely near the emitter, but this weak coupling also leads to highly tunable emission properties with a similar degree of polarization and directionality compared to resonant antennas.
doi:10.1038/srep06456
PMCID: PMC4173036  PMID: 25248420
21.  Measuring bacterial cells size with AFM 
Brazilian Journal of Microbiology  2012;43(1):341-347.
Atomic Force Microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria revealing surface details and cell integrity. During scanning however, the interactions between the AFM probe and the membrane results in distortion of the images. Such distortions or artifacts are the result of geometrical effects related to bacterial cell height, specimen curvature and the AFM probe geometry. The most common artifact in imaging is surface broadening, what can lead to errors in bacterial sizing. Several methods of correction have been proposed to compensate for these artifacts and in this study we describe a simple geometric model for the interaction between the tip (a pyramidal shaped AFM probe) and the bacterium (Escherichia coli JM-109 strain) to minimize the enlarging effect. Approaches to bacteria immobilization and examples of AFM images analysis are also described.
doi:10.1590/S1517-838220120001000040
PMCID: PMC3768968  PMID: 24031837
Atomic force microscopy (AFM); Escherichia coli; cell dimensions; bacteria visualization
22.  Investigation on Blind Tip Reconstruction Errors Caused by Sample Features 
Sensors (Basel, Switzerland)  2014;14(12):23159-23175.
Precision measurements of a nanoscale sample surface using an atomic force microscope (AFM) require a precise quantitative knowledge of the 3D tip shape. Blind tip reconstruction (BTR), established by Villarrubia, gives an outer bound with larger errors if the tip characterizer is not appropriate. In order to explore the errors of BTR, a series of simulation experiments based on a conical model were carried out. The results show that, to reconstruct the tip precisely, the cone angle of the tip characterizer must be smaller than that of the tip. Furthermore, the errors decrease as a function of the tip cone angle and increase linearly with the sample radius of curvature, irrespective of the tip radius of curvature. In particular, for sharp (20 nm radius) and blunt (80 nm radius) tips, the radius of curvature of the tip characterizer must be smaller than 5 nm. Based on these simulation results, a local error model of BTR was established. The maximum deviation between the errors derived from the model and the simulated experiments is 1.22 nm. Compared with the lateral resolution used in the above simulated experiments (4 nm/pixel), it is valid to ignore the deviations and consider the local error model of BTR is indeed in quantitative agreement with the simulation results. Finally, two simulated ideal structures are proposed here, together with their corresponding real samples. The simulation results show they are suitable for BTR.
doi:10.3390/s141223159
PMCID: PMC4299057  PMID: 25490584
blind tip reconstruction; 3D tip shape; AFM; tip characterizer
23.  Modeling viscoelasticity through spring–dashpot models in intermittent-contact atomic force microscopy 
Summary
We examine different approaches to model viscoelasticity within atomic force microscopy (AFM) simulation. Our study ranges from very simple linear spring–dashpot models to more sophisticated nonlinear systems that are able to reproduce fundamental properties of viscoelastic surfaces, including creep, stress relaxation and the presence of multiple relaxation times. Some of the models examined have been previously used in AFM simulation, but their applicability to different situations has not yet been examined in detail. The behavior of each model is analyzed here in terms of force–distance curves, dissipated energy and any inherent unphysical artifacts. We focus in this paper on single-eigenmode tip–sample impacts, but the models and results can also be useful in the context of multifrequency AFM, in which the tip trajectories are very complex and there is a wider range of sample deformation frequencies (descriptions of tip–sample model behaviors in the context of multifrequency AFM require detailed studies and are beyond the scope of this work).
doi:10.3762/bjnano.5.224
PMCID: PMC4273292  PMID: 25551043
atomic force microscopy; creep; dissipated energy; multifrequency; stress relaxation; tapping mode; viscoelasticity
24.  Indentation of poroviscoelastic vocal fold tissue using an atomic force microscope☆ 
Journal of the mechanical behavior of biomedical materials  2013;28:10.1016/j.jmbbm.2013.05.026.
The elastic properties of the vocal folds (VFs) vary as a function of depth relative to the epithelial surface. The poroelastic anisotropic properties of porcine VFs, at various depths, were measured using atomic force microscopy (AFM)-based indentation. The minimum tip diameter to effectively capture the local properties was found to be 25 µm, based on nonlinear laser scanning microscopy data and image analysis. The effects of AFM tip dimensions and AFM cantilever stiffness were systematically investigated. The indentation tests were performed along the sagittal and coronal planes for an evaluation of the VF anisotropy. Hertzian contact theory was used along with the governing equations of linear poroelasticity to calculate the diffusivity coefficient of the tissue from AFM indentation creep testing. The permeability coefficient of the porcine VF was found to be 1.80 ± 0.32 × 10−15 m4/N s.
doi:10.1016/j.jmbbm.2013.05.026
PMCID: PMC3833877  PMID: 23829979
Indentation; Anisotropy; Permeability; Atomic force microscopy; Nonlinear optics; Vocal folds
25.  Determination of the Elastic Properties of Tomato Fruit Cells with an Atomic Force Microscope 
Sensors (Basel, Switzerland)  2013;13(9):12175-12191.
Since the mechanical properties of single cells together with the intercellular adhesive properties determine the macro-mechanical properties of plants, a method for evaluation of the cell elastic properties is needed to help explanation of the behavior of fruits and vegetables in handling and food processing. For this purpose, indentation of tomato mesocarp cells with an atomic force microscope was used. The Young's modulus of a cell using the Hertz and Sneddon models, and stiffness were calculated from force-indentation curves. Use of two probes of distinct radius of curvature (20 nm and 10,000nm) showed that the measured elastic properties were significantly affected by tip geometry. The Young's modulus was about 100 kPa ± 35 kPa and 20 kPa ± 14 kPa for the sharper tip and a bead tip, respectively. Moreover, large variability regarding elastic properties (>100%) among cells sampled from the same region in the fruit was observed. We showed that AFM provides the possibility of combining nano-mechanical properties with topography imaging, which could be very useful for the study of structure-related properties of fruits and vegetables at the cellular and sub-cellular scale.
doi:10.3390/s130912175
PMCID: PMC3821342  PMID: 24030683
AFM; indentation; tomato; cell; Young's modulus; Hertz; Sneddon; stiffness; texture; biomechanics

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