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Time-Resolved Imaging of Bacterial Surfaces Using Atomic Force Microscopy. Methods Mol Biol 2018. [PMID: 29956245 DOI: 10.1007/978-1-4939-8591-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Time-resolved atomic force microscopy (AFM) offers countless new modes by which to study bacterial cell physiology on relevant time scales, from mere milliseconds to hours and days on end. In addition, time-lapse AFM acts as a complementary tool to optical fluorescence microscopy (OFM), for which the combination offers a correlative link between the physical manifestation of bacterial phenotypes and molecular mechanisms obeying those principles. Herein we describe the essential materials and methods necessary for conducting time-resolved AFM and dual AFM/OFM experiments on bacteria.
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Adams JD, Erickson BW, Grossenbacher J, Brugger J, Nievergelt A, Fantner GE. Harnessing the damping properties of materials for high-speed atomic force microscopy. NATURE NANOTECHNOLOGY 2016; 11:147-151. [PMID: 26595334 DOI: 10.1038/nnano.2015.254] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
The success of high-speed atomic force microscopy in imaging molecular motors, enzymes and microbes in liquid environments suggests that the technique could be of significant value in a variety of areas of nanotechnology. However, the majority of atomic force microscopy experiments are performed in air, and the tapping-mode detection speed of current high-speed cantilevers is an order of magnitude lower in air than in liquids. Traditional approaches to increasing the imaging rate of atomic force microscopy have involved reducing the size of the cantilever, but further reductions in size will require a fundamental change in the detection method of the microscope. Here, we show that high-speed imaging in air can instead be achieved by changing the cantilever material. We use cantilevers fabricated from polymers, which can mimic the high damping environment of liquids. With this approach, SU-8 polymer cantilevers are developed that have an imaging-in-air detection bandwidth that is 19 times faster than those of conventional cantilevers of similar size, resonance frequency and spring constant.
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Affiliation(s)
- Jonathan D Adams
- Laboratory for Bio- and Nano-Instrumentation, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Blake W Erickson
- Laboratory for Bio- and Nano-Instrumentation, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Jonas Grossenbacher
- Microsystems Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Juergen Brugger
- Microsystems Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Adrian Nievergelt
- Laboratory for Bio- and Nano-Instrumentation, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Georg E Fantner
- Laboratory for Bio- and Nano-Instrumentation, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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Studying biological membranes with extended range high-speed atomic force microscopy. Sci Rep 2015; 5:11987. [PMID: 26169348 PMCID: PMC4500952 DOI: 10.1038/srep11987] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/11/2015] [Indexed: 11/28/2022] Open
Abstract
High—speed atomic force microscopy has proven to be a valuable tool for the study of biomolecular systems at the nanoscale. Expanding its application to larger biological specimens such as membranes or cells has, however, proven difficult, often requiring fundamental changes in the AFM instrument. Here we show a way to utilize conventional AFM instrumentation with minor alterations to perform high-speed AFM imaging with a large scan range. Using a two—actuator design with adapted control systems, a 130 × 130 × 5 μm scanner with nearly 100 kHz open—loop small-signal Z—bandwidth is implemented. This allows for high-speed imaging of biologically relevant samples as well as high-speed measurements of nanomechanical surface properties. We demonstrate the system performance by real-time imaging of the effect of charged polymer nanoparticles on the integrity of lipid membranes at high imaging speeds and peak force tapping measurements at 32 kHz peak force rate.
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Ahmad A, Schuh A, Rangelow IW. Adaptive AFM scan speed control for high aspect ratio fast structure tracking. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:103706. [PMID: 25362402 DOI: 10.1063/1.4897141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Improved imaging rates in Atomic Force Microscopes (AFM) are of high interest for disciplines such as life sciences and failure analysis of semiconductor wafers, where the sample topology shows high aspect ratios. Also, fast imaging is necessary to cover a large surface under investigation in reasonable times. Since AFMs are composed of mechanical components, they are associated with comparably low resonance frequencies that undermine the effort to increase the acquisition rates. In particular, high and steep structures are difficult to follow, which causes the cantilever to temporarily loose contact to or crash into the sample. Here, we report on a novel approach that does not affect the scanner dynamics, but adapts the lateral scanning speed of the scanner. The controller monitors the control error signal and, only when necessary, decreases the scan speed to allow the z-piezo more time to react to changes in the sample's topography. In this case, the overall imaging rate can be significantly increased, because a general scan speed trade-off decision is not needed and smooth areas are scanned fast. In contrast to methods trying to increase the z-piezo bandwidth, our method is a comparably simple approach that can be easily adapted to standard systems.
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Affiliation(s)
- Ahmad Ahmad
- Department of Microelectronic and Nanoelectronic Systems, Faculty of Electrical Engineering and Information Technology Ilmenau University of Technology, Gustav-Kirchhoffstr. 1, 98684 Ilmenau, Germany
| | - Andreas Schuh
- Department of Microelectronic and Nanoelectronic Systems, Faculty of Electrical Engineering and Information Technology Ilmenau University of Technology, Gustav-Kirchhoffstr. 1, 98684 Ilmenau, Germany
| | - Ivo W Rangelow
- Department of Microelectronic and Nanoelectronic Systems, Faculty of Electrical Engineering and Information Technology Ilmenau University of Technology, Gustav-Kirchhoffstr. 1, 98684 Ilmenau, Germany
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Adams JD, Nievergelt A, Erickson BW, Yang C, Dukic M, Fantner GE. High-speed imaging upgrade for a standard sample scanning atomic force microscope using small cantilevers. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:093702. [PMID: 25273731 DOI: 10.1063/1.4895460] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present an atomic force microscope (AFM) head for optical beam deflection on small cantilevers. Our AFM head is designed to be small in size, easily integrated into a commercial AFM system, and has a modular architecture facilitating exchange of the optical and electronic assemblies. We present two different designs for both the optical beam deflection and the electronic readout systems, and evaluate their performance. Using small cantilevers with our AFM head on an otherwise unmodified commercial AFM system, we are able to take tapping mode images approximately 5-10 times faster compared to the same AFM system using large cantilevers. By using additional scanner turnaround resonance compensation and a controller designed for high-speed AFM imaging, we show tapping mode imaging of lipid bilayers at line scan rates of 100-500 Hz for scan areas of several micrometers in size.
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Affiliation(s)
| | | | | | - Chen Yang
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maja Dukic
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Georg E Fantner
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Schlecker B, Dukic M, Erickson B, Ortmanns M, Fantner G, Anders J. Single-cycle-PLL detection for real-time FM-AFM applications. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2014; 8:206-215. [PMID: 24760947 DOI: 10.1109/tbcas.2014.2307696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this paper we present a novel architecture for phase-locked loop (PLL) based high-speed demodulation of frequency-modulated (FM) atomic force microscopy (AFM) signals. In our approach, we use single-sideband (SSB) frequency upconversion to translate the AFM signal from the position sensitive detector to a fixed intermediate frequency (IF) of 10 MHz. In this way, we fully benefit from the excellent noise performance of PLL-based FM demodulators still avoiding the intrinsic bandwidth limitation of such systems. In addition, the upconversion to a fixed IF renders the PLL demodulator independent of the cantilever's resonance frequency, allowing the system to work with a large range of cantilever frequencies. To investigate if the additional noise introduced by the SSB upconverter degrades the system noise figure we present a model of the AM-to-FM noise conversion in PLLs incorporating a phase-frequency detector. Using this model, we can predict an upper corner frequency for the demodulation bandwidth above which the converted noise from the single-sideband upconverter becomes the dominant noise source and therefore begins to deteriorate the overall system performance. The approach is validated by both electrical and AFM measurements obtained with a PCB-based prototype implementing the proposed demodulator architecture.
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Brown BP, Picco L, Miles MJ, Faul CFJ. Opportunities in high-speed atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3201-3211. [PMID: 23609982 DOI: 10.1002/smll.201203223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Indexed: 06/02/2023]
Abstract
The atomic force microscope (AFM) has become integrated into standard characterisation procedures in many different areas of research. Nonetheless, typical imaging rates of commercial microscopes are still very slow, much to the frustration of the user. Developments in instrumentation for "high-speed AFM" (HSAFM) have been ongoing since the 1990s, and now nanometer resolution imaging at video rate is readily achievable. Despite thorough investigation of samples of a biological nature, use of HSAFM instruments to image samples of interest to materials scientists, or to carry out AFM lithography, has been minimal. This review gives a summary of different approaches to and advances in the development of high-speed AFMs, highlights important discoveries made with new instruments, and briefly discusses new possibilities for HSAFM in materials science.
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Affiliation(s)
- Benjamin P Brown
- Bristol Centre for Functional Nanomaterials, Centre for NSQI, University of Bristol, Tyndall Avenue, Bristol, BS8 1FD, UK
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Erickson BW, Coquoz S, Adams JD, Burns DJ, Fantner GE. Large-scale analysis of high-speed atomic force microscopy data sets using adaptive image processing. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2012; 3:747-758. [PMID: 23213638 PMCID: PMC3512124 DOI: 10.3762/bjnano.3.84] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 10/08/2012] [Indexed: 05/27/2023]
Abstract
Modern high-speed atomic force microscopes generate significant quantities of data in a short amount of time. Each image in the sequence has to be processed quickly and accurately in order to obtain a true representation of the sample and its changes over time. This paper presents an automated, adaptive algorithm for the required processing of AFM images. The algorithm adaptively corrects for both common one-dimensional distortions as well as the most common two-dimensional distortions. This method uses an iterative thresholded processing algorithm for rapid and accurate separation of background and surface topography. This separation prevents artificial bias from topographic features and ensures the best possible coherence between the different images in a sequence. This method is equally applicable to all channels of AFM data, and can process images in seconds.
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Affiliation(s)
- Blake W Erickson
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
| | - Séverine Coquoz
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
| | - Jonathan D Adams
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
| | - Daniel J Burns
- Mechatronics Laboratory, Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Georg E Fantner
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
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Payton OD, Picco L, Miles MJ, Homer ME, Champneys AR. Improving the signal-to-noise ratio of high-speed contact mode atomic force microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:083710. [PMID: 22938306 DOI: 10.1063/1.4747455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
During high-speed contact mode atomic force microscopy, higher eigenmode flexural oscillations of the cantilever have been identified as the main source of noise in the resultant topography images. We show that by selectively filtering out the frequencies corresponding to these oscillations in the time domain prior to transforming the data into the spatial domain, significant improvements in image quality can be achieved.
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Affiliation(s)
- O D Payton
- University of Bristol, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom.
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Bozchalooi IS, Youcef-Toumi K, Burns DJ, Fantner GE. Compensator design for improved counterbalancing in high speed atomic force microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:113712. [PMID: 22128989 PMCID: PMC3298558 DOI: 10.1063/1.3663070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 10/31/2011] [Indexed: 05/28/2023]
Abstract
High speed atomic force microscopy can provide the possibility of many new scientific observations and applications ranging from nano-manufacturing to the study of biological processes. However, the limited imaging speed has been an imperative drawback of the atomic force microscopes. One of the main reasons behind this limitation is the excitation of the AFM dynamics at high scan speeds, severely undermining the reliability of the acquired images. In this research, we propose a piezo based, feedforward controlled, counter actuation mechanism to compensate for the excited out-of-plane scanner dynamics. For this purpose, the AFM controller output is properly filtered via a linear compensator and then applied to a counter actuating piezo. An effective algorithm for estimating the compensator parameters is developed. The information required for compensator design is extracted from the cantilever deflection signal, hence eliminating the need for any additional sensors. The proposed approach is implemented and experimentally evaluated on the dynamic response of a custom made AFM. It is further assessed by comparing the imaging performance of the AFM with and without the application of the proposed technique and in comparison with the conventional counterbalancing methodology. The experimental results substantiate the effectiveness of the method in significantly improving the imaging performance of AFM at high scan speeds.
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Affiliation(s)
- I S Bozchalooi
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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